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Conserved domains on  [gi|2240506762|ref|XP_048153358|]
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DNA (cytosine-5)-methyltransferase 3A isoform X1 [Corvus hawaiiensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PWWP_DNMT3A cd20154
PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA ...
 303-436 7.58e-104

PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. It contains a PWWP domain that binds methylated histone.


:

Pssm-ID: 438982  Cd Length: 134  Bit Score: 318.45  E-value: 7.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 303 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNKQPM 382
Cdd:cd20154     1 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFSSAFHQATYNKQPM 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2240506762 383 YRKAIYEVLQVASSRAGKIFPACPENDETDTSKVVEIQNKQMIEWALGGFQPSG 436
Cdd:cd20154    81 YRKAIYEVLQVASSRAGKLFPVCPESDESDTSKAVEVQNKQMIEWALGGFQPSG 134
ADDz_Dnmt3a cd11729
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a ...
 506-633 8.95e-89

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a member of the Dnmt3 family and is a protein with de novo DNA methyltransferase activity. Dnmt3 family members are Dnmt3a, Dnmt3b, and Dnmt3l the non-enzymatic regulatory factor. Dnmt3a is recruited by Dnmt3l to unmethylated histone H3 and methylates the target. Dnmt3a has a variable region at the N-terminus, followed by a conserved PWWP region and the cysteine-rich ADDz domain. ADDz_Dnmt3a is an active catalytic domain of Dnmt3a. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3a has been shown to be lethal in the mouse model.


:

Pssm-ID: 277255 [Multi-domain]  Cd Length: 128  Bit Score: 278.43  E-value: 8.95e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 506 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 585
Cdd:cd11729     1 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2240506762 586 VGPGAAQAAIKEDPWNCYMCGHKGVYGLLRRREDWPSRLQMFFANNHD 633
Cdd:cd11729    81 VGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHD 128
Dcm super family cl43082
DNA-cytosine methylase [Replication, recombination and repair];
650-928 1.32e-20

DNA-cytosine methylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0270:

Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 92.95  E-value: 1.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 650 RKPIRVLSLFDGI---ATGLlvlKDLGIQVdrYIASEVCEDSITVGMVRHQGKIMYVGDVRNVTQKHIQewGPFDLVIGG 726
Cdd:COG0270     1 SKKLTVIDLFAGAgglSLGF---EKAGFEV--VFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELI--PDVDLLIGG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 727 SPCNDLSIVNPaRKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVSDK----RDISRFLES-----NPV 797
Cdd:COG0270    74 PPCQPFSVAGK-RKGLEDPRGTLFFEFIRIVEELRPK-------AFVLENVPGLLSSDKgktfEEILKELEElgyrvDYK 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 798 MIDAKEVSAA-HRARYF----WGNLPGMNRPLASTVNDKLELQECLEH----GRIAKFSKvrTITTRSNsikqgkdqHFP 868
Cdd:COG0270   146 VLNAADYGVPqNRERVFivgfRKDLDLFEFPEPTHLKPYVTVGDALEDlpdaHEARYLSE--TITAGYG--------GGG 215

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2240506762 869 VFMNEKEDIlWCT--EMERVFGFPVHYTDVSNMSRLARQrlLGRSWSVPVIRHLFAPLKEYF 928
Cdd:COG0270   216 RFLHPGEPR-RLTvrEAARLQGFPDDFKFPGSKTQAYRQ--IGNAVPPPLAEAIAKAILKAL 274
PHA03169 super family cl27451
hypothetical protein; Provisional
 8-154 6.37e-05

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PHA03169:

Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 46.50  E-value: 6.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   8 DAGSP-APSREALDTHKGEEEPEENPSKEEKQEPGTPMRKAGRPGRKRKHAQQVESSDTPKDiaavpkcppprPEASPAE 86
Cdd:PHA03169  116 SGLSPeNTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEE-----------PEPPTSE 184

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2240506762  87 PLPNGDVEGDAEEAAESPKGGraEEDETESLPDGETGRALENGRcTPKEGLDAPADEGELAPSDPQKK 154
Cdd:PHA03169  185 PEPDSPGPPQSETPTSSPPPQ--SPPDEPGEPQSPTPQQAPSPN-TQQAVEHEDEPTEPEREGPPFPG 249
 
Name Accession Description Interval E-value
PWWP_DNMT3A cd20154
PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA ...
 303-436 7.58e-104

PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. It contains a PWWP domain that binds methylated histone.


Pssm-ID: 438982  Cd Length: 134  Bit Score: 318.45  E-value: 7.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 303 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNKQPM 382
Cdd:cd20154     1 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFSSAFHQATYNKQPM 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2240506762 383 YRKAIYEVLQVASSRAGKIFPACPENDETDTSKVVEIQNKQMIEWALGGFQPSG 436
Cdd:cd20154    81 YRKAIYEVLQVASSRAGKLFPVCPESDESDTSKAVEVQNKQMIEWALGGFQPSG 134
ADDz_Dnmt3a cd11729
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a ...
 506-633 8.95e-89

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a member of the Dnmt3 family and is a protein with de novo DNA methyltransferase activity. Dnmt3 family members are Dnmt3a, Dnmt3b, and Dnmt3l the non-enzymatic regulatory factor. Dnmt3a is recruited by Dnmt3l to unmethylated histone H3 and methylates the target. Dnmt3a has a variable region at the N-terminus, followed by a conserved PWWP region and the cysteine-rich ADDz domain. ADDz_Dnmt3a is an active catalytic domain of Dnmt3a. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3a has been shown to be lethal in the mouse model.


Pssm-ID: 277255 [Multi-domain]  Cd Length: 128  Bit Score: 278.43  E-value: 8.95e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 506 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 585
Cdd:cd11729     1 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2240506762 586 VGPGAAQAAIKEDPWNCYMCGHKGVYGLLRRREDWPSRLQMFFANNHD 633
Cdd:cd11729    81 VGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHD 128
ADD_DNMT3 pfam17980
Cysteine rich ADD domain in DNMT3; This is a cysteine-rich domain termed ADD ...
 494-549 9.88e-31

Cysteine rich ADD domain in DNMT3; This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. Furthermore, the ADD domain of DNMMT3A (ADD-3A) competes with the chromodomain (CD) of heterochromatin protein 1 alpha (HP1alpha, CDHP1alpha) for binding to the H3 tail. The DNA methyltransferase (DNMT) 3 family members DNMT3A and DNMT3B and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development.


Pssm-ID: 465603  Cd Length: 56  Bit Score: 114.69  E-value: 9.88e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2240506762 494 TRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDD 549
Cdd:pfam17980   1 SREQMVYEVRENKRNIEDFCLSCGSLNVHTFHPLFEGGLCQKCKDNFLETLYRYDE 56
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
650-928 1.32e-20

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 92.95  E-value: 1.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 650 RKPIRVLSLFDGI---ATGLlvlKDLGIQVdrYIASEVCEDSITVGMVRHQGKIMYVGDVRNVTQKHIQewGPFDLVIGG 726
Cdd:COG0270     1 SKKLTVIDLFAGAgglSLGF---EKAGFEV--VFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELI--PDVDLLIGG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 727 SPCNDLSIVNPaRKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVSDK----RDISRFLES-----NPV 797
Cdd:COG0270    74 PPCQPFSVAGK-RKGLEDPRGTLFFEFIRIVEELRPK-------AFVLENVPGLLSSDKgktfEEILKELEElgyrvDYK 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 798 MIDAKEVSAA-HRARYF----WGNLPGMNRPLASTVNDKLELQECLEH----GRIAKFSKvrTITTRSNsikqgkdqHFP 868
Cdd:COG0270   146 VLNAADYGVPqNRERVFivgfRKDLDLFEFPEPTHLKPYVTVGDALEDlpdaHEARYLSE--TITAGYG--------GGG 215

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2240506762 869 VFMNEKEDIlWCT--EMERVFGFPVHYTDVSNMSRLARQrlLGRSWSVPVIRHLFAPLKEYF 928
Cdd:COG0270   216 RFLHPGEPR-RLTvrEAARLQGFPDDFKFPGSKTQAYRQ--IGNAVPPPLAEAIAKAILKAL 274
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 308-366 2.75e-20

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 85.09  E-value: 2.75e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2240506762  308 FGIGELVWGKLRGFSWWPGRIVSWWMTG----RSRAAEGTRWVMWFGDGKFSVVCVEKLLPLS 366
Cdd:smart00293   1 FKPGDLVWAKMKGFPWWPALVISPKMTPdnimKRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 311-395 2.65e-17

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 77.85  E-value: 2.65e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 311 GELVWGKLRGFSWWPGRIVSWWMTGRS----RAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNK---QPMY 383
Cdd:pfam00855   1 GDLVWAKLKGYPWWPARVVDPEELPENvlkpKKKDGEYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKKkkkKKAF 80

                          90
                  ....*....|..
gi 2240506762 384 RKAIYEVLQVAS 395
Cdd:pfam00855  81 KKALEEAEEALK 92
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 653-926 9.36e-14

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 72.65  E-value: 9.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 653 IRVLSLFDGIATGLLVLKDLGIQVdrYIASEVCEDSITVGMVRHqGKIMYVGDVRNVTQKHIQEwgPFDLVIGGSPCNDL 732
Cdd:cd00315     1 LRVIDLFAGIGGFRLGLEKAGFEI--VAANEIDKSAAETYEANF-PNKLIEGDITKIDEKDFIP--DIDLLTGGFPCQPF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 733 SIVNpARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVSDKR----DISRFLESN-----PVMIDAKE 803
Cdd:cd00315    76 SIAG-KRKGFEDTRGTLFFEIIRILKEKKPK-------YFLLENVKGLLTHDNGntlkVILNTLEELgynvyWKLLNASD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 804 VSAAH-RARYFW-GNLPGMNRPLASTV----NDKLELQECLehgRIAKFSKV-RTITTRSNSIKQGKDQHFPVFMNEKED 876
Cdd:cd00315   148 YGVPQnRERVFIiGIRKDLILNFFSPFpkpsEKKKTLKDIL---RIRDPDEPsPTLTASYGKGTGSVHPTAPDMIGKESN 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2240506762 877 ILWCT--EMERVFGFPVHYtDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKE 926
Cdd:cd00315   225 IRRLTprECARLQGFPDDF-EFPGKSVTQAYRQIGNSVPVPVAEAIAKAIKE 275
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 704-918 3.09e-11

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 65.43  E-value: 3.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 704 GDVRNVTQKHIQEwgpFDLVIGGSPCNDLSIvNPARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVS 783
Cdd:TIGR00675  47 GDITKISPSDIPD---FDILLGGFPCQPFSI-AGKRKGFEDTRGTLFFEIVRILKEKKPK-------FFLLENVKGLVSH 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 784 DK-RDISRFLES--------NPVMIDAKEVSAA-HRAR-------YFWGNLPgMNRPLASTVNDKLELQECLEHG----- 841
Cdd:TIGR00675 116 DKgRTFKVIIETleelgykvYYKVLNAKDFGVPqNRERiyivgfrDFDDKLN-FEFPKPIYVAKKKRIGDLLDLSvdlee 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 842 ----------------------------------RIAKFSKVRTITTRSNSIKQGKDQ------HFPVFMNEKEDILWCT 881
Cdd:TIGR00675 195 kyylseekknglllllenmrkkegtgeqigsfynRESKSSIIRTLSARGYTFVKGGKSvlivphKSTVVHPGRIRRLTPR 274

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2240506762 882 EMERVFGFPVHYTDvsNMSRLARQRLLGRSWSVPVIR 918
Cdd:TIGR00675 275 ECARLQGFPDDFKF--PVSDSQLYKQAGNAVVVPVIE 309
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
653-777 8.83e-09

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 58.09  E-value: 8.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 653 IRVLSLFDGIATGLLVLKDLGIQVdrYIASEVCEDSITVGMVRHQGKImyVGDVRNVTQKHIQEwgpFDLVIGGSPCNDL 732
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLEQAGFEC--VAANEIDKSAAKTYEANFPKVP--IGDITLIDIKDIPD---IDILTGGFPCQDF 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2240506762 733 SIVNpARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENV 777
Cdd:pfam00145  74 SIAG-KQKGFEDTRGTLFFEIIRIIKEKKPK-------AFLLENV 110
PHA03169 PHA03169
hypothetical protein; Provisional
 8-154 6.37e-05

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 46.50  E-value: 6.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   8 DAGSP-APSREALDTHKGEEEPEENPSKEEKQEPGTPMRKAGRPGRKRKHAQQVESSDTPKDiaavpkcppprPEASPAE 86
Cdd:PHA03169  116 SGLSPeNTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEE-----------PEPPTSE 184

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2240506762  87 PLPNGDVEGDAEEAAESPKGGraEEDETESLPDGETGRALENGRcTPKEGLDAPADEGELAPSDPQKK 154
Cdd:PHA03169  185 PEPDSPGPPQSETPTSSPPPQ--SPPDEPGEPQSPTPQQAPSPN-TQQAVEHEDEPTEPEREGPPFPG 249
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 9-158 7.78e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 42.83  E-value: 7.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   9 AGSPAPSREALDTHKGEEEPEENPSKEekqePGTPMRKAGRPGRKRKHAQQVESSDTpkdiaAVPKCPPPRPEASPAEPL 88
Cdd:NF040712  200 ATVPRLAREPADARPEEVEPAPAAEGA----PATDSDPAEAGTPDDLASARRRRAGV-----EQPEDEPVGPGAAPAAEP 270

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  89 PngdveGDAEEAAESPKGGRAEEDETESlPDGETGRALENgrcTPKEGLDAPADEGELAPSDPQKKRGRR 158
Cdd:NF040712  271 D-----EATRDAGEPPAPGAAETPEAAE-PPAPAPAAPAA---PAAPEAEEPARPEPPPAPKPKRRRRRA 331
CDC27 pfam09507
DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It ...
 3-173 1.88e-03

DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.


Pssm-ID: 462819 [Multi-domain]  Cd Length: 427  Bit Score: 41.73  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   3 SSGTLDAGSPAPSREALdthKGEEEPEENPsKEEKQEPGTPMRKAGRPgrkrkhAQQVESSDTPKDIAAVPKCPPPRPEA 82
Cdd:pfam09507 213 KSNIMSAFFKAKPKNKK---KKTSASEQKV-QEESAEESGKEDVTLED------DSAAEEEEDEQLPTKKDKRRQKRGES 282

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  83 SPAEPlPNGDVEGDAEEAAESPKGGRAEEDETESLPDGETGRALENGRcTPKEGLDAPADEGELAPSDPQKKRGRRKLLe 162
Cdd:pfam09507 283 SDSEE-STRESRKEKRERLKKMMEDDSDDDEMEDVPESPVATEEEETG-SPPPLLKKEVEKEEVTESGDGRRRKRRKVM- 359

                         170
                  ....*....|.
gi 2240506762 163 ateKSKDEKEE 173
Cdd:pfam09507 360 ---KKKTFKDE 367
 
Name Accession Description Interval E-value
PWWP_DNMT3A cd20154
PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA ...
 303-436 7.58e-104

PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. It contains a PWWP domain that binds methylated histone.


Pssm-ID: 438982  Cd Length: 134  Bit Score: 318.45  E-value: 7.58e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 303 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNKQPM 382
Cdd:cd20154     1 EDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFSSAFHQATYNKQPM 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2240506762 383 YRKAIYEVLQVASSRAGKIFPACPENDETDTSKVVEIQNKQMIEWALGGFQPSG 436
Cdd:cd20154    81 YRKAIYEVLQVASSRAGKLFPVCPESDESDTSKAVEVQNKQMIEWALGGFQPSG 134
ADDz_Dnmt3a cd11729
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a ...
 506-633 8.95e-89

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a); Dnmt3a is a member of the Dnmt3 family and is a protein with de novo DNA methyltransferase activity. Dnmt3 family members are Dnmt3a, Dnmt3b, and Dnmt3l the non-enzymatic regulatory factor. Dnmt3a is recruited by Dnmt3l to unmethylated histone H3 and methylates the target. Dnmt3a has a variable region at the N-terminus, followed by a conserved PWWP region and the cysteine-rich ADDz domain. ADDz_Dnmt3a is an active catalytic domain of Dnmt3a. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3a has been shown to be lethal in the mouse model.


Pssm-ID: 277255 [Multi-domain]  Cd Length: 128  Bit Score: 278.43  E-value: 8.95e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 506 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 585
Cdd:cd11729     1 CRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2240506762 586 VGPGAAQAAIKEDPWNCYMCGHKGVYGLLRRREDWPSRLQMFFANNHD 633
Cdd:cd11729    81 VGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFANNHD 128
ADDz cd11672
ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is ...
 509-607 2.67e-61

ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277250 [Multi-domain]  Cd Length: 99  Bit Score: 202.79  E-value: 2.67e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 509 IEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGP 588
Cdd:cd11672     1 IEDICIACGSLVVIYRHPLFQGGICKNCKKYFLSDDISYDDDGYQSYCRICCEGGNLLCCGNNFCHRCFCKECVDRLVGP 80

                          90
                  ....*....|....*....
gi 2240506762 589 GAAQAAIKEDPWNCYMCGH 607
Cdd:cd11672    81 GELSTMDENNQWYCYICHP 99
ADDz_Dnmt3b cd11728
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b); ADDz_Dnmt3b ...
 509-628 1.12e-57

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b); ADDz_Dnmt3b is an active catalytic domain of Dnmt3b. Dnmt3b is a member of the Dnmt3 family and is a de novo DNA methyltransferases that has an N-terminal variable region followed by a conserved PWWP region and the cysteine-rich ADDz domain. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. Dnmt3b is ubiquitously expressed in most adult tissues. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3b has been shown to be lethal in the mouse model.


Pssm-ID: 277254 [Multi-domain]  Cd Length: 120  Bit Score: 193.53  E-value: 1.12e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 509 IEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGP 588
Cdd:cd11728     1 IEDFCLSCGRSNPATFHPLFEGGLCITCKDRFLELFYMYDDDGYQSYCTVCCEGRELLLCGNASCCRCFCVDCLEVLVGP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2240506762 589 GAAQAAIKEDPWNCYMCGHKGVYGLLRRREDWPSRLQMFF 628
Cdd:cd11728    81 GTAAKAKEQDPWSCYMCLPQRCYGVLKRRTDWSVRLQEFF 120
ADDz_Dnmt3 cd11725
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de ...
 509-614 1.38e-54

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de novo DNA methyltransferase family that includes two active enzymes Dnmt3a and -3b and one regulatory factor Dnmt3l. The ADDz domain of Dnmt3 is located in the C-terminal region of Dnmt3, which is an active catalytic domain in Dnmt3a and -b, but lacks some residues for enzymatic activity in Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277251 [Multi-domain]  Cd Length: 108  Bit Score: 184.51  E-value: 1.38e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 509 IEDICISCGSLNV--TLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLV 586
Cdd:cd11725     1 IEDICLACGSLEVseTSDHPFFEGGLCKNCKERFLECIFLFDDDGYQMYCTICGGGGEVVLCDNPDCTRVYCTECLDLLL 80

                          90       100
                  ....*....|....*....|....*...
gi 2240506762 587 GPGAAQAAIKEDPWNCYMCGHKGVYGLL 614
Cdd:cd11725    81 GPGAVAKILESDPWFCFLCSPESNSLLG 108
PWWP_DNMT3B cd20155
PWWP domain found in DNA (cytosine-5)-methyltransferase 3B (DNMT3B); DNMT3B, also called DNA ...
 309-432 5.62e-50

PWWP domain found in DNA (cytosine-5)-methyltransferase 3B (DNMT3B); DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalies) syndrome, a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438983  Cd Length: 117  Bit Score: 171.98  E-value: 5.62e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 309 GIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNKQPMYRKAIY 388
Cdd:cd20155     1 GIGELVWGKIKGFSWWPAMVVSWRATGKRQASSGMRWLQWFGDGKFSEVSADKLVSLTAFSQHFNLSTYNKLVSYRKAMY 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2240506762 389 EVLQVASSRAGKIFPacPENDETdtskvVEIQNKQMIEWALGGF 432
Cdd:cd20155    81 HALEVARVRAGKTFP--SSPGES-----LEDQLKPMLDWAHGGF 117
ADDz_Dnmt3l cd11727
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 like (Dnmt3l); Dnmt3l ...
 507-628 3.89e-48

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 like (Dnmt3l); Dnmt3l is a regulator of DNA methylation, which acts by recognizing unmethylated histone H3 tails and interacting with Dnmt3a to stimulate its de novo DNA methylation activity. The ADDz_Dnmt3l domain is located in the C-terminal region of Dnmt3l that otherwise lacks some residues required for DNA methyltransferase activity. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. Dnmt3l is also associating with HDAC1 and acts as a transcriptional repressor. The ADDz_Dnmt3l domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277253 [Multi-domain]  Cd Length: 123  Bit Score: 166.95  E-value: 3.89e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 507 RNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLV 586
Cdd:cd11727     1 RSIEEICICCGSLQIHTQHPLFHGGICAPCTEKFLEAFFLYDEDGYQAYCTICCSGETLLMCDDPDCTRCYCFECVDSLV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2240506762 587 GPGAAQAAIKEDPWNCYMCGHKGVYGLLRRREDWPSRLQMFF 628
Cdd:cd11727    81 GPGTSEKVKATNNWVCFLCLPSSRSGLLQRKRKWRSQLKAFY 122
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
 310-398 9.62e-38

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 135.85  E-value: 9.62e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 310 IGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQaTYNKQPMYRKAIYE 389
Cdd:cd05835     2 IGDLVWAKLKGSPWWPGIVVSHKDCGQKPPAEGSVWVFWFGDHKVSEVPLDKILPFAEFFNKFYI-SKNSSKLYKKAVYE 80


                  ....*....
gi 2240506762 390 VLQVASSRA 398
Cdd:cd05835    81 ALKEAAERS 89
ADD_DNMT3 pfam17980
Cysteine rich ADD domain in DNMT3; This is a cysteine-rich domain termed ADD ...
 494-549 9.88e-31

Cysteine rich ADD domain in DNMT3; This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. Furthermore, the ADD domain of DNMMT3A (ADD-3A) competes with the chromodomain (CD) of heterochromatin protein 1 alpha (HP1alpha, CDHP1alpha) for binding to the H3 tail. The DNA methyltransferase (DNMT) 3 family members DNMT3A and DNMT3B and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development.


Pssm-ID: 465603  Cd Length: 56  Bit Score: 114.69  E-value: 9.88e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2240506762 494 TRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDD 549
Cdd:pfam17980   1 SREQMVYEVRENKRNIEDFCLSCGSLNVHTFHPLFEGGLCQKCKDNFLETLYRYDE 56
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
650-928 1.32e-20

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 92.95  E-value: 1.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 650 RKPIRVLSLFDGI---ATGLlvlKDLGIQVdrYIASEVCEDSITVGMVRHQGKIMYVGDVRNVTQKHIQewGPFDLVIGG 726
Cdd:COG0270     1 SKKLTVIDLFAGAgglSLGF---EKAGFEV--VFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELI--PDVDLLIGG 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 727 SPCNDLSIVNPaRKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVSDK----RDISRFLES-----NPV 797
Cdd:COG0270    74 PPCQPFSVAGK-RKGLEDPRGTLFFEFIRIVEELRPK-------AFVLENVPGLLSSDKgktfEEILKELEElgyrvDYK 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 798 MIDAKEVSAA-HRARYF----WGNLPGMNRPLASTVNDKLELQECLEH----GRIAKFSKvrTITTRSNsikqgkdqHFP 868
Cdd:COG0270   146 VLNAADYGVPqNRERVFivgfRKDLDLFEFPEPTHLKPYVTVGDALEDlpdaHEARYLSE--TITAGYG--------GGG 215

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2240506762 869 VFMNEKEDIlWCT--EMERVFGFPVHYTDVSNMSRLARQrlLGRSWSVPVIRHLFAPLKEYF 928
Cdd:COG0270   216 RFLHPGEPR-RLTvrEAARLQGFPDDFKFPGSKTQAYRQ--IGNAVPPPLAEAIAKAILKAL 274
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 308-366 2.75e-20

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 85.09  E-value: 2.75e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2240506762  308 FGIGELVWGKLRGFSWWPGRIVSWWMTG----RSRAAEGTRWVMWFGDGKFSVVCVEKLLPLS 366
Cdd:smart00293   1 FKPGDLVWAKMKGFPWWPALVISPKMTPdnimKRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 311-395 2.65e-17

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 77.85  E-value: 2.65e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 311 GELVWGKLRGFSWWPGRIVSWWMTGRS----RAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNK---QPMY 383
Cdd:pfam00855   1 GDLVWAKLKGYPWWPARVVDPEELPENvlkpKKKDGEYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKKkkkKKAF 80

                          90
                  ....*....|..
gi 2240506762 384 RKAIYEVLQVAS 395
Cdd:pfam00855  81 KKALEEAEEALK 92
PWWP_PWWP2 cd20140
PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family ...
 305-396 8.56e-14

PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438968  Cd Length: 92  Bit Score: 67.67  E-value: 8.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 305 GRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRW--VMWFGDGKFSVVCVEKLLPlssFASAFHQaTYNKQP- 381
Cdd:cd20140     1 GRTLRVGDIVWGKIHGFPWWPGRILSITVSRDDNGELSTQEahVSWFGSSTTSYMPCSQLYP---FLEDFKL-RYNKKKr 76

                          90
                  ....*....|....*.
gi 2240506762 382 -MYRKAIYEVLQVASS 396
Cdd:cd20140    77 gPYKEAVRQALEAAKQ 92
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 653-926 9.36e-14

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 72.65  E-value: 9.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 653 IRVLSLFDGIATGLLVLKDLGIQVdrYIASEVCEDSITVGMVRHqGKIMYVGDVRNVTQKHIQEwgPFDLVIGGSPCNDL 732
Cdd:cd00315     1 LRVIDLFAGIGGFRLGLEKAGFEI--VAANEIDKSAAETYEANF-PNKLIEGDITKIDEKDFIP--DIDLLTGGFPCQPF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 733 SIVNpARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVSDKR----DISRFLESN-----PVMIDAKE 803
Cdd:cd00315    76 SIAG-KRKGFEDTRGTLFFEIIRILKEKKPK-------YFLLENVKGLLTHDNGntlkVILNTLEELgynvyWKLLNASD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 804 VSAAH-RARYFW-GNLPGMNRPLASTV----NDKLELQECLehgRIAKFSKV-RTITTRSNSIKQGKDQHFPVFMNEKED 876
Cdd:cd00315   148 YGVPQnRERVFIiGIRKDLILNFFSPFpkpsEKKKTLKDIL---RIRDPDEPsPTLTASYGKGTGSVHPTAPDMIGKESN 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2240506762 877 ILWCT--EMERVFGFPVHYtDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKE 926
Cdd:cd00315   225 IRRLTprECARLQGFPDDF-EFPGKSVTQAYRQIGNSVPVPVAEAIAKAIKE 275
PWWP_PWWP2B cd20153
PWWP domain found in PWWP domain-containing protein 2B (PWWP2B); PWWP2B is a paralog of PWWP2A, ...
 303-394 1.04e-13

PWWP domain found in PWWP domain-containing protein 2B (PWWP2B); PWWP2B is a paralog of PWWP2A, a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438981  Cd Length: 116  Bit Score: 68.45  E-value: 1.04e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 303 EDGRGFGIGELVWGKLRGFSWWPGRIVSwwmTGRSRAAEGT-RW----VMWFGDGKFSVVCVEKLLPLSSfasaFHQATY 377
Cdd:cd20153     9 EEGRTVSVGDIVWGKIHGFPWWPARVLS---ISLSQKEDGEpSWqeakVSWFGSPTTSLLSVSKLSPFSE----FFKLRF 81

                          90
                  ....*....|....*....
gi 2240506762 378 N--KQPMYRKAIYEVLQVA 394
Cdd:cd20153    82 NrkKKGMYRKAITEAAKAA 100
PWWP_MBD5 cd20141
PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is ...
 308-375 1.60e-13

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438969  Cd Length: 92  Bit Score: 66.96  E-value: 1.60e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2240506762 308 FGIGELVWGKLRGFSWWPGRIVSwwMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQA 375
Cdd:cd20141     1 FNVGDLVWGQIRGFPSWPGKLVS--ENDVGKTNEGKVWVSWFGDHSFGQVEPDKLKTLSEGLEAHHRA 66
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 311-389 2.56e-13

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 66.37  E-value: 2.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 311 GELVWGKLRGFSWWPGRIVSWWMTG---RSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFHQATYNKQPMYRKAI 387
Cdd:cd05162     1 GDLVWAKLKGYPWWPARVVDPEELPeevGKKKKKGGVLVQFFGDNDYAWVKSKNIKPFEEGFKKEFKKKKKKSKKFKKAV 80


                  ..
gi 2240506762 388 YE 389
Cdd:cd05162    81 EE 82
PWWP_PWWP2A cd20152
PWWP domain found in PWWP domain-containing protein 2A (PWWP2A); PWWP2A is a H2A.Z-specific ...
 304-395 1.08e-12

PWWP domain found in PWWP domain-containing protein 2A (PWWP2A); PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438980  Cd Length: 122  Bit Score: 65.80  E-value: 1.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 304 DGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAA--EGTRWVMWFGDGKFSVVCVEKLLP-LSSFASAFHQatyNKQ 380
Cdd:cd20152    16 DGRTICVGDIVWAKIYGFPWWPARILAITVSRKDNGLlvRQEARISWFGSPTTSFLALSQLAPfLENFQSRFNK---KRK 92

                          90
                  ....*....|....*
gi 2240506762 381 PMYRKAIYEVLQVAS 395
Cdd:cd20152    93 GLYRKAITEAAKAAK 107
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
 513-605 2.69e-12

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277252 [Multi-domain]  Cd Length: 102  Bit Score: 63.86  E-value: 2.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 513 CISCG-SLNVT----LEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCgnNNCCRCFCVECVDLLVG 587
Cdd:cd11726     5 CTACGeQLNHFskevHRHPVLKVLICKSCLKFYNSGEFSKDEDGSDEYCRWCGQGGDLICC--DFCPNVFCKKCIKRNLG 82

                          90
                  ....*....|....*...
gi 2240506762 588 PGAAQAAIKEDPWNCYMC 605
Cdd:cd11726    83 RAELSRIEESDKWKCFVC 100
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 704-918 3.09e-11

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 65.43  E-value: 3.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 704 GDVRNVTQKHIQEwgpFDLVIGGSPCNDLSIvNPARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENVVAMGVS 783
Cdd:TIGR00675  47 GDITKISPSDIPD---FDILLGGFPCQPFSI-AGKRKGFEDTRGTLFFEIVRILKEKKPK-------FFLLENVKGLVSH 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 784 DK-RDISRFLES--------NPVMIDAKEVSAA-HRAR-------YFWGNLPgMNRPLASTVNDKLELQECLEHG----- 841
Cdd:TIGR00675 116 DKgRTFKVIIETleelgykvYYKVLNAKDFGVPqNRERiyivgfrDFDDKLN-FEFPKPIYVAKKKRIGDLLDLSvdlee 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 842 ----------------------------------RIAKFSKVRTITTRSNSIKQGKDQ------HFPVFMNEKEDILWCT 881
Cdd:TIGR00675 195 kyylseekknglllllenmrkkegtgeqigsfynRESKSSIIRTLSARGYTFVKGGKSvlivphKSTVVHPGRIRRLTPR 274

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2240506762 882 EMERVFGFPVHYTDvsNMSRLARQRLLGRSWSVPVIR 918
Cdd:TIGR00675 275 ECARLQGFPDDFKF--PVSDSQLYKQAGNAVVVPVIE 309
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
653-777 8.83e-09

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 58.09  E-value: 8.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 653 IRVLSLFDGIATGLLVLKDLGIQVdrYIASEVCEDSITVGMVRHQGKImyVGDVRNVTQKHIQEwgpFDLVIGGSPCNDL 732
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLEQAGFEC--VAANEIDKSAAKTYEANFPKVP--IGDITLIDIKDIPD---IDILTGGFPCQDF 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2240506762 733 SIVNpARKGLYEGTGRLFFEFYRLLHEARPKegddrpfFWLFENV 777
Cdd:pfam00145  74 SIAG-KQKGFEDTRGTLFFEIIRIIKEKKPK-------AFLLENV 110
PWWP_AtATX3-like cd20143
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 311-395 2.79e-07

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also called protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also called protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also called protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain containing protein that consists of an N-terminal PWWP domain, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438971 [Multi-domain]  Cd Length: 100  Bit Score: 49.68  E-value: 2.79e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 311 GELVWGKLRGFSWWPGRIV---SWWMTGRSRAAEGTRWVMWFGDGK---FSVVCVEKLLPLSSFASAFHQATY--NKQP- 381
Cdd:cd20143     3 GDLVWAKVGTHPFWPARVVepaEQAEEVRRRCVPGSLCVYFFGPGGsrdYGWVRRSMIFPFTDDLARFQTQKIknKKRPq 82

                          90
                  ....*....|....
gi 2240506762 382 MYRKAIYEVLQVAS 395
Cdd:cd20143    83 EFQEALEEAKLADA 96
PWWP_GLYR1 cd05836
PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called ...
 308-390 5.24e-06

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438961 [Multi-domain]  Cd Length: 86  Bit Score: 45.29  E-value: 5.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 308 FGIGELVWGKLRGFSWWPGRIVS-WWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLLPLSSFASAFhqATYNKQPMYRKA 386
Cdd:cd05836     1 FKIGDLVWAKMKGFPPWPGKIVNpPPDLKKPPRKKKMHCVYFFGSENYAWIEDENIKPYEEFKEEM--LKSKKSAGFKDA 78


                  ....
gi 2240506762 387 IYEV 390
Cdd:cd05836    79 VEAI 82
PHA03169 PHA03169
hypothetical protein; Provisional
 8-154 6.37e-05

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 46.50  E-value: 6.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   8 DAGSP-APSREALDTHKGEEEPEENPSKEEKQEPGTPMRKAGRPGRKRKHAQQVESSDTPKDiaavpkcppprPEASPAE 86
Cdd:PHA03169  116 SGLSPeNTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEE-----------PEPPTSE 184

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2240506762  87 PLPNGDVEGDAEEAAESPKGGraEEDETESLPDGETGRALENGRcTPKEGLDAPADEGELAPSDPQKK 154
Cdd:PHA03169  185 PEPDSPGPPQSETPTSSPPPQ--SPPDEPGEPQSPTPQQAPSPN-TQQAVEHEDEPTEPEREGPPFPG 249
PTZ00121 PTZ00121
MAEBL; Provisional
 15-258 8.54e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 46.67  E-value: 8.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   15 SREALDTHKGEEEP----EENPSKEEKQEPGTPMRKA--GRPGRKRKHAQQVESSDTPKDIAAVPKcppprpeaspAEPL 88
Cdd:PTZ00121  1482 AKKADEAKKKAEEAkkkaDEAKKAAEAKKKADEAKKAeeAKKADEAKKAEEAKKADEAKKAEEKKK----------ADEL 1551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   89 PNGDVEGDAEEAAESPKGGRAEEDETESLPDGETGRALENGRCTPKEGLDAP-----------ADEGELAPSDPQKKRGR 157
Cdd:PTZ00121  1552 KKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEekkmkaeeakkAEEAKIKAEELKKAEEE 1631

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  158 RKLLEATEKsKDEKEENNFDTLKMEGSRGRLRGglgwESSLRQRPMQRHTFQAGDPYYISKRKRDEWLarwKREAEKKAK 237
Cdd:PTZ00121  1632 KKKVEQLKK-KEAEEKKKAEELKKAEEENKIKA----AEEAKKAEEDKKKAEEAKKAEEDEKKAAEAL---KKEAEEAKK 1703

                          250       260
                   ....*....|....*....|...
gi 2240506762  238 VIAVMNVVEEPARA--EAQKEEE 258
Cdd:PTZ00121  1704 AEELKKKEAEEKKKaeELKKAEE 1726
PHA03169 PHA03169
hypothetical protein; Provisional
 4-178 2.50e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 44.58  E-value: 2.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   4 SGTLDAGSPAPSrealdtHKGEEEPEENPSKEEKQEPGTPMRKAGRPGRKRKHAQQVESSDTpkdiaavpkcPPPRPEAS 83
Cdd:PHA03169   95 SGSESVGSPTPS------PSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPA----------PPESHNPS 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  84 PAEPlPNGDVEGDAEEAAESPKGGRAE-EDETESLPDGETGRALENgrctPKEGLDAPADEGELAPSDPQKKRGRRKLLE 162
Cdd:PHA03169  159 PNQQ-PSSFLQPSHEDSPEEPEPPTSEpEPDSPGPPQSETPTSSPP----PQSPPDEPGEPQSPTPQQAPSPNTQQAVEH 233

                         170
                  ....*....|....*.
gi 2240506762 163 ATEKSKDEKEENNFDT 178
Cdd:PHA03169  234 EDEPTEPEREGPPFPG 249
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 9-158 7.78e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 42.83  E-value: 7.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   9 AGSPAPSREALDTHKGEEEPEENPSKEekqePGTPMRKAGRPGRKRKHAQQVESSDTpkdiaAVPKCPPPRPEASPAEPL 88
Cdd:NF040712  200 ATVPRLAREPADARPEEVEPAPAAEGA----PATDSDPAEAGTPDDLASARRRRAGV-----EQPEDEPVGPGAAPAAEP 270

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  89 PngdveGDAEEAAESPKGGRAEEDETESlPDGETGRALENgrcTPKEGLDAPADEGELAPSDPQKKRGRR 158
Cdd:NF040712  271 D-----EATRDAGEPPAPGAAETPEAAE-PPAPAPAAPAA---PAAPEAEEPARPEPPPAPKPKRRRRRA 331
PWWP_HRP cd05834
PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The ...
 308-389 1.70e-03

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438959 [Multi-domain]  Cd Length: 82  Bit Score: 38.30  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762 308 FGIGELVWGKLRGFSWWPGRIvswwmtgrSRAAEGTRW------VMWFGDGKFSVVCVEKLLPLSSFasAFHQATYNKQP 381
Cdd:cd05834     1 FKPGDLVFAKVKGYPPWPARI--------DEIPEGAKIpknkypVFFYGTHETAFLKPKDLFPYEEN--KEKYGKPRKRK 70


                  ....*...
gi 2240506762 382 MYRKAIYE 389
Cdd:cd05834    71 GFNEGLWE 78
CDC27 pfam09507
DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It ...
 3-173 1.88e-03

DNA polymerase subunit Cdc27; This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.


Pssm-ID: 462819 [Multi-domain]  Cd Length: 427  Bit Score: 41.73  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762   3 SSGTLDAGSPAPSREALdthKGEEEPEENPsKEEKQEPGTPMRKAGRPgrkrkhAQQVESSDTPKDIAAVPKCPPPRPEA 82
Cdd:pfam09507 213 KSNIMSAFFKAKPKNKK---KKTSASEQKV-QEESAEESGKEDVTLED------DSAAEEEEDEQLPTKKDKRRQKRGES 282

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2240506762  83 SPAEPlPNGDVEGDAEEAAESPKGGRAEEDETESLPDGETGRALENGRcTPKEGLDAPADEGELAPSDPQKKRGRRKLLe 162
Cdd:pfam09507 283 SDSEE-STRESRKEKRERLKKMMEDDSDDDEMEDVPESPVATEEEETG-SPPPLLKKEVEKEEVTESGDGRRRKRRKVM- 359

                         170
                  ....*....|.
gi 2240506762 163 ateKSKDEKEE 173
Cdd:pfam09507 360 ---KKKTFKDE 367
PWWP_MSH6 cd05837
PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called ...
 308-326 3.77e-03

PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines.


Pssm-ID: 438962  Cd Length: 103  Bit Score: 37.65  E-value: 3.77e-03
                          10
                  ....*....|....*....
gi 2240506762 308 FGIGELVWGKLRGFSWWPG 326
Cdd:cd05837     1 FSPGDLVWAKLEGYPWWPS 19
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 311-328 6.52e-03

PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438974  Cd Length: 113  Bit Score: 37.28  E-value: 6.52e-03
                          10
                  ....*....|....*...
gi 2240506762 311 GELVWGKLRGFSWWPGRI 328
Cdd:cd20146    12 GSLVWAKMTGYPRWPAIL 29
PWWP_ScIOC4-like cd05840
PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar ...
 311-366 8.28e-03

PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins; ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438965  Cd Length: 94  Bit Score: 36.51  E-value: 8.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2240506762 311 GELVWGKLRGFSWWPGRIVS--------WWMTGRSRAAEGTRW-VMWFGDGKFSVVCVEKLLPLS 366
Cdd:cd05840     1 GDLVLAKVKGYPPWPAMVLPeellpknvLKAKKRKPKSKKTVYpVQFFPDNEYYWVSPSSLKPLT 65
 
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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