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Conserved domains on  [gi|1039771187|ref|XP_017176313|]
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histone-lysine N-methyltransferase 2C isoform X18 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4767-4919 7.39e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


:

Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.39e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4767 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4846
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4847 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4411-4515 2.06e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


:

Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.06e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1584-1664 1.82e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


:

Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.82e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1584 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1663
Cdd:cd22026      1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                   .
gi 1039771187 1664 N 1664
Cdd:cd22026     81 N 81
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 8.44e-54

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


:

Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.99  E-value: 8.44e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696      7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                   ....
gi 1039771187  327 CPEH 330
Cdd:cd15696     87 CPTH 90
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 907-963 3.45e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


:

Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.45e-36
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  907 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 963
Cdd:cd15596      1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1041-1091 3.20e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


:

Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.80  E-value: 3.20e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1091
Cdd:cd15600      1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 964-1010 4.30e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


:

Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.88  E-value: 4.30e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 8.30e-29

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


:

Pssm-ID: 277069  Cd Length: 46  Bit Score: 111.18  E-value: 8.30e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 1.68e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


:

Pssm-ID: 276986  Cd Length: 52  Bit Score: 107.57  E-value: 1.68e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511      1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4617-4701 8.78e-25

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


:

Pssm-ID: 461788  Cd Length: 83  Bit Score: 100.76  E-value: 8.78e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4617 RPVFVIRIVEqgHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENY 4696
Cdd:pfam05965    1 GPLFRVTVEE--DPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1039771187 4697 TFRYG 4701
Cdd:pfam05965   79 KFRYG 83
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 1.83e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


:

Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.84  E-value: 1.83e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1824-2314 2.16e-21

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 104.25  E-value: 2.16e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1824 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1899
Cdd:PHA03247  2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1900 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 1977
Cdd:PHA03247  2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1978 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2051
Cdd:PHA03247  2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2052 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2126
Cdd:PHA03247  2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2127 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2185
Cdd:PHA03247  2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2186 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2262
Cdd:PHA03247  2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2263 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2314
Cdd:PHA03247  2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4560-4611 4.67e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


:

Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.67e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 4560 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4611
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2090-2697 7.02e-13

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 76.13  E-value: 7.02e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2090 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2155
Cdd:PHA03247  2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2156 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2231
Cdd:PHA03247  2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2232 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2310
Cdd:PHA03247  2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2311 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2389
Cdd:PHA03247  2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2390 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2469
Cdd:PHA03247  2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2470 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2547
Cdd:PHA03247  2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2548 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2606
Cdd:PHA03247  2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2607 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2672
Cdd:PHA03247  2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                          650       660
                   ....*....|....*....|....*.
gi 1039771187 2673 NLNL-DTEDGKGDDLDTLDNlETNDP 2697
Cdd:PHA03247  3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
Myosin_tail_1 super family cl37647
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3136-3218 9.96e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


The actual alignment was detected with superfamily member pfam01576:

Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3136 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3212
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 1039771187 3213 HAELIE 3218
Cdd:pfam01576  536 DAGTLE 541
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3233-3545 3.08e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.99  E-value: 3.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3233 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3301
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3302 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3374
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3375 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3445
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3446 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3521
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 1039771187 3522 NSNVPCGQDPAVTQGQNYSGSSQS 3545
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4767-4919 7.39e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.39e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4767 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4846
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4847 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4411-4515 2.06e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.06e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1584-1664 1.82e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.82e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1584 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1663
Cdd:cd22026      1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                   .
gi 1039771187 1664 N 1664
Cdd:cd22026     81 N 81
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 8.44e-54

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.99  E-value: 8.44e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696      7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                   ....
gi 1039771187  327 CPEH 330
Cdd:cd15696     87 CPTH 90
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4779-4918 4.97e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 140.48  E-value: 4.97e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgvYMFRMDNDHVIDATLTGGPARYINH 4858
Cdd:COG2940      5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINH 82

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4859 SCAPNCVAEvvtfERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHkiPCHCGavNCRKW 4918
Cdd:COG2940     83 SCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 907-963 3.45e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.45e-36
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  907 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 963
Cdd:cd15596      1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4781-4902 1.17e-35

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 133.61  E-value: 1.17e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  4781 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNR-GVYMFRMDNDHVIDATLTGGPARYINHS 4859
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 1039771187  4860 CAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDD 4902
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1041-1091 3.20e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.80  E-value: 3.20e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1091
Cdd:cd15600      1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 964-1010 4.30e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.88  E-value: 4.30e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4791-4896 3.89e-29

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 114.54  E-value: 3.89e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGT-IIRNEVANRKEKLYESQNR----GVYMFRMDND--HVIDATLT--GGPARYINHSCA 4861
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDseYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1039771187 4862 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYK 4896
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 8.30e-29

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 111.18  E-value: 8.30e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 1.68e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 107.57  E-value: 1.68e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511      1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4617-4701 8.78e-25

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 100.76  E-value: 8.78e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4617 RPVFVIRIVEqgHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENY 4696
Cdd:pfam05965    1 GPLFRVTVEE--DPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1039771187 4697 TFRYG 4701
Cdd:pfam05965   79 KFRYG 83
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4619-4706 9.13e-25

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 100.83  E-value: 9.13e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  4619 VFVIRIVEQGheDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYTF 4698
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1039771187  4699 RYGRNPLM 4706
Cdd:smart00542   79 RYHRSPLL 86
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 1.83e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.84  E-value: 1.83e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1824-2314 2.16e-21

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 104.25  E-value: 2.16e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1824 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1899
Cdd:PHA03247  2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1900 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 1977
Cdd:PHA03247  2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1978 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2051
Cdd:PHA03247  2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2052 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2126
Cdd:PHA03247  2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2127 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2185
Cdd:PHA03247  2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2186 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2262
Cdd:PHA03247  2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2263 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2314
Cdd:PHA03247  2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4560-4611 4.67e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.67e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 4560 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4611
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4570-4613 1.45e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 76.17  E-value: 1.45e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1039771187  4570 LLPQQMQAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEE 4613
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4438-4515 2.10e-14

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 71.59  E-value: 2.10e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4438 HLNCALWSTEVYetQAGA------LINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKT 4509
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 1039771187 4510 ----MLCPMH 4515
Cdd:pfam13771   79 gtfkSYCKKH 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1828-2249 2.29e-14

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 80.58  E-value: 2.29e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1828 QSQNSQPPSPQMFSPGSShsrPPSPVDPYAKMVGTPRPPPGGHSFPrrnsvtpvencvplssvprpihmnetsatrpspa 1907
Cdd:pfam03154  165 QILQTQPPVLQAQSGAAS---PPSPPPPGTTQAATAGPTPSAPSVP---------------------------------- 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1908 rdlcassmtnsdPYAKPPDTPRPMMTDQFSKPFSLPRSpviseqstkgplttgtsdhftkpsprTDAFQRQRLPDPYagP 1987
Cdd:pfam03154  208 ------------PQGSPATSQPPNQTQSTAAPHTLIQQ--------------------------TPTLHPQRLPSPH--P 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1988 SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERP-ALTPRPVDNFSH-SQSNDPYSHPPLTPHPAMTESFT 2065
Cdd:pfam03154  248 PLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPQPFPLTPQsSQSQVPPGPSPAAPGQSQQRIHT 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2066 HASRAFPQPGTISRSASQDP-------YSQPPGTPRP-LIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS----QQP 2133
Cdd:pfam03154  328 PPSQSQLQSQQPPREQPLPPaplsmphIKPPPTTPIPqLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslstHHP 407

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2134 PTPRPSPQTDMFVSS----------VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR--PSSARPALMPN 2201
Cdd:pfam03154  408 PSAHPPPLQLMPQSQqlppppaqppVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPitPPSGPPTSTSS 487

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2202 QDPFLQAAQNRVPGLPGPLI--------------RPPDTCSQTPRPPGPGR--------IDTFTHASSSA 2249
Cdd:pfam03154  488 AMPGIQPPSSASVSSSGPVPaavscplppvqikeEALDEAEEPESPPPPPRspspeptvVNTPSHASQSA 557
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2090-2697 7.02e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 76.13  E-value: 7.02e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2090 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2155
Cdd:PHA03247  2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2156 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2231
Cdd:PHA03247  2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2232 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2310
Cdd:PHA03247  2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2311 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2389
Cdd:PHA03247  2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2390 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2469
Cdd:PHA03247  2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2470 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2547
Cdd:PHA03247  2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2548 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2606
Cdd:PHA03247  2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2607 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2672
Cdd:PHA03247  2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                          650       660
                   ....*....|....*....|....*.
gi 1039771187 2673 NLNL-DTEDGKGDDLDTLDNlETNDP 2697
Cdd:PHA03247  3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 252-330 1.42e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 66.20  E-value: 1.42e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  252 HHRCVEWSLGICQ-----MEEPLLvNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTFQDFSH--- 322
Cdd:pfam13771    1 HVVCALWSPELVQrgndsMGFPIE-DIEKIPKRRWKLKCYLCKKkGGACIQCSKKNCRRAFHVTCALEAGLLMQFDEdng 79


                   ....*....
gi 1039771187  323 -FFLLCPEH 330
Cdd:pfam13771   80 tFKSYCKKH 88
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 964-1010 1.85e-12

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 64.82  E-value: 1.85e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCV 1010
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 964-1009 2.43e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.46  E-value: 2.43e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1039771187   964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1009
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 390-438 5.61e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.58  E-value: 5.61e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV--MKSVPTNGWKCKNCRIC 438
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPldPAEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 390-435 4.65e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.61  E-value: 4.65e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1039771187   390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 915-965 7.42e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.12  E-value: 7.42e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  915 CVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLECTVC 965
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 914-962 8.87e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 8.87e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1039771187   914 MCVVCGSFGqgAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 962
Cdd:smart00249    1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 344-391 1.15e-08

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 54.04  E-value: 1.15e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT--PLKRAGWQCPECKVC 391
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 344-388 8.25e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.75  E-value: 8.25e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1039771187   344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 467-517 9.47e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 9.47e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187   467 CPFCGKCYHPElqkDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPP--LLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 467-518 2.01e-06

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.49  E-value: 2.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  467 CPFCGKcyhPELQKDMLHCNMCKRWVHLECDKPTDQELDsQLKEDYICMYCK 518
Cdd:pfam00628    2 CAVCGK---SDDGGELVQCDGCDDWFHLACLGPPLDPAE-IPSGEWLCPECK 49
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2119-2541 2.32e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 54.39  E-value: 2.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2119 GTPRPNTIDPYSQQPPTPRPSPQ---TDMFVSSVANQRHTDP-----YTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR 2190
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSPSIPSPQdneSDSDSSAQQQILQTQPpvlqaQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2191 PSSarPALMPNQDPFLQAA-----QNRVPGLPGPLIRPPDTCSQTPRPPGPGRIdtfthaSSSAVRDPYDQPPVTPRPHS 2265
Cdd:pfam03154  210 GSP--ATSQPPNQTQSTAAphtliQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV------SPQPLPQPSLHGQMPPMPHS 281

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2266 ESFGTSQVVHDLVDRPVPGSegnfstssnlPVSSQGQQfssvsqLPGPVPTSGGTDTQNTvnMSQADTEKLRQRQKLREI 2345
Cdd:pfam03154  282 LQTGPSHMQHPVPPQPFPLT----------PQSSQSQV------PPGPSPAAPGQSQQRI--HTPPSQSQLQSQQPPREQ 343

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2346 ILQQQQqkkIASRQEKGPQDTAVVPHPVPLPHWQPESINQAF------TRPPPPY--PGSTRSPVIPPLG--PRYAVFPK 2415
Cdd:pfam03154  344 PLPPAP---LSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSpfqmnsNLPPPPAlkPLSSLSTHHPPSAhpPPLQLMPQ 420

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2416 DQRGPYPPE-----VAGMGMRPHGFRFGFPGAGHgPMPSQDRFhvPQQIQGSGIPPHIRRPMSmemprpsnnPPLNNPVG 2490
Cdd:pfam03154  421 SQQLPPPPAqppvlTQSQSLPPPAASHPPTSGLH-QVPSQSPF--PQHPFVPGGPPPITPPSG---------PPTSTSSA 488

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2491 LPQHFPPQGLPVQQHNILGQAF------IELRHRAPD----GRSRLPFAASPS---SVIESPSH 2541
Cdd:pfam03154  489 MPGIQPPSSASVSSSGPVPAAVscplppVQIKEEALDeaeePESPPPPPRSPSpepTVVNTPSH 552
HMG_box pfam00505
HMG (high mobility group) box;
1605-1656 1.24e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.24e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 1605 VLYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1656
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
HMG smart00398
high mobility group;
1603-1656 1.36e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 1.36e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039771187  1603 APVLYTNINFPNLKEEFPDWTT--RVKQIAKLWRKASSQERAPYVQKARDNRAALR 1656
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1042-1093 7.30e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 43.25  E-value: 7.30e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 1042 CPVCcRNYREEDLILQCRQCDRWMHAVCqnLNTEEEVENVADIGFDCSMCRP 1093
Cdd:pfam00628    2 CAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECKP 50
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 1968-2285 2.74e-04

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 47.37  E-value: 2.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1968 PSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQ--DPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2045
Cdd:COG5180    138 TREATSASAGVALAAALLQRSDPILAKDPDGDSASTLPPPAEklDKVLTEPRDALKDSPEKLDRPKVEVKDEAQEEPPDL 217

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2046 NDPYSHPPLtphPAMTESFthasraFPQPGTiSRSASQDPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPPGTPRPNt 2125
Cdd:COG5180    218 TGGADHPRP---EAASSPK------VDPPST-SEARSRPATVDAQPEMRPPADA-------KERRRAAIGDTPAAEPPG- 279

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2126 idpysQQPPTPRPSPQTDMfvSSVANQRHTDPYTHHLGPP--RPGISVPYSQPPAVPRPRTSEGftRPSSA-RPALMPNQ 2202
Cdd:COG5180    280 -----LPVLEAGSEPQSDA--PEAETARPIDVKGVASAPPatRPVRPPGGARDPGTPRPGQPTE--RPAGVpEAASDAGQ 350

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2203 DP-FLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGpgridtfthasssavrDPYDQPPVTPRPHSESFGTSQVVHDLVDRP 2281
Cdd:COG5180    351 PPsAYPPAEEAVPGKPLEQGAPRPGSSGGDGAPF----------------QPPNGAPQPGLGRRGAPGPPMGAGDLVQAA 414


                   ....
gi 1039771187 2282 VPGS 2285
Cdd:COG5180    415 LDGG 418
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3136-3218 9.96e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3136 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3212
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 1039771187 3213 HAELIE 3218
Cdd:pfam01576  536 DAGTLE 541
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4436-4519 1.31e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 1.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4436 WVHLNCALWSTEVY--ETQAGALINVELALRRGL-QMKCVFCHKTGATS-GCHRFRCTNIYHFTCATKAqCMFFK----- 4506
Cdd:COG5141    268 WGHVICAMFNPELSfgHLLSKDPIDNIASVSSSRwKLGCLICKEFGGTCiQCSYFNCTRAYHVTCARRA-GYFDLniysh 346

                           90       100
                   ....*....|....*....|
gi 1039771187 4507 -------DKTMLCPMHKPKG 4519
Cdd:COG5141    347 ngisyciDHEPLCRKHYPLG 366
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4471-4515 1.88e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 1.88e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1039771187  4471 CVFCHKTGATS---GCHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1042-1091 1.99e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 1.99e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  1042 CPVCcRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1091
Cdd:smart00249    2 CSVC-GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDG---KWYCPKC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3233-3545 3.08e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.99  E-value: 3.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3233 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3301
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3302 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3374
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3375 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3445
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3446 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3521
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 1039771187 3522 NSNVPCGQDPAVTQGQNYSGSSQS 3545
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
mukB PRK04863
chromosome partition protein MukB;
3133-3223 5.49e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 43.41  E-value: 5.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3133 KQYEEWLQETQQLLQMQQKY--LEEQIGAHRKSKKALsakQRTAKKAGREFPEEDA---------EQLKHVTEQQSMVQK 3201
Cdd:PRK04863   503 RRLREQRHLAEQLQQLRMRLseLEQRLRQQQRAERLL---AEFCKRLGKNLDDEDEleqlqeeleARLESLSESVSEARE 579

                           90       100
                   ....*....|....*....|..
gi 1039771187 3202 QLEQIRKQQKEHAELIEDYRIK 3223
Cdd:PRK04863   580 RRMALRQQLEQLQARIQRLAAR 601
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 3127-3218 5.80e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 5.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3127 VNDSQRKQYEEwLQETQQLLQMQQKYLEEQigahRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQI 3206
Cdd:COG4942    144 LAPARREQAEE-LRADLAELAALRAELEAE----RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAEL 218

                           90
                   ....*....|..
gi 1039771187 3207 RKQQKEHAELIE 3218
Cdd:COG4942    219 QQEAEELEALIA 230
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4767-4919 7.39e-118

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 369.84  E-value: 7.39e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4767 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDA 4846
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4847 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 4766-4919 9.36e-108

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival.


Pssm-ID: 380985 [Multi-domain]  Cd Length: 154  Bit Score: 340.84  E-value: 9.36e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4766 SKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVID 4845
Cdd:cd19208      1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 4846 ATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd19208     81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 4765-4919 1.35e-94

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 303.54  E-value: 1.35e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4765 HSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVI 4844
Cdd:cd19209      1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 4845 DATLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd19209     81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4411-4515 2.06e-73

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 240.72  E-value: 2.06e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 4768-4916 1.40e-72

SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380916  Cd Length: 150  Bit Score: 240.19  E-value: 1.40e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4768 SSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQN-RGVYMFRMDNDHVIDA 4846
Cdd:cd10518      2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4847 TLTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNCR 4916
Cdd:cd10518     82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4411-4515 7.59e-70

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 230.27  E-value: 7.59e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15666      1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15666     81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4411-4516 1.10e-64

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 215.69  E-value: 1.10e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*.
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMHK 4516
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHK 106
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 4768-4920 3.81e-59

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 201.85  E-value: 3.81e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4768 SSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDAT 4847
Cdd:cd19170      2 AMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDAT 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4848 LTGGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4920
Cdd:cd19170     82 MHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1584-1664 1.82e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 1.82e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1584 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 1663
Cdd:cd22026      1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                   .
gi 1039771187 1664 N 1664
Cdd:cd22026     81 N 81
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 4779-4916 2.87e-54

SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated.


Pssm-ID: 380946  Cd Length: 148  Bit Score: 187.54  E-value: 2.87e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRG-VYMFRMDNDHVIDATLTGGPARYIN 4857
Cdd:cd19169     12 KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEAIGIGsSYLFRVDDDTIIDATKCGNLARFIN 91

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4858 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCR 4916
Cdd:cd19169     92 HSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIEDE--KIPCLCGAPQCR 148
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 247-330 8.44e-54

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 183.99  E-value: 8.44e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15696      7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                   ....
gi 1039771187  327 CPEH 330
Cdd:cd15696     87 CPTH 90
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 4779-4916 6.94e-49

SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3).


Pssm-ID: 380998  Cd Length: 148  Bit Score: 172.22  E-value: 6.94e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRG-VYMFRMDNDHVIDATLTGGPARYIN 4857
Cdd:cd20072     12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4858 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCR 4916
Cdd:cd20072     92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 4770-4920 6.68e-47

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac).


Pssm-ID: 380983 [Multi-domain]  Cd Length: 154  Bit Score: 166.74  E-value: 6.68e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4770 QYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLT 4849
Cdd:cd19206      4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 4850 GGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4920
Cdd:cd19206     84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 4770-4920 4.70e-44

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation.


Pssm-ID: 380984 [Multi-domain]  Cd Length: 154  Bit Score: 158.65  E-value: 4.70e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4770 QYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLT 4849
Cdd:cd19207      4 RFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 4850 GGPARYINHSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4920
Cdd:cd19207     84 GNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 247-330 2.18e-42

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 151.32  E-value: 2.18e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15665      7 GEVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                   ....
gi 1039771187  327 CPEH 330
Cdd:cd15665     87 CPEH 90
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 1589-1655 1.03e-41

high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins; This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, and farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. All subfamily members contain one HMG-box domain.


Pssm-ID: 438813  Cd Length: 67  Bit Score: 148.66  E-value: 1.03e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187 1589 KWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAAL 1655
Cdd:cd21997      1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1580-1661 2.26e-40

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 145.23  E-value: 2.26e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1580 LSNAQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINK 1659
Cdd:cd22027      2 LSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRINK 81


                   ..
gi 1039771187 1660 VQ 1661
Cdd:cd22027     82 VQ 83
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 4779-4920 1.20e-39

SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression.


Pssm-ID: 380981 [Multi-domain]  Cd Length: 153  Bit Score: 145.94  E-value: 1.20e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGV-YMFRMDNDHVIDATLTGGPARYIN 4857
Cdd:cd19204     13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4858 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4920
Cdd:cd19204     93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4779-4918 4.97e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 140.48  E-value: 4.97e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgvYMFRMDNDHVIDATLTGGPARYINH 4858
Cdd:COG2940      5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINH 82

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4859 SCAPNCVAEvvtfERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHkiPCHCGavNCRKW 4918
Cdd:COG2940     83 SCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 4779-4920 9.70e-38

SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.


Pssm-ID: 380982 [Multi-domain]  Cd Length: 153  Bit Score: 140.58  E-value: 9.70e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGV-YMFRMDNDHVIDATLTGGPARYIN 4857
Cdd:cd19205     13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4858 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDqhKIPCHCGAVNCRKWMN 4920
Cdd:cd19205     93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 4411-4515 1.47e-37

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 138.31  E-value: 1.47e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15664      1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15664     81 NYHFMCARKAECVFQDDKKVFCPAH 105
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 907-963 3.45e-36

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 132.45  E-value: 3.45e-36
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  907 KFTLQQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 963
Cdd:cd15596      1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4781-4902 1.17e-35

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 133.61  E-value: 1.17e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  4781 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNR-GVYMFRMDNDHVIDATLTGGPARYINHS 4859
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 1039771187  4860 CAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDD 4902
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 4409-4516 3.99e-34

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 128.58  E-value: 3.99e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4409 RKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRC 4488
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100
                   ....*....|....*....|....*...
gi 1039771187 4489 TNIYHFTCATKAQCMFFKDKTMLCPMHK 4516
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHK 108
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1041-1091 3.20e-32

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 120.80  E-value: 3.20e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1091
Cdd:cd15600      1 TCPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 4781-4916 6.41e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins.


Pssm-ID: 380929  Cd Length: 136  Bit Score: 123.13  E-value: 6.41e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4781 NVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQN-RGVYMFRMDNDHVIDATLTGGPARYINHS 4859
Cdd:cd10531      1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERLDEYEELGkSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 4860 CAPNCVAEvVTFERGHKII-ISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNCR 4916
Cdd:cd10531     81 CEPNCETQ-KWIVNGEYRIgIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 4780-4919 6.76e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.


Pssm-ID: 380949 [Multi-domain]  Cd Length: 142  Bit Score: 123.46  E-value: 6.76e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4780 SNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRM-DNDHVIDATLTGGPARYINH 4858
Cdd:cd19172      2 AKVEVFRTEKKGWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYAREGNRHYYFMAlKSDEIIDATKKGNLSRFINH 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4859 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFD--FEDDQhkiPCHCGAVNCRKWM 4919
Cdd:cd19172     82 SCEPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFEryGKEAQ---KCYCGSPNCRGYI 141
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 4791-4919 2.75e-31

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).


Pssm-ID: 380952 [Multi-domain]  Cd Length: 139  Bit Score: 121.37  E-value: 2.75e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVAnrKEKLYESQNRG---VYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAE 4867
Cdd:cd19175     11 GWGLVADEDINAGEFIIEYVGEVIDDKTC--EERLWDMKHKGeknFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQ 88

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4868 VVTFERGHKIIISSNRRIQKGEELCYDYKF-DFEDDQHkipCHCGAVNCRKWM 4919
Cdd:cd19175     89 KWQVDGETRIGVFAIRDIKKGEELTYDYQFvQFGADQD---CHCGSKNCRGKL 138
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 4782-4895 3.59e-31

SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380917  Cd Length: 117  Bit Score: 120.43  E-value: 3.59e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4782 VYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGvYMFRMDNDHVIDATLTGGPARYINHSCA 4861
Cdd:cd10519      3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1039771187 4862 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd10519     82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDY 115
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 4791-4915 4.76e-31

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.


Pssm-ID: 380950 [Multi-domain]  Cd Length: 142  Bit Score: 120.88  E-value: 4.76e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4869
Cdd:cd19173     13 GWGLRTKRDIKKGDFVIEYVGELIdEEECRRRLKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187 4870 TFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNC 4915
Cdd:cd19173     93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 964-1010 4.30e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.88  E-value: 4.30e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 914-962 2.50e-29

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 112.56  E-value: 2.50e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  914 MCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 962
Cdd:cd15512      1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4791-4896 3.89e-29

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 114.54  E-value: 3.89e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGT-IIRNEVANRKEKLYESQNR----GVYMFRMDND--HVIDATLT--GGPARYINHSCA 4861
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDseYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1039771187 4862 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYK 4896
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4791-4919 6.14e-29

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.


Pssm-ID: 380940 [Multi-domain]  Cd Length: 245  Bit Score: 118.55  E-value: 6.14e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMD-----NDHVIDATLTGGPARYINHSCAPN-- 4863
Cdd:cd10542     99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNla 177

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4864 ---CVAEVVtFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQH----------KIPCHCGAVNCRKWM 4919
Cdd:cd10542    178 vyaVWINHL-DPRLPRIAFFAKRDIKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 390-435 8.30e-29

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 111.18  E-value: 8.30e-29
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 247-330 1.46e-28

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 111.93  E-value: 1.46e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  247 GTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLL 326
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1039771187  327 CPEH 330
Cdd:cd15695     87 CPEH 90
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 4411-4515 5.19e-28

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 111.14  E-value: 5.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPArLLNLDLDLWVHLNCALWSTEVYETQAGAL--INVELALRRGLQMKCVFCHKT-GATSGCHRFR 4487
Cdd:cd15571      1 CALCPRSGGALKGGGA-LKTTSDGLWVHVVCALWSPEVYFDDGTLLevEGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1039771187 4488 CTNIYHFTCATKAQCMF-----FKDKTMLCPMH 4515
Cdd:cd15571     80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 466-517 1.68e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 107.57  E-value: 1.68e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  466 LCPFCGKCYHPELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYC 517
Cdd:cd15511      1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 4411-4515 2.93e-27

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 108.59  E-value: 2.93e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15694      1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4491 IYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15694     81 NFHFMCARASRCCFQDDKKVFCQKH 105
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 913-962 6.78e-27

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 105.89  E-value: 6.78e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  913 DMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 962
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 50
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 4791-4920 6.90e-26

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).


Pssm-ID: 380951 [Multi-domain]  Cd Length: 141  Bit Score: 106.22  E-value: 6.90e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYeSQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCvaEVV 4869
Cdd:cd19174     11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQY-HNHSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNC--EMQ 87

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4870 TFE-RG-HKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN 4920
Cdd:cd19174     88 KWSvNGvYRIGLFALKDIPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 390-435 3.08e-25

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 100.97  E-value: 3.08e-25
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15510      1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4617-4701 8.78e-25

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 100.76  E-value: 8.78e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4617 RPVFVIRIVEqgHEDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENY 4696
Cdd:pfam05965    1 GPLFRVTVEE--DPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1039771187 4697 TFRYG 4701
Cdd:pfam05965   79 KFRYG 83
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4619-4706 9.13e-25

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 100.83  E-value: 9.13e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  4619 VFVIRIVEQGheDLVLSDSSPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYTF 4698
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1039771187  4699 RYGRNPLM 4706
Cdd:smart00542   79 RYHRSPLL 86
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1041-1091 1.42e-24

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 99.28  E-value: 1.42e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1091
Cdd:cd15514      1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 4778-4897 1.54e-23

SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380995  Cd Length: 120  Bit Score: 98.83  E-value: 1.54e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4778 WKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsQNRGVYMFRMDNDHVIDATLTGGPARYIN 4857
Cdd:cd19218      2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYD-KYMCSFLFNLNNDFVVDATRKGNKIRFAN 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1039771187 4858 HSCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKF 4897
Cdd:cd19218     81 HSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 343-388 1.83e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 95.84  E-value: 1.83e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TPLKRAGWQCPEC 388
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVrpTPLVRAGWQCPEC 48
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 390-435 7.52e-23

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 93.91  E-value: 7.52e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1041-1091 3.90e-22

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 92.28  E-value: 3.90e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMC 1091
Cdd:cd15601      1 TCPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 4779-4901 5.00e-22

SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380994  Cd Length: 136  Bit Score: 95.13  E-value: 5.00e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsQNRGVYMFRMDNDHVIDATLTGGPARYINH 4858
Cdd:cd19217      5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD-KYMSSFLFNLNNDFVVDATRKGNKIRFANH 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1039771187 4859 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFED 4901
Cdd:cd19217     84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1824-2314 2.16e-21

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 104.25  E-value: 2.16e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1824 ESLSQSQNSQPP---SPQMFSPGSSHSRPPSPvdpYAkmvgtPRPP-PGGHSFPRRNSVTPvencvplssvprpihmnet 1899
Cdd:PHA03247  2541 EELASDDAGDPPpplPPAAPPAAPDRSVPPPR---PA-----PRPSePAVTSRARRPDAPP------------------- 2593

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1900 SATRPSPARDLCASSMTNSDPYAKPPDTPRPmmtdqfsKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPS--PRTDAFQR 1977
Cdd:PHA03247  2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-------DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPapGRVSRPRR 2666

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1978 QRLPDPYAGPSLTPaplgNGPfktplHPPPSQDPYGSVSQTSRRLSVDPYERPA------LTPRPVDNFSHSQSNDPYSH 2051
Cdd:PHA03247  2667 ARRLGRAAQASSPP----QRP-----RRRAARPTVGSLTSLADPPPPPPTPEPAphalvsATPLPPGPAAARQASPALPA 2737

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2052 PPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTP-----RPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTI 2126
Cdd:PHA03247  2738 APAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPprrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2127 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYT------------HHLGPPRPGISVPYSQP---------PAVPRPRTS 2185
Cdd:PHA03247  2818 LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLplggsvapggdvRRRPPSRSPAAKPAAPArppvrrlarPAVSRSTES 2897

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2186 EGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPdtcsqtPRPPGPGRIDTFTHAS---SSAVRDPYDQPPVTPR 2262
Cdd:PHA03247  2898 FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP------PRPQPPLAPTTDPAGAgepSGAVPQPWLGALVPGR 2971

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2263 PHSESFGTSQvvhDLVDRPVPGSEGNFSTSSNLP-VSSQGQQFS-SVSQLPGPV 2314
Cdd:PHA03247  2972 VAVPRFRVPQ---PAPSREAPASSTPPLTGHSLSrVSSWASSLAlHEETDPPPV 3022
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4786-4895 2.05e-20

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 93.20  E-value: 2.05e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4786 RSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYeSQNRGVYMFRMDND---------HVIDATLTGGPARYI 4856
Cdd:cd10538     95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIY-DKSGGSYLFDLDEFsdsdgdgeeLCVDATFCGNVSRFI 173

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1039771187 4857 NHSCAPN----CVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd10538    174 NHSCDPNlfpfNVVIDHDDLRYPRIALFATRDILPGEELTFDY 216
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 4784-4915 6.25e-20

SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS).


Pssm-ID: 380988 [Multi-domain]  Cd Length: 142  Bit Score: 89.28  E-value: 6.25e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4784 LARSRIQGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAP 4862
Cdd:cd19211      6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIdEEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4863 NCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIpCHCGAVNC 4915
Cdd:cd19211     86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTV-CRCGAPNC 137
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 4411-4515 1.73e-19

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 86.59  E-value: 1.73e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFC--HEEGDGLTD--GPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGCHRF 4486
Cdd:cd15668      1 CVFCkrGPHYKGLGDlfGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039771187 4487 RCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4515
Cdd:cd15668     74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 241-330 7.45e-19

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 84.94  E-value: 7.45e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  241 ALFDSTGTCWAHHRCVEWS--LGICQMEEPLLVNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTF 317
Cdd:cd15571     16 ALKTTSDGLWVHVVCALWSpeVYFDDGTLLEVEGVSKIPKRRKKLKCSICGKrGGACIQCSYPGCPRSFHVSCAIRAGCL 95

                           90
                   ....*....|....*..
gi 1039771187  318 QDFS----HFFLLCPEH 330
Cdd:cd15571     96 FEFEdgpgNFVVYCPKH 112
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 4788-4895 1.09e-18

SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes.


Pssm-ID: 380926 [Multi-domain]  Cd Length: 141  Bit Score: 85.71  E-value: 1.09e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4788 RIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYES-QNRGVYM--FRMDN-DHVIDATL-TGGPARYINHSC-A 4861
Cdd:cd10528     25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGkTYCVDATKeSGRLGRLINHSKkK 104

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1039771187 4862 PNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd10528    105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4560-4611 4.67e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 80.63  E-value: 4.67e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 4560 GSLIFHTIGQLLPQQMqAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSI 4611
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4779-4916 4.76e-18

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380941 [Multi-domain]  Cd Length: 231  Bit Score: 86.62  E-value: 4.76e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4779 KSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyESqnrgvYMFRMDND----HVIDATLTGGPAR 4854
Cdd:cd10543     90 RYRLQLFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED--DS-----YLFDLDNKdgetYCIDARRYGNISR 162

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4855 YINHSCAPNCVAevVTFERGH------KIIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCR 4916
Cdd:cd10543    163 FINHLCEPNLIP--VRVFVEHqdlrfpRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4411-4515 1.36e-17

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 80.44  E-value: 1.36e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCheegdgltdgparllNLDlDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTN 4490
Cdd:cd15665      1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                           90       100
                   ....*....|....*....|....*.
gi 1039771187 4491 IYHFTCATKAQCM-FFKDKTMLCPMH 4515
Cdd:cd15665     65 SFHFPCAAAAGCFqDIKTLTLFCPEH 90
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4790-4915 1.45e-17

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy.


Pssm-ID: 380989 [Multi-domain]  Cd Length: 142  Bit Score: 82.28  E-value: 1.45e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEV 4868
Cdd:cd19212     12 RGWGLRTKRSIKKGEFVNEYVGELIdEEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187 4869 VTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIpCHCGAVNC 4915
Cdd:cd19212     92 WTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTE-CHCGADNC 137
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1905-2550 6.26e-17

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 89.61  E-value: 6.26e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1905 SPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPfSLPRSPVISEQS-TKGPLTTGTSdhftkPSPRTDAfqrqrLPDP 1983
Cdd:PHA03247  2438 SPGGDVLAGLAADGDPFFARTILGAPFSLSLLLGE-LFPGAPVYRRPAeARFPFAAGAA-----PDPGGGG-----PPDP 2506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1984 YAGP---SLTPAPLGNGPFKTPLHPppsqdpygsvsqtsrrlsvdpyeRPALTPRPVDNFSHSQSNDPYSHPPLTPHPAM 2060
Cdd:PHA03247  2507 DAPPapsRLAPAILPDEPVGEPVHP-----------------------RMLTWIRGLEELASDDAGDPPPPLPPAAPPAA 2563

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2061 TESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPlidsysqtsgtaRSNPDPYSQPPGTPRPNTIDPYSQQPPTPRPSP 2140
Cdd:PHA03247  2564 PDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARP------------RAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSP 2631

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2141 qtdmfvSSVANQRhtdPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSA--------RPALMPNQDPFLQAAQNR 2212
Cdd:PHA03247  2632 ------SPAANEP---DPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQAssppqrprRRAARPTVGSLTSLADPP 2702

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2213 VPGlPGPLIRPPDTCSQTPRPPGPgridtfthassSAVRDPYDQPPVTPRPHSESFGTSqvvhdlvdrpVPGSEGNFSTs 2292
Cdd:PHA03247  2703 PPP-PTPEPAPHALVSATPLPPGP-----------AAARQASPALPAAPAPPAVPAGPA----------TPGGPARPAR- 2759

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2293 snlPVSSQGQQFSSVSQLP--GPVPTSggtdTQNTVNMSQADTEKLrqrqklreiilqqqqqkkiasrqeKGPQDTAVVP 2370
Cdd:PHA03247  2760 ---PPTTAGPPAPAPPAAPaaGPPRRL----TRPAVASLSESRESL------------------------PSPWDPADPP 2808

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2371 HPVPLPH-WQPESINQAFTRPPPPY-----PGSTRSPVIPPLGPRYAVFPK---DQRGP--YPPEVAGMGMRPHGFRFGF 2439
Cdd:PHA03247  2809 AAVLAPAaALPPAASPAGPLPPPTSaqptaPPPPPGPPPPSLPLGGSVAPGgdvRRRPPsrSPAAKPAAPARPPVRRLAR 2888

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2440 PGaghgPMPSQDRFHVPQ-QIQGSGIPPHIRRPMSMEMPRPSNNPPLNNPV-GLPQ-HFPPQGLPVQQHNILGQA-FIEL 2515
Cdd:PHA03247  2889 PA----VSRSTESFALPPdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPpPRPQpPLAPTTDPAGAGEPSGAVpQPWL 2964

                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 1039771187 2516 RHRAPDG----RSRLPFAASPSSVIESPSHPRHGNFLPR 2550
Cdd:PHA03247  2965 GALVPGRvavpRFRVPQPAPSREAPASSTPPLTGHSLSR 3003
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1814-2317 7.40e-17

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 89.23  E-value: 7.40e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1814 PSTPSRIPVQESLS-QSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKmvgTPRPPPGGHSfPRRNSVTPVEncvPLSSVPR 1892
Cdd:PHA03247  2577 PSEPAVTSRARRPDaPPQSARPRAPVDDRGDPRGPAPPSPLPPDTH---APDPPPPSPS-PAANEPDPHP---PPTVPPP 2649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1893 PIHMNETSATRPSPARDlcASSMTNSDPYAKPPDTPRPMMTDQFSKP---FSLPRSPVISEQSTKGPLTTGTsdhftkPS 1969
Cdd:PHA03247  2650 ERPRDDPAPGRVSRPRR--ARRLGRAAQASSPPQRPRRRAARPTVGSltsLADPPPPPPTPEPAPHALVSAT------PL 2721

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1970 PRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPyERPALTPRPVDNFSHSQSN--- 2046
Cdd:PHA03247  2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAG-PPRRLTRPAVASLSESRESlps 2800

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2047 --DPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNP--DPYSQPPGTPR 2122
Cdd:PHA03247  2801 pwDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPsrSPAAKPAAPAR 2880

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2123 P-----------NTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRP 2191
Cdd:PHA03247  2881 PpvrrlarpavsRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2192 SSARPALMPNQDPflqAAQNRVPGlPGPLIRPPDTCSQTPRPPGPGRIDTFthASSSAVRDPYDQPPVT-------PRPH 2264
Cdd:PHA03247  2961 QPWLGALVPGRVA---VPRFRVPQ-PAPSREAPASSTPPLTGHSLSRVSSW--ASSLALHEETDPPPVSlkqtlwpPDDT 3034

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 2265 SESFGTSQVVHDLVDR------PVPGSEGNFSTSSNLPVSSQGQQFSSVSQLPGPVPTS 2317
Cdd:PHA03247  3035 EDSDADSLFDSDSERSdlealdPLPPEPHDPFAHEPDPATPEAGARESPSSQFGPPPLS 3093
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 4791-4901 9.30e-17

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.


Pssm-ID: 380920 [Multi-domain]  Cd Length: 122  Bit Score: 79.31  E-value: 9.30e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNrgvYMFRMDNDH-VIDATLTGGPARYINHSCAPNCVAEVV 4869
Cdd:cd10522     14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1039771187 4870 TFERGHKIIISSNRRIQKGEELCYDYKFDFED 4901
Cdd:cd10522     91 TLKGEQHIGFVAIRDIKPGEELFISYGPKYWK 122
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1838-2414 1.21e-16

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 88.46  E-value: 1.21e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1838 QMFSPGSSHSRPPSPVDPYAkmvGTPRPPPGGhsfprrnSVTPVENCVPLSSVPRPIHMNETSATRPSPARDLC------ 1911
Cdd:PHA03247  2472 ELFPGAPVYRRPAEARFPFA---AGAAPDPGG-------GGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTwirgle 2541

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1912 --ASSMTNSDPYAKPPDtPRPMMTDQfSKPFSLP-------------RSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQ 1976
Cdd:PHA03247  2542 elASDDAGDPPPPLPPA-APPAAPDR-SVPPPRPaprpsepavtsraRRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPP 2619

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1977 RQRLPDPyagPSLTPAPLGN-----GPFKTPLHPPPSQDPYGSVSQTSRRLSvdpyeRPALTPRPvdnfshsqsndpySH 2051
Cdd:PHA03247  2620 DTHAPDP---PPPSPSPAANepdphPPPTVPPPERPRDDPAPGRVSRPRRAR-----RLGRAAQA-------------SS 2678

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2052 PPLTPHPamtesfthasRAFPqPGTISRSASQDPYSQPPgTPRPlidsysqtSGTARSNPDPysQPPGTPRPNTIDPYSQ 2131
Cdd:PHA03247  2679 PPQRPRR----------RAAR-PTVGSLTSLADPPPPPP-TPEP--------APHALVSATP--LPPGPAAARQASPALP 2736

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2132 QPPTPRPSPQTDmfVSSVANQRHTDPYTHHlGPPRPgisVPYSQPPAVPRPRTsegfTRPSSARPALMPNQDPFLQAAQN 2211
Cdd:PHA03247  2737 AAPAPPAVPAGP--ATPGGPARPARPPTTA-GPPAP---APPAAPAAGPPRRL----TRPAVASLSESRESLPSPWDPAD 2806

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2212 RVPGLPGPliRPPDTCSQTPRPPGPgridTFTHASSSAvrdpydqPPVTPRPHSESFGTSQVVH---DLVDRPVPGSEGN 2288
Cdd:PHA03247  2807 PPAAVLAP--AAALPPAASPAGPLP----PPTSAQPTA-------PPPPPGPPPPSLPLGGSVApggDVRRRPPSRSPAA 2873

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2289 FSTSSNLPvssqgqqfsSVSQLPGPVPTsggtdtQNTVNMSQADTEKLRQRQklreiilqqqqqkkiasrqekgpqdtav 2368
Cdd:PHA03247  2874 KPAAPARP---------PVRRLARPAVS------RSTESFALPPDQPERPPQ---------------------------- 2910

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187 2369 vPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFP 2414
Cdd:PHA03247  2911 -PQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEP 2955
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4570-4613 1.45e-16

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 76.17  E-value: 1.45e-16
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1039771187  4570 LLPQQMQAFHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEE 4613
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 4791-4919 2.25e-16

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.


Pssm-ID: 380942 [Multi-domain]  Cd Length: 254  Bit Score: 82.35  E-value: 2.25e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyeSQNRG----VYMFR--MDNDHV----IDATLTGGPARYINHSC 4860
Cdd:cd10544    101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGdmnyIIVLRehLSSGKVletfVDPTYIGNIGRFLNHSC 177

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 4861 APNCVAEVVtfeRGH----KIIISSNRRIQKGEELCYDY------------KFDFEDDQHKIPCHCGAVNCRKWM 4919
Cdd:cd10544    178 EPNLFMVPV---RVDsmvpKLALFAARDIVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRGFL 249
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 4790-4919 2.50e-16

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.


Pssm-ID: 380999 [Multi-domain]  Cd Length: 259  Bit Score: 82.23  E-value: 2.50e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYEsqNRGV-YMFRMD-------NDHVIDATLTGGPARYINHSCA 4861
Cdd:cd20073    103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFDLDlfedqvdEYYTVDAQYCGDVTRFINHSCD 180

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 4862 PNCVAEVV----TFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQ----------------HKIPCHCGAVNCRKWM 4919
Cdd:cd20073    181 PNLAIYSVlrdkSDSKIYDLAFFAIKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4780-4915 8.03e-16

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation.


Pssm-ID: 380987 [Multi-domain]  Cd Length: 142  Bit Score: 77.27  E-value: 8.03e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4780 SNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTII-RNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINH 4858
Cdd:cd19210      2 PEVEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIdEEECRARIRYAQEHDITNFYMLTLDKDRIIDAGPKGNYARFMNH 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187 4859 SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFEDDQhKIPCHCGAVNC 4915
Cdd:cd19210     82 CCQPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYNLECLGNG-KTVCKCGAPNC 137
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4767-4916 8.36e-16

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380933 [Multi-domain]  Cd Length: 231  Bit Score: 79.98  E-value: 8.36e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4767 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyesqnrGVYMFRMDND----H 4842
Cdd:cd10535     78 RNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4843 VIDATLTGGPARYINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKI-PCHCGAVNCR 4916
Cdd:cd10535    151 CIDARFYGNVSRFINHHCEPNLVPVRVFMAhqdlRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 4781-4895 1.88e-15

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


Pssm-ID: 380914 [Multi-domain]  Cd Length: 72  Bit Score: 73.82  E-value: 1.88e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4781 NVYLARSRIQGLGLYAARDIEKhtmvieyiGTIIrnevanrkeklyesqnrgvymfrmdndhvidatltgGPARYINHSC 4860
Cdd:cd08161      1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1039771187 4861 APNCVAEVVTFERGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd08161     37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 4782-4899 2.31e-15

SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380945  Cd Length: 124  Bit Score: 75.30  E-value: 2.31e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4782 VYLARSRIQ-GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMDNDHVIDATLTGGPARYINH-- 4858
Cdd:cd19168      3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1039771187 4859 --SCAPNCVAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDF 4899
Cdd:cd19168     82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNYGDNF 124
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 4791-4919 2.45e-15

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.


Pssm-ID: 380996 [Multi-domain]  Cd Length: 274  Bit Score: 79.67  E-value: 2.45e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVAN-RKEKLYESQNRGVYMFRMD---NDHVIDATLTG-----------GPARY 4855
Cdd:cd19473    117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFALDkfsDPDSLDPRLRGdpyeidgefmsGPTRF 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4856 INHSCAPNC-VAEVVT------FergHKIIISSNRRIQKGEELCYDY----------KFDFEDDQHKIPCHCGAVNCRKW 4918
Cdd:cd19473    197 INHSCDPNLrIFARVGdhadkhI---HDLAFFAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGY 273


                   .
gi 1039771187 4919 M 4919
Cdd:cd19473    274 L 274
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 964-1009 3.05e-15

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 72.50  E-value: 3.05e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15519      1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 4793-4899 3.44e-15

SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380927  Cd Length: 127  Bit Score: 75.00  E-value: 3.44e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4793 GLYAARDIEKHTMVIEYIGTI-IRNEVANRKEKLYESQNRgVYMF--RMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4869
Cdd:cd10529     18 GLVATEDISPGEPILEYKGEVsLRSEFKEDNGFFKRPSPF-VFFYdgFEGLPLCVDARKYGNEARFIRRSCRPNAELRHV 96

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1039771187 4870 TFERG-HKIIISSNRRIQKGEELCYDYKFDF 4899
Cdd:cd10529     97 VVSNGeLRLFIFALKDIRKGTEITIPFDYDY 127
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4790-4919 3.80e-15

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380930 [Multi-domain]  Cd Length: 243  Bit Score: 78.39  E-value: 3.80e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRgVYMFRMD---NDHVIDATLTGGPARYINHSCAPNCVA 4866
Cdd:cd10532     95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYDSKGI-TYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQV 173

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4867 EVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDD-------------QHKIPCHCGAVNCRKWM 4919
Cdd:cd10532    174 FNVFIDnldtRLPRIALFSTRTIKAGEELTFDYQMKGSGDlssdsidnspakkRVRTVCKCGAVTCRGYL 243
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4790-4919 6.73e-15

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380923 [Multi-domain]  Cd Length: 255  Bit Score: 78.01  E-value: 6.73e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNrGVYMFRMD---NDHVIDATLTGGPARYINHSCAPNCVA 4866
Cdd:cd10525     97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDLDyveDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4867 EVVTF----ERGHKIIISSNRRIQKGEELCYDYKF-----DFEDDQH-----------------KIPCHCGAVNCRKWM 4919
Cdd:cd10525    176 YNVFIdnldERLPRIALFATRTIRAGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 964-1009 8.76e-15

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 71.14  E-value: 8.76e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15603      1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 391-435 8.84e-15

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 71.27  E-value: 8.84e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 964-1009 1.29e-14

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 70.50  E-value: 1.29e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 249-330 1.46e-14

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 72.44  E-value: 1.46e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  249 CWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAG-TFQDFSHFFllC 327
Cdd:cd15664     25 EWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCARKAEcVFQDDKKVF--C 102


                   ...
gi 1039771187  328 PEH 330
Cdd:cd15664    103 PAH 105
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4438-4515 2.10e-14

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 71.59  E-value: 2.10e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4438 HLNCALWSTEVYetQAGA------LINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKT 4509
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 1039771187 4510 ----MLCPMH 4515
Cdd:pfam13771   79 gtfkSYCKKH 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1828-2249 2.29e-14

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 80.58  E-value: 2.29e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1828 QSQNSQPPSPQMFSPGSShsrPPSPVDPYAKMVGTPRPPPGGHSFPrrnsvtpvencvplssvprpihmnetsatrpspa 1907
Cdd:pfam03154  165 QILQTQPPVLQAQSGAAS---PPSPPPPGTTQAATAGPTPSAPSVP---------------------------------- 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1908 rdlcassmtnsdPYAKPPDTPRPMMTDQFSKPFSLPRSpviseqstkgplttgtsdhftkpsprTDAFQRQRLPDPYagP 1987
Cdd:pfam03154  208 ------------PQGSPATSQPPNQTQSTAAPHTLIQQ--------------------------TPTLHPQRLPSPH--P 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1988 SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERP-ALTPRPVDNFSH-SQSNDPYSHPPLTPHPAMTESFT 2065
Cdd:pfam03154  248 PLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPQPFPLTPQsSQSQVPPGPSPAAPGQSQQRIHT 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2066 HASRAFPQPGTISRSASQDP-------YSQPPGTPRP-LIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS----QQP 2133
Cdd:pfam03154  328 PPSQSQLQSQQPPREQPLPPaplsmphIKPPPTTPIPqLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslstHHP 407

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2134 PTPRPSPQTDMFVSS----------VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR--PSSARPALMPN 2201
Cdd:pfam03154  408 PSAHPPPLQLMPQSQqlppppaqppVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPitPPSGPPTSTSS 487

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2202 QDPFLQAAQNRVPGLPGPLI--------------RPPDTCSQTPRPPGPGR--------IDTFTHASSSA 2249
Cdd:pfam03154  488 AMPGIQPPSSASVSSSGPVPaavscplppvqikeEALDEAEEPESPPPPPRspspeptvVNTPSHASQSA 557
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 4411-4515 4.09e-14

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 71.10  E-value: 4.09e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGD----GLTDGPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGCHRF 4486
Cdd:cd15699      1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLV-CGRLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039771187 4487 RCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4515
Cdd:cd15699     74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 250-330 4.16e-14

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 71.18  E-value: 4.16e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT--FQDFShffLLC 327
Cdd:cd15666     26 WVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGCmfFKDKT---MLC 102


                   ...
gi 1039771187  328 PEH 330
Cdd:cd15666    103 PSH 105
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4767-4916 6.74e-14

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380931 [Multi-domain]  Cd Length: 239  Bit Score: 74.67  E-value: 6.74e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4767 KSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKlyesqnrGVYMFRMDND----H 4842
Cdd:cd10533     78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4843 VIDATLTGGPARYINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCR 4916
Cdd:cd10533    151 CIDARYYGNISRFINHLCDPNIIPVRVFMLhqdlRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 965-1009 9.26e-14

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 68.06  E-value: 9.26e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 964-1009 1.05e-13

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 68.04  E-value: 1.05e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 250-330 1.68e-13

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 69.26  E-value: 1.68e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICqMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15668     24 WVHEDCAVWAPGVY-LVGGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENFSLLCPK 102


                   .
gi 1039771187  330 H 330
Cdd:cd15668    103 H 103
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 964-1009 1.99e-13

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 67.09  E-value: 1.99e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15605      1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 964-1009 2.62e-13

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 67.07  E-value: 2.62e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15510      1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1754-2192 2.63e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 77.67  E-value: 2.63e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1754 APGSDTPSSGAQSPLTPqagngnvSPAQTfhkdlfskHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPVQE------SLS 1827
Cdd:PHA03247  2600 APVDDRGDPRGPAPPSP-------LPPDT--------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDpapgrvSRP 2664

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1828 QSQNSQPPSPQMFSPGSSHSRP--PSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVENCVPLSSVPRPIHMNETSATRPS 1905
Cdd:PHA03247  2665 RRARRLGRAAQASSPPQRPRRRaaRPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAV 2744

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1906 PARDLCASSMTN--SDPYAKPPDTPRPMMTDQFSKPFSLPRSPV--ISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLP 1981
Cdd:PHA03247  2745 PAGPATPGGPARpaRPPTTAGPPAPAPPAAPAAGPPRRLTRPAVasLSESRESLPSPWDPADPPAAVLAPAAALPPAASP 2824

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1982 DPYAGPSLTPAPLGngPFKTPLHPPPSQDPYGSVS---QTSRR-LSVDPYERPALTPRP----VDNFSHSQSNDPYSHPP 2053
Cdd:PHA03247  2825 AGPLPPPTSAQPTA--PPPPPGPPPPSLPLGGSVApggDVRRRpPSRSPAAKPAAPARPpvrrLARPAVSRSTESFALPP 2902

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2054 LTPHPAMTESFTHASRAFPQPGTISRSASQD---PYSQPPGTPRPLIDSYSQTSGTArSNPDPYSQPPG----------T 2120
Cdd:PHA03247  2903 DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPpppPRPQPPLAPTTDPAGAGEPSGAV-PQPWLGALVPGrvavprfrvpQ 2981

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2121 PRPNTIDPYSQQPP----------------------TPRPS-------PQTDMFVSSVANQRHTDPYTHHLGPPRPGISV 2171
Cdd:PHA03247  2982 PAPSREAPASSTPPltghslsrvsswasslalheetDPPPVslkqtlwPPDDTEDSDADSLFDSDSERSDLEALDPLPPE 3061

                          490       500
                   ....*....|....*....|.
gi 1039771187 2172 PYSQPPAVPRPRTSEGFTRPS 2192
Cdd:PHA03247  3062 PHDPFAHEPDPATPEAGARES 3082
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 965-1009 2.77e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 67.03  E-value: 2.77e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4434-4515 2.98e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 68.43  E-value: 2.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4434 DLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMF-FKDKTMLC 4512
Cdd:cd15696      8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQdFSRRLLLC 87


                   ...
gi 1039771187 4513 PMH 4515
Cdd:cd15696     88 PTH 90
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4434-4515 3.16e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 68.02  E-value: 3.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4434 DLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATkAQCMFFKDKT--ML 4511
Cdd:cd15695      8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAA-ASGSFQSMKTllLL 86


                   ....
gi 1039771187 4512 CPMH 4515
Cdd:cd15695     87 CPEH 90
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 964-1010 3.60e-13

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 66.51  E-value: 3.60e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15602      1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCV 47
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 250-330 3.74e-13

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 68.54  E-value: 3.74e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAG-TFqdFSHFFLLCP 328
Cdd:cd15697     26 WVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTCAIKAQcMF--FKDKTMLCP 103


                   ..
gi 1039771187  329 EH 330
Cdd:cd15697    104 MH 105
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 391-435 4.83e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 66.18  E-value: 4.83e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 4411-4515 5.22e-13

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 67.98  E-value: 5.22e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEegdgltdgPARLLNL-DL------DLWVHLNCALWSTEVYETqAGALINVELALRRGLQMKCVFCHKTGATSGC 4483
Cdd:cd15700      1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1039771187 4484 HRFRCTNIYHFTCATKAQCMFFKDK-TMLCPMH 4515
Cdd:cd15700     72 CHKGCTQSYHYICAVEAGCLFEEENfSLRCPKH 104
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 965-1009 6.79e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 65.90  E-value: 6.79e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2090-2697 7.02e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 76.13  E-value: 7.02e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2090 PGTP---RPLIDSYSQTSGTArsnPDPYSQPPgtPRPNTIDPYSQQPPTPRPSPQTDMFV-----------SSVANQRHT 2155
Cdd:PHA03247  2475 PGAPvyrRPAEARFPFAAGAA---PDPGGGGP--PDPDAPPAPSRLAPAILPDEPVGEPVhprmltwirglEELASDDAG 2549

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2156 DPythhlGPPRPGISVP----YSQPPAVPRPRTSEGFTRPSSARPALMPnqdpflQAAQNRVPGlpGPLIRPPDTCSQTP 2231
Cdd:PHA03247  2550 DP-----PPPLPPAAPPaapdRSVPPPRPAPRPSEPAVTSRARRPDAPP------QSARPRAPV--DDRGDPRGPAPPSP 2616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2232 RPPGPgridtfthasssavrDPYDQPPVTPRPH-SESFGTSQVVHDLVDRPVPGSEGNfSTSSNLPVSSQGQQFSSVSQL 2310
Cdd:PHA03247  2617 LPPDT---------------HAPDPPPPSPSPAaNEPDPHPPPTVPPPERPRDDPAPG-RVSRPRRARRLGRAAQASSPP 2680

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2311 PGPVPTSGGTDTQNTVNMSQA-DTEKLRQRQKLREIILQQQQQKKIASRQEKGPQDTAVVPHPVPLPHWQPESINQAFTR 2389
Cdd:PHA03247  2681 QRPRRRAARPTVGSLTSLADPpPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP 2760

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2390 PPPPYPGSTRSPVIPPLGPRyavfpkdQRGPYPPEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPhir 2469
Cdd:PHA03247  2761 PTTAGPPAPAPPAAPAAGPP-------RRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--- 2830

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2470 rPMSMemprpsnnpplnnpvgLPQHFPPQGLPVQQHNILGQAFielrhrAPDGR-SRLPFAASPSSVIESPSHPRHGNF- 2547
Cdd:PHA03247  2831 -PTSA----------------QPTAPPPPPGPPPPSLPLGGSV------APGGDvRRRPPSRSPAAKPAAPARPPVRRLa 2887

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2548 ---LPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP------------------LNHP 2606
Cdd:PHA03247  2888 rpaVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPttdpagagepsgavpqpwLGAL 2967

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2607 LSGEFS-------------EAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKE-LDVKDlegvevkDLDDEDLE 2672
Cdd:PHA03247  2968 VPGRVAvprfrvpqpapsrEAPASSTPPLTGHSLSRVSSWASSLALHEETDPPPVSLKQtLWPPD-------DTEDSDAD 3040

                          650       660
                   ....*....|....*....|....*.
gi 1039771187 2673 NLNL-DTEDGKGDDLDTLDNlETNDP 2697
Cdd:PHA03247  3041 SLFDsDSERSDLEALDPLPP-EPHDP 3065
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 4411-4515 8.39e-13

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 67.80  E-value: 8.39e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGParLLNLDLDLWVHLNCALWSTEVYETQ-------AGALIN-VELALRRGLQMKCVFCHKTGATSG 4482
Cdd:cd15673      1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1039771187 4483 CHRFRCTNIYHFTCATKAQCMFFKDK-----TMLCPMH 4515
Cdd:cd15673     79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 390-435 1.15e-12

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 65.19  E-value: 1.15e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 252-330 1.42e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 66.20  E-value: 1.42e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  252 HHRCVEWSLGICQ-----MEEPLLvNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCAAGAGTFQDFSH--- 322
Cdd:pfam13771    1 HVVCALWSPELVQrgndsMGFPIE-DIEKIPKRRWKLKCYLCKKkGGACIQCSKKNCRRAFHVTCALEAGLLMQFDEdng 79


                   ....*....
gi 1039771187  323 -FFLLCPEH 330
Cdd:pfam13771   80 tFKSYCKKH 88
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 964-1010 1.85e-12

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 64.82  E-value: 1.85e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCV 1010
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECK 49
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 251-330 1.91e-12

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 66.50  E-value: 1.91e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  251 AHHRCVEWSLGICQMEEP-------LLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT-FQDFSH 322
Cdd:cd15669     25 AHYFCLLFSSGLPQRGEDnegiygfLPEDIRKEVRRASRLRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFGE 104


                   ....*...
gi 1039771187  323 FFLLCPEH 330
Cdd:cd15669    105 YRSFCWEH 112
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 964-1009 2.37e-12

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 64.09  E-value: 2.37e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15604      1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4791-4917 2.66e-12

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 70.78  E-value: 2.66e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLY--------------ESQNRGVYMFRMDNDHVIDATLTGGPARYI 4856
Cdd:cd10517    140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievvEKLKEGYESDVEEHCYIIDAKSEGNLGRYL 219

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187 4857 NHSCAPNCVAEVVtFERGHKIIIS-----SNRRIQKGEELCYDYKFDFEDDQHKI-PCHCGAVNCRK 4917
Cdd:cd10517    220 NHSCSPNLFVQNV-FVDTHDLRFPwvaffASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 250-330 3.58e-12

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 65.67  E-value: 3.58e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLvNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15700     25 WVHEACAVWTTGVYLVAGKLF-GLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENFSLRCPK 103


                   .
gi 1039771187  330 H 330
Cdd:cd15700    104 H 104
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 390-435 4.20e-12

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 63.48  E-value: 4.20e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQpvMKSVPTNGWKCKNC 435
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 391-435 5.38e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 63.20  E-value: 5.38e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 391-435 9.12e-12

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 62.67  E-value: 9.12e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 250-311 1.03e-11

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 64.64  E-value: 1.03e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15693     28 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCS 89
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 965-1009 1.03e-11

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 62.43  E-value: 1.03e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 965-1009 1.11e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 62.39  E-value: 1.11e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKCKWC 1009
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 965-1009 1.27e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 62.29  E-value: 1.27e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVP-KGGWKCKWC 1009
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
4409-4504 1.79e-11

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 63.90  E-value: 1.79e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4409 RKCCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLQMKCVFCHK-TGATSG 4482
Cdd:pfam13832    1 VRCCLCPLRGGALkqtSDG----------RWVHVLCAIFVPEVRfgNVATMEPIDVSRIPPERWKLKCVFCKKrSGACIQ 70

                           90       100
                   ....*....|....*....|..
gi 1039771187 4483 CHRFRCTNIYHFTCATKAQCMF 4504
Cdd:pfam13832   71 CSKGRCTTAFHVTCAQAAGVYM 92
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 4790-4919 2.28e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380921 [Multi-domain]  Cd Length: 266  Bit Score: 67.55  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTI---IRNEVANRKEKLYESQNRGVYMFRM-----------DNDHVIDATLTGGPARY 4855
Cdd:cd10523    118 KGWGVRCLDDIDKGTFVCIYAGRVlsrARSPTEPLPPKLELPSENEVEVVTSwlilskkrklrENVCFLDASKEGNVGRF 197

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187 4856 INHSCAPNCVAEVVTFERGHK----IIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCRKWM 4919
Cdd:cd10523    198 LNHSCCPNLFVQNVFVDTHDKnfpwVAFFTNRVVKAGTELTWDYSYDAGTSPEQeIPCLCGVNKCQKKI 266
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 964-1009 2.29e-11

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 61.55  E-value: 2.29e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 964-1009 2.43e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.46  E-value: 2.43e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1039771187   964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1009
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 4790-4917 2.48e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380939 [Multi-domain]  Cd Length: 236  Bit Score: 67.18  E-value: 2.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4790 QGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVV 4869
Cdd:cd10541    102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 4870 tFERGHK-----IIISSNRRIQKGEELCYDYKFDFEDDQHK-IPCHCGAVNCRK 4917
Cdd:cd10541    182 -FVDTHDlrfpwVAFFASKRIKAGTELTWDYNYEVGSVEGKeLLCCCGSNECRG 234
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 250-330 3.33e-11

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 63.14  E-value: 3.33e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA-AGAGTFQDFSHFFllCP 328
Cdd:cd15694     26 WTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCArASRCCFQDDKKVF--CQ 103


                   ..
gi 1039771187  329 EH 330
Cdd:cd15694    104 KH 105
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 390-438 5.61e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 60.58  E-value: 5.61e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV--MKSVPTNGWKCKNCRIC 438
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPldPAEIPSGEWLCPECKPK 51
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 4411-4515 5.74e-11

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 62.65  E-value: 5.74e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGlTDGPARLLNLDlDLWVHLNCALWSTEVYETQ------AGALIN-VELALRRGLQMKCVFCHKTGATSGC 4483
Cdd:cd15669      1 CVLCGRSDDD-PDKYGEKLQKD-GICAHYFCLLFSSGLPQRGednegiYGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1039771187 4484 HRFRCTNIYHFTCATKAQC--MFFKDKTMLCPMH 4515
Cdd:cd15669     79 AVKGCRRSFHFPCGLENGCvtQFFGEYRSFCWEH 112
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 962-1009 7.26e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 60.08  E-value: 7.26e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  962 CTVCEACGKATDpgrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15527      2 CSVCQDSGNADN---LLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 965-1009 7.90e-11

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 59.70  E-value: 7.90e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 965-1009 8.07e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 60.02  E-value: 8.07e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 390-435 9.93e-11

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 59.71  E-value: 9.93e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
GGN pfam15685
Gametogenetin; GGN is a family of proteins largely found in mammals. It reacts with POG in the ...
 1834-2321 1.31e-10

Gametogenetin; GGN is a family of proteins largely found in mammals. It reacts with POG in the maturation of sperm and is expressed virtually only in the testis. It is found to be associated with the intracellular membrane, binds with GGNBP1 and may be involved in vesicular trafficking.


Pssm-ID: 434857 [Multi-domain]  Cd Length: 668  Bit Score: 67.87  E-value: 1.31e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1834 PPSPQMF-SPGSSHSRPPSPVDP-----YAKMVGTPRPPPGGhsfprrnsvtpvencvplSSVPRPIHMNETSATRPSPA 1907
Cdd:pfam15685   64 PPEPQASpSPLPLTLELPLPVTPppeeaAAAAVSTAPPPAVG------------------SLLPAPSKWRKPTGTAVARI 125

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1908 RDLC-ASSMTNSDPYAKPPDTprPMMTDQFSKPFSLPRSPViseqstkGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAG 1986
Cdd:pfam15685  126 RGLLeASHRGQGDPLSLRPLL--PLLPRQLIEKDPAPGAPA-------PPPPTPLEPRKPPPLPPSDRQPPNRGITPALA 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1987 PSLTPaplgngpfktplhPPPSQDPYGSVSQTSRrlSVDPYERPALTPRPVDNFSHSQSNDPY-------SHPPLTPHPA 2059
Cdd:pfam15685  197 TSATS-------------PTDSQAKHIAEGKTAG--GACGGAPPQAGEGEMARFAASESGLSLlckvtfkSAAPLCPAAA 261

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2060 MTESFTHASRAFPQPGTISRSASQDPYSQ-------PPGTPRPL--IDSYSQTSGTARSNPDPYSQPPGTPRPNTidpYS 2130
Cdd:pfam15685  262 SGPLAAKASLGGGGGGGLFAASGAISCAEvlkqgplAPGAARPLgeVPRAALETEGGEGDGEGCSGGPAAPASHA---RA 338

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2131 QQPPT----PRPSPQTDMFVSSVANQRH--TDPYTHHLGPPR---PGISVPYSQPPavPRPRTSEGFTRPSSARPALMPN 2201
Cdd:pfam15685  339 LPPPAyttfPGSKPKFDWVSPPDGPERHfrFNGAGGGIGAPRrraAALSGPWGSPP--PPPGKAHPIPGPRRPAPALLAP 416

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2202 QDPFLQAAQNRVPGLPGplirPPDTCSQTPRPPGPGRIDTFTHASSSAVRDPYDQPPVTP--RPHSESFGTSQVVHDLVD 2279
Cdd:pfam15685  417 PMFIFPAPTNGEPVRPG----PPAPQALLPRPPPPTPPATPPPVPPPIPQLPALQPMPLAaaRPPTPRPCPGHGESALAP 492

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|..
gi 1039771187 2280 RPVPgsegnfSTSSNLPVSSQGQQFSSVSQLPGPVPTSGGTD 2321
Cdd:pfam15685  493 APTA------PLPPALAADQAPAPALAAAPAPSPAPAPATAD 528
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 4791-4895 1.49e-10

SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions.


Pssm-ID: 380997 [Multi-domain]  Cd Length: 122  Bit Score: 61.62  E-value: 1.49e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4791 GLGLYAARDIEKhtmvieyiGTIIRNE------VANRKEKLYESQNRGVYMFRMdndhvidatltggpARYINHSCAPNC 4864
Cdd:cd20071     10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1039771187 4865 VaevVTFERGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd20071     68 V---VVFDGNGTLRVRALRDIKAGEELTISY 95
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 390-435 1.80e-10

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 58.70  E-value: 1.80e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15604      1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 965-1009 2.65e-10

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 58.43  E-value: 2.65e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKG-GWKCKWC 1009
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 391-435 2.77e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 58.22  E-value: 2.77e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 250-330 2.82e-10

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 60.45  E-value: 2.82e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGT--FQDFShffLLC 327
Cdd:cd15698     26 WVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIRAKCmfFKDKT---MLC 102


                   ...
gi 1039771187  328 PEH 330
Cdd:cd15698    103 PMH 105
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 391-435 3.43e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 57.94  E-value: 3.43e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1754-2141 3.45e-10

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 66.71  E-value: 3.45e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1754 APGSDTPSSGAQ-SPLTPQAGNGNVSPA----------QTFHKDLFSKHLPGTPASTPSdgvfvkpqppPPPSTPSRIPV 1822
Cdd:pfam03154  198 GPTPSAPSVPPQgSPATSQPPNQTQSTAaphtliqqtpTLHPQRLPSPHPPLQPMTQPP----------PPSQVSPQPLP 267

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1823 QESLsqsQNSQPPSPQMFSPGSSHSRPPSPVDPYakmvgtPRPPPGGHSfprrnsvtpveNCVPLSSVPRPIHMNETSAT 1902
Cdd:pfam03154  268 QPSL---HGQMPPMPHSLQTGPSHMQHPVPPQPF------PLTPQSSQS-----------QVPPGPSPAAPGQSQQRIHT 327

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1903 RPSpardlcASSMTNSDPYAKPPDTPRPMMTDQFSKPFSLPRSPVISEQSTKGPlttgtsDHFTKPSPrtdaFQ-RQRLP 1981
Cdd:pfam03154  328 PPS------QSQLQSQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQSHKHP------PHLSGPSP----FQmNSNLP 391

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1982 DPYA-----------GPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTsrrlsvdpyerpaLTPRPVDNFSHSQSNDPYS 2050
Cdd:pfam03154  392 PPPAlkplsslsthhPPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQS-------------LPPPAASHPPTSGLHQVPS 458

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2051 HPPLTPHPAMTESfthASRAFPQPGTISRSASQDPYSQPPGTPRPlidSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYS 2130
Cdd:pfam03154  459 QSPFPQHPFVPGG---PPPITPPSGPPTSTSSAMPGIQPPSSASV---SSSGPVPAAVSCPLPPVQIKEEALDEAEEPES 532

                          410
                   ....*....|.
gi 1039771187 2131 QQPPTPRPSPQ 2141
Cdd:pfam03154  533 PPPPPRSPSPE 543
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 4792-4906 4.02e-10

SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression.


Pssm-ID: 380960  Cd Length: 173  Bit Score: 62.04  E-value: 4.02e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4792 LGLYAARDIEKHTMVIEYIGtiirnEVANRKEKLYESQNRgvY----------MFRMDNDHVIDATLTGGPARYINHSCA 4861
Cdd:cd19183     14 FGLFADRPIPAGDPIQELLG-----EIGLQSEYIADPENQ--YqilgapkphvFFHPQSPLYIDTRRSGSVARFIRRSCR 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187 4862 PNCVAEVVTFERGH--KIIISSNRRIQKGEELCYDYKFDFEDDQHKI 4906
Cdd:cd19183     87 PNAELVTVASDSGSvlKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 390-435 4.65e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.61  E-value: 4.65e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1039771187   390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 390-435 4.68e-10

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 57.68  E-value: 4.68e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15532      1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 390-435 7.15e-10

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 57.07  E-value: 7.15e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15605      1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 915-965 7.42e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.12  E-value: 7.42e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  915 CVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLECTVC 965
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1748-2227 7.60e-10

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 65.96  E-value: 7.60e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1748 SQHLLVAPGSD---TPSSGAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPpstpsripvqe 1824
Cdd:PHA03307    46 DSAELAAVTVVagaAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSP----------- 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1825 slsqsqnsqPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGG--------HSFPRRNSVTPVENCVPLSSVPrpihm 1896
Cdd:PHA03307   115 ---------DPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAAsppaagasPAAVASDAASSRQAALPLSSPE----- 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1897 nETSATRPSPArdlcASSMTNSDPYAKPPDTPRPMMTDQFSKPFSLPRSPviseQSTKGPLTTGTSDHFTKPSPRTDAFQ 1976
Cdd:PHA03307   181 -ETARAPSSPP----AEPPPSTPPAAASPRPPRRSSPISASASSPAPAPG----RSAADDAGASSSDSSSSESSGCGWGP 251

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1977 RQRLPDPYAGPSLTPAPLGNGpfKTPLHPPPSQDPYGSVSQTSRRlsvdpyerpalTPRPvdnfshsQSNDPYSHPPLTP 2056
Cdd:PHA03307   252 ENECPLPRPAPITLPTRIWEA--SGWNGPSSRPGPASSSSSPRER-----------SPSP-------SPSSPGSGPAPSS 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2057 HPAMtesfthASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPySQPPGTPRPNTIDPYSQQPPTP 2136
Cdd:PHA03307   312 PRAS------SSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADP-SSPRKRPRPSRAPSSPAASAGR 384

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2137 RPSPQTDMFVSSVANQRHTdpythhlGPPRPGisvpySQPPAVPrPRTSEGFTRPSSARPALMPNQDPFlqaaqnrvPGL 2216
Cdd:PHA03307   385 PTRRRARAAVAGRARRRDA-------TGRFPA-----GRPRPSP-LDAGAASGAFYARYPLLTPSGEPW--------PGS 443

                          490
                   ....*....|.
gi 1039771187 2217 PGPlirPPDTC 2227
Cdd:PHA03307   444 PPP---PPGRV 451
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 914-962 8.87e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 8.87e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1039771187   914 MCVVCGSFGqgAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 962
Cdd:smart00249    1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 388-435 1.27e-09

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 56.62  E-value: 1.27e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  388 CKVCQNckqSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15527      2 CSVCQD---SGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 964-1009 1.29e-09

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 56.55  E-value: 1.29e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1009
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 964-1009 1.46e-09

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 56.13  E-value: 1.46e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGkatDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15532      1 FCRVCK---DGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 250-330 1.74e-09

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 58.00  E-value: 1.74e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGIcQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHFFLLCPE 329
Cdd:cd15699     24 WVHEGCILWANGI-YLVCGRLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCLLNEENFSVRCPK 102


                   .
gi 1039771187  330 H 330
Cdd:cd15699    103 H 103
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 965-1009 2.06e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 55.91  E-value: 2.06e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 964-1009 3.47e-09

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 55.09  E-value: 3.47e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  964 VCEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15523      1 FCSVCRKS---GELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 961-1009 4.07e-09

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 54.76  E-value: 4.07e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  961 ECTVCeacgkaTDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15539      1 ECAVC------GDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 390-435 4.24e-09

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 54.96  E-value: 4.24e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15602      1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 391-435 5.24e-09

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 54.73  E-value: 5.24e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 964-1009 5.93e-09

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 54.72  E-value: 5.93e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKG----GWKCKWC 1009
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKtknsGWQCSEC 50
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 4434-4515 6.25e-09

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 56.83  E-value: 6.25e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4434 DLWVHLNCALWSTEVYETQAGALINVELA---------LRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMF 4504
Cdd:cd15712     20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALCDDAAI 99

                           90
                   ....*....|....*.
gi 1039771187 4505 FKDKT-----MLCPMH 4515
Cdd:cd15712    100 ETDEVrgiyrVFCQKH 115
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1753-2090 6.54e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 63.03  E-value: 6.54e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1753 VAPGSDTPssgaqsPLTPQAGNGNVSPAQtfhkdlfskhlPGTPASTPSDGVFVKPQPPPPPSTPSRIPVQESLSQSQNS 1832
Cdd:PHA03247  2749 ATPGGPAR------PARPPTTAGPPAPAP-----------PAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAV 2811

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1833 QPPSPQMfspgSSHSRPPSPVDPYAKMVGTPRPPPGGhsfPRRNSVTPVENCVPLSSV-----PRPIHMNETSATRPsPA 1907
Cdd:PHA03247  2812 LAPAAAL----PPAASPAGPLPPPTSAQPTAPPPPPG---PPPPSLPLGGSVAPGGDVrrrppSRSPAAKPAAPARP-PV 2883

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1908 RDLCASSMTNS-DPYAKPPDTPRPMMTDQFSKPFSLPRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQR--LPDPY 1984
Cdd:PHA03247  2884 RRLARPAVSRStESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSgaVPQPW 2963

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1985 AGP----------SLTPAPLGNGPFKTPLHPPPSQDPYGSVSQ--TSRRLSVDPYERPA---LTPRPVDN---------- 2039
Cdd:PHA03247  2964 LGAlvpgrvavprFRVPQPAPSREAPASSTPPLTGHSLSRVSSwaSSLALHEETDPPPVslkQTLWPPDDtedsdadslf 3043

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 2040 FSHSQSNDPYSHPPLTPHPamTESFTHAsrafPQPGTISRSASQDPYSQ--PP 2090
Cdd:PHA03247  3044 DSDSERSDLEALDPLPPEP--HDPFAHE----PDPATPEAGARESPSSQfgPP 3090
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 390-435 7.80e-09

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 54.19  E-value: 7.80e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15603      1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 964-1009 1.06e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 53.86  E-value: 1.06e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  964 VCEACGKATD-PGRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1009
Cdd:cd15489      1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 344-391 1.15e-08

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 54.04  E-value: 1.15e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT--PLKRAGWQCPECKVC 391
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2062-2405 1.20e-08

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 62.11  E-value: 1.20e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2062 ESFTHASRAFPQPGTISRSASQDPYSQPPG----TPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTIDPYSQQPPTPR 2137
Cdd:PHA03307    12 EAAAEGGEFFPRPPATPGDAADDLLSGSQGqlvsDSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWS 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2138 PSPQTdmfVSSVANQRHTDPYTHHLGPPRPGISVPYSQPP-----AVPRPRTSEGFTRPSSARPALMPNQDPFLQAAQNR 2212
Cdd:PHA03307    92 LSTLA---PASPAREGSPTPPGPSSPDPPPPTPPPASPPPspapdLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAAS 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2213 VPGLPGPLIRPPDT--CSQTPRPPGPGRIDTFTHASSSAVRDPYDQPPV---TPRP----------------HSESFGTS 2271
Cdd:PHA03307   169 SRQAALPLSSPEETarAPSSPPAEPPPSTPPAAASPRPPRRSSPISASAsspAPAPgrsaaddagasssdssSSESSGCG 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2272 QVVHDLVDRPVP-----------GSEGNFSTSSNLPVSSqgqqfSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRq 2340
Cdd:PHA03307   249 WGPENECPLPRPapitlptriweASGWNGPSSRPGPASS-----SSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSR- 322

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 2341 klreiilqqqqQKKIASRQEKGPQDTAVVPHPVPLPHWQPESinqafTRPPPPYPGSTRSPVIPP 2405
Cdd:PHA03307   323 -----------ESSSSSTSSSSESSRGAAVSPGPSPSRSPSP-----SRPPPPADPSSPRKRPRP 371
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 390-435 1.24e-08

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 53.62  E-value: 1.24e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15519      1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 249-330 1.96e-08

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 55.48  E-value: 1.96e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  249 CWAHHRCVEWSLGICQMEEPLLVN--------VDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAA--GAGTFQ 318
Cdd:cd15673     23 IAAHHNCMLFSSGLVQYVSPNENDfggfdiedVKKEIKRGRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKkdDAKIIE 102

                           90
                   ....*....|....
gi 1039771187  319 DFSH--FFLLCPEH 330
Cdd:cd15673    103 RNSQgiYRVYCKNH 116
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 391-435 2.39e-08

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 52.77  E-value: 2.39e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 965-1010 2.80e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 52.55  E-value: 2.80e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 388-435 3.73e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 52.32  E-value: 3.73e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  388 CKVCQNCKQSGEDskMLVCDTCDKGYHTFCLQPVMKS-VPTNGWKCKNC 435
Cdd:cd15489      2 CIVCGKGGDLGGE--LLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 466-517 5.22e-08

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 52.30  E-value: 5.22e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  466 LCPFCGKCYHP-ELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15592      1 FCPLCDKCYDDdDYESKMMQCGKCDRWVHSKCENLSDEmyEILSNLPESvaYTCINC 57
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 388-435 6.47e-08

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 51.60  E-value: 6.47e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  388 CKVCQNcKQsgEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG-WKCKNC 435
Cdd:cd15525      2 CHVCGG-KQ--DPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 467-517 6.66e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 51.55  E-value: 6.66e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  467 CPFCGKCYHPElqKDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:cd15489      2 CIVCGKGGDLG--GELLQCDGCGKWFHADCLGPP--LSSFVPNGKWICPVC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 914-962 6.66e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 51.55  E-value: 6.66e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  914 MCVVCGSFGQGaEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 962
Cdd:cd15489      1 SCIVCGKGGDL-GGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 964-1009 6.92e-08

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 51.59  E-value: 6.92e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  964 VCEACGkatDPGRLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1009
Cdd:cd15533      1 YCDSCG---EGGDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 961-1009 1.23e-07

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 50.86  E-value: 1.23e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  961 ECTVCEACGKATDpgrLLLCDDCDISYHTYCLDPPLQTVPKG---GWKCKWC 1009
Cdd:cd15563      1 ECCVCKQTGDNSQ---LVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 4778-4917 1.55e-07

SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions.


Pssm-ID: 380922 [Multi-domain]  Cd Length: 141  Bit Score: 53.44  E-value: 1.55e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4778 WKSNVYLARSRiQGLGLYAARDIEKHTMVIEYIGTIIRNEVAnrkEKLYESQNRG----VYMFRMDNDHVIDatltgGPA 4853
Cdd:cd10524      7 CPCNRYSLENH-YGAKIIATKPIKKGEKIHELCGCIAELSEE---EEALLRPGGNdfsvMYSSRKKCSQLWL-----GPA 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 4854 RYINHSCAPNCvaEVVTFERGhKIIISSNRRIQKGEELCYDYKFDFEDDQHkipCHCGAVNCRK 4917
Cdd:cd10524     78 AFINHDCRPNC--KFVPTGKS-TACVKVLRDIEPGEEITVYYGDNYFGENN---EECECETCER 135
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 391-435 2.28e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 49.91  E-value: 2.28e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15531      2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1041-1091 2.38e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 50.01  E-value: 2.38e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1041 SCPVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1091
Cdd:cd15489      1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNG---KWICPVC 48
PHA03377 PHA03377
EBNA-3C; Provisional
 1755-2137 2.39e-07

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 57.37  E-value: 2.39e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1755 PGSDTPSSGAQSPLTPQAGNGNVSPAQTFHKDLfSKHLPGTPASTPSDgvfvKPQPPPPPSTPSRIPVQESLSQSQNSQP 1834
Cdd:PHA03377   568 PVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQ-AKCKDGPPASGPHE----KQPPSSAPRDMAPSVVRMFLRERLLEQS 642

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1835 --PSPQMF------SPGSSHSRPPSPVDPYAKMVGTPRPP--PGGHSFPrrnsVTPVENCVPLSSVprpiHMNETSATRP 1904
Cdd:PHA03377   643 tgPKPKSFwemragRDGSGIQQEPSSRRQPATQSTPPRPSwlPSVFVLP----SVDAGRAQPSEES----HLSSMSPTQP 714

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1905 SPA------RDLCASSMTNSDPYAKPPDTPR--------PMMTDQFSKPFSLPRSPVISEQSTKGPLTTGTSDH----FT 1966
Cdd:PHA03377   715 ISHeeqpryEDPDDPLDLSLHPDQAPPPSHQapysgheePQAQQAPYPGYWEPRPPQAPYLGYQEPQAQGVQVSsypgYA 794

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1967 KPSPRTDAFQRQRLP------DPYAGPSLTP-APlgngpfkTPLHPPPSQDPYGSVSQTSrrlsvdpyerpaltprpVDN 2039
Cdd:PHA03377   795 GPWGLRAQHPRYRHSwaywsqYPGHGHPQGPwAP-------RPPHLPPQWDGSAGHGQDQ-----------------VSQ 850

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2040 FSHSQSNDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPY-SQPPGTPRPLIDSYS---QTSGTARSN---PD 2112
Cdd:PHA03377   851 FPHLQSETGPPRLQLSQVPQLPYSQTLVSSSAPSWSSPQPRAPIRPIpTRFPPPPMPLQDSMAvgcDSSGTACPSmpfAS 930

                          410       420
                   ....*....|....*....|....*
gi 1039771187 2113 PYSQPPGTPrpntIDPYSQQPPTPR 2137
Cdd:PHA03377   931 DYSQGAFTP----LDINAQTPKRPR 951
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 466-517 2.61e-07

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 50.17  E-value: 2.61e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  466 LCPFCGKCYHP--ELQKDMLHCNMCKRWVHLECDKPTDQELDSQLKED---YICMYC 517
Cdd:cd15615      1 FCILCGQVYEEneGDEKEWVQCDSCSEWVHFECDGRTGLGAFKYAKSDglqYVCPRC 57
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 390-435 3.08e-07

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 49.70  E-value: 3.08e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15523      1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2034-2263 3.31e-07

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.08  E-value: 3.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2034 PRPVDNFSHSQSNDPYS------------HPPLTPHPAMTESFTHASRAFPQPGTISRSASQDP-YSQPPGTPRPLIDSY 2100
Cdd:pfam03154  149 PSPQDNESDSDSSAQQQilqtqppvlqaqSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPaTSQPPNQTQSTAAPH 228

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2101 SQTSGTarsnpdPYSQPPGTPRPNT-------IDPYSQQPPTPRPSPQTDMFVSSVANQRHTDP-YTHHLGPPRPGISVP 2172
Cdd:pfam03154  229 TLIQQT------PTLHPQRLPSPHPplqpmtqPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPsHMQHPVPPQPFPLTP 302

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2173 YSQPPAVPrPRTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPG-----PLIRPPDTcsqTPRPPGPGRiDTFTHASS 2247
Cdd:pfam03154  303 QSSQSQVP-PGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPaplsmPHIKPPPT---TPIPQLPNP-QSHKHPPH 377

                          250
                   ....*....|....*.
gi 1039771187 2248 SAVRDPYDQPPVTPRP 2263
Cdd:pfam03154  378 LSGPSPFQMNSNLPPP 393
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 965-1010 3.32e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 49.59  E-value: 3.32e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1010
Cdd:cd15630      3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACI 48
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 965-1009 3.44e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 49.52  E-value: 3.44e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15531      2 CEVCQQG---GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 961-1009 3.66e-07

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 49.26  E-value: 3.66e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  961 ECTVCEacgkatDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15541      1 WCAVCQ------NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 390-435 4.05e-07

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 49.31  E-value: 4.05e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTN---GWKCKNC 435
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 391-435 4.29e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 49.59  E-value: 4.29e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15630      3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 344-388 8.25e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.75  E-value: 8.25e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1039771187   344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 344-388 8.43e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 48.47  E-value: 8.43e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  344 CAVCDSPGDLLDQF-FCTTCGQHYHGMCLDIAVTPL-KRAGWQCPEC 388
Cdd:cd15489      2 CIVCGKGGDLGGELlQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 467-517 9.47e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 48.36  E-value: 9.47e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187   467 CPFCGKCYHPElqkDMLHCNMCKRWVHLECDKPTdqELDSQLKEDYICMYC 517
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPP--LLEEEPDGKWYCPKC 47
PHA03378 PHA03378
EBNA-3B; Provisional
 1945-2332 9.58e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 55.46  E-value: 9.58e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1945 SPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSV 2024
Cdd:PHA03378   579 SPTTSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPLRMQPITFNVLVFPTPHQPPQVE 658

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2025 DPYERPALTPRPVDNFSHSQSNDPYSH-----------PPLTPHPAMTESFTHASRAFPQ--PGTISRSASQDPYSQPPG 2091
Cdd:PHA03378   659 ITPYKPTWTQIGHIPYQPSPTGANTMLpiqwapgtmqpPPRAPTPMRPPAAPPGRAQRPAaaTGRARPPAAAPGRARPPA 738

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2092 TPRPLIDSYSQTSGTAR---SNPDPYSQPPGTPRPNTIDPYSQQPPTPRPSPQTdmfVSSVANQRHTDPYTHHLGPPRPg 2168
Cdd:PHA03378   739 AAPGRARPPAAAPGRARppaAAPGRARPPAAAPGAPTPQPPPQAPPAPQQRPRG---APTPQPPPQAGPTSMQLMPRAA- 814

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2169 isvPYSQPPA--VPRPRTSEGFT--RPSSARPALMPNQDPflqAAQNRVPG-------LPGPLIRPP-DTCSQTPRPPGP 2236
Cdd:PHA03378   815 ---PGQQGPTkqILRQLLTGGVKrgRPSLKKPAALERQAA---AGPTPSPGsgtsdkiVQAPVFYPPvLQPIQVMRQLGS 888

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2237 GRIDTFTHASSSAVRDPYDQPPVTPRPHSESFGTSQVVHD-LVDRPVPGSEGNFSTSSNLPVSSQGQQfssvsqlpgPVP 2315
Cdd:PHA03378   889 VRAAAASTVTQAPTEYTGERRGVGPMHPTDIPPSKRAKTDaYVESQPPHGGQSHSFSVIWENVSQGQQ---------QTL 959

                          410
                   ....*....|....*..
gi 1039771187 2316 TSGGTDTQNTVNMSQAD 2332
Cdd:PHA03378   960 ECGGTTKQERAMLGTGD 976
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 466-517 1.25e-06

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 48.21  E-value: 1.25e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187  466 LCPFCGKCYH-PELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15508      1 YCPLCEKCYDdDDYDSKMMQCSQCDHWVHAKCEGLSDEmyEILSYLPESieYTCSLC 57
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 390-435 1.32e-06

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 48.17  E-value: 1.32e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVP----TNGWKCKNC 435
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPkktkNSGWQCSEC 50
PHA03377 PHA03377
EBNA-3C; Provisional
 2026-2467 1.48e-06

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 55.06  E-value: 1.48e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2026 PYERPALTP---RPVDNFSHSQSNDPYSHPPLTP--HPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSY 2100
Cdd:PHA03377   391 PYIDPNMEPvqqRPVMFVSRVPWRKPRTLPWPTPktHPVKRTLVKTSGRSDEAEQAQSTPERPGPSDQPSVPVEPAHLTP 470

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2101 SQTSGTArsnpdpYSQPPGTPRPNTIDPYSQ--------------------------------QPPTPRPSPQTDMFVSS 2148
Cdd:PHA03377   471 VEHTTVI------LHQPPQSPPTVAIKPAPPpsrrrrgacvvydddiievidvetteeeesvtQPAKPHRKVQDGFQRSG 544

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2149 VANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPalmPNQDPFLQAAQNRVPGLPGPLIRPPDtcS 2228
Cdd:PHA03377   545 RRQKRATPPKVSPSDRGPPKASPPVMAPPSTGPRVMATPSTGPRDMAP---PSTGPRQQAKCKDGPPASGPHEKQPP--S 619

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2229 QTPRPPGPGRIDTFThasssavRDPYDQPPVTPRPhsESFGTSQVVHDLVD-RPVPGSEGNFSTSSNLPVSSqgqQFSSV 2307
Cdd:PHA03377   620 SAPRDMAPSVVRMFL-------RERLLEQSTGPKP--KSFWEMRAGRDGSGiQQEPSSRRQPATQSTPPRPS---WLPSV 687

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2308 SQLPGpVPTSGGTDTQNTVNMSQADTEKLRQRQKLReiilqqqqqkkiaSRQEKGPQDTAVVPHPVPLP-HWQPESINQA 2386
Cdd:PHA03377   688 FVLPS-VDAGRAQPSEESHLSSMSPTQPISHEEQPR-------------YEDPDDPLDLSLHPDQAPPPsHQAPYSGHEE 753

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2387 FTRPPPPYPG--STRSPVIPPLGPRYAVFPKDQRGPYPPEVAGMGMRPHGFRF--------GFPGAGHGPMPSQDRF-HV 2455
Cdd:PHA03377   754 PQAQQAPYPGywEPRPPQAPYLGYQEPQAQGVQVSSYPGYAGPWGLRAQHPRYrhswaywsQYPGHGHPQGPWAPRPpHL 833

                          490
                   ....*....|..
gi 1039771187 2456 PQQIQGSGIPPH 2467
Cdd:PHA03377   834 PPQWDGSAGHGQ 845
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 964-1015 1.93e-06

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 47.88  E-value: 1.93e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187  964 VCEACG--KATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKcKWcvWCRHC 1015
Cdd:cd15499      1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDE-KW--FCSRC 51
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1606-1653 1.98e-06

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 47.90  E-value: 1.98e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1606 LYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRA 1653
Cdd:cd00084      8 LFSKEKRPKLKKENPDLSFTeiSKLLGERWKELSEEEKQPYEEKAKEDKE 57
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 467-518 2.01e-06

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 47.49  E-value: 2.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  467 CPFCGKcyhPELQKDMLHCNMCKRWVHLECDKPTDQELDsQLKEDYICMYCK 518
Cdd:pfam00628    2 CAVCGK---SDDGGELVQCDGCDDWFHLACLGPPLDPAE-IPSGEWLCPECK 49
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1041-1091 2.01e-06

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 47.83  E-value: 2.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 1041 SCPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLnTEEEVENVAD----IGFDCSMC 1091
Cdd:cd15508      1 YCPLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGL-SDEMYEILSYlpesIEYTCSLC 57
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2119-2541 2.32e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 54.39  E-value: 2.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2119 GTPRPNTIDPYSQQPPTPRPSPQ---TDMFVSSVANQRHTDP-----YTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTR 2190
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSPSIPSPQdneSDSDSSAQQQILQTQPpvlqaQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2191 PSSarPALMPNQDPFLQAA-----QNRVPGLPGPLIRPPDTCSQTPRPPGPGRIdtfthaSSSAVRDPYDQPPVTPRPHS 2265
Cdd:pfam03154  210 GSP--ATSQPPNQTQSTAAphtliQQTPTLHPQRLPSPHPPLQPMTQPPPPSQV------SPQPLPQPSLHGQMPPMPHS 281

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2266 ESFGTSQVVHDLVDRPVPGSegnfstssnlPVSSQGQQfssvsqLPGPVPTSGGTDTQNTvnMSQADTEKLRQRQKLREI 2345
Cdd:pfam03154  282 LQTGPSHMQHPVPPQPFPLT----------PQSSQSQV------PPGPSPAAPGQSQQRI--HTPPSQSQLQSQQPPREQ 343

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2346 ILQQQQqkkIASRQEKGPQDTAVVPHPVPLPHWQPESINQAF------TRPPPPY--PGSTRSPVIPPLG--PRYAVFPK 2415
Cdd:pfam03154  344 PLPPAP---LSMPHIKPPPTTPIPQLPNPQSHKHPPHLSGPSpfqmnsNLPPPPAlkPLSSLSTHHPPSAhpPPLQLMPQ 420

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2416 DQRGPYPPE-----VAGMGMRPHGFRFGFPGAGHgPMPSQDRFhvPQQIQGSGIPPHIRRPMSmemprpsnnPPLNNPVG 2490
Cdd:pfam03154  421 SQQLPPPPAqppvlTQSQSLPPPAASHPPTSGLH-QVPSQSPF--PQHPFVPGGPPPITPPSG---------PPTSTSSA 488

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2491 LPQHFPPQGLPVQQHNILGQAF------IELRHRAPD----GRSRLPFAASPS---SVIESPSH 2541
Cdd:pfam03154  489 MPGIQPPSSASVSSSGPVPAAVscplppVQIKEEALDeaeePESPPPPPRSPSpepTVVNTPSH 552
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 965-1009 2.59e-06

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 47.03  E-value: 2.59e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  965 CEACGKatdPGRLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1009
Cdd:cd15535      2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
SET_SpSet7-like cd10540
SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces ...
 4782-4901 3.52e-06

SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces pombe Set7 is a novel histone-lysine N-methyltransferase. The family also includes a viral histone H3 lysine 27 methyltransferase from Paramecium bursaria Chlorella virus 1 (PBCV-1).


Pssm-ID: 380938  Cd Length: 112  Bit Score: 48.79  E-value: 3.52e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4782 VYLARSRIQGLGLYAARDIEKHTmVIEYIGTIIrneVANRKEKLYESQNRGVYMFRMDNDHVidATLTGGPARYiNHSCA 4861
Cdd:cd10540      2 LEVKPSTLKGRGVFATRPIKKGE-VIEEAPVIV---LPKEEYQHLCKTVLDHYVFSWGDGCL--ALALGYGSMF-NHSYT 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1039771187 4862 PNcvAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDFED 4901
Cdd:cd10540     75 PN--AEYEIDFENQTIVFYALRDIEAGEELTINYGDDLWD 112
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 391-435 3.61e-06

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 46.67  E-value: 3.61e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15539      2 CAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHA03379 PHA03379
EBNA-3A; Provisional
 1830-2287 4.40e-06

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 53.52  E-value: 4.40e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1830 QNSQPPSPQMFSPGSSHSR-----------PPSPVDPYAKMVGTPRPPPGGhsfprRNSVTPVEncVPLSSVPRPIHMNE 1898
Cdd:PHA03379   441 QVPEPPPVHDLEPGPLHDQhsmapcpvaqlPPGPLQDLEPGDQLPGVVQDG-----RPACAPVP--APAGPIVRPWEASL 513

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1899 TSATRPSPArdlcassMTNSDPYAKPPDtPRPmmtdqfSKPFSLPRSPVISEQSTKGPLTTGTSdhftkpsprtdafqrQ 1978
Cdd:PHA03379   514 SQVPGVAFA-------PVMPQPMPVEPV-PVP------TVALERPVCPAPPLIAMQGPGETSGI---------------V 564

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1979 RLPDPYAGPSLTPAPLgNGPFKTPLHPPPSQ-DPYGSVSQTSrrLSVDPYERPALTPRpvdnfshsqsnDPYSHpPLTPH 2057
Cdd:PHA03379   565 RVRERWRPAPWTPNPP-RSPSQMSVRDRLARlRAEAQPYQAS--VEVQPPQLTQVSPQ-----------QPMEY-PLEPE 629

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2058 PAMtesftHASRAFPQPGTISRsASQDPYSQPPGTPRPLIDSYSQTSGTArsnPDPYSQPPGTPRPNTIDPYSQQPPTPR 2137
Cdd:PHA03379   630 QQM-----FPGSPFSQVADVMR-AGGVPAMQPQYFDLPLQQPISQGAPLA---PLRASMGPVPPVPATQPQYFDIPLTEP 700

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2138 PSPQTDMFvssvanqrhtdpythHLGPPRPgisvpySQPPAVPRPRTSEGFTRPSSARPALMPNQD---PFLQAAQNRVP 2214
Cdd:PHA03379   701 INQGASAA---------------HFLPQQP------MEGPLVPERWMFQGATLSQSVRPGVAQSQYfdlPLTQPINHGAP 759

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 2215 GLPGPlirppdtcsqtPRPPGPGRIdtfthassSAVRDPYDQPPVTPR----PHS-ESFGtsQVVHDLVDRPVPGSEG 2287
Cdd:PHA03379   760 AAHFL-----------HQPPMEGPW--------VPEQWMFQGAPPSQGtdvvQHQlDALG--YVLHVLNHPGVPVSPA 816
dnaA PRK14086
chromosomal replication initiator protein DnaA;
1982-2212 5.69e-06

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 52.91  E-value: 5.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1982 DPYAGPSLTPAPlgngpfktplHPPPSQDPYGSvsqTSRRLSVDPYERPALTPRPvdnfshsQSNDPYSHPPlTPHPAMT 2061
Cdd:PRK14086    89 DPSAGEPAPPPP----------HARRTSEPELP---RPGRRPYEGYGGPRADDRP-------PGLPRQDQLP-TARPAYP 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2062 eSFTHASRAFPQPGT-ISRSASQDPYSQPPGTPRPLIDSYS-------QTSGTARSNPDPYSQPPGTPRPNTIDPYSQQP 2133
Cdd:PRK14086   148 -AYQQRPEPGAWPRAaDDYGWQQQRLGFPPRAPYASPASYApeqerdrEPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRT 226

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2134 PTPRPSPQTdmfvssvanqrHTDPYTHHLGPPRPGISVPYSQPPAvPRPRTSEGFTRPSSARPALMPNQ----DPFLQAA 2209
Cdd:PRK14086   227 DRPEPPPGA-----------GHVHRGGPGPPERDDAPVVPIRPSA-PGPLAAQPAPAPGPGEPTARLNPkytfDTFVIGA 294


                   ...
gi 1039771187 2210 QNR 2212
Cdd:PRK14086   295 SNR 297
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 915-962 5.92e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 46.15  E-value: 5.92e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  915 CVVCGSFGQGAEgrLLACSQCGQCYHPYCV--SIKITKVVLSkGWRCLEC 962
Cdd:cd15509      2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLdpAVRPTPLVRA-GWQCPEC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 965-1009 6.86e-06

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 45.87  E-value: 6.86e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15559      2 CRVCHKL---GDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 964-1006 8.09e-06

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 45.80  E-value: 8.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1039771187  964 VCEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKC 1006
Cdd:cd15534      1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 965-1009 8.11e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 45.76  E-value: 8.11e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVP--KGGWKCKWC 1009
Cdd:cd15509      2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 4794-4915 8.12e-06

SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression.


Pssm-ID: 380958  Cd Length: 150  Bit Score: 48.85  E-value: 8.12e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4794 LYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRMDN--DHVIDATLTGGPARYINHSCAPNCVAEVVTF 4871
Cdd:cd19181     21 LRAARDLALDTLIIEYRGKVMLRQQFEVNGHFFKRPYPFVLFYSKFNgvEMCVDARTFGNDARFIRRSCTPNAEVRHMIA 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187 4872 ERGHKIIISSNRRIQKGEELCYDYKFDFEDDQHKIPCHC--GAVNC 4915
Cdd:cd19181    101 DGMIHLCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 391-435 8.16e-06

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 45.73  E-value: 8.16e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPT-NGWKCKNC 435
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1981-2222 9.31e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 52.19  E-value: 9.31e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1981 PDPYAGPSLTP------APLGNGPFKTPlhPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPL 2054
Cdd:PRK12323   347 PDEYAGFTMTLlrmlafRPGQSGGGAGP--ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPA 424

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2055 TPHPAMTESFTHASRAFPQPGTISRSASQdPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPP--------GTPRPNTI 2126
Cdd:PRK12323   425 RRSPAPEALAAARQASARGPGGAPAPAPA-PAAAPAAAARPAAAG-------PRPVAAAAAAAParaapaaaPAPADDDP 496

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2127 DPYSQQPPT-PRPSP-QTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGF---TRPSSARPALMPN 2201
Cdd:PRK12323   497 PPWEELPPEfASPAPaQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVvapRPPRASASGLPDM 576

                          250       260
                   ....*....|....*....|....
gi 1039771187 2202 QD---PFLqAAQNRVPGLPGPLIR 2222
Cdd:PRK12323   577 FDgdwPAL-AARLPVRGLAQQLAR 599
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 4806-4895 1.08e-05

SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380943 [Multi-domain]  Cd Length: 232  Bit Score: 50.09  E-value: 1.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4806 VIEYIGTIIRNEVANRKEKlyesqnRGVYMFRMDN-------------------------------DHVIDATLTGGPAR 4854
Cdd:cd10545    112 ICEYVGELLDTSEADTRSG------NDDYLFDIDNrqtnrgwdggqrldvgmsdgerssaedeessEFTIDAGSFGNVAR 185

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187 4855 YINHSCAPNCVAEVVTFE----RGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd10545    186 FINHSCSPNLFVQCVLYDhndlRLPRVMLFAADNIPPLQELTYDY 230
HMG_box pfam00505
HMG (high mobility group) box;
1605-1656 1.24e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 45.68  E-value: 1.24e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 1605 VLYTNINFPNLKEEFPDWTTR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1656
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
250-330 1.30e-05

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 46.95  E-value: 1.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  250 WAHHRCVEWSLGIC-----QMEeplLVNVDKAVVSGSTERCAFCKHL-GATIKCCEEKCTQMYHYPCAAGAG---TFQDF 320
Cdd:pfam13832   21 WVHVLCAIFVPEVRfgnvaTME---PIDVSRIPPERWKLKCVFCKKRsGACIQCSKGRCTTAFHVTCAQAAGvymEPEDW 97

                           90
                   ....*....|..
gi 1039771187  321 SHF--FLLCPEH 330
Cdd:pfam13832   98 PNVvvIAYCQKH 109
HMG smart00398
high mobility group;
1603-1656 1.36e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 1.36e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039771187  1603 APVLYTNINFPNLKEEFPDWTT--RVKQIAKLWRKASSQERAPYVQKARDNRAALR 1656
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4438-4501 1.67e-05

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 46.88  E-value: 1.67e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 4438 HLNCALWSTEVYETQAG-------ALINVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCA--TKAQ 4501
Cdd:cd15710     26 HHKCMLFSSALVSSHSDsenlggfSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCAlhDKAQ 98
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1758-2201 1.97e-05

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 51.23  E-value: 1.97e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1758 DTPSSGAQSPLTPQAGNGNVSPAQTFHKDLFSKHLP---GTPASTPSDGVFVKPQPPPPPSTPSRIPV-------QESLS 1827
Cdd:PTZ00449   508 DEPPEGPEASGLPPKAPGDKEGEEGEHEDSKESDEPkegGKPGETKEGEVGKKPGPAKEHKPSKIPTLskkpefpKDPKH 587

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1828 QSQNSQPPSPQMFSPGSSHSRPPSPVDP-YAKMVGTPRPPPGGHSfPRRnsvtPVencvplssvprpihmnetSATRP-S 1905
Cdd:PTZ00449   588 PKDPEEPKKPKRPRSAQRPTRPKSPKLPeLLDIPKSPKRPESPKS-PKR----PP------------------PPQRPsS 644

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1906 PARDLCASSMTNSdpyaKPPDTPRPMMTDQFSKPFSLPRSPVISEqsTKGPLTTGTSDHftkpspRTDAFQRQRLPDPYA 1985
Cdd:PTZ00449   645 PERPEGPKIIKSP----KPPKSPKPPFDPKFKEKFYDDYLDAAAK--SKETKTTVVLDE------SFESILKETLPETPG 712

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1986 GPSLTPAPLgngPFKTPLHPPPSQDPygsvsqtsrrlsvdPYERPALTPRPVDNFSHSQSNDPYSH--PPLTPHPAMT-- 2061
Cdd:PTZ00449   713 TPFTTPRPL---PPKLPRDEEFPFEP--------------IGDPDAEQPDDIEFFTPPEEERTFFHetPADTPLPDILae 775

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2062 ---ESFTHASRAFPQPgTISRSASQDPYS-QPPGT------PRPLIDSYSQTSGTARSNP-----DPYSQPPGTPRPNTI 2126
Cdd:PTZ00449   776 efkEEDIHAETGEPDE-AMKRPDSPSEHEdKPPGDhpslpkKRHRLDGLALSTTDLESDAgriakDASGKIVKLKRSKSF 854

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 2127 DPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHhlgPP--RPGISVPYSQPPAVP-RPRTSEGFTRPSSARPALMPN 2201
Cdd:PTZ00449   855 DDLTTVEEAEEMGAEARKIVVDDDGTEADDEDTH---PPeeKHKSEVRRRRPPKKPsKPKKPSKPKKPKKPDSAFIPS 929
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 251-330 2.36e-05

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 46.43  E-value: 2.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  251 AHHRCVEWSLGICQMEEPLLVNVD---------KAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA----AGAGTF 317
Cdd:cd15712     23 AHQNCLLYSSGFVESEEYNPLNLDrrfdvesvlNEIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCAlcddAAIETD 102

                           90
                   ....*....|...
gi 1039771187  318 QDFSHFFLLCPEH 330
Cdd:cd15712    103 EVRGIYRVFCQKH 115
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 965-1009 2.56e-05

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 44.11  E-value: 2.56e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKAtdpGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15524      2 CAACKRG---GNLQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
SET_SETD7 cd10530
SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2. ...
 4782-4895 2.59e-05

SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2.1.1.43; also termed histone H3-K4 methyltransferase SETD7, H3-K4-HMTase SETD7, lysine N-methyltransferase 7 (KMT7) or SET7/9) is a histone-lysine N-methyltransferase that specifically monomethylates 'Lys-4' of histone H3. It plays a central role in the transcriptional activation of genes such as collagenase or insulin. Set7/9 also methylates non-histone proteins, including estrogen receptor alpha (ERa), suggesting it has a role in diverse biological processes. ERa methylation by Set7/9 stabilizes ERa and activates its transcriptional activities, which are involved in the carcinogenesis of breast cancer. In a high-throughput screen, treatment of human breast cancer cells (MCF7 cells) with cyproheptadine, a Set7/9 inhibitor, decreased the expression and transcriptional activity of ERa, thereby inhibiting estrogen-dependent cell growth.


Pssm-ID: 380928  Cd Length: 130  Bit Score: 46.91  E-value: 2.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4782 VYLARSRIQ--GLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESqnrgvYMFRMDNDHVID------------AT 4847
Cdd:cd10530      9 VYVAESLIPsaGEGLFAKVAVGPNTVMSFYNGVRITHQEVDSRDWSLNG-----NTISLDEETVIDvpepynsvskycAS 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187 4848 LtGGPAryiNHSCAPNCVAEVVTFER-GHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd10530     84 L-GHKA---NHSFTPNCIYDPFVHPRfGPIKCIRTLRAVEAGEELTVAY 128
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 965-1009 2.63e-05

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 44.22  E-value: 2.63e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  965 CEACGKATDPGRLLLCDDCDISYHTYCLDPPLQTVPKGG--WKCKWC 1009
Cdd:cd15497      2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 928-962 2.78e-05

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 44.65  E-value: 2.78e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1039771187  928 RLLACSQCGQCYHPYCV--SIKITKVVLSKGWRCLEC 962
Cdd:cd15526     20 ELISCADCGSSGHPSCLkfSPGLTDAVKSYRWQCIEC 56
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2043-2267 3.01e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.75  E-value: 3.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2043 SQSNDPYSHPPLTPHPAmtesfthaSRAFPQPGTISRSASQDPYSQPPGTPrplidsYSQTSGTARSNPDPYSQPPGTPR 2122
Cdd:PRK07764   606 SGPPEEAARPAAPAAPA--------APAAPAPAGAAAAPAEASAAPAPGVA------APEHHPKHVAVPDASDGGDGWPA 671

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2123 PNTIDPYSQQPPTPRPSPQtdmfvssVANQRHTDPYTHHLGPPRPGiSVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQ 2202
Cdd:PRK07764   672 KAGGAAPAAPPPAPAPAAP-------AAPAGAAPAQPAPAPAATPP-AGQADDPAAQPPQAAQGASAPSPAADDPVPLPP 743

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 2203 DPFLQAAQNRVPGLPGPlIRPPDTCSQTPRPPGPgridtfTHASSSAVRDPYDQPPVTPRPHSES 2267
Cdd:PRK07764   744 EPDDPPDPAGAPAQPPP-PPAPAPAAAPAAAPPP------SPPSEEEEMAEDDAPSMDDEDRRDA 801
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 246-330 3.29e-05

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 45.90  E-value: 3.29e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  246 TGTCWAHHRCVEW----SLGICQMEEPLlVNVDKAVVSGSTERCAFCK-HLGATIKCCEEKCTQMYHYPCAAGAG----- 315
Cdd:cd15671     16 SGTKWVHVSCALWipevSIGCPEKMEPI-TKISHIPMSRWALVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQHGlemkt 94

                           90
                   ....*....|....*...
gi 1039771187  316 ---TFQDFSHFFLLCPEH 330
Cdd:cd15671     95 ileDEDDEVKFKSYCPKH 112
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 390-434 3.60e-05

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 43.87  E-value: 3.60e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  390 VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG-WKCKN 434
Cdd:cd15534      1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMCPN 46
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 964-1009 3.68e-05

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 43.96  E-value: 3.68e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187  964 VCEACGKAT--DPGRLLLCD-DCDISYHTYCLDPPLQT--VPKG--GWKCKWC 1009
Cdd:cd15504      1 FCAKCQSGEasPDNDILLCDgGCNRAYHQKCLEPPLLTedIPPEdeGWLCPLC 53
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4411-4507 3.79e-05

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 46.23  E-value: 3.79e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHE-EGDGLTDGPARLLNLDlDLWVHLNCALWST---EVYETQAGALINVELA-----LRRGLQMKCVFCHKTGATS 4481
Cdd:cd15711      1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                           90       100
                   ....*....|....*....|....*.
gi 1039771187 4482 GCHRFRCTNIYHFTCATKAQCMFFKD 4507
Cdd:cd15711     80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 962-1009 3.80e-05

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 43.96  E-value: 3.80e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  962 CTVCEaCGKATDPGRLLLCDDCDISYHTYCLDPPLQT----VPKGGWKCKWC 1009
Cdd:cd15502      2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1947-2234 3.88e-05

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 49.92  E-value: 3.88e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1947 VISEqsTKGPLTTgTSDHFTK-PSprtdafQRQRLPDPYAGPSLTPAPLGNGPFKTPLhPPPSQDPYGSVSQTSRRLSvd 2025
Cdd:PLN03209   305 VIAE--TTAPLTP-MEELLAKiPS------QRVPPKESDAADGPKPVPTKPVTPEAPS-PPIEEEPPQPKAVVPRPLS-- 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2026 PYE-----RPALTPRPVdnfshsqsndPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLidsy 2100
Cdd:PLN03209   373 PYTayedlKPPTSPIPT----------PPSSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTRPL---- 438

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2101 sqtsgtarsnpDPYS-----QPPGTPRPNTIDPY----------SQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPP 2165
Cdd:PLN03209   439 -----------SPYAryedlKPPTSPSPTAPTGVspsvsstssvPAVPDTAPATAATDAAAPPPANMRPLSPYAVYDDLK 507

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039771187 2166 RPGISVPYSQPPAVPRPRTSEGFTRPSSARP-ALMPNQDpflQAAQNRVPGLPGPL---IRPPdtCSQTPRPP 2234
Cdd:PLN03209   508 PPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPtALADEQH---HAQPKPRPLSPYTMyedLKPP--TSPTPSPV 575
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 387-435 4.79e-05

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 43.49  E-value: 4.79e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  387 ECKVCQNckqsGEDSkmLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15541      1 WCAVCQN----GGEL--LCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1943-2184 5.01e-05

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 49.54  E-value: 5.01e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1943 PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLP---DPYAG-------PSLTPAPLGNGPFKTP----LHPPPS 2008
Cdd:PLN03209   330 PKESDAADGPKPVPTKPVTPEAPSPPIEEEPPQPKAVVPrplSPYTAyedlkppTSPIPTPPSSSPASSKsvdaVAKPAE 409

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2009 QDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQDPYSQ 2088
Cdd:PLN03209   410 PDVVPSPGSASNVPEVEPAQVEAKKTRPLSPYARYEDLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAP 489

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2089 PPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTidpySQQPPTPRPSPQTdmfvSSVANQRHTDPythhlgPPRPg 2168
Cdd:PLN03209   490 PPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSST----NEVVKVGNSAPPT----ALADEQHHAQP------KPRP- 554

                          250       260
                   ....*....|....*....|.
gi 1039771187 2169 ISvPYS-----QPPAVPRPRT 2184
Cdd:PLN03209   555 LS-PYTmyedlKPPTSPTPSP 574
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 4411-4504 5.04e-05

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 45.43  E-value: 5.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLQMKCVFCHK-------TG 4478
Cdd:cd15675      1 CCLCCLRGGALkptTDG----------RWAHVVCAIAIPEVRfsNVPERGPIDISKIPPARLKLKCIYCSKitksmshMG 70

                           90       100
                   ....*....|....*....|....*.
gi 1039771187 4479 ATSGCHRFRCTNIYHFTCATKAQCMF 4504
Cdd:cd15675     71 ACIQCSTGKCTTSFHVTCAHAAGVQM 96
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 962-1009 5.13e-05

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 43.61  E-value: 5.13e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  962 CTVCEACGKATDPgrLLLCDDCDISYHTYCLDPPLQTVP---KGGWKCKWC 1009
Cdd:cd15507      2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPtrkKKTWICSKC 50
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 388-435 5.21e-05

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 43.64  E-value: 5.21e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  388 CKVCQNcKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG---WKCKNC 435
Cdd:cd15499      2 CSICGG-AEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 388-435 5.36e-05

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 43.58  E-value: 5.36e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  388 CKVCQnCKQSGEDSKMLVCDTCDKGYHTFCLQPVMK----SVPTNGWKCKNC 435
Cdd:cd15502      2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDdevvEDPDAEWFCKKC 52
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2005-2197 5.40e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.60  E-value: 5.40e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2005 PPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDnfshsqsnDPYSHPPLTPHPAMTESFTHASRAFPQPGTISRSASQD 2084
Cdd:PRK07764   590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAA--------PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPD 661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2085 PYSQPPGTPRPLID-----------SYSQTSGTARSNPDPYSQPPGTPRPntiDPYSQQPPTPRPSPQTDMFVSSVANQR 2153
Cdd:PRK07764   662 ASDGGDGWPAKAGGaapaapppapaPAAPAAPAGAAPAQPAPAPAATPPA---GQADDPAAQPPQAAQGASAPSPAADDP 738

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1039771187 2154 HTDPYTHHLgPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPA 2197
Cdd:PRK07764   739 VPLPPEPDD-PPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSE 781
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1042-1091 5.80e-05

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 43.82  E-value: 5.80e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039771187 1042 CPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLNTE--EEVENVAD-IGFDCSMC 1091
Cdd:cd15592      2 CPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENLSDEmyEILSNLPEsVAYTCINC 57
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 4411-4507 6.83e-05

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 44.96  E-value: 6.83e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGparllnlDLDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLQMKCVFCHK-----TGATSG 4482
Cdd:cd15713      1 CCLCSLRGGALQRA-------NDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQR-FKLKCIFCKKrrkrtAGCCVQ 72

                           90       100
                   ....*....|....*....|....*
gi 1039771187 4483 CHRFRCTNIYHFTCATKAQCMFFKD 4507
Cdd:cd15713     73 CSHGRCPTSFHASCAQAAGVMMQPD 97
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1042-1093 7.30e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 43.25  E-value: 7.30e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 1042 CPVCcRNYREEDLILQCRQCDRWMHAVCqnLNTEEEVENVADIGFDCSMCRP 1093
Cdd:pfam00628    2 CAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECKP 50
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 343-388 9.31e-05

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 42.77  E-value: 9.31e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  343 NCAVCDSPGDLLDQFFCTTCGQHYHGMCLD--IAVTPLKRA-GWQCPEC 388
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDppLKKSPKQRGyGWVCEEC 49
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1605-1659 9.56e-05

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 43.46  E-value: 9.56e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 1605 VLYTNINFPNLKEEFPDWTTRV--KQIAKLWRKASSQERAPYVQKARD-NRAALRINK 1659
Cdd:cd21977      9 IMFCRLNRKNYIDKHPGLASTEltKELGQLWRELSAEEKKPYCVRARElSQLHNRKVK 66
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 344-388 9.56e-05

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 42.78  E-value: 9.56e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  344 CAVCDSPGD--LLDQffCTTCGQHYHGMCLDIAVT--PLKRA--GWQCPEC 388
Cdd:cd15562      2 CGICKKSNDqhLLAL--CDTCKLYYHLGCLDPPLTrmPKKTKnsGWQCSEC 50
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 4794-4899 1.12e-04

SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide.


Pssm-ID: 380959  Cd Length: 129  Bit Score: 44.88  E-value: 1.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4794 LYAARDIEKHTMVIEYIGTIIRNEV--AN-----RKEK--LYESQNRGVYMfrmdndhVIDATLTGGPARYINHSCAPNC 4864
Cdd:cd19182     21 LKAAKDLPPDTLIIEYRGKFMLREQfeANgyffkRPYPfvLFYSKFHGLEM-------CVDARTFGNEARFIRRSCTPNA 93

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1039771187 4865 VAEVVTFERGHKIIISSNRRIQKGEELCYDYKFDF 4899
Cdd:cd19182     94 EVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDFDY 128
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 4411-4500 1.21e-04

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 44.54  E-value: 1.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGL---TDgparllnldlDLWVHLNCALWSTEVYETQA--GALINVELALRRGLQMKCVFCHKT-----GAT 4480
Cdd:cd15714      1 CCLCNLRGGALqmtTD----------ERWVHVICAIAVPEARFLNVieRHPVDVSAIPEQRWKLKCVYCRKRmkkvsGAC 70

                           90       100
                   ....*....|....*....|
gi 1039771187 4481 SGCHRFRCTNIYHFTCATKA 4500
Cdd:cd15714     71 IQCSYDHCSTSFHVTCAHAA 90
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 467-517 1.35e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 42.53  E-value: 1.35e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039771187  467 CPFCGKCYHP-ELQKDMLHCNMCKRWVHLECDKPTDQ--ELDSQLKED--YICMYC 517
Cdd:cd15593      2 CPICLKCYEDnDYESKMMQCAKCDHWVHAKCEGLSDElyEILSSLPDSvvYSCAPC 57
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1042-1075 1.67e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 42.53  E-value: 1.67e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1039771187 1042 CPVCCRNYREEDL---ILQCRQCDRWMHAVCQNLNTE 1075
Cdd:cd15593      2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGLSDE 38
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 965-1009 1.86e-04

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 41.71  E-value: 1.86e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKatdPGRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1009
Cdd:cd15623      2 CRVCQK---AGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
dnaA PRK14086
chromosomal replication initiator protein DnaA;
2125-2323 1.87e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 47.90  E-value: 1.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2125 TIDPYSQQPPTPRPSPQtdmfvssvanqRHTDPYTHHLGP-PRPGisvpYSQPPAVPRPRTSEGFTRPSSARPALMPNQD 2203
Cdd:PRK14086    87 TVDPSAGEPAPPPPHAR-----------RTSEPELPRPGRrPYEG----YGGPRADDRPPGLPRQDQLPTARPAYPAYQQ 151

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2204 PflqaaqnrvpGLPGPLIRPPDTCSQTPRPPGPGRIDTFTHASSSA-----VRDPYD----------QPPVTPRPHSEsf 2268
Cdd:PRK14086   152 R----------PEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYApeqerDREPYDagrpeydqrrRDYDHPRPDWD-- 219

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039771187 2269 gtsQVVHDLVDRPV--PGSEGNFSTSSNLPVSSQGQQFSSVSQLPG-------PVPTSGGTDTQ 2323
Cdd:PRK14086   220 ---RPRRDRTDRPEppPGAGHVHRGGPGPPERDDAPVVPIRPSAPGplaaqpaPAPGPGEPTAR 280
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 390-435 2.11e-04

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 41.58  E-value: 2.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  390 VCQNCKQSGEDsKMLVCDTCDKGYHTFCLQPVMKSVPTNG--WKCKNC 435
Cdd:cd15506      1 LCFLCGSAGLN-ELLYCSVCCEPYHTFCLEEAERPLNINKdnWCCRRC 47
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 391-435 2.26e-04

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 41.53  E-value: 2.26e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNG--WKCKNC 435
Cdd:cd15497      2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 391-435 2.60e-04

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 41.25  E-value: 2.60e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15559      2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 1968-2285 2.74e-04

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 47.37  E-value: 2.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1968 PSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQ--DPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2045
Cdd:COG5180    138 TREATSASAGVALAAALLQRSDPILAKDPDGDSASTLPPPAEklDKVLTEPRDALKDSPEKLDRPKVEVKDEAQEEPPDL 217

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2046 NDPYSHPPLtphPAMTESFthasraFPQPGTiSRSASQDPYSQPPGTPRPLIDSysqtsgtARSNPDPYSQPPGTPRPNt 2125
Cdd:COG5180    218 TGGADHPRP---EAASSPK------VDPPST-SEARSRPATVDAQPEMRPPADA-------KERRRAAIGDTPAAEPPG- 279

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2126 idpysQQPPTPRPSPQTDMfvSSVANQRHTDPYTHHLGPP--RPGISVPYSQPPAVPRPRTSEGftRPSSA-RPALMPNQ 2202
Cdd:COG5180    280 -----LPVLEAGSEPQSDA--PEAETARPIDVKGVASAPPatRPVRPPGGARDPGTPRPGQPTE--RPAGVpEAASDAGQ 350

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2203 DP-FLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGpgridtfthasssavrDPYDQPPVTPRPHSESFGTSQVVHDLVDRP 2281
Cdd:COG5180    351 PPsAYPPAEEAVPGKPLEQGAPRPGSSGGDGAPF----------------QPPNGAPQPGLGRRGAPGPPMGAGDLVQAA 414


                   ....
gi 1039771187 2282 VPGS 2285
Cdd:COG5180    415 LDGG 418
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 926-962 2.85e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 41.16  E-value: 2.85e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1039771187  926 EGRLLACSQCGQCYHPYCVSIKITkvvLSKGWRCLEC 962
Cdd:cd15538      8 EGQVLCCSLCPRVYHKKCLKLTSE---PDEDWVCPEC 41
PHA03379 PHA03379
EBNA-3A; Provisional
 2360-2663 3.09e-04

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 47.36  E-value: 3.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2360 EKGPQDTAVVPHP-VPLPHWQ-PESINQAFTRPPP--PYPGSTRSPVIPPLGPRYAVFP----KDQRGPYPPEVAGmGMR 2431
Cdd:PHA03379   406 EKASEPTYGTPRPpVEKPRPEvPQSLETATSHGSAqvPEPPPVHDLEPGPLHDQHSMAPcpvaQLPPGPLQDLEPG-DQL 484

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2432 PHGFRFGFPGAGHGPMPSQDRFH----VPQQIQGSGIPPHIRRPMSMEMPRPSNNPPLNNPVGLPQHFPPQGlPVQQHNI 2507
Cdd:PHA03379   485 PGVVQDGRPACAPVPAPAGPIVRpweaSLSQVPGVAFAPVMPQPMPVEPVPVPTVALERPVCPAPPLIAMQG-PGETSGI 563

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2508 LGqafIELRHRAPDGRSRLPFAASPSSVIESPSHPR-------HGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPnLE 2580
Cdd:PHA03379   564 VR---VRERWRPAPWTPNPPRSPSQMSVRDRLARLRaeaqpyqASVEVQPPQLTQVSPQQPMEYPLEPEQQMFPGSP-FS 639

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2581 QVPPSQQEQGHPAHQSSIVMRPLNHPLSGEFSEAPLSTST-----PAETSPDNLEIAgqssagLEEKLDSDDPSVKELDV 2655
Cdd:PHA03379   640 QVADVMRAGGVPAMQPQYFDLPLQQPISQGAPLAPLRASMgpvppVPATQPQYFDIP------LTEPINQGASAAHFLPQ 713


                   ....*...
gi 1039771187 2656 KDLEGVEV 2663
Cdd:PHA03379   714 QPMEGPLV 721
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2058-2282 3.23e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 47.47  E-value: 3.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2058 PAMTESFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLidsysqtSGTARSNPDPYSQPPGT----PRPNTIDPYSQQP 2133
Cdd:PHA03307   761 PSLVPAKLAEALALLEPAEPQRGAGSSPPVRAEAAFRRP-------GRLRRSGPAADAASRTAskrkSRSHTPDGGSESS 833

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2134 PTPRPSPQTdmFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPAlmpnqdpflqaaqnRV 2213
Cdd:PHA03307   834 GPARPPGAA--ARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAA--------------PP 897

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 2214 PGLPGPLIRPPDTCSQTPRPPGpGRidtfthASSSAVRDPYDQPPVTPRP---HSESFGTSQVVHDLVDRPV 2282
Cdd:PHA03307   898 AGAPAPRPRPAPRVKLGPMPPG-GP------DPRGGFRRVPPGDLHTPAPsaaALAAYCPPEVVAELVDHPL 962
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 391-435 3.28e-04

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 41.09  E-value: 3.28e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  391 CQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTN-GWKCKNC 435
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 388-435 3.56e-04

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 41.27  E-value: 3.56e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187  388 CKVCQNcKQSGEDSKMLVCD-TCDKGYHTFCLQPVMKSV----PTNGWKCKNC 435
Cdd:cd15504      2 CAKCQS-GEASPDNDILLCDgGCNRAYHQKCLEPPLLTEdippEDEGWLCPLC 53
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
 915-962 3.70e-04

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.


Pssm-ID: 276976  Cd Length: 52  Bit Score: 41.18  E-value: 3.70e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  915 CVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLS---KGWRCLEC 962
Cdd:cd15501      2 CVVCKQMDVTSGNQLVECQECHNLYHQECHKPPVTDKDVNdprLVWYCSRC 52
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 344-388 3.87e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 41.54  E-value: 3.87e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  344 CAVCDS-----PGDLLDqffCTTCGQHYHGMCLDIAVTP-LKRAGWQCPEC 388
Cdd:cd15596      9 CVVCGSfgqgaEGRLLA---CSQCGQCYHPYCVSIKITKvVLSKGWRCLEC 56
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 4436-4499 3.98e-04

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 42.82  E-value: 3.98e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039771187 4436 WVHLNCALWSTEV-------YEtqagALINVELALRRGLQMKCVFCH-KTGATSGCHRFRCTNIYHFTCATK 4499
Cdd:cd15671     20 WVHVSCALWIPEVsigcpekME----PITKISHIPMSRWALVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQ 87
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
4904-4920 4.47e-04

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 40.08  E-value: 4.47e-04
                            10
                    ....*....|....*..
gi 1039771187  4904 HKIPCHCGAVNCRKWMN 4920
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
SET_SMYD4 cd10536
SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing ...
 4856-4912 4.61e-04

SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins; SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. In zebrafish, SMYD4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart; mutants show a strong defect in cardiomyocyte proliferation, which lead to a severe cardiac malformation.


Pssm-ID: 380934 [Multi-domain]  Cd Length: 218  Bit Score: 44.98  E-value: 4.61e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039771187 4856 INHSCAPNCvaeVVTFErGHKIIISSNRRIQKGEEL--CYDYKF---DFED------DQHKIPCHCGA 4912
Cdd:cd10536    154 LNHSCDPNT---IRSFY-GNTIVVRATRPIKKGEEItiCYGPHFsrmKRSErqrllkEQYFFDCSCEA 217
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 1983-2122 5.06e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 46.61  E-value: 5.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1983 PYAGPSLTPAPLGNGPFKtplHPPPSQDPYgsvsqtsrrlSVDPYERPALTPRPVDNFSHsqSNDPYSHPP---LTPHPA 2059
Cdd:PTZ00395   418 GNSNPGYNNAPNSNTPYN---NPPNSNTPY----------SNPPNSNPPYSNLPYSNTPY--SNAPLSNAPpssAKDHHS 482

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039771187 2060 MTESfTHASRAFPQPG----TISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR 2122
Cdd:PTZ00395   483 AYHA-AYQHRAANQPAanlpTANQPAANNFHGAAGNSVGNPFASRPFGSAPYGGNAATTADPNGIAK 548
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 240-311 5.47e-04

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 42.64  E-value: 5.47e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187  240 QALFDSTGTCWAHHRCVEWSLGICQME---EPL----LVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15710     14 QLLISENQKVAAHHKCMLFSSALVSSHsdsENLggfsIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCA 92
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 344-388 6.08e-04

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 40.46  E-value: 6.08e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15523      2 CSVCRKSGELL---MCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 4411-4500 6.31e-04

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 42.25  E-value: 6.31e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4411 CCFCHEEGDGLTDGPArllnldlDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLQMKCVFCHK-----TGATSG 4482
Cdd:cd15715      1 CCLCNLRGGALKQTSD-------DKWAHVMCAVALPEVRFINVVERTPIDISripLQR-LKLKCIFCRNrikrvSGACIQ 72

                           90
                   ....*....|....*...
gi 1039771187 4483 CHRFRCTNIYHFTCATKA 4500
Cdd:cd15715     73 CSYGRCPASFHVTCAHAA 90
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 388-435 7.00e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 40.52  E-value: 7.00e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  388 CKVCQNCKQsGEDSKMLVCDTCDKGYHTFCLQ-PVMKSVPTNGWKCKNC 435
Cdd:cd15512      2 CVSCGSFGR-GAEGRLIACSQCGQCYHPYCVNvKVTKVILSKGWRCLDC 49
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 467-517 8.25e-04

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 40.35  E-value: 8.25e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039771187  467 CPFCGKCYHPElqkDML-HCNMCKRWVHLECDK-PTDQELDSQLKEDYICMYC 517
Cdd:cd15514      2 CPVCSRSYNEG---ELIiQCSQCERWLHGACDSlRTEEEAERAADNGYRCLLC 51
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 914-962 8.49e-04

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 40.09  E-value: 8.49e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039771187  914 MCVVC---GSFGQGAEGRLLACSQCGQCYHPYCVSI--KITKVVLSKGWRCLEC 962
Cdd:cd15528      1 VCGICekgGKSNKGEPEELIHCSQCGNSGHPSCLEMsdEMVAVIKTYPWQCMEC 54
SET_SMYD3 cd19203
SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 ...
 4857-4895 8.52e-04

SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins; SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. It is overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers.


Pssm-ID: 380980 [Multi-domain]  Cd Length: 210  Bit Score: 43.89  E-value: 8.52e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1039771187 4857 NHSCAPNCVAevvTFErGHKIIISSNRRIQKGEELCYDY 4895
Cdd:cd19203    147 NHSCDPNCVI---VFN-GPHLLLRAIREIEVGEELTISY 181
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1966-2160 8.55e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 8.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1966 TKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQS 2045
Cdd:PRK07764   600 PPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPA 679

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2046 NDPYSHPPLTPHPAMTESFT---HASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR 2122
Cdd:PRK07764   680 APPPAPAPAAPAAPAGAAPAqpaPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPP 759

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1039771187 2123 PNTID-PYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTH 2160
Cdd:PRK07764   760 PPPAPaPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDR 798
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 965-1008 8.61e-04

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 39.95  E-value: 8.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  965 CEACGkatDPGRLLLCD--DCDISYHTYCLDppLQTVPKGGWKCKW 1008
Cdd:cd15661      2 CFQCG---DGGELVMCDkkDCPKAYHLLCLN--LTQPPYGKWECPW 42
DUF3824 pfam12868
Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It ...
 2028-2140 8.63e-04

Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.


Pssm-ID: 372351 [Multi-domain]  Cd Length: 145  Bit Score: 42.81  E-value: 8.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2028 ERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESFTHaSRAFPQPgtisrsasqdpysqPPGTPRPLIDsYSQTSGTA 2107
Cdd:pfam12868   40 ERRRYEDDYRDYYEDPYSPSPYPPSPAGPYASQGQYYPE-TNYFPPP--------------PGSTPQPPVD-PQPNAPPP 103

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1039771187 2108 RSNPDPYSQPPGTPRPNtidPYSQQPPTPRPSP 2140
Cdd:pfam12868  104 PYNPADYPPPPGAAPPP---QPYQYPPPPGPDP 133
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1985-2210 8.92e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 8.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 1985 AGPSLTPAPLGNGPFKTPLHPPPSQDPYGSVSQtsrrlsvdPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTESF 2064
Cdd:PRK07764   595 AGGEGPPAPASSGPPEEAARPAAPAAPAAPAAP--------APAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGG 666

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2065 THASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNP--DPYSQPPGTPRPNTIDPYS---QQPPTPRPS 2139
Cdd:PRK07764   667 DGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQadDPAAQPPQAAQGASAPSPAaddPVPLPPEPD 746

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 2140 PQTDmfvssvanqrhtdPYTHHLGPPRPGISVPYSQPPAvpRPRTSEGFTRPSSARPALMPNQDPFLQAAQ 2210
Cdd:PRK07764   747 DPPD-------------PAGAPAQPPPPPAPAPAAAPAA--APPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 914-962 9.14e-04

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 40.04  E-value: 9.14e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  914 MCVVCGSFGQGaegRLLACSQCGQCYHPYCVSIKITKVVLSKG-WRCLEC 962
Cdd:cd15506      1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 344-388 9.16e-04

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 40.05  E-value: 9.16e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  344 CAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3136-3218 9.96e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 45.55  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3136 EEWLQETQQLLQmqqkylEEQigahrKSKKALSAKQRT--AKKAG-REFPEEDAEQLKHVTEQQSMVQKQLEQIRKQQKE 3212
Cdd:pfam01576  467 ESQLQDTQELLQ------EET-----RQKLNLSTRLRQleDERNSlQEQLEEEEEAKRNVERQLSTLQAQLSDMKKKLEE 535


                   ....*.
gi 1039771187 3213 HAELIE 3218
Cdd:pfam01576  536 DAGTLE 541
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 962-1009 1.04e-03

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 39.91  E-value: 1.04e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  962 CTVCEAcGKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1009
Cdd:cd15492      2 CDVCLD-GESEDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 251-311 1.17e-03

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 41.99  E-value: 1.17e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039771187  251 AHHRCVEWSLGICQMEEPL--------LVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15711     27 AHYKCMLFSSGTVQLTTTSraefgdfdIKTVIQEIKRGKRMKCTLCSQLGATIGCEIKACVKTYHYHCG 95
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 241-319 1.22e-03

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 41.69  E-value: 1.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  241 ALFDSTGTCWAHHRCVEW-----SLGICQMEeplLVNVDKAVvsgSTER----CAFCKH-LGATIKCCEEKCTQMYHYPC 310
Cdd:cd15662     10 ALKPTTDGRWAHLACAIWipetcLLDVKTME---PVDGINAI---SKERwelsCTICKQrYGACIQCSNNSCRVAYHPLC 83


                   ....*....
gi 1039771187  311 AAGAGTFQD 319
Cdd:cd15662     84 ARAAGLCME 92
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2073-2330 1.26e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 1.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2073 QPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPpgTPRPN----------TIDPYSQQPPTPRPSPQT 2142
Cdd:pfam09770  106 QPAARAAQSSAQPPASSLPQYQYASQQSQQPSKPVRTGYEKYKEP--EPIPDlqvdaslwgvAPKKAAAPAPAPQPAAQP 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2143 DMFVSSV----------ANQRHTDPythhlGPPRPGISVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQDPfLQAAQNR 2212
Cdd:pfam09770  184 ASLPAPSrkmmsleeveAAMRAQAK-----KPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQP-QQPQQHP 257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2213 VPGLP-GPLIRPPdtcSQTPRPPGPgridtftHASSSAVRDPYDQPPVTPRPhsesfgtSQVVHD---LVDRPVPGSEGN 2288
Cdd:pfam09770  258 GQGHPvTILQRPQ---SPQPDPAQP-------SIQPQAQQFHQQPPPVPVQP-------TQILQNpnrLSAARVGYPQNP 320

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1039771187 2289 FSTSSNLPVSSQGQQFSSVSQLPGPVptsggTDTQNTVNMSQ 2330
Cdd:pfam09770  321 QPGVQPAPAHQAHRQQGSFGRQAPII-----THPQQLAQLSE 357
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 4436-4500 1.27e-03

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 41.55  E-value: 1.27e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 4436 WVHLNCALWSTEVYetqagaLIN-VELALRRGLQ--------MKCVFC-HKTGATSGCHRFRCTNIYHFTCATKA 4500
Cdd:cd15670     19 WAHVVCALWIPEVS------FANtVFLEPIDGIQnipkarwkLTCYICkKRMGACIQCHKKNCYTAFHVTCAQQA 87
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4436-4519 1.31e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 1.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4436 WVHLNCALWSTEVY--ETQAGALINVELALRRGL-QMKCVFCHKTGATS-GCHRFRCTNIYHFTCATKAqCMFFK----- 4506
Cdd:COG5141    268 WGHVICAMFNPELSfgHLLSKDPIDNIASVSSSRwKLGCLICKEFGGTCiQCSYFNCTRAYHVTCARRA-GYFDLniysh 346

                           90       100
                   ....*....|....*....|
gi 1039771187 4507 -------DKTMLCPMHKPKG 4519
Cdd:COG5141    347 ngisyciDHEPLCRKHYPLG 366
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 388-435 1.49e-03

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 39.61  E-value: 1.49e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  388 CKVCQNCKQsGEDSKMLVCDTCDKGYHTFCLQ-PVMKSVPTNGWKCKNC 435
Cdd:cd15596      9 CVVCGSFGQ-GAEGRLLACSQCGQCYHPYCVSiKITKVVLSKGWRCLEC 56
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 3131-3223 1.62e-03

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 44.14  E-value: 1.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3131 QRKQ--YEEWLQETQQLLQMQQKYLEEQigahrksKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQIRK 3208
Cdd:pfam13868   87 QKRQeeYEEKLQEREQMDEIVERIQEED-------QAEAEEKLEKQRQLREEIDEFNEEQAEWKELEKEEEREEDERILE 159

                           90
                   ....*....|....*
gi 1039771187 3209 QQKEHAELIEDYRIK 3223
Cdd:pfam13868  160 YLKEKAEREEEREAE 174
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 915-962 1.74e-03

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 38.95  E-value: 1.74e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  915 CVVCGSfgQGAEGRLLACSQCGQCYHPYCVSIKITKVVlSKGWRCLEC 962
Cdd:cd15510      2 CQACRQ--PGDDTKMLVCETCDKGYHTSCLRPVMSSIP-KYGWKCKNC 46
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 915-962 1.81e-03

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 39.15  E-value: 1.81e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  915 CVVCGSFGQGAEgRLLACSQCGQCYHPYCVSIKITKVVLSK--GWRCLEC 962
Cdd:cd15591      2 CHVCGRKNKESK-PLLECERCRNCYHPACLGPNYPKPANRKkrPWICSAC 50
PHA03418 PHA03418
hypothetical E4 protein; Provisional
 2085-2265 1.84e-03

hypothetical E4 protein; Provisional


Pssm-ID: 177646 [Multi-domain]  Cd Length: 230  Bit Score: 43.19  E-value: 1.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2085 PYSQPPGTPRPLIDSysqtsgtaRSNPDPYSQPPGTPRPNTIDPYSQQPP-TPRPSPQTdmfvssvANQRHTDPYTHHL- 2162
Cdd:PHA03418    34 PLLPAPHHPNPQEDP--------DKNPSPPPDPPLTPRPPAQPNGHNKPPvTKQPGGEG-------TEEDHQAPLAADAd 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2163 GPPRPGisvpysqppavprPRTSEGFTRPSSARPALMP-----NQDPfLQAAQNRVPGLPGPL-IRPPDTCSQTPRPPGP 2236
Cdd:PHA03418    99 DDPRPG-------------KRSKADEHGPAPGRAALAPfkldlDQDP-LHGDPDPPPGATGGQgEEPPEGGEESQPPLGE 164

                          170       180
                   ....*....|....*....|....*....
gi 1039771187 2237 GRIDTFTHAsssavrdPYDQPPVTPRPHS 2265
Cdd:PHA03418   165 GEGAVEGHP-------PPLPPAPEPKPHN 186
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4471-4515 1.88e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 1.88e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1039771187  4471 CVFCHKTGATS---GCHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1042-1091 1.99e-03

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 1.99e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  1042 CPVCcRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVadiGFDCSMC 1091
Cdd:smart00249    2 CSVC-GKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDG---KWYCPKC 47
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2090-2287 2.01e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 2.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2090 PGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPRPNTidpysQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGI 2169
Cdd:PRK07764   588 VGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAA-----PAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDA 662

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2170 SVPYSQPPAVPRPRTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPliRPPDTCSQTPRPPgpgridtftHASSSA 2249
Cdd:PRK07764   663 SDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAG--QADDPAAQPPQAA---------QGASAP 731

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1039771187 2250 VRDPYDQPPVTPRPHSESFGtSQVVHDLVDRPVPGSEG 2287
Cdd:PRK07764   732 SPAADDPVPLPPEPDDPPDP-AGAPAQPPPPPAPAPAA 768
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
 968-1008 2.07e-03

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 38.76  E-value: 2.07e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1039771187  968 CGKATDPGRLLLCDD--CDISYHTYCLDppLQTVPKGGWKCKW 1008
Cdd:cd15660      2 CFRCGDGGQLVLCDRksCTKAYHLSCLG--LTKRPFGKWECPW 42
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 388-435 2.08e-03

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 39.02  E-value: 2.08e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1039771187  388 CKVCQnckqsgEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15623      2 CRVCQ------KAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 344-388 2.14e-03

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 38.97  E-value: 2.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15539      2 CAVCGDGGELL---CCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
959-1095 2.26e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.20  E-value: 2.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187  959 CLECTVCEACgKATDPGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWCVWCRHcgatsaglrcewqnNYTQCAPCAS 1038
Cdd:COG5141    193 DDICTKCTST-HNENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIYGEY--------------QIRCCSFCPS 255

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 1039 lsscpvccrnyreEDLILQCRQCDRWMHAVC---------QNLNTEEEVENVADIG-----FDCSMCRPYM 1095
Cdd:COG5141    256 -------------SDGAFKQTSDGRWGHVICamfnpelsfGHLLSKDPIDNIASVSssrwkLGCLICKEFG 313
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
 473-518 2.39e-03

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 38.87  E-value: 2.39e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  473 CYHPELQKDMLHCNMCKRWVHLECDKPTdqelDSQLKEDYICMYCK 518
Cdd:cd15632      6 CMKPFAGRPMIECNECHTWIHLSCAKIR----KSNVPEVYVCQKCR 47
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 914-959 2.41e-03

PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger.


Pssm-ID: 277040  Cd Length: 51  Bit Score: 38.95  E-value: 2.41e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  914 MCVVCGSFGQGAEGrLLACSQ--CGQCYHPYCVS-IKITKVVLSKGWRC 959
Cdd:cd15565      1 SCFVCKKLGSVGGE-VFKCSVasCGKFYHEECLKkWPLTTISDSKKFRC 48
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 388-435 2.76e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 38.60  E-value: 2.76e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  388 CKVCQNCKQSgeDSKMLVCDTCDKGYHTFCLQPVMKSVPT---NGWKCKNC 435
Cdd:cd15507      2 CHVCGRKGQA--QKQLLECEKCQRGYHVDCLGPSYPTKPTrkkKTWICSKC 50
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1612-1648 2.91e-03

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 39.32  E-value: 2.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1039771187 1612 FPNLKEEFPDWTtrVKQIAK----LWRKASSQERAPYVQKA 1648
Cdd:cd21979     18 RPKIKGEHPGLS--IGDVAKklgeMWNNTSAKDKQPYEKKA 56
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3233-3545 3.08e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.99  E-value: 3.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3233 LAPPILM----PGVQPQPPLV-------PGATSLTMSQPNFPMVPQQLQHQQHTAVISGHTSPARMPSLPgwQSNSASAH 3301
Cdd:pfam03154  169 TQPPVLQaqsgAASPPSPPPPgttqaatAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLH--PQRLPSPH 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3302 LPLNPPRIQPPIAQLSLKTcTPAPGTVSSANP-----QNGPPPRVEFDDNNPFSESFQERERKERLREQQE--RQRVQLM 3374
Cdd:pfam03154  247 PPLQPMTQPPPPSQVSPQP-LPQPSLHGQMPPmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAapGQSQQRI 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3375 QEVDRQRALQQRMEMEQHCLMGAELA-------NRTPVSQMPFYGSDRPCDFLQPPRP--LQQSPQHQQQIGPVLQQQNV 3445
Cdd:pfam03154  326 HTPPSQSQLQSQQPPREQPLPPAPLSmphikppPTTPIPQLPNPQSHKHPPHLSGPSPfqMNSNLPPPPALKPLSSLSTH 405

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3446 QQGSVNSPPNQTFMQTneqRQVGPPsfvPDSPSASGGSPNFHSvkPGHGNLPGSSFQQSPLRPPFT--PILPGTSP--VA 3521
Cdd:pfam03154  406 HPPSAHPPPLQLMPQS---QQLPPP---PAQPPVLTQSQSLPP--PAASHPPTSGLHQVPSQSPFPqhPFVPGGPPpiTP 477

                          330       340
                   ....*....|....*....|....
gi 1039771187 3522 NSNVPCGQDPAVTQGQNYSGSSQS 3545
Cdd:pfam03154  478 PSGPPTSTSSAMPGIQPPSSASVS 501
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 388-435 3.23e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 38.53  E-value: 3.23e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  388 CKVCQNcKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSV---PTNGWKCKNC 435
Cdd:cd15578      2 CTVCQD-GSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQC 51
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 3129-3222 3.36e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 40.63  E-value: 3.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3129 DSQRKQYEEW---LQETQQLLQMQQKYLEEQIGAHRKSKKALSAKQRTA-KKAgrefpEEDAEQLKHVTEQQSMVQKQLE 3204
Cdd:pfam13863   16 DAKREEIERLeelLKQREEELEKKEQELKEDLIKFDKFLKENDAKRRRAlKKA-----EEETKLKKEKEKEIKKLTAQIE 90

                           90
                   ....*....|....*...
gi 1039771187 3205 QIRKQQKEHAELIEDYRI 3222
Cdd:pfam13863   91 ELKSEISKLEEKLEEYKP 108
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 4436-4500 3.57e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 40.42  E-value: 3.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 4436 WVHLNCALWSTEVYETQAGALINVE----LALRRgLQMKCVFCHKTG--ATSGCHRFRCTNIYHFTCATKA 4500
Cdd:cd15703     19 WAHVVCAIWIPEVCFANTVFLEPVEgvnnIPPAR-WKLTCYLCKQKGrgAAIQCHKVNCYTAFHVTCAQRA 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2278-2635 3.65e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.99  E-value: 3.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2278 VDRPVPGSEGNFSTSSNLPVSSQGQ---------QFSSVSQLPGPvptsggtdtqntvNMSQADTEKLRQRQKLREIILQ 2348
Cdd:pfam03154  107 ISRPNSPSEGEGESSDGRSVNDEGSsdpkdidqdNRSTSPSIPSP-------------QDNESDSDSSAQQQILQTQPPV 173

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2349 QQQQKKIASRQEKGPQDTAVVPHPVPLPhwqpesinQAFTRPPPPYPGSTRSPV--IPPLGP----RYAVFPKDQRGPYP 2422
Cdd:pfam03154  174 LQAQSGAASPPSPPPPGTTQAATAGPTP--------SAPSVPPQGSPATSQPPNqtQSTAAPhtliQQTPTLHPQRLPSP 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2423 -PEVAGMGMRPHGFRFGF----PGAGHGPMPSqdrfhVPQQIQGSgiPPHIRRPMsmemprpsnnpplnnpvglpqhfPP 2497
Cdd:pfam03154  246 hPPLQPMTQPPPPSQVSPqplpQPSLHGQMPP-----MPHSLQTG--PSHMQHPV-----------------------PP 295

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 2498 QGLPVQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHPRHgnflpRPDFPGPRHTDPIRQPSQCLSNQLpvhp 2577
Cdd:pfam03154  296 QPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPRE-----QPLPPAPLSMPHIKPPPTTPIPQL---- 366

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187 2578 nleqvpPSQQEQGHPAHQSSIVMRPLNHPLSGEFSEAPLS---TSTPAETSPDNLEIAGQS 2635
Cdd:pfam03154  367 ------PNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSslsTHHPPSAHPPPLQLMPQS 421
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 246-311 3.79e-03

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 40.27  E-value: 3.79e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  246 TGTCWAHHRCVEW----SLGICQMEEPLlVNVDKAVVSGSTERCAFCKH-LGATIKCCEEKCTQMYHYPCA 311
Cdd:cd15707     16 SGTKWAHVSCALWipevSIGCVEKMEPI-TKISSIPASRWALICVLCRErTGACIQCSVKTCKTAYHVTCG 85
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 965-1009 3.89e-03

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 38.00  E-value: 3.89e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  965 CEACGKAtdpGRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1009
Cdd:cd15567      2 CFICSEG---GSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
 391-436 4.06e-03

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 38.40  E-value: 4.06e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1039771187  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCR 436
Cdd:cd15625      5 CAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCR 47
PHD1_DPF3 cd15692
PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed ...
 924-962 4.27e-03

PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277162  Cd Length: 57  Bit Score: 38.51  E-value: 4.27e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1039771187  924 GAEGRLLACSQCGQCYHPYCV--SIKITKVVLSKGWRCLEC 962
Cdd:cd15692     16 GRPEELVSCADCGRSGHPTCLqfTVNMTEAVKTYQWQCIEC 56
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 914-962 4.67e-03

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 37.82  E-value: 4.67e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  914 MCVVCGsfgqgAEGRLLACSQCGQCYHPYCVSIKITKVVlSKGWRCLEC 962
Cdd:cd15539      1 ECAVCG-----DGGELLCCDGCPRAFHLACLVPPLTLIP-SGTWRCSSC 43
mukB PRK04863
chromosome partition protein MukB;
3133-3223 5.49e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 43.41  E-value: 5.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3133 KQYEEWLQETQQLLQMQQKY--LEEQIGAHRKSKKALsakQRTAKKAGREFPEEDA---------EQLKHVTEQQSMVQK 3201
Cdd:PRK04863   503 RRLREQRHLAEQLQQLRMRLseLEQRLRQQQRAERLL---AEFCKRLGKNLDDEDEleqlqeeleARLESLSESVSEARE 579

                           90       100
                   ....*....|....*....|..
gi 1039771187 3202 QLEQIRKQQKEHAELIEDYRIK 3223
Cdd:PRK04863   580 RRMALRQQLEQLQARIQRLAAR 601
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 388-436 5.58e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 37.72  E-value: 5.58e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  388 CKVCQNckqsGEDskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCR 436
Cdd:cd15624      2 CAVCQN----GGD--LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCR 44
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 390-435 5.75e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 37.91  E-value: 5.75e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  390 VCQNCKQSGEDSKML--VCDTCDKGYHTFC--LQPVMKSVPTNgWKCKNC 435
Cdd:cd15517      1 VCGICNLETAAVDELwvQCDGCDKWFHQFClgLSNERYADEDK-FKCPNC 49
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 3127-3218 5.80e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 5.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3127 VNDSQRKQYEEwLQETQQLLQMQQKYLEEQigahRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQLEQI 3206
Cdd:COG4942    144 LAPARREQAEE-LRADLAELAALRAELEAE----RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAEL 218

                           90
                   ....*....|..
gi 1039771187 3207 RKQQKEHAELIE 3218
Cdd:COG4942    219 QQEAEELEALIA 230
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 344-388 5.82e-03

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 37.71  E-value: 5.82e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15541      2 CAVCQNGGELL---CCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 915-962 5.93e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 37.68  E-value: 5.93e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187  915 CVVCGSFGQgaEGRLLACSQCGQCYHPYCVSIKITKVvlSKG-WRCLEC 962
Cdd:cd15545      2 CQICRSGDN--EDQLLLCDGCDRGYHTYCFKPKMTNV--PEGdWFCPEC 46
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 344-388 6.45e-03

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 37.71  E-value: 6.45e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039771187  344 CAVCDS-----PGDLLDqffCTTCGQHYHGMCLDIAVTPLK-RAGWQCPEC 388
Cdd:cd15597      3 CVVCGSfgrgsEGHLLA---CSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
SET_SMYD1 cd10526
SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 ...
 4856-4910 6.47e-03

SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 (SMYD1) and similar proteins; SMYD1 (EC 2.1.1.43), also termed BOP, is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD1 plays a critical role in cardiomyocyte differentiation, cardiac morphogenesis and myofibril organization, as well as in the regulation of endothelial cells (ECs). It is expressed in vascular endothelial cells, it has beenshown that knockdown of SMYD1 in endothelial cells impairs EC migration and tube formation.


Pssm-ID: 380924 [Multi-domain]  Cd Length: 210  Bit Score: 41.25  E-value: 6.47e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039771187 4856 INHSCAPNCvaeVVTFERGhKIIISSNRRIQKGEELCYDYkFDF----ED------DQHKIPCHC 4910
Cdd:cd10526    146 VNHDCWPNC---TVIFNNG-RIELRALGKISEGDELTVSY-IDFlntsEDrkeqlkKQYYFDCTC 205
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 4471-4515 6.51e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 37.68  E-value: 6.51e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1039771187 4471 CVFCHKTGATSG----CHRfrCTNIYHFTCATKAQCMFFKDKTMLCPMH 4515
Cdd:cd15489      2 CIVCGKGGDLGGellqCDG--CGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 470-517 6.58e-03

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 37.58  E-value: 6.58e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1039771187  470 CGKCYHPELQKDML-HCNMCKRWVHLECDKP-TDQELDSQLKEDYICMYC 517
Cdd:cd15601      2 CPVCRAKYVEEDLLiQCRHCDRWVHAVCESLfTEDEVEQAADEGFDCSSC 51
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 344-388 6.68e-03

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 37.58  E-value: 6.68e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  344 CAVCDSPGDLLdqfFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC 388
Cdd:cd15531      2 CEVCQQGGEII---LCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 962-1010 6.69e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 37.76  E-value: 6.69e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1039771187  962 CTVCEAcGKATDPGRLLLCDDCDISYHTYCLDPPLQTV---PKGGWKCKWCV 1010
Cdd:cd15578      2 CTVCQD-GSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCV 52
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 4436-4517 7.40e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 39.68  E-value: 7.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 4436 WVHLNCALWSTEVYETQAGAL---INVELALRRGLQMKCVFCHK--TGATSGCHRFRCTNIYHFTCATKAQcMFFK---- 4506
Cdd:cd15701     19 WAHVVCALWIPEVCFANTVFLepiDSIEHIPPARWKLTCYICKQrgSGACIQCHKANCYTAFHVTCAQQAG-LYMKmepv 97

                           90       100
                   ....*....|....*....|...
gi 1039771187 4507 ------------DKTMLCPMHKP 4517
Cdd:cd15701     98 retgangtsfsvRKTAYCDIHTP 120
PHD_ASH1L cd15548
PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like ...
 1046-1077 7.78e-03

PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like protein, or absent small and homeotic disks protein 1 homolog, or lysine N-methyltransferase 2H, is a protein belonging to the Trithorax family. It methylates Lys36 of histone H3 independently of transcriptional elongation to promote the establishment of Hox gene expression by counteracting Polycomb silencing. It can suppress interleukin-6 (IL-6), and tumor necrosis factor (TNF) production in Toll-like receptor (TLR)-triggered macrophages, and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. ASH1L contains an associated with SET domain (AWS), a SET domain, a post-SET domain, a bromodomain, a bromo-adjacent homology domain (BAH), and a plant homeodomain (PHD) finger.


Pssm-ID: 277023  Cd Length: 43  Bit Score: 37.06  E-value: 7.78e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1039771187 1046 CRNYREEDLILQCRQCDRWMHAVCQNLNTEEE 1077
Cdd:cd15548      5 CGLYKDEGLMIQCEKCMVWQHCDCMGVNDDVE 36
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 391-435 8.14e-03

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 37.18  E-value: 8.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039771187  391 CQNCKQSGEdskMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNC 435
Cdd:cd15524      2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 3130-3218 8.33e-03

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 42.51  E-value: 8.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039771187 3130 SQRKQYEEWLQETQQLLQMQQKY---LEEQIGAHRKSKKALSAKQ-RTAKKAGREFPEEDAEQLKHVTEQQSMVQ----- 3200
Cdd:PRK00409   527 ELERELEQKAEEAEALLKEAEKLkeeLEEKKEKLQEEEDKLLEEAeKEAQQAIKEAKKEADEIIKELRQLQKGGYasvka 606

                           90
                   ....*....|....*...
gi 1039771187 3201 KQLEQIRKQQKEHAELIE 3218
Cdd:PRK00409   607 HELIEARKRLNKANEKKE 624
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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