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Conserved domains on  [gi|1174697597|ref|XP_020561094|]
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nuclear body protein SP140-like protein isoform X3 [Oryzias latipes]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
184-256 1.11e-25

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


:

Pssm-ID: 396076  Cd Length: 75  Bit Score: 100.33  E-value: 1.11e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174697597 184 FFKNQLPVTCGSIKGILNHDKLAKG--EKCIKVKDQWFTPAEFEKFAGKEKSRNWKSSIRCENITLGKLIQEGHL 256
Cdd:pfam01342   1 FHSPVLPVTCGEAKGILHKEKFKQGisGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
488-580 6.82e-15

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: 70.48  E-value: 6.82e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRN--TDKEQIFNTNP-ELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAE 564
Cdd:cd04369     4 KLRSLLDALKKlkRDLSEPFLEPVdPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSP 83
                          90
                  ....*....|....*.
gi 1174697597 565 FLEIGKRLKETFDKEF 580
Cdd:cd04369    84 IYKDAKKLEKLFEKLL 99
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
413-458 1.77e-12

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  Cd Length: 43  Bit Score: 61.98  E-value: 1.77e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 413 ECYICEDVGDLVVCDHCPKSFHPNCHLPHIEEammSDNNPWMCTFC 458
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPE---FPSGEWSCSLC 43
HSR super family cl03917
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
11-107 4.53e-11

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


The actual alignment was detected with superfamily member pfam03172:

Pssm-ID: 397335  Cd Length: 99  Bit Score: 59.47  E-value: 4.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  11 QLQQFFHSRKTELS-CLENPQTFLSQLRDYNLIPEDRYKKVIKMK-SKDRRRMAIYEFLDWMERERSehiPLFWRCVFKE 88
Cdd:pfam03172   4 ALFQHFKENKVEIAyAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1174697597  89 IILSQYPIFRLMRNSLMDG 107
Cdd:pfam03172  81 VNLKEYPDLIEILRSFPNV 99
SAND super family cl02536
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
324-386 2.13e-10

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


The actual alignment was detected with superfamily member pfam01342:

Pssm-ID: 413362  Cd Length: 75  Bit Score: 56.81  E-value: 2.13e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 324 NATFEVSCGQ---------FL-GTRGLSIRTEDKWMSPVEFVMEATSQTDATWRKDIIYNEEPLNALIEAKVL 386
Cdd:pfam01342   3 SPVLPVTCGEakgilhkekFKqGISGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
 
Name Accession Description Interval E-value
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
184-256 1.11e-25

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 396076  Cd Length: 75  Bit Score: 100.33  E-value: 1.11e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174697597 184 FFKNQLPVTCGSIKGILNHDKLAKG--EKCIKVKDQWFTPAEFEKFAGKEKSRNWKSSIRCENITLGKLIQEGHL 256
Cdd:pfam01342   1 FHSPVLPVTCGEAKGILHKEKFKQGisGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
SAND smart00258
SAND domain;
189-256 1.91e-21

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 88.17  E-value: 1.91e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  189 LPVTCGSIKGILNHDKLAKG--EKCIKVKDQWFTPAEFEKFAGKEKSRNWKSSIRCENITLGKLIQEGHL 256
Cdd:smart00258   3 LPVTCGTVKGILYKKKFKCGisVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTL 72
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
488-580 6.82e-15

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: 70.48  E-value: 6.82e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRN--TDKEQIFNTNP-ELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAE 564
Cdd:cd04369     4 KLRSLLDALKKlkRDLSEPFLEPVdPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSP 83
                          90
                  ....*....|....*.
gi 1174697597 565 FLEIGKRLKETFDKEF 580
Cdd:cd04369    84 IYKDAKKLEKLFEKLL 99
BROMO smart00297
bromo domain;
485-583 1.59e-14

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 69.61  E-value: 1.59e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  485 HIVECQYLLLFLRNTDKEQ----IFNTNPELN-LENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYN 559
Cdd:smart00297   4 LQKKLQELLKAVLDKLDSHplswPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83
                           90       100
                   ....*....|....*....|....
gi 1174697597  560 RDNAEFLEIGKRLKETFDKEFKKA 583
Cdd:smart00297  84 GPDSEVYKDAKKLEKFFEKKLREL 107
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
413-458 1.77e-12

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  Cd Length: 43  Bit Score: 61.98  E-value: 1.77e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 413 ECYICEDVGDLVVCDHCPKSFHPNCHLPHIEEammSDNNPWMCTFC 458
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPE---FPSGEWSCSLC 43
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
489-571 1.17e-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: 395352  Cd Length: 84  Bit Score: 60.79  E-value: 1.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 489 CQYLLLFLRNTDKEQIF-NTNPELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLE 567
Cdd:pfam00439   1 CLEILDKLMEHPLAAPFlEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTYNGPGSVIYK 80

                  ....
gi 1174697597 568 IGKR 571
Cdd:pfam00439  81 AAEK 84
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
11-107 4.53e-11

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 397335  Cd Length: 99  Bit Score: 59.47  E-value: 4.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  11 QLQQFFHSRKTELS-CLENPQTFLSQLRDYNLIPEDRYKKVIKMK-SKDRRRMAIYEFLDWMERERSehiPLFWRCVFKE 88
Cdd:pfam03172   4 ALFQHFKENKVEIAyAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1174697597  89 IILSQYPIFRLMRNSLMDG 107
Cdd:pfam03172  81 VNLKEYPDLIEILRSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
324-386 2.13e-10

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 396076  Cd Length: 75  Bit Score: 56.81  E-value: 2.13e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 324 NATFEVSCGQ---------FL-GTRGLSIRTEDKWMSPVEFVMEATSQTDATWRKDIIYNEEPLNALIEAKVL 386
Cdd:pfam01342   3 SPVLPVTCGEakgilhkekFKqGISGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
488-582 2.67e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 55.97  E-value: 2.67e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRNTDKEQIFNTN-------PELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNR 560
Cdd:COG5076   146 DNKAIAKFKKQLFLRDGRFLSsiflglpSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNG 225
                          90       100
                  ....*....|....*....|..
gi 1174697597 561 DNAEFLEIGKRLKETFDKEFKK 582
Cdd:COG5076   226 PDSSVYVDAKELEKYFLKLIEE 247
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
414-461 6.03e-07

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: 395503  Cd Length: 51  Bit Score: 46.33  E-value: 6.03e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1174697597 414 CYICEDV---GDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNpWMCTFCIFK 461
Cdd:pfam00628   2 CSVCGKSdddGELVQCDGCDDWFHLACLGPPLDPAEIPSGE-WLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
414-458 1.71e-06

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: 44.90  E-value: 1.71e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1174697597  414 CYICEDV---GDLVVCDHCPKSFHPNCHLPHIEEAMMSDNnpWMCTFC 458
Cdd:smart00249   2 CSVCGKPddgGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47
 
Name Accession Description Interval E-value
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
184-256 1.11e-25

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 396076  Cd Length: 75  Bit Score: 100.33  E-value: 1.11e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174697597 184 FFKNQLPVTCGSIKGILNHDKLAKG--EKCIKVKDQWFTPAEFEKFAGKEKSRNWKSSIRCENITLGKLIQEGHL 256
Cdd:pfam01342   1 FHSPVLPVTCGEAKGILHKEKFKQGisGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
SAND smart00258
SAND domain;
189-256 1.91e-21

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 88.17  E-value: 1.91e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  189 LPVTCGSIKGILNHDKLAKG--EKCIKVKDQWFTPAEFEKFAGKEKSRNWKSSIRCENITLGKLIQEGHL 256
Cdd:smart00258   3 LPVTCGTVKGILYKKKFKCGisVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTL 72
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
488-580 6.82e-15

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: 70.48  E-value: 6.82e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRN--TDKEQIFNTNP-ELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAE 564
Cdd:cd04369     4 KLRSLLDALKKlkRDLSEPFLEPVdPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSP 83
                          90
                  ....*....|....*.
gi 1174697597 565 FLEIGKRLKETFDKEF 580
Cdd:cd04369    84 IYKDAKKLEKLFEKLL 99
BROMO smart00297
bromo domain;
485-583 1.59e-14

bromo domain;


Pssm-ID: 197636  Cd Length: 107  Bit Score: 69.61  E-value: 1.59e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  485 HIVECQYLLLFLRNTDKEQ----IFNTNPELN-LENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYN 559
Cdd:smart00297   4 LQKKLQELLKAVLDKLDSHplswPFLKPVSRKeAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83
                           90       100
                   ....*....|....*....|....
gi 1174697597  560 RDNAEFLEIGKRLKETFDKEFKKA 583
Cdd:smart00297  84 GPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
491-578 4.11e-13

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: 65.41  E-value: 4.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 491 YLLLFLRNTD--KEQIFNTNP----ELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAE 564
Cdd:cd05500     8 FLLSSIRSLKrlKDARPFLVPvdpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHP 87
                          90
                  ....*....|....
gi 1174697597 565 FLEIGKRLKETFDK 578
Cdd:cd05500    88 VSQMGKRLQAAFEK 101
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
413-458 1.77e-12

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  Cd Length: 43  Bit Score: 61.98  E-value: 1.77e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 413 ECYICEDVGDLVVCDHCPKSFHPNCHLPHIEEammSDNNPWMCTFC 458
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPE---FPSGEWSCSLC 43
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
515-582 4.16e-12

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: 63.18  E-value: 4.16e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKEFKK 582
Cdd:cd05504    44 DYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRK 111
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
511-579 7.35e-12

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: 61.92  E-value: 7.35e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174697597 511 LNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKE 579
Cdd:cd05499    33 LNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
489-571 1.17e-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: 395352  Cd Length: 84  Bit Score: 60.79  E-value: 1.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 489 CQYLLLFLRNTDKEQIF-NTNPELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLE 567
Cdd:pfam00439   1 CLEILDKLMEHPLAAPFlEPVDPDEYPDYYSVIKRPMDLSTIKKKLENGEYKSLAEFEADVKLMFSNARTYNGPGSVIYK 80

                  ....
gi 1174697597 568 IGKR 571
Cdd:pfam00439  81 AAEK 84
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
515-582 4.30e-11

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  Cd Length: 101  Bit Score: 59.49  E-value: 4.30e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKEFKK 582
Cdd:cd05509    33 DYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
11-107 4.53e-11

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 397335  Cd Length: 99  Bit Score: 59.47  E-value: 4.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597  11 QLQQFFHSRKTELS-CLENPQTFLSQLRDYNLIPEDRYKKVIKMK-SKDRRRMAIYEFLDWMERERSehiPLFWRCVFKE 88
Cdd:pfam03172   4 ALFQHFKENKVEIAyAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1174697597  89 IILSQYPIFRLMRNSLMDG 107
Cdd:pfam03172  81 VNLKEYPDLIEILRSFPNV 99
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
489-586 1.43e-10

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: 58.21  E-value: 1.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 489 CQYLLLFLRNTDKEQIFNTNPELNLENYRCFVEtPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNaEFLEI 568
Cdd:cd05501     7 CEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKE-PMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD-DFGQV 84
                          90
                  ....*....|....*...
gi 1174697597 569 GKRLKETFDKEFKKAFNI 586
Cdd:cd05501    85 GITLEKKFEKNFKEVFAI 102
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
324-386 2.13e-10

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 396076  Cd Length: 75  Bit Score: 56.81  E-value: 2.13e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 324 NATFEVSCGQ---------FL-GTRGLSIRTEDKWMSPVEFVMEATSQTDATWRKDIIYNEEPLNALIEAKVL 386
Cdd:pfam01342   3 SPVLPVTCGEakgilhkekFKqGISGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGGKPLRELIEKGIL 75
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
508-580 6.50e-10

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: 56.52  E-value: 6.50e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174697597 508 NPE-LNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKEF 580
Cdd:cd05498    29 DPEaLGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDRW 102
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
516-578 1.16e-09

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: 55.46  E-value: 1.16e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 516 YRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDK 578
Cdd:cd05503    33 YRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFFEK 95
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
414-458 1.99e-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  Cd Length: 45  Bit Score: 53.13  E-value: 1.99e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNpWMCTFC 458
Cdd:cd15533     2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLDEEDLPPGE-WLCHRC 45
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
489-584 2.30e-09

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  Cd Length: 109  Bit Score: 54.99  E-value: 2.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 489 CQYLLLFLRNTDKEQIFNTNPELNLENYRCFVETPMWLGKITDKLQE---NQYKTVGQFESDIQLIFSNCGCYNRDNAEF 565
Cdd:cd05502     9 CERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTPMDLSLIRKKLQPkspQHYSSPEEFVADVRLMFKNCYKFNEEDSEV 88
                          90
                  ....*....|....*....
gi 1174697597 566 LEIGKRLKETFDKEFKKAF 584
Cdd:cd05502    89 AQAGKELELFFEEQLKEIL 107
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
488-580 4.04e-09

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: 53.87  E-value: 4.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRNTDKEQIFNTNPE---LNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAE 564
Cdd:cd05506     4 QCGTLLRKLMKHKWGWVFNAPVDvvaLGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGND 83
                          90
                  ....*....|....*.
gi 1174697597 565 FLEIGKRLKETFDKEF 580
Cdd:cd05506    84 VHTMAKELLKIFETRW 99
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
413-458 4.53e-09

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: 52.04  E-value: 4.53e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 413 ECYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMMsdnnPWMCTFC 458
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRS----PWSCTFC 42
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
414-460 7.37e-09

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: 52.01  E-value: 7.37e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1174697597 414 CYICED-----VGDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNPWMCTFCIF 460
Cdd:cd15578     2 CTVCQDgssesPNEIVLCDKCGQGYHQLCHNPKIDSSVLDPDVPWLCRQCVF 53
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
410-458 7.50e-09

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  Cd Length: 49  Bit Score: 51.88  E-value: 7.50e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1174697597 410 NDDECYICEDVGDLVVCDHCPKSFHPNCHLPhieeAMMS-DNNPWMCTFC 458
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVP----ALLSfPVGEWVCTLC 46
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
492-574 1.75e-08

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: 52.02  E-value: 1.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 492 LLLFLRNTDKEQIFNTNPELN-LENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGK 570
Cdd:cd05512     9 TLDQLQEKDTAEIFSEPVDLSeVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAV 88

                  ....
gi 1174697597 571 RLKE 574
Cdd:cd05512    89 RLRD 92
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
488-582 2.67e-08

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 55.97  E-value: 2.67e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 488 ECQYLLLFLRNTDKEQIFNTN-------PELNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNR 560
Cdd:COG5076   146 DNKAIAKFKKQLFLRDGRFLSsiflglpSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNG 225
                          90       100
                  ....*....|....*....|..
gi 1174697597 561 DNAEFLEIGKRLKETFDKEFKK 582
Cdd:COG5076   226 PDSSVYVDAKELEKYFLKLIEE 247
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
502-579 3.36e-08

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: 51.68  E-value: 3.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 502 EQIFNTNPE------------LNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIG 569
Cdd:cd05495    13 EKLYKQDPEslpfrqpvdpklLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYC 92
                          90
                  ....*....|
gi 1174697597 570 KRLKETFDKE 579
Cdd:cd05495    93 TKLAEVFEQE 102
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
395-458 3.96e-08

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: 51.15  E-value: 3.96e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174697597 395 CRKCKAELKDKDNQKNDD----ECYICEDVGDLVVCDHCPKSFHPNC---HLPHIEEAMMSDNNPWMCTFC 458
Cdd:cd11726    30 CKSCLKFYNSGEFSKDEDgsdeYCRWCGQGGDLICCDFCPNVFCKKCikrNLGRAELSRIEESDKWKCFVC 100
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
414-460 7.25e-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: 49.04  E-value: 7.25e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1174697597 414 CYIC-----EDVGDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNPWMCTFCIF 460
Cdd:cd15499     2 CSICggaeaRDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDEKWFCSRCVF 53
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
414-458 1.51e-07

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: 48.12  E-value: 1.51e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIeeaMMSDNNPWMCTFC 458
Cdd:cd15624     2 CAVCQNGGDLLCCEKCPKVFHLTCHVPTL---LSFPSGDWICTFC 43
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
414-458 1.57e-07

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: 47.75  E-value: 1.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIeeaMMSDNNPWMCTFC 458
Cdd:cd15622     2 CAVCQNGGELLCCEKCPKVFHLSCHVPTL---MNFPSGEWICTFC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
413-458 3.20e-07

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  Cd Length: 43  Bit Score: 47.06  E-value: 3.20e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 413 ECYICEDVGDLVVCDHCPKSFHPNCHLPHIEEaMMSDNnpWMCTFC 458
Cdd:cd15539     1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTL-IPSGT--WRCSSC 43
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
413-455 3.76e-07

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  Cd Length: 43  Bit Score: 46.55  E-value: 3.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 413 ECYICEDVGDLVVCDH--CPKSFHPNChlphIEEAMMSDNNpWMC 455
Cdd:cd15568     1 ECFRCGDGGDLVLCDFkgCPKVYHLSC----LGLEKPPGGK-WIC 40
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
414-461 6.03e-07

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: 395503  Cd Length: 51  Bit Score: 46.33  E-value: 6.03e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1174697597 414 CYICEDV---GDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNpWMCTFCIFK 461
Cdd:pfam00628   2 CSVCGKSdddGELVQCDGCDDWFHLACLGPPLDPAEIPSGE-WLCPECKPK 51
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
515-566 7.02e-07

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  Cd Length: 112  Bit Score: 48.21  E-value: 7.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFL 566
Cdd:cd05510    40 DYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPL 91
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
414-458 1.31e-06

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  Cd Length: 43  Bit Score: 44.96  E-value: 1.31e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAmmsDNNPWMCTFC 458
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEI---PDGDWFCPRC 43
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
414-458 1.63e-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: 1.63e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1174697597 414 CYICEDVGD---LVVCDHCPKSFHPNCHLPHIEEAmmsDNNPWMCTFC 458
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRM---PKGKWVCQIC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
414-458 1.71e-06

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: 44.90  E-value: 1.71e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1174697597  414 CYICEDV---GDLVVCDHCPKSFHPNCHLPHIEEAMMSDNnpWMCTFC 458
Cdd:smart00249   2 CSVCGKPddgGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
414-458 2.93e-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  Cd Length: 45  Bit Score: 44.33  E-value: 2.93e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNpWMCTFC 458
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEEDNLPDDE-WFCNEC 45
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
414-458 3.04e-06

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: 44.03  E-value: 3.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMMSDnnpWMCTFC 458
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGED---WKCLLC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
414-458 1.64e-05

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  Cd Length: 43  Bit Score: 42.20  E-value: 1.64e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAmmsDNNPWMCTFC 458
Cdd:cd15531     2 CEVCQQGGEIILCDTCPRAYHLVCLDPELEKA---PEGKWSCPHC 43
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
414-458 2.24e-05

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  Cd Length: 48  Bit Score: 41.92  E-value: 2.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1174697597 414 CYICEDVGD----LVVCDHCPKSFHPNCHLPHIEEAMmsDNNPWMCTFC 458
Cdd:cd15489     2 CIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSSFV--PNGKWICPVC 48
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
515-578 2.74e-05

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: 43.86  E-value: 2.74e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDK 578
Cdd:cd05529    60 DYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLR 123
PHD1_PHF1 cd15500
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ...
423-458 2.78e-05

PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with 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. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger.


Pssm-ID: 276975  Cd Length: 51  Bit Score: 41.74  E-value: 2.78e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1174697597 423 LVVCDHCPKSFHPNCHLPHIEEAMMSDNNPWMCTFC 458
Cdd:cd15500    16 LVNCEKCHHAYHQECHVPRVPLESAGDGDSWMCRQC 51
PHD1_PHF19 cd15579
PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
413-460 2.86e-05

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: 41.79  E-value: 2.86e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 413 ECYICED-----VGDLVVCDHCPKSFHPNCHLPHIEEAMMSDNNPWMCTFCIF 460
Cdd:cd15579     1 KCNVCLGkssgpLNEILICGKCGLGYHQQCHIPVVDSSDDPPLTPWFCRRCIF 53
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
414-458 8.19e-05

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  Cd Length: 41  Bit Score: 39.92  E-value: 8.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNChlphIEEAMMSDNNpWMCTFC 458
Cdd:cd15567     2 CFICSEGGSLICCESCPASFHPEC----LGLEPPPEGK-FYCEDC 41
ADDz_Dnmt3 cd11725
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de ...
395-458 1.04e-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: 41.61  E-value: 1.04e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1174697597 395 CRKCKAELKDKDNQKNDD--ECY--ICEDVGDLVVCDH--CPKSFhpnCH------LPHIEEAMMSDNNPWMCTFC 458
Cdd:cd11725    27 CKNCKERFLECIFLFDDDgyQMYctICGGGGEVVLCDNpdCTRVY---CTecldllLGPGAVAKILESDPWFCFLC 99
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
414-458 1.71e-04

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


Pssm-ID: 277034  Cd Length: 43  Bit Score: 39.32  E-value: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMMSDnnpWMCTFC 458
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEED---WQCEVC 43
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
515-576 1.80e-04

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  Cd Length: 104  Bit Score: 41.07  E-value: 1.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETF 576
Cdd:cd05522    39 EYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEA 100
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
511-560 2.02e-04

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: 40.87  E-value: 2.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1174697597 511 LNLENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNR 560
Cdd:cd05497    35 LNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
414-458 2.37e-04

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: 38.74  E-value: 2.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNCHLPHIEEAMmsdnnpWMCTFC 458
Cdd:cd15658     2 CFVCARGGRLLCCESCPASFHPECLSIEMPEGC------WNCNEC 40
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
520-565 2.43e-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  Cd Length: 112  Bit Score: 40.71  E-value: 2.43e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 520 VETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEF 565
Cdd:cd05511    37 IKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVY 82
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
515-559 2.54e-04

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: 40.90  E-value: 2.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYN 559
Cdd:cd05496    37 DYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
515-579 5.34e-04

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 39.29  E-value: 5.34e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174697597 515 NYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKE 579
Cdd:cd05508    34 DYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICEQE 98
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
514-562 6.42e-04

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: 39.65  E-value: 6.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1174697597 514 ENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDN 562
Cdd:cd05528    34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDR 82
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
414-455 6.86e-04

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: 37.71  E-value: 6.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGD---LVVCDHCPKSFHPNCHLPHIeeAMMSDNNPWMC 455
Cdd:cd15534     2 CFKCNRSCRvapLIQCDYCPLLFHLDCLDPPL--THPPATGRWMC 44
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
414-437 1.00e-03

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: 37.02  E-value: 1.00e-03
                          10        20
                  ....*....|....*....|....*....
gi 1174697597 414 CYICEDVGD-----LVVCDHCPKSFHPNC 437
Cdd:cd15566     2 CATCEASGDgssgkLVRCIRCPRAYHAGC 30
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
414-437 2.20e-03

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: 36.14  E-value: 2.20e-03
                          10        20
                  ....*....|....*....|....
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNC 437
Cdd:cd15657     2 CFVCSKGGSLLCCESCPAAFHPDC 25
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
514-576 2.76e-03

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: 37.52  E-value: 2.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 514 ENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETF 576
Cdd:cd05505    31 EDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQCC 93
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
414-458 2.84e-03

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: 35.77  E-value: 2.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNChlphIEEAMMSDNNpWMCTFC 458
Cdd:cd15538     2 CWRCHKEGQVLCCSLCPRVYHKKC----LKLTSEPDED-WVCPEC 41
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
513-582 3.08e-03

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: 37.41  E-value: 3.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174697597 513 LENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKEFKK 582
Cdd:cd05516    37 LPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFKSARQK 106
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
504-580 4.58e-03

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: 36.93  E-value: 4.58e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1174697597 504 IFNTNPELNL-ENYRCFVETPMWLGKITDKLQENQYKTVGQFESDIQLIFSNCGCYNRDNAEFLEIGKRLKETFDKEF 580
Cdd:cd05519    26 LFLEKPSKKLyPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFKKKY 103
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
423-458 5.33e-03

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: 35.10  E-value: 5.33e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1174697597 423 LVVCDHCPKSFHPNCHLPHIEEAMMSDNNP-WMCTFC 458
Cdd:cd15502    16 IVFCDGCNTPYHQLCHDPSIDDEVVEDPDAeWFCKKC 52
ADDz cd11672
ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is ...
395-458 6.42e-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: 36.39  E-value: 6.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174697597 395 CRKCKAELKDKDNQKNDD----ECYICEDVGDLVVCDH--CPKSFHPNCHLPHI---EEAMMSDNNPWMCTFC 458
Cdd:cd11672    25 CKNCKKYFLSDDISYDDDgyqsYCRICCEGGNLLCCGNnfCHRCFCKECVDRLVgpgELSTMDENNQWYCYIC 97
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
414-458 8.69e-03

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: 34.24  E-value: 8.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1174697597 414 CYICEDVGDLVVCDHCPKSFHPNChlphIEEAMMSDNNP-WMCTFC 458
Cdd:cd15537     2 CFECHAPGEVLPCSGCFRVYHSDC----LSEDFRPDSTShWTCPVC 43
PHD2_AIRE cd15540
PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
413-440 8.79e-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: 34.49  E-value: 8.79e-03
                          10        20
                  ....*....|....*....|....*....
gi 1174697597 413 ECYICED-VGDLVVCDHCPKSFHPNCHLP 440
Cdd:cd15540     1 RCGVCRGgRGDLLRCPQCLQAFHWHCHFP 29
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
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