NCBI Conserved Domain Search

Conserved domains on [gi|281362149|ref|NP_001163665|]

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bonus, isoform B [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

Bromo_tif1_like

cd05502

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...

955-1064

3.18e-52

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99934 [Multi-domain] Cd Length: 109 Bit Score: 178.25 E-value: 3.18e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  955 LSALELRILQRICLELYCQyEQSLNFREPESPANTSYYEIVSSPMSLDVIRTRLDPSSPNHYKDIAGFVSDVRLIFSNTY 1034
Cdd:cd05502     1 LSPIDQRKCERLLLELYCH-ELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCY 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 281362149 1035 LFYQEDTKTYSNAKYLENFFEEQLAKWLPQ 1064
Cdd:cd05502    80 KFNEEDSEVAQAGKELELFFEEQLKEILPD 109

BBC

smart00502

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

284-409

6.94e-36

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

Pssm-ID: 128778 Cd Length: 127 Bit Score: 132.39 E-value: 6.94e-36

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149    284 RQALSTLVSEINYKRFLLSSATKVIDDRQQLIHDKKKDLIKEITAMAVKITNTVNTRGKQLIMRLNEVCDSKLKVLVEKK 363
Cdd:smart00502    2 REALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQL 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*.
gi 281362149    364 ETLQLLSDNTDHCIDFMQNALEKGSDFAILSSKKSLVRHLQKLKCQ 409
Cdd:smart00502   82 ESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

Bbox1_TIF1

cd19805

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

177-220

7.28e-24

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 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. TIF1-alpha and TIF1-beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, 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).

Pssm-ID: 380863 Cd Length: 44 Bit Score: 95.14 E-value: 7.28e-24

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  177 QCSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPK 220
Cdd:cd19805     1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

Bbox2_TIF1_C-VI

cd19775

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

238-278

1.27e-23

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 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 and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. 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).

Pssm-ID: 380833 Cd Length: 43 Bit Score: 94.32 E-value: 1.27e-23

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 281362149  238 HMCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHE 278
Cdd:cd19775     2 LFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEE 42

PHD_TIF1_like

cd15541

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...

891-935

7.02e-20

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: 83.55 E-value: 7.02e-20

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFP--SGEWSCSLC 43

RING_Ubox super family

cl17238

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...

92-130

1.34e-03

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.

The actual alignment was detected with superfamily member cd16555:

Pssm-ID: 473075 [Multi-domain] Cd Length: 55 Bit Score: 37.80 E-value: 1.34e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 281362149   92 SNDRPKLLECLHVACAQCVStKFSELDRSLPPLIHCPVC 130
Cdd:cd16555    14 RQRRPKVLECCHRVCAKCLY-KIVDLGDSSPSVLVCPFC 51

Med15 super family

cl26621

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...

486-735

1.74e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.

The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 42.30 E-value: 1.74e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   486 PAGLSPNGPPvnfGPQNGPPLYSNAAQQQFNNLSMSRSFPGdgsvrfGGMPPVGMQRHGQPHVSSSTHPQNMDISLRGLL 565
Cdd:pfam09606  101 PMGPGPGGPM---GQQMGGPGTASNLLASLGRPQMPMGGAG------FPSQMSRVGRMQPGGQAGGMMQPSSGQPGSGTP 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   566 NNQ-AAQSPNAHMAFNGPPSYPGGPQGAPAPAhqpMGPQMRPHFMPGQQGFSQGGGPGGGprdanfMNSNARFQSQYQRM 644
Cdd:pfam09606  172 NQMgPNGGPGQGQAGGMNGGQQGPMGGQMPPQ---MGVPGMPGPADAGAQMGQQAQANGG------MNPQQMGGAPNQVA 242

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   645 ANHAQQAaaaaamagaagggggqiPSPGALQRPQMMSNPMQNSLGFHGSQ----AGFNTGPPQTSPQLGGGGMHSLAKWH 720
Cdd:pfam09606  243 MQQQQPQ-----------------QQGQQSQLGMGINQMQQMPQGVGGGAgqggPGQPMGPPGQQPGAMPNVMSIGDQNN 305

                          250
                   ....*....|....*
gi 281362149   721 IPQSAQQSNMCSQQG 735
Cdd:pfam09606  306 YQQQQTRQQQQQQGG 320

Name

Accession

Description

Interval

E-value

Bromo_tif1_like

cd05502

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...

955-1064

3.18e-52

Pssm-ID: 99934 [Multi-domain] Cd Length: 109 Bit Score: 178.25 E-value: 3.18e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  955 LSALELRILQRICLELYCQyEQSLNFREPESPANTSYYEIVSSPMSLDVIRTRLDPSSPNHYKDIAGFVSDVRLIFSNTY 1034
Cdd:cd05502     1 LSPIDQRKCERLLLELYCH-ELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCY 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 281362149 1035 LFYQEDTKTYSNAKYLENFFEEQLAKWLPQ 1064
Cdd:cd05502    80 KFNEEDSEVAQAGKELELFFEEQLKEILPD 109

BBC

smart00502

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

284-409

6.94e-36

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

Pssm-ID: 128778 Cd Length: 127 Bit Score: 132.39 E-value: 6.94e-36

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149    284 RQALSTLVSEINYKRFLLSSATKVIDDRQQLIHDKKKDLIKEITAMAVKITNTVNTRGKQLIMRLNEVCDSKLKVLVEKK 363
Cdd:smart00502    2 REALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQL 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*.
gi 281362149    364 ETLQLLSDNTDHCIDFMQNALEKGSDFAILSSKKSLVRHLQKLKCQ 409
Cdd:smart00502   82 ESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

Bbox1_TIF1

cd19805

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

177-220

7.28e-24

Pssm-ID: 380863 Cd Length: 44 Bit Score: 95.14 E-value: 7.28e-24

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  177 QCSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPK 220
Cdd:cd19805     1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

Bbox2_TIF1_C-VI

cd19775

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

238-278

1.27e-23

Pssm-ID: 380833 Cd Length: 43 Bit Score: 94.32 E-value: 1.27e-23

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 281362149  238 HMCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHE 278
Cdd:cd19775     2 LFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEE 42

BROMO

smart00297

bromo domain;

959-1060

3.60e-21

bromo domain;

Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 89.65 E-value: 3.60e-21

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149    959 ELRILQRICLELYCQ---YEQSLNFREPESPANTS-YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTY 1034
Cdd:smart00297    4 LQKKLQELLKAVLDKldsHPLSWPFLKPVSRKEAPdYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*.
gi 281362149   1035 LFYQEDTKTYSNAKYLENFFEEQLAK 1060
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLRE 106

PHD_TIF1_like

cd15541

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...

891-935

7.02e-20

Pssm-ID: 277016 [Multi-domain] Cd Length: 43 Bit Score: 83.55 E-value: 7.02e-20

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFP--SGEWSCSLC 43

BBOX

smart00336

B-Box-type zinc finger;

239-275

2.52e-11

B-Box-type zinc finger;

Pssm-ID: 197662 [Multi-domain] Cd Length: 42 Bit Score: 59.27 E-value: 2.52e-11

                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 281362149    239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKF 275
Cdd:smart00336    5 KCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVL 41

Bromodomain

pfam00439

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...

980-1049

2.91e-11

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 425683 [Multi-domain] Cd Length: 84 Bit Score: 60.40 E-value: 2.91e-11

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149   980 FREPESPANT-SYYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKY 1049
Cdd:pfam00439   17 FLEPVDPDEYpDYYSVIKKPMDLSTIKKKLEN---GEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84

PHD

pfam00628

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

891-937

1.76e-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: 1.76e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 281362149   891 WCAVCL---DGGELMCCDKCPKVFHQNCHIPAISSLPDESESWQCLLCVN 937
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKP 50

zf-B_box

pfam00643

B-box zinc finger;

236-274

3.44e-10

B-box zinc finger;

Pssm-ID: 459886 [Multi-domain] Cd Length: 42 Bit Score: 56.33 E-value: 3.44e-10

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 281362149   236 KLHMCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYK 274
Cdd:pfam00643    2 KERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVV 40

COG5076

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...

991-1061

5.02e-10

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];

Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 62.90 E-value: 5.02e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  991 YYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLAKW 1061
Cdd:COG5076   181 YYEIIKSPMDLLTIQKKL---KNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEI 248

PHD

smart00249

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

891-935

3.36e-08

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: 50.67 E-value: 3.36e-08

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 281362149    891 WCAVC---LDGGELMCCDKCPKVFHQNCHIPAISSlPDESESWQCLLC 935
Cdd:smart00249    1 YCSVCgkpDDGGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47

CC_brat-like

cd20482

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...

286-404

6.77e-06

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.

Pssm-ID: 467844 [Multi-domain] Cd Length: 122 Bit Score: 46.38 E-value: 6.77e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  286 ALSTLVSEINYKRFLLSSATKVIDDRQQLIHDKKKDLIKEITAMAVKITNTVNTRGKQLIMRLNEVCDSKLKVLVEKKET 365
Cdd:cd20482     4 SLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLNEQQQK 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 281362149  366 LQLLSDNTDHCIDFMQNALEKGSDFAILSSKKSLVRHLQ 404
Cdd:cd20482    84 LQETIEKIQQGCEFTERLLKHGSETEVLLFKKLLEARLQ 122

RING-HC_RNF182

cd16555

RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; ...

92-130

1.34e-03

RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; RNF182 is a brain-enriched E3 ubiquitin-protein ligase that stimulates E2-dependent polyubiquitination in vitro. It is upregulated in Alzheimer"s disease (AD) brains and neuronal cells exposed to injurious insults. It interacts with ATP6V0C and promotes its degradation by the ubiquitin-proteosome pathway, suggesting a very specific role in controlling the turnover of an essential component of the neurotransmitter release machinery. RNF182 contains an N-terminal C3HC4-type RING-HC finger, and a C-terminal transmembrane domain.

Pssm-ID: 438217 [Multi-domain] Cd Length: 55 Bit Score: 37.80 E-value: 1.34e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 281362149   92 SNDRPKLLECLHVACAQCVStKFSELDRSLPPLIHCPVC 130
Cdd:cd16555    14 RQRRPKVLECCHRVCAKCLY-KIVDLGDSSPSVLVCPFC 51

Med15

pfam09606

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...

486-735

1.74e-03

Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 42.30 E-value: 1.74e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   486 PAGLSPNGPPvnfGPQNGPPLYSNAAQQQFNNLSMSRSFPGdgsvrfGGMPPVGMQRHGQPHVSSSTHPQNMDISLRGLL 565
Cdd:pfam09606  101 PMGPGPGGPM---GQQMGGPGTASNLLASLGRPQMPMGGAG------FPSQMSRVGRMQPGGQAGGMMQPSSGQPGSGTP 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   566 NNQ-AAQSPNAHMAFNGPPSYPGGPQGAPAPAhqpMGPQMRPHFMPGQQGFSQGGGPGGGprdanfMNSNARFQSQYQRM 644
Cdd:pfam09606  172 NQMgPNGGPGQGQAGGMNGGQQGPMGGQMPPQ---MGVPGMPGPADAGAQMGQQAQANGG------MNPQQMGGAPNQVA 242

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   645 ANHAQQAaaaaamagaagggggqiPSPGALQRPQMMSNPMQNSLGFHGSQ----AGFNTGPPQTSPQLGGGGMHSLAKWH 720
Cdd:pfam09606  243 MQQQQPQ-----------------QQGQQSQLGMGINQMQQMPQGVGGGAgqggPGQPMGPPGQQPGAMPNVMSIGDQNN 305

                          250
                   ....*....|....*
gi 281362149   721 IPQSAQQSNMCSQQG 735
Cdd:pfam09606  306 YQQQQTRQQQQQQGG 320

Name

Accession

Description

Interval

E-value

Bromo_tif1_like

cd05502

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...

955-1064

3.18e-52

Pssm-ID: 99934 [Multi-domain] Cd Length: 109 Bit Score: 178.25 E-value: 3.18e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  955 LSALELRILQRICLELYCQyEQSLNFREPESPANTSYYEIVSSPMSLDVIRTRLDPSSPNHYKDIAGFVSDVRLIFSNTY 1034
Cdd:cd05502     1 LSPIDQRKCERLLLELYCH-ELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCY 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 281362149 1035 LFYQEDTKTYSNAKYLENFFEEQLAKWLPQ 1064
Cdd:cd05502    80 KFNEEDSEVAQAGKELELFFEEQLKEILPD 109

BBC

smart00502

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

284-409

6.94e-36

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains

Pssm-ID: 128778 Cd Length: 127 Bit Score: 132.39 E-value: 6.94e-36

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149    284 RQALSTLVSEINYKRFLLSSATKVIDDRQQLIHDKKKDLIKEITAMAVKITNTVNTRGKQLIMRLNEVCDSKLKVLVEKK 363
Cdd:smart00502    2 REALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQL 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*.
gi 281362149    364 ETLQLLSDNTDHCIDFMQNALEKGSDFAILSSKKSLVRHLQKLKCQ 409
Cdd:smart00502   82 ESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127

Bbox1_TIF1

cd19805

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

177-220

7.28e-24

Pssm-ID: 380863 Cd Length: 44 Bit Score: 95.14 E-value: 7.28e-24

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  177 QCSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPK 220
Cdd:cd19805     1 VCTSCEDNAPATSFCVECSEWLCDTCVQAHQRVKVTKDHTIRSK 44

Bbox2_TIF1_C-VI

cd19775

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...

238-278

1.27e-23

Pssm-ID: 380833 Cd Length: 43 Bit Score: 94.32 E-value: 1.27e-23

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 281362149  238 HMCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHE 278
Cdd:cd19775     2 LFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHKYQFAEE 42

BROMO

smart00297

bromo domain;

959-1060

3.60e-21

bromo domain;

Pssm-ID: 197636 [Multi-domain] Cd Length: 107 Bit Score: 89.65 E-value: 3.60e-21

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149    959 ELRILQRICLELYCQ---YEQSLNFREPESPANTS-YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTY 1034
Cdd:smart00297    4 LQKKLQELLKAVLDKldsHPLSWPFLKPVSRKEAPdYYDIIKKPMDLKTIKKKLEN---GKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*.
gi 281362149   1035 LFYQEDTKTYSNAKYLENFFEEQLAK 1060
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLRE 106

PHD_TIF1_like

cd15541

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...

891-935

7.02e-20

Pssm-ID: 277016 [Multi-domain] Cd Length: 43 Bit Score: 83.55 E-value: 7.02e-20

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFP--SGEWSCSLC 43

Bbox1_TRIM71_C-VII

cd19812

B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar ...

177-217

1.35e-18

B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380870 Cd Length: 44 Bit Score: 80.14 E-value: 1.35e-18

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 281362149  177 QCSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTI 217
Cdd:cd19812     1 RCSSCDEGNAATSRCKDCNEYLCDNCVRAHQRVRLTKDHFI 41

Bbox1_TIF1b_C-VI

cd19846

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...

174-223

1.73e-18

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the 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 the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, 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. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

Pssm-ID: 380904 Cd Length: 52 Bit Score: 80.13 E-value: 1.73e-18

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  174 ASIQ-CSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPKDEA 223
Cdd:cd19846     1 ETIQcCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRVKSSS 51

Bromodomain

cd04369

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...

959-1058

2.13e-17

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

Pssm-ID: 99922 [Multi-domain] Cd Length: 99 Bit Score: 78.57 E-value: 2.13e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  959 ELRILQRICLELYCQYEQ-SLNFREPESPANTS-YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLF 1036
Cdd:cd04369     1 LKKKLRSLLDALKKLKRDlSEPFLEPVDPKEAPdYYEVIKNPMDLSTIKKKLKN---GEYKSLEEFEADVRLIFSNAKTY 77

                          90       100
                  ....*....|....*....|..
gi 281362149 1037 YQEDTKTYSNAKYLENFFEEQL 1058
Cdd:cd04369    78 NGPGSPIYKDAKKLEKLFEKLL 99

PHD_TIF1delta

cd15625

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...

888-938

2.15e-17

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: 76.92 E-value: 2.15e-17

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  888 NEDWCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLCVNI 938
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFP--VGEWVCTLCRNL 49

Bbox1_TIF1a_C-VI

cd19845

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...

178-220

5.74e-15

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

Pssm-ID: 380903 Cd Length: 45 Bit Score: 69.71 E-value: 5.74e-15

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 281362149  178 CSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPK 220
Cdd:cd19845     3 CTSCEDNAEANGFCVECVEWLCKTCIEAHQRVKFTKDHTVRQK 45

Bromo_Brdt_II_like

cd05498

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...

980-1061

9.09e-15

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99930 Cd Length: 102 Bit Score: 71.16 E-value: 9.09e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  980 FREPESPANT---SYYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEE 1056
Cdd:cd05498    24 FYKPVDPEALglhDYHDIIKHPMDLSTIKKKLDN---REYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFED 100


                  ....*
gi 281362149 1057 qlaKW 1061
Cdd:cd05498   101 ---RW 102

Bbox2_TIF1b_C-VI

cd19829

B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...

240-275

1.28e-14

B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD) and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-beta acts as a nuclear co-repressor that plays a role in transcription and in the 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 the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, 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. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

Pssm-ID: 380887 Cd Length: 44 Bit Score: 68.70 E-value: 1.28e-14

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKF 275
Cdd:cd19829     4 CSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQF 39

Bbox2_TIF1g_C-VI

cd19830

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); ...

240-278

1.60e-14

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma 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 actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.

Pssm-ID: 380888 Cd Length: 53 Bit Score: 68.93 E-value: 1.60e-14

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHE 278
Cdd:cd19830     9 CPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEE 47

PHD_TIF1alpha

cd15622

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...

891-935

3.50e-14

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha 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: 277092 Cd Length: 43 Bit Score: 67.40 E-value: 3.50e-14

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15622     1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFP--SGEWICTFC 43

Bbox2_TIF1a_C-VI

cd19828

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...

240-291

9.81e-14

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

Pssm-ID: 380886 Cd Length: 57 Bit Score: 66.61 E-value: 9.81e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHEIATESRQALSTLV 291
Cdd:cd19828     6 CPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVIIDTLI 57

PHD_TIF1gamma

cd15624

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...

891-938

4.15e-13

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: 64.68 E-value: 4.15e-13

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLCVNI 938
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFP--SGDWICTFCRDI 46

Bbox2_TRIM45_C-X

cd19785

B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar ...

240-275

4.93e-13

B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380843 Cd Length: 43 Bit Score: 64.36 E-value: 4.93e-13

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKF 275
Cdd:cd19785     4 CPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDF 39

Bbox2_TRIM66-like

cd19794

B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar ...

239-274

8.21e-13

B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 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. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380852 Cd Length: 43 Bit Score: 63.63 E-value: 8.21e-13

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYK 274
Cdd:cd19794     2 MCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEHRFK 37

PHD1_AIRE

cd15539

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...

892-935

3.30e-12

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: 62.08 E-value: 3.30e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15539     2 CAVCGDGGELLCCDGCPRAFHLACLVPPLTLIP--SGTWRCSSC 43

Bromo_gcn5_like

cd05509

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...

980-1061

3.51e-12

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99941 [Multi-domain] Cd Length: 101 Bit Score: 63.73 E-value: 3.51e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  980 FREP----ESPantSYYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFE 1055
Cdd:cd05509    22 FLEPvdkeEAP---DYYDVIKKPMDLSTMEEKLEN---GYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFW 95


                  ....*.
gi 281362149 1056 EQLAKW 1061
Cdd:cd05509    96 KKLKEL 101

Bromo_cbp_like

cd05495

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...

960-1058

4.01e-12

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99927 Cd Length: 108 Bit Score: 63.62 E-value: 4.01e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  960 LRILQRICLELYCQYEQSLNFREPESPANTS---YYEIVSSPMSLDVIRTRLDPSspnHYKDIAGFVSDVRLIFSNTYLF 1036
Cdd:cd05495     5 RQALMPTLEKLYKQDPESLPFRQPVDPKLLGipdYFDIVKNPMDLSTIRRKLDTG---QYQDPWQYVDDVWLMFDNAWLY 81

                          90       100
                  ....*....|....*....|..
gi 281362149 1037 YQEDTKTYSNAKYLENFFEEQL 1058
Cdd:cd05495    82 NRKTSRVYKYCTKLAEVFEQEI 103

Bbox1_TIF1g_C-VI

cd19847

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); ...

178-224

6.09e-12

B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma 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, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma 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.

Pssm-ID: 380905 Cd Length: 54 Bit Score: 61.70 E-value: 6.09e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  178 CSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPKDEAN 224
Cdd:cd19847     8 CTSCEDNASAVGFCVECGEWLCKTCIEAHQRVKFTKDHMIRKKEDVS 54

Bromo_Rsc1_2_II

cd05522

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...

977-1054

6.43e-12

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99953 [Multi-domain] Cd Length: 104 Bit Score: 63.03 E-value: 6.43e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362149  977 SLNF-REPESPANTSYYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFF 1054
Cdd:cd05522    25 TLHFeKLPDKAREPEYYQEISNPISLDDIKKKV---KRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEA 100

BBOX

smart00336

B-Box-type zinc finger;

239-275

2.52e-11

B-Box-type zinc finger;

Pssm-ID: 197662 [Multi-domain] Cd Length: 42 Bit Score: 59.27 E-value: 2.52e-11

                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 281362149    239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKF 275
Cdd:smart00336    5 KCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVL 41

Bromodomain

pfam00439

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...

980-1049

2.91e-11

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 425683 [Multi-domain] Cd Length: 84 Bit Score: 60.40 E-value: 2.91e-11

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149   980 FREPESPANT-SYYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKY 1049
Cdd:pfam00439   17 FLEPVDPDEYpDYYSVIKKPMDLSTIKKKLEN---GEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84

PHD_SP110_140

cd15626

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...

892-935

1.06e-10

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator 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. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, 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's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.

Pssm-ID: 277096 Cd Length: 42 Bit Score: 57.44 E-value: 1.06e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSlpdESESWQCLLC 935
Cdd:cd15626     2 CEVCGQEGKLFCCCTCSRVFHEDCHIPPVEA---QRSPWSCTFC 42

PHD

pfam00628

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...

891-937

1.76e-10

Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 57.12 E-value: 1.76e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 281362149   891 WCAVCL---DGGELMCCDKCPKVFHQNCHIPAISSLPDESESWQCLLCVN 937
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKP 50

PHD2_CHD_II

cd15532

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...

892-935

2.11e-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: 56.91 E-value: 2.11e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPD--GDWFCPRC 43

Bromo_SNF2

cd05519

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...

963-1056

2.55e-10

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99950 Cd Length: 103 Bit Score: 58.51 E-value: 2.55e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  963 LQRICLELY-----CQYEQ----SLNFREPESPAN-TSYYEIVSSPMSLDVIRTRLDPSspnHYKDIAGFVSDVRLIFSN 1032
Cdd:cd05519     1 LKAAMLEIYdavlnCEDETgrklSELFLEKPSKKLyPDYYVIIKRPIALDQIKRRIEGR---AYKSLEEFLEDFHLMFAN 77

                          90       100
                  ....*....|....*....|....
gi 281362149 1033 TYLFYQEDTKTYSNAKYLENFFEE 1056
Cdd:cd05519    78 ARTYNQEGSIVYEDAVEMEKAFKK 101

Bbox2

cd19756

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of ...

239-272

2.90e-10

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2).

Pssm-ID: 380814 [Multi-domain] Cd Length: 39 Bit Score: 56.27 E-value: 2.90e-10

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLS-DHRDHK 272
Cdd:cd19756     1 LCPEHPEEPLKLFCETCQELVCVLCLLSgEHRGHK 35

zf-B_box

pfam00643

B-box zinc finger;

236-274

3.44e-10

B-box zinc finger;

Pssm-ID: 459886 [Multi-domain] Cd Length: 42 Bit Score: 56.33 E-value: 3.44e-10

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 281362149   236 KLHMCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYK 274
Cdd:pfam00643    2 KERLCPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVV 40

Bbox1

cd19757

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...

177-219

3.54e-10

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).

Pssm-ID: 380815 [Multi-domain] Cd Length: 44 Bit Score: 56.35 E-value: 3.54e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  177 QCSSCSDGAvATSWCVDCSEYICDSCVQA-HQRLKITKDHTIKP 219
Cdd:cd19757     1 LCDECEERE-ATVYCLECEEFLCDDCSDAiHRRGKLTRSHKLVP 43

COG5076

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...

991-1061

5.02e-10

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];

Pssm-ID: 227408 [Multi-domain] Cd Length: 371 Bit Score: 62.90 E-value: 5.02e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  991 YYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLAKW 1061
Cdd:COG5076   181 YYEIIKSPMDLLTIQKKL---KNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEI 248

ADDz_ATRX

cd11726

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...

875-935

6.11e-10

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: 57.32 E-value: 6.11e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281362149  875 QEVNNKNEQKDDP-NEDWCAVCLDGGELMCCDKCPKVFHQNChI-----PAISSLPDESESWQCLLC 935
Cdd:cd11726    35 KFYNSGEFSKDEDgSDEYCRWCGQGGDLICCDFCPNVFCKKC-IkrnlgRAELSRIEESDKWKCFVC 100

Bromo_SP100C_like

cd05501

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...

954-1040

1.74e-09

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99933 Cd Length: 102 Bit Score: 55.90 E-value: 1.74e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  954 ELSALELrILQRIclelYCQYEQSLNFREPESpaNTSYYEIVSSPMSLDVIRTRLDPSSpnhYKDIAGFVSDVRLIFSNT 1033
Cdd:cd05501     3 ELLKCEF-LLLKV----YCMSKSGFFISKPYY--IRDYCQGIKEPMWLNKVKERLNERV---YHTVEGFVRDMRLIFHNH 72


                  ....*..
gi 281362149 1034 YLFYQED 1040
Cdd:cd05501    73 KLFYKDD 79

Bromo_WDR9_I_like

cd05529

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...

925-1054

2.50e-09

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99958 Cd Length: 128 Bit Score: 56.58 E-value: 2.50e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  925 DESESWQCLLCVNIKELTKTEGSEKSssgeLSALElRILQRICLELYCQYEQSLNFREpespANTSYYEIVSSPMSLDVI 1004
Cdd:cd05529     4 PLSSEWELFDPGWEQPHIRDEERERL----ISGLD-KLLLSLQLEIAEYFEYPVDLRA----WYPDYWNRVPVPMDLETI 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 281362149 1005 RTRLDpssPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFF 1054
Cdd:cd05529    75 RSRLE---NRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121

Bromo_BDF1_2_I

cd05500

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...

977-1058

2.58e-09

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99932 Cd Length: 103 Bit Score: 55.78 E-value: 2.58e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  977 SLNFREPESPANTS---YYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENF 1053
Cdd:cd05500    22 ARPFLVPVDPVKLNiphYPTIIKKPMDLGTIERKL---KSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98


                  ....*
gi 281362149 1054 FEEQL 1058
Cdd:cd05500    99 FEKHL 103

Bbox1_TRIM45_C-X

cd19809

B-box-type 1 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar ...

176-217

4.90e-09

B-box-type 1 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1, and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription, and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380867 Cd Length: 46 Bit Score: 53.15 E-value: 4.90e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 281362149  176 IQCSSCSDG-AVATSWCVDCSEYICDSCVQAHQRLKITKDHTI 217
Cdd:cd19809     1 LLCDLCTDGnSSAEYRCFDCSENLCEFCKQAHRRQRKTASHRI 43

Bbox2_TRIM71_C-VII

cd19796

B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar ...

240-284

5.60e-09

B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7), and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs through mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380854 [Multi-domain] Cd Length: 48 Bit Score: 52.69 E-value: 5.60e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKYKFAHEIATESR 284
Cdd:cd19796     4 CEIHEHEVLRLYCDTCSVPICRECTMGEHRGHSFIYLQEAVQDSK 48

PHD1_PHF12

cd15533

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...

892-935

6.18e-09

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: 52.74 E-value: 6.18e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDESESWQCLLC 935
Cdd:cd15533     2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLDEEDLPPGEWLCHRC 45

Bromo_BDF1_2_II

cd05499

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...

959-1055

7.49e-09

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99931 Cd Length: 102 Bit Score: 54.21 E-value: 7.49e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  959 ELRILQRICLELYCQYEQSLN--FREPESPANT---SYYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNT 1033
Cdd:cd05499     1 ELKFCEEVLKELMKPKHSAYNwpFLDPVDPVALnipNYFSIIKKPMDLGTISKKL---QNGQYQSAKEFERDVRLIFKNC 77

                          90       100
                  ....*....|....*....|..
gi 281362149 1034 YLFYQEDTKTYSNAKYLENFFE 1055
Cdd:cd05499    78 YTFNPEGTDVYMMGHQLEEVFN 99

Bbox2_BRAT-like

cd19798

B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...

239-276

1.12e-08

B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. This family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380856 Cd Length: 44 Bit Score: 51.91 E-value: 1.12e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHR--DHKYKFA 276
Cdd:cd19798     5 FCPKHPNEVLKFFCKTCNIPICKDCTLLDHNkgLHDYEYL 44

PHD_TIF1beta

cd15623

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...

892-935

1.33e-08

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: 51.73 E-value: 1.33e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVP--GEDWKCLLC 43

Bromo_Acf1_like

cd05504

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...

991-1060

1.38e-08

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99936 Cd Length: 115 Bit Score: 53.94 E-value: 1.38e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  991 YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLAK 1060
Cdd:cd05504    45 YYDIIKKPMDLGTIKEKLNM---GEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRK 111

PHD5_NSD

cd15568

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...

891-932

3.08e-08

PHD finger 5 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 fifth PHD finger.

Pssm-ID: 277043 [Multi-domain] Cd Length: 43 Bit Score: 50.79 E-value: 3.08e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  891 WCAVCLDGGELMCCDK--CPKVFHQNChipaISSLPDESESWQC 932
Cdd:cd15568     1 ECFRCGDGGDLVLCDFkgCPKVYHLSC----LGLEKPPGGKWIC 40

PHD

smart00249

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...

891-935

3.36e-08

Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 50.67 E-value: 3.36e-08

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 281362149    891 WCAVC---LDGGELMCCDKCPKVFHQNCHIPAISSlPDESESWQCLLC 935
Cdd:smart00249    1 YCSVCgkpDDGGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47

PHD1_MTF2_PHF19_like

cd15499

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...

892-937

5.76e-08

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: 50.19 E-value: 5.76e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 281362149  892 CAVCL-----DGGELMCCDKCPKVFHQNCHIPAISSLP-DESESWQCLLCVN 937
Cdd:cd15499     2 CSICGgaearDGNEILICDKCDKGYHQLCHSPKVRTSPlEGDEKWFCSRCVF 53

PHD1_MTF2

cd15578

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...

892-936

7.25e-08

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: 49.70 E-value: 7.25e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  892 CAVCLDG-----GELMCCDKCPKVFHQNCHIPAI-SSLPDESESWQCLLCV 936
Cdd:cd15578     2 CTVCQDGssespNEIVLCDKCGQGYHQLCHNPKIdSSVLDPDVPWLCRQCV 52

PHD4_NSD

cd15567

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...

891-935

8.48e-08

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: 49.17 E-value: 8.48e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNChipaISSLPDESESWQCLLC 935
Cdd:cd15567     1 WCFICSEGGSLICCESCPASFHPEC----LGLEPPPEGKFYCEDC 41

Bromo_polybromo_I

cd05524

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...

982-1060

1.36e-07

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

Pssm-ID: 99954 [Multi-domain] Cd Length: 113 Bit Score: 51.18 E-value: 1.36e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362149  982 EPEspantsYYEIVSSPMSLDVIRTRLDPSSpnhYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLAK 1060
Cdd:cd05524    38 EPE------YYEVVSNPIDLLKIQQKLKTEE---YDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNE 107

Bromo_WSTF_like

cd05505

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...

962-1058

1.55e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99937 Cd Length: 97 Bit Score: 50.23 E-value: 1.55e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  962 ILQRIClelycQYEQSLNFREPESPANT-SYYEIVSSPMSLDVIRTRLDPSSpnhYKDIAGFVSDVRLIFSNTYLFYQED 1040
Cdd:cd05505     8 ILSKIL-----KYRFSWPFREPVTADEAeDYKKVITNPMDLQTMQTKCSCGS---YSSVQEFLDDMKLVFSNAEKYYENG 79

                          90
                  ....*....|....*...
gi 281362149 1041 TKTYSNAKYLENFFEEQL 1058
Cdd:cd05505    80 SYVLSCMRKTEQCCVNLL 97

Bromo_WDR9_II

cd05496

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...

965-1074

2.11e-07

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99928 Cd Length: 119 Bit Score: 50.53 E-value: 2.11e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  965 RICLELYCQYEQSLNFREP-ESPANTSYYEIVSSPMSLDVIRTRLDPSSpnhYKDIAGFVSDVRLIFSNTYLFY-QEDTK 1042
Cdd:cd05496    11 KELVNLMWDCEDSEPFRQPvDLLKYPDYRDIIDTPMDLGTVKETLFGGN---YDDPMEFAKDVRLIFSNSKSYTpNKRSR 87

                          90       100       110
                  ....*....|....*....|....*....|..
gi 281362149 1043 TYSNAKYLENFFEEQLAKWLPQFEGTKPQGKR 1074
Cdd:cd05496    88 IYSMTLRLSALFEEHIKKIISDWKSALKRNEK 119

PHD_SF

cd15489

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...

892-935

2.68e-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: 48.08 E-value: 2.68e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 281362149  892 CAVC----LDGGELMCCDKCPKVFHQNCHIPAISSlPDESESWQCLLC 935
Cdd:cd15489     2 CIVCgkggDLGGELLQCDGCGKWFHADCLGPPLSS-FVPNGKWICPVC 48

Bbox1_TRIM19_C-V

cd19804

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; ...

175-222

3.77e-07

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380862 [Multi-domain] Cd Length: 47 Bit Score: 47.84 E-value: 3.77e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 281362149  175 SIQCSSCSDGAvATSWCVDCSEYICDSCVQAHQRLKITKDHTIKPKDE 222
Cdd:cd19804     1 ELMCNRCSESE-AEFWCSECEEFLCRKCFEAHQRFKKRKKHEALRLAE 47

Bromo_plant1

cd05506

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...

991-1061

8.85e-07

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99938 Cd Length: 99 Bit Score: 48.10 E-value: 8.85e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  991 YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEqlaKW 1061
Cdd:cd05506    35 YFDIIKKPMDLGTVKKKLEK---GEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFET---RW 99

Bbox1_BRAT-like

cd19813

B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...

178-217

1.15e-06

B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. The family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380871 Cd Length: 44 Bit Score: 46.25 E-value: 1.15e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 281362149  178 CSSCSDGAVATSWCVDCSEYICDSCVQAHQRLKITKDHTI 217
Cdd:cd19813     2 CTGCKSKETAVARCFDCQVLLCANCVTAHQFMHCFKDHRV 41

Bromo_SPT7_like

cd05510

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...

963-1044

2.24e-06

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99942 [Multi-domain] Cd Length: 112 Bit Score: 47.44 E-value: 2.24e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  963 LQRICLELYCQYEQSLNFREPESPANT-SYYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDT 1041
Cdd:cd05510    12 LDKVLNELKTYTEHSTPFLTKVSKREApDYYDIIKKPMDLGTMLKKL---KNLQYKSKAEFVDDLNLIWKNCLLYNSDPS 88


                  ...
gi 281362149 1042 KTY 1044
Cdd:cd05510    89 HPL 91

PHD_BS69

cd15537

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...

891-935

2.44e-06

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.

Pssm-ID: 277012 Cd Length: 43 Bit Score: 45.41 E-value: 2.44e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNChIPAiSSLPDESESWQCLLC 935
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDC-LSE-DFRPDSTSHWTCPVC 43

PHD1_Rco1

cd15535

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...

892-935

2.79e-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: 45.10 E-value: 2.79e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDESESWQCLLC 935
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEEDNLPDDEWFCNEC 45

PHD2_KAT6A_6B

cd15527

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...

892-935

2.94e-06

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: 45.06 E-value: 2.94e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVCLDGGE---LMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMP--KGKWVCQIC 46

PHD1_CHD_II

cd15531

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...

891-935

3.18e-06

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: 44.90 E-value: 3.18e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPE--GKWSCPHC 43

PHD1_BPTF

cd15559

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...

892-935

3.24e-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: 45.10 E-value: 3.24e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPE--EDWQCEVC 43

Bromo_AAA

cd05528

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...

958-1042

3.27e-06

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

Pssm-ID: 99957 Cd Length: 112 Bit Score: 46.97 E-value: 3.27e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  958 LELRILQRICLELYCQYEQSLNFREPESPANT-SYYEIVSSPMSLDVIRTRLDPSSPNHYKDiagFVSDVRLIFSNTYLF 1036
Cdd:cd05528     2 RELRLFLRDVLKRLASDKRFNAFTKPVDEEEVpDYYEIIKQPMDLQTILQKLDTHQYLTAKD---FLKDIDLIVTNALEY 78


                  ....*.
gi 281362149 1037 YQEDTK 1042
Cdd:cd05528    79 NPDRDP 84

Bromo_BAZ2A_B_like

cd05503

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...

959-1061

5.41e-06

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99935 Cd Length: 97 Bit Score: 45.83 E-value: 5.41e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  959 ELRILQRICLELYCQyEQSLNFREPESPANTS-YYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFY 1037
Cdd:cd05503     1 DLALCETILDEMEAH-EDAWPFLEPVNTKLVPgYRKIIKKPMDFSTIREKL---ESGQYKTLEEFAEDVRLVFDNCETFN 76

                          90       100
                  ....*....|....*....|....
gi 281362149 1038 QEDTKTYSNAKYLENFFEeqlAKW 1061
Cdd:cd05503    77 EDDSEVGRAGHNMRKFFE---KRW 97

CC_brat-like

cd20482

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...

286-404

6.77e-06

Pssm-ID: 467844 [Multi-domain] Cd Length: 122 Bit Score: 46.38 E-value: 6.77e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  286 ALSTLVSEINYKRFLLSSATKVIDDRQQLIHDKKKDLIKEITAMAVKITNTVNTRGKQLIMRLNEVCDSKLKVLVEKKET 365
Cdd:cd20482     4 SLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLNEQQQK 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 281362149  366 LQLLSDNTDHCIDFMQNALEKGSDFAILSSKKSLVRHLQ 404
Cdd:cd20482    84 LQETIEKIQQGCEFTERLLKHGSETEVLLFKKLLEARLQ 122

PHD_PRKCBP1

cd15538

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...

892-935

7.82e-06

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: 43.85 E-value: 7.82e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNChipaISSLPDESESWQCLLC 935
Cdd:cd15538     2 CWRCHKEGQVLCCSLCPRVYHKKC----LKLTSEPDEDWVCPEC 41

PHD4_NSD1

cd15656

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...

891-915

1.80e-05

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). 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 fourth PHD finger.

Pssm-ID: 277126 Cd Length: 40 Bit Score: 42.69 E-value: 1.80e-05

                          10        20
                  ....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNC 915
Cdd:cd15656     1 WCFVCSEGGSLLCCESCPAAFHREC 25

Bbox2_TRIM37_C-VIII

cd19779

B-box-type 2 zinc finger found in tripartite motif-containing protein 37 (TRIM37) and similar ...

239-274

1.87e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 37 (TRIM37) and similar proteins; TRIM37, also known as Mulibrey nanism protein, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380837 Cd Length: 40 Bit Score: 42.70 E-value: 1.87e-05

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 281362149  239 MCQLHpQEKLSLFCETCDKLTCRDCQLSD--HRDHKYK 274
Cdd:cd19779     2 KCETH-NEKLSVYCWTCKKCICHQCALWGgtHSGHTFK 38

PHD_PHF21A

cd15523

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...

892-935

2.66e-05

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: 42.38 E-value: 2.66e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15523     2 CSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPK--GMWICPKC 43

Bromo_Rsc1_2_I

cd05521

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...

989-1053

2.69e-05

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99952 Cd Length: 106 Bit Score: 44.24 E-value: 2.69e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281362149  989 TSYYEIVSSPMSLDVIRTRLdpsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENF 1053
Cdd:cd05521    38 PDYYKIIKNPLSLNTVKKRL-----PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKY 97

Bromo_SNF2L2

cd05516

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...

991-1060

4.33e-05

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99947 Cd Length: 107 Bit Score: 43.57 E-value: 4.33e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  991 YYEIVSSPMSLDVIRTRLDpsspNH-YKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLAK 1060
Cdd:cd05516    40 YYELIRKPVDFKKIKERIR----NHkYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQK 106

PHD4_NSD3

cd15658

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...

891-915

5.14e-05

PHD finger 4 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 fourth PHD finger.

Pssm-ID: 277128 Cd Length: 40 Bit Score: 41.44 E-value: 5.14e-05

                          10        20
                  ....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNC 915
Cdd:cd15658     1 FCFVCARGGRLLCCESCPASFHPEC 25

Bromo_Brdt_I_like

cd05497

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...

991-1059

5.44e-05

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99929 Cd Length: 107 Bit Score: 43.56 E-value: 5.44e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362149  991 YYEIVSSPMSLDVIRTRLDpssPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLA 1059
Cdd:cd05497    40 YHKIIKTPMDLGTIKKRLE---NNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLA 105

Bbox2_TRIM56_C-V

cd19789

B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar ...

239-273

7.22e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380847 Cd Length: 47 Bit Score: 41.37 E-value: 7.22e-05

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHKY 273
Cdd:cd19789     4 MCREHRDERLLLYCTPCEAAVCRECRLRPHLSLTH 38

PHD_PRHA_like

cd15504

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...

892-935

8.02e-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: 41.27 E-value: 8.02e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 281362149  892 CAVCLDGGE------LMCCDKCPKVFHQNCHIP--AISSLPDESESWQCLLC 935
Cdd:cd15504     2 CAKCQSGEAspdndiLLCDGGCNRAYHQKCLEPplLTEDIPPEDEGWLCPLC 53

PHD_Phf1p_Phf2p_like

cd15502

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...

892-935

9.32e-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: 41.27 E-value: 9.32e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  892 CAVCLDG-----GELMCCDKCPKVFHQNCHIPAISSLP--DESESWQCLLC 935
Cdd:cd15502     2 CIVCQRGhspksNRIVFCDGCNTPYHQLCHDPSIDDEVveDPDAEWFCKKC 52

Bromo_TFIID

cd05511

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...

991-1059

1.11e-04

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99943 [Multi-domain] Cd Length: 112 Bit Score: 42.64 E-value: 1.11e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362149  991 YYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLENFFEEQLA 1059
Cdd:cd05511    33 YYKIIKRPMDLQTIRKKI---SKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLA 98

Bromo_polybromo_V

cd05515

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...

991-1051

1.15e-04

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

Pssm-ID: 99946 Cd Length: 105 Bit Score: 42.29 E-value: 1.15e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  991 YYEIVSSPMSLDVIRTRLDPsspNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLE 1051
Cdd:cd05515    39 YYDVIKKPIDMEKIRSKIEG---NQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQ 96

PHD4_NSD2

cd15657

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...

891-915

1.15e-04

PHD finger 4 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 fourth PHD finger.

Pssm-ID: 277127 Cd Length: 41 Bit Score: 40.37 E-value: 1.15e-04

                          10        20
                  ....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNC 915
Cdd:cd15657     1 WCFVCSKGGSLLCCESCPAAFHPDC 25

Bbox2_TRIM36_C-I

cd19778

B-box-type 2 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar ...

239-272

1.36e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar proteins; TRIM36, human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation through interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380836 Cd Length: 45 Bit Score: 40.59 E-value: 1.36e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLS-DHRDHK 272
Cdd:cd19778     2 MCPEHEMEKVNMYCEACRRPVCHLCKLGgSHANHR 36

PHD1_PHF19

cd15579

PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...

892-936

1.37e-04

PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the first PHD finger.

Pssm-ID: 277054 Cd Length: 53 Bit Score: 40.63 E-value: 1.37e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  892 CAVCLD-----GGELMCCDKCPKVFHQNCHIPAISSLPDES-ESWQCLLCV 936
Cdd:cd15579     2 CNVCLGkssgpLNEILICGKCGLGYHQQCHIPVVDSSDDPPlTPWFCRRCI 52

Bromo_brd1_like

cd05512

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...

960-1047

1.41e-04

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

Pssm-ID: 99944 Cd Length: 98 Bit Score: 42.00 E-value: 1.41e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149  960 LRILQRICLELYCQYEQSLNFREPespANTS----YYEIVSSPMSLDVIRTRLDpssPNHYKDIAGFVSDVRLIFSNTYL 1035
Cdd:cd05512     2 LEVLLRKTLDQLQEKDTAEIFSEP---VDLSevpdYLDHIKQPMDFSTMRKKLE---SQRYRTLEDFEADFNLIINNCLA 75

                          90
                  ....*....|..
gi 281362149 1036 FYQEDTKTYSNA 1047
Cdd:cd05512    76 YNAKDTIFYRAA 87

Bbox_SF

cd00021

B-box-type zinc finger superfamily; The B-box-type zinc finger is a short zinc binding domain ...

239-272

1.80e-04

B-box-type zinc finger superfamily; The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2).

Pssm-ID: 380813 [Multi-domain] Cd Length: 39 Bit Score: 39.89 E-value: 1.80e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLSD-HRDHK 272
Cdd:cd00021     1 MCQEHDEEKANKYCVTCEVLYCALCKKSGaHPDHE 35

Bbox2_MID

cd19758

B-box-type 2 zinc finger found in midline (MID) family; The MID family includes MID1 and MID2. ...

239-271

2.65e-04

B-box-type 2 zinc finger found in midline (MID) family; The MID family includes MID1 and MID2. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is highly related to MID1. It associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis, and functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380816 Cd Length: 40 Bit Score: 39.38 E-value: 2.65e-04

                          10        20        30
                  ....*....|....*....|....*....|....
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQL-SDHRDH 271
Cdd:cd19758     2 MCSEHEEEKVNMYCLTDDQLICSLCKLvGKHKDH 35

PHD3_NSD

cd15566

PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...

892-919

3.23e-04

PHD finger 3 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 third PHD finger.

Pssm-ID: 277041 Cd Length: 48 Bit Score: 39.33 E-value: 3.23e-04

                          10        20        30
                  ....*....|....*....|....*....|...
gi 281362149  892 CAVC-----LDGGELMCCDKCPKVFHQNChIPA 919
Cdd:cd15566     2 CATCeasgdGSSGKLVRCIRCPRAYHAGC-IPA 33

PHD2_KMT2D

cd15595

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...

892-935

4.33e-04

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: 39.21 E-value: 4.33e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVCLDGGE---LMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15595     2 CQTCRKPGEdskMLVCEACDKGYHTFCLKPAMESLP--TDSWKCKAC 46

Bbox2_TRIM16-like

cd19769

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, ...

238-271

5.20e-04

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, such as TRIM16, TRIM29 and TRIM47. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor through affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. TRIM16 and TRIM29 belong to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. TRIM47 belongs to the C-IV subclass of TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380827 [Multi-domain] Cd Length: 46 Bit Score: 38.85 E-value: 5.20e-04

                          10        20        30
                  ....*....|....*....|....*....|....
gi 281362149  238 HMCQLHpQEKLSLFCETCDKLTCRDCQLSDHRDH 271
Cdd:cd19769     1 RVCPIH-KKPLELFCRTDQMCICELCAKEEHRGH 33

Bbox2_TRIM23_C-IX_rpt2

cd19774

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...

237-280

7.61e-04

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.

Pssm-ID: 380832 Cd Length: 50 Bit Score: 38.55 E-value: 7.61e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 281362149  237 LHMCQLHPQEKLSLFC--ETC--DKLTCRDCQLS-DHRDHKYKFAHEIA 280
Cdd:cd19774     2 KPKCPIHPDHLIEFVCleEDCqeSPLMCIICKEYgKHQGHKHELLEEEA 50

ADDz_Dnmt3

cd11725

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de ...

885-936

8.38e-04

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: 40.06 E-value: 8.38e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362149  885 DDPNEDWCAVCLDGGELMCCDK--CPKVFhqnCHI-------PAISSLPDESESWQCLLCV 936
Cdd:cd11725    43 DDGYQMYCTICGGGGEVVLCDNpdCTRVY---CTEcldlllgPGAVAKILESDPWFCFLCS 100

Bbox2_TRIM2-like

cd19759

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and ...

239-272

1.05e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380817 [Multi-domain] Cd Length: 42 Bit Score: 37.81 E-value: 1.05e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQLSDHRDHK 272
Cdd:cd19759     3 VCPNHDGETLEFYCESCETAVCRECTAGEHNEHR 36

Bbox1_TRIM8-like

cd19802

B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM8, TRIM16, TRIM25, ...

177-215

1.28e-03

B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM8, TRIM16, TRIM25, TRIM29, TRIM44, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, including TRIM8, TRIM16, TRIM25, TRIM29, TRIM44 and TRIM47. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53, impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM16, also termed estrogen-responsive B box protein (EBBP), may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor by affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM25, also termed estrogen-responsive finger protein (EFP), or ubiquitin/ISG15-conjugating enzyme TRIM25, or zinc finger protein 147 (ZNF147), or E3 ubiquitin/ISG15 ligase TRIM25, is induced by estrogen and is particularly abundant in placenta and uterus. It has been implicated in cell proliferation, protein modification, and the retinoic acid inducible gene I (RIG-I)-mediated antiviral signaling pathway. It functions as an E3-ubiquitin ligase able to transfer ubiquitin and ISG15 to target proteins. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. The TRIM (tripartite motif) family of proteins are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380860 Cd Length: 46 Bit Score: 37.79 E-value: 1.28e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 281362149  177 QCSSCSDGA--VATSWCVDCSEYICDSCVQAHQRLKITKDH 215
Cdd:cd19802     1 LCDFCDPGKalKAVKSCLTCEASLCEIHLRPHLESPALKSH 41

RING-HC_RNF182

cd16555

RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; ...

92-130

1.34e-03

Pssm-ID: 438217 [Multi-domain] Cd Length: 55 Bit Score: 37.80 E-value: 1.34e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 281362149   92 SNDRPKLLECLHVACAQCVStKFSELDRSLPPLIHCPVC 130
Cdd:cd16555    14 RQRRPKVLECCHRVCAKCLY-KIVDLGDSSPSVLVCPFC 51

PHD_BAZ1B

cd15628

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...

892-935

1.39e-03

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: 37.42 E-value: 1.39e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVCLDGGE---LMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15628     2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPD--GEWMCPAC 46

PHD_UHRF1_2

cd15525

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...

892-935

1.47e-03

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: 37.73 E-value: 1.47e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 281362149  892 CAVCldGGE-----LMCCDKCPKVFHQNCHIPAISSLPDESEsWQCLLC 935
Cdd:cd15525     2 CHVC--GGKqdpekQLLCDECDMAYHLYCLDPPLTSLPDDDE-WYCPDC 47

Bromo_polybromo_III

cd05520

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...

980-1051

1.49e-03

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

Pssm-ID: 99951 Cd Length: 103 Bit Score: 39.24 E-value: 1.49e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 281362149  980 FREPESPANTSYYEIVSSPMSLDVIRTRLdpsSPNHYKDIAGFVSDVRLIFSNTYLFYQEDTKTYSNAKYLE 1051
Cdd:cd05520    28 LKLPSKRKYPDYYQEIKNPISLQQIRTKL---KNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96

PHD1_Lid2p_like

cd15519

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...

892-935

1.49e-03

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: 37.45 E-value: 1.49e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVC---LDGGELMCCDKCPKVFHQNCHIPAISSLPDesESWQCLLC 935
Cdd:cd15519     2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPP--GTWFCPSC 46

PHD_PHF21B

cd15524

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...

891-935

1.67e-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: 1.67e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  891 WCAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15524     1 HCAACKRGGNLQPCGTCPRAYHLDCLDPPLKTAP--KGVWVCPKC 43

Med15

pfam09606

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...

486-735

1.74e-03

Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 42.30 E-value: 1.74e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   486 PAGLSPNGPPvnfGPQNGPPLYSNAAQQQFNNLSMSRSFPGdgsvrfGGMPPVGMQRHGQPHVSSSTHPQNMDISLRGLL 565
Cdd:pfam09606  101 PMGPGPGGPM---GQQMGGPGTASNLLASLGRPQMPMGGAG------FPSQMSRVGRMQPGGQAGGMMQPSSGQPGSGTP 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   566 NNQ-AAQSPNAHMAFNGPPSYPGGPQGAPAPAhqpMGPQMRPHFMPGQQGFSQGGGPGGGprdanfMNSNARFQSQYQRM 644
Cdd:pfam09606  172 NQMgPNGGPGQGQAGGMNGGQQGPMGGQMPPQ---MGVPGMPGPADAGAQMGQQAQANGG------MNPQQMGGAPNQVA 242

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   645 ANHAQQAaaaaamagaagggggqiPSPGALQRPQMMSNPMQNSLGFHGSQ----AGFNTGPPQTSPQLGGGGMHSLAKWH 720
Cdd:pfam09606  243 MQQQQPQ-----------------QQGQQSQLGMGINQMQQMPQGVGGGAgqggPGQPMGPPGQQPGAMPNVMSIGDQNN 305

                          250
                   ....*....|....*
gi 281362149   721 IPQSAQQSNMCSQQG 735
Cdd:pfam09606  306 YQQQQTRQQQQQQGG 320

PHD_Int12

cd15501

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...

892-935

1.85e-03

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: 37.32 E-value: 1.85e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 281362149  892 CAVCLD-----GGELMCCDKCPKVFHQNCHIPAIS--SLPDESESWQCLLC 935
Cdd:cd15501     2 CVVCKQmdvtsGNQLVECQECHNLYHQECHKPPVTdkDVNDPRLVWYCSRC 52

RING-HC_TRIM13_like_C-V

cd16581

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...

93-130

1.93e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.

Pssm-ID: 438243 [Multi-domain] Cd Length: 50 Bit Score: 37.49 E-value: 1.93e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 281362149   93 NDRPKLLECLHVACAQCVSTKFSELDRSLPPLIHCPVC 130
Cdd:cd16581    12 FDDPKILPCSHTFCKNCLEKLLAASGYYLLASLKCPTC 49

Med15

pfam09606

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...

473-736

2.19e-03

Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 42.30 E-value: 2.19e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   473 MAPPLRP---GLPPGMPAGLSPNGPPvnfGPQNGPPLYSNAAQQQFNNL-------------SMSRSFPGDGSVRFGGMP 536
Cdd:pfam09606  204 MGVPGMPgpaDAGAQMGQQAQANGGM---NPQQMGGAPNQVAMQQQQPQqqgqqsqlgmginQMQQMPQGVGGGAGQGGP 280

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   537 PVGMQRHGQphvSSSTHPQNMDISLRGLLNNQAAQSPNAHMAFNGPPSYPGGP--QGAPAPAHQPMGPQMRPhfmpgqqg 614
Cdd:pfam09606  281 GQPMGPPGQ---QPGAMPNVMSIGDQNNYQQQQTRQQQQQQGGNHPAAHQQQMnqSVGQGGQVVALGGLNHL-------- 349

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   615 fsqgggPGGGPRDANFMNSNARFQSQYQRMAnhaqqaaaaaAMAGAAGGGGGQIPSPGALQRPQMMSNPMQNSLGFHGSQ 694
Cdd:pfam09606  350 ------ETWNPGNFGGLGANPMQRGQPGMMS----------SPSPVPGQQVRQVTPNQFMRQSPQPSVPSPQGPGSQPPQ 413

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 281362149   695 agfnTGPPQTSPQLGGGGMHSLAKWhipQSAQQSNMCSQQGP 736
Cdd:pfam09606  414 ----SHPGGMIPSPALIPSPSPQMS---QQPAQQRTIGQDSP 448

PHD_BAZ1A_like

cd15544

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...

892-935

2.32e-03

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: 37.01 E-value: 2.32e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVCL---DGGELMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15544     2 CKVCRkkgDPDNMILCDGCDKAFHLYCLRPALREVP--SGDWFCPAC 46

PHD2_PHF12_Rco1

cd15534

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...

892-932

3.28e-03

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: 36.56 E-value: 3.28e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGE---LMCCDKCPKVFHQNCHIPAISSLPDeSESWQC 932
Cdd:cd15534     2 CFKCNRSCRvapLIQCDYCPLLFHLDCLDPPLTHPPA-TGRWMC 44

PHD_UHRF1

cd15616

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...

892-935

3.51e-03

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: 36.48 E-value: 3.51e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 281362149  892 CAVCLDGGELMCCDKCPKVFHQNCHIPAISSLPDEsESWQCLLC 935
Cdd:cd15616     5 CGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDD-EDWYCPEC 47

PHD1_PHF14

cd15561

PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...

892-935

3.71e-03

PHD finger 1 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 first PHD finger.

Pssm-ID: 277036 Cd Length: 56 Bit Score: 36.65 E-value: 3.71e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 281362149  892 CAVCL-----DGGELMCCDKCPKVFHQNCH--IPAISSLPDES----ESWQCLLC 935
Cdd:cd15561     2 CCVCLgdrsnDADEIIECDKCGISVHEGCYgvIDESDSSSSASssstEPWFCEPC 56

Pro-rich

pfam15240

Proline-rich protein; This family includes several eukaryotic proline-rich proteins.

486-606

4.26e-03

Proline-rich protein; This family includes several eukaryotic proline-rich proteins.

Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 39.25 E-value: 4.26e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   486 PAGLSPNGPPVNFGPQNGPPLYSNAAQQQFNNLSMSRSFPGDGSvrfGGMPPVGMQRHGQPHVSSSTHPQNMDislrgll 565
Cdd:pfam15240   59 PASDDPPGPPPPGGPQQPPPQGGKQKPQGPPPQGGPRPPPGKPQ---GPPPQGGNQQQGPPPPGKPQGPPPQG------- 128

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 281362149   566 nnqaaqspnahmafNGPPSYPGGPQGAPAPAH-QPMGPQMRP 606
Cdd:pfam15240  129 --------------GGPPPQGGNQQGPPPPPPgNPQGPPQRP 156

RING-HC_TRIM45_C-VII

cd16588

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar ...

81-131

4.60e-03

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain.

Pssm-ID: 438250 [Multi-domain] Cd Length: 59 Bit Score: 36.73 E-value: 4.60e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362149   81 FKCVYCAQLLGSndrPKLLECLHVACAQCVST--KFSEL-----DRSLPP--LIHCPVCD 131
Cdd:cd16588     1 TRCPVCGKLFQE---PRLLPCLHTLCSPCLRQlePFSVCglrggDRSEKSnySVLCPVCD 57

PHD5_NSD3

cd15661

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...

891-915

4.83e-03

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: 36.10 E-value: 4.83e-03

                          10        20
                  ....*....|....*....|....*..
gi 281362149  891 WCAVCLDGGELMCCDK--CPKVFHQNC 915
Cdd:cd15661     1 YCFQCGDGGELVMCDKkdCPKAYHLLC 27

Bbox1_TRIM56_C-V

cd19810

B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar ...

187-217

4.88e-03

B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

Pssm-ID: 380868 Cd Length: 49 Bit Score: 36.08 E-value: 4.88e-03

                          10        20        30
                  ....*....|....*....|....*....|.
gi 281362149  187 ATSWCVDCSEYICDSCVQAHQRLKITKDHTI 217
Cdd:cd19810    16 ATSRCLDCADFLCDACASGHRCSRLTHDHRV 46

Bbox2_TRIM14

cd19768

B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar ...

240-280

5.07e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar proteins; TRIM14 is a mitochondrial adaptor that facilitates innate immune signaling. It also plays a critical role in tumor development. TRIM14 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 zinc finger as well as a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380826 [Multi-domain] Cd Length: 44 Bit Score: 35.86 E-value: 5.07e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 281362149  240 CQLHPQEKLSLFCETCDKLTCRDCQ-LSDHRDHKYKFAHEIA 280
Cdd:cd19768     3 CPEHKDRPLELFCKTCKRCVCALCPiLGQHRGHDVRLIDEEA 44

Bbox2_MID2_C-I

cd19823

B-box-type 2 zinc finger found in midline-2 (MID2) and similar proteins; MID2, also known as ...

239-272

5.40e-03

B-box-type 2 zinc finger found in midline-2 (MID2) and similar proteins; MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase that is highly related to MID1 that associate with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. It heterodimerizes in vitro with its paralog MID1. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380881 Cd Length: 40 Bit Score: 35.72 E-value: 5.40e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 281362149  239 MCQLHPQEKLSLFCETCDKLTCRDCQL-SDHRDHK 272
Cdd:cd19823     2 TCLEHENEKVNMYCVVDDQLICALCKLvGRHRDHQ 36

ADDz

cd11672

ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is ...

885-935

5.78e-03

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: 37.54 E-value: 5.78e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 281362149  885 DDPNEDWCAVCLDGGELMCCDK--CPKVFHQNCHI----PAISSLPDESESWQCLLC 935
Cdd:cd11672    41 DDGYQSYCRICCEGGNLLCCGNnfCHRCFCKECVDrlvgPGELSTMDENNQWYCYIC 97

RING-HC_TRIM32_C-VII

cd16587

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...

95-130

6.68e-03

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.

Pssm-ID: 438249 [Multi-domain] Cd Length: 51 Bit Score: 35.84 E-value: 6.68e-03

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 281362149   95 RPKLLECLHVACAQCVstkfSELDRSLPPL-IHCPVC 130
Cdd:cd16587    16 RPKLLHCGHTICEQCL----EKLLASLSINgVRCPFC 48

RING-HC_PML_C-V

cd16579

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...

81-130

7.43e-03

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.

Pssm-ID: 438241 [Multi-domain] Cd Length: 52 Bit Score: 35.61 E-value: 7.43e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 281362149   81 FKCVYCAQLLGSNDRPKLLECLHVACAQCVSTkfSELDRSLPPLIHCPVC 130
Cdd:cd16579     2 FKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEA--LAEQASETTEFQCPIC 49

RING-HC_TRIM39_C-IV

cd16601

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...

81-130

7.50e-03

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438263 [Multi-domain] Cd Length: 44 Bit Score: 35.54 E-value: 7.50e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 281362149   81 FKCVYCAQLLGSndrPKLLECLHVACAQCVSTKFSELDRSLPplihCPVC 130
Cdd:cd16601     2 ASCSLCKEYLKD---PVIIECGHNFCRACITRFWEELDGDFP----CPQC 44

PHD2_AIRE

cd15540

PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...

892-935

8.65e-03

PHD finger 2 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 second PHD finger that may play a critical role in the activation of gene transcription.

Pssm-ID: 277015 Cd Length: 42 Bit Score: 35.26 E-value: 8.65e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 281362149  892 CAVCLDG-GELMCCDKCPKVFHQNCHIPAISSlpdeSESWQCLLC 935
Cdd:cd15540     2 CGVCRGGrGDLLRCPQCLQAFHWHCHFPSGSS----GGRMRCKSC 42

PHD2_KMT2C_like

cd15510

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...

892-935

8.65e-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: 35.49 E-value: 8.65e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 281362149  892 CAVCLDGGE---LMCCDKCPKVFHQNCHIPAISSLPdeSESWQCLLC 935
Cdd:cd15510     2 CQACRQPGDdtkMLVCETCDKGYHTSCLRPVMSSIP--KYGWKCKNC 46

Bbox2_xNF7-like

cd19800

B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; ...

239-274

8.80e-03

B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; xNF7 is a maternally expressed novel zinc finger nuclear phosphoprotein. It acts as a transcription factor that determines dorsal-ventral body axis. xNF7 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380858 [Multi-domain] Cd Length: 39 Bit Score: 35.07 E-value: 8.80e-03

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 281362149  239 MCQLHpQEKLSLFCETCDKLTCRDCQLSD-HRDHKYK 274
Cdd:cd19800     2 VCSEH-DEPLKLFCKDDKRLICVICRDSRkHRGHRFL 37

RING-HC_TRIM71_C-VII

cd16589

RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar ...

68-131

9.15e-03

RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and is therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438251 [Multi-domain] Cd Length: 91 Bit Score: 36.62 E-value: 9.15e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281362149   68 SESNSSASAKFTLFKCVYCAqllGSNDRPKLLECLHVACAQCVSTKFSELDRSlPPLIHCPVCD 131
Cdd:cd16589    25 LSSNSSTSSTSSGGGGGSAG---AATRRLHVLPCLHAFCRQCLEAQRSPGAGP-ALKLRCPVCD 84

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