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Conserved domains on  [gi|1958803196|ref|XP_038939827|]
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nuclear autoantigen Sp-100 isoform X2 [Rattus norvegicus]

Protein Classification

nuclear body protein( domain architecture ID 10504730)

nuclear body protein similar to human Sp110 nuclear body protein that may be a nuclear hormone receptor coactivator that enhances transcription of genes with retinoic acid response elements (RARE)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
23-119 1.07e-45

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: 460835  Cd Length: 99  Bit Score: 158.08  E-value: 1.07e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196  23 ELIFQHFKRQKVAISNAIKNPFPFLEGLRDHELITAKMYEDLQDSYRALVRVQEVIYRALDKLEKIFSMKVLYEVFSNVN 102
Cdd:pfam03172   3 EALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDVN 82
                          90
                  ....*....|....*..
gi 1958803196 103 MEKYPDLQLIYQSFERV 119
Cdd:pfam03172  83 LKEYPDLIEILKSFPNV 99
Bromodomain super family cl02556
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
646-746 1.82e-44

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


The actual alignment was detected with superfamily member cd05501:

Pssm-ID: 445827  Cd Length: 102  Bit Score: 154.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 646 PEEQLKCELLLLTIYCCPKSGFFIRKPKKRKEDFPDLQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYK-SR 724
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKdDD 80
                          90       100
                  ....*....|....*....|..
gi 1958803196 725 FKNLGVIVGNKFEKTFKSVFSI 746
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
472-548 2.81e-32

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: 460167  Cd Length: 76  Bit Score: 119.61  E-value: 2.81e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958803196 472 DFSSNELLVTCGKVVGTLYKEKLNQGIHVKSIQsTEGKWFTPLEFEIEGGYEKCKNWRQSIRCSGWPLKELIKRGEL 548
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQ-NEDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
578-619 2.57e-21

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: 87.10  E-value: 2.57e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 578 ACKVCGQRRRVRPCATCRKCYHKNCHIPPVEVQSGPWHCAFC 619
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
23-119 1.07e-45

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: 460835  Cd Length: 99  Bit Score: 158.08  E-value: 1.07e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196  23 ELIFQHFKRQKVAISNAIKNPFPFLEGLRDHELITAKMYEDLQDSYRALVRVQEVIYRALDKLEKIFSMKVLYEVFSNVN 102
Cdd:pfam03172   3 EALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDVN 82
                          90
                  ....*....|....*..
gi 1958803196 103 MEKYPDLQLIYQSFERV 119
Cdd:pfam03172  83 LKEYPDLIEILKSFPNV 99
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
646-746 1.82e-44

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: 154.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 646 PEEQLKCELLLLTIYCCPKSGFFIRKPKKRKEDFPDLQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYK-SR 724
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKdDD 80
                          90       100
                  ....*....|....*....|..
gi 1958803196 725 FKNLGVIVGNKFEKTFKSVFSI 746
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
472-548 2.81e-32

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: 460167  Cd Length: 76  Bit Score: 119.61  E-value: 2.81e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958803196 472 DFSSNELLVTCGKVVGTLYKEKLNQGIHVKSIQsTEGKWFTPLEFEIEGGYEKCKNWRQSIRCSGWPLKELIKRGEL 548
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQ-NEDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
477-549 1.16e-26

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 103.58  E-value: 1.16e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958803196  477 ELLVTCGKVVGTLYKEKLNQGIHVKSIQStEGKWFTPLEFEIEGGYEKCKNWRQSIRCSGWPLKELIKRGELQ 549
Cdd:smart00258   2 ELPVTCGTVKGILYKKKFKCGISVKCIQY-EDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTLD 73
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
578-619 2.57e-21

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: 87.10  E-value: 2.57e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 578 ACKVCGQRRRVRPCATCRKCYHKNCHIPPVEVQSGPWHCAFC 619
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
BROMO smart00297
bromo domain;
645-741 1.08e-13

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 67.69  E-value: 1.08e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196  645 SPEEQLKCELLLLTIYCC----PKSGFFIRKPKKRK-EDFPDL-QEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHS 718
Cdd:smart00297   1 DPKLQKKLQELLKAVLDKldshPLSWPFLKPVSRKEaPDYYDIiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                           90       100
                   ....*....|....*....|....*
gi 1958803196  719 KFYK--SRFKNLGVIVGNKFEKTFK 741
Cdd:smart00297  81 TYNGpdSEVYKDAKKLEKFFEKKLR 105
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
634-745 1.39e-06

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 51.34  E-value: 1.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 634 HKESEVLKRKMS-------PEEQLKCELL---LLTIYCCPKSGFFIRKPKKRkeDFPDL----QEHMWLNKIKHRLNKKA 699
Cdd:COG5076   125 HLKTSVKKRKTPkiedellYADNKAIAKFkkqLFLRDGRFLSSIFLGLPSKR--EYPDYyeiiKSPMDLLTIQKKLKNGR 202
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1958803196 700 YHSVQHFVGDMRLIFQNhskFYKSRFKNLGVIV-GNKFEKTFKSVFS 745
Cdd:COG5076   203 YKSFEEFVSDLNLMFDN---CKLYNGPDSSVYVdAKELEKYFLKLIE 246
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
668-725 8.11e-05

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 41.92  E-value: 8.11e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 668 FIRKPKKR-KEDFPDLQEH-MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYKSRF 725
Cdd:pfam00439  17 FLEPVDPDeYPDYYSVIKKpMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGS 76
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
579-619 1.53e-03

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 37.19  E-value: 1.53e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958803196  579 CKVCGQRRRVRP---CATCRKCYHKNCHIPP--VEVQSGPWHCAFC 619
Cdd:smart00249   2 CSVCGKPDDGGEllqCDGCDRWYHQTCLGPPllEEEPDGKWYCPKC 47
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
23-119 1.07e-45

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: 460835  Cd Length: 99  Bit Score: 158.08  E-value: 1.07e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196  23 ELIFQHFKRQKVAISNAIKNPFPFLEGLRDHELITAKMYEDLQDSYRALVRVQEVIYRALDKLEKIFSMKVLYEVFSNVN 102
Cdd:pfam03172   3 EALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDVN 82
                          90
                  ....*....|....*..
gi 1958803196 103 MEKYPDLQLIYQSFERV 119
Cdd:pfam03172  83 LKEYPDLIEILKSFPNV 99
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
646-746 1.82e-44

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: 154.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 646 PEEQLKCELLLLTIYCCPKSGFFIRKPKKRKEDFPDLQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYK-SR 724
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKdDD 80
                          90       100
                  ....*....|....*....|..
gi 1958803196 725 FKNLGVIVGNKFEKTFKSVFSI 746
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
472-548 2.81e-32

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: 460167  Cd Length: 76  Bit Score: 119.61  E-value: 2.81e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958803196 472 DFSSNELLVTCGKVVGTLYKEKLNQGIHVKSIQsTEGKWFTPLEFEIEGGYEKCKNWRQSIRCSGWPLKELIKRGEL 548
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQ-NEDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
477-549 1.16e-26

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 103.58  E-value: 1.16e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958803196  477 ELLVTCGKVVGTLYKEKLNQGIHVKSIQStEGKWFTPLEFEIEGGYEKCKNWRQSIRCSGWPLKELIKRGELQ 549
Cdd:smart00258   2 ELPVTCGTVKGILYKKKFKCGISVKCIQY-EDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTLD 73
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
578-619 2.57e-21

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: 87.10  E-value: 2.57e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 578 ACKVCGQRRRVRPCATCRKCYHKNCHIPPVEVQSGPWHCAFC 619
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
BROMO smart00297
bromo domain;
645-741 1.08e-13

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 67.69  E-value: 1.08e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196  645 SPEEQLKCELLLLTIYCC----PKSGFFIRKPKKRK-EDFPDL-QEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHS 718
Cdd:smart00297   1 DPKLQKKLQELLKAVLDKldshPLSWPFLKPVSRKEaPDYYDIiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80
                           90       100
                   ....*....|....*....|....*
gi 1958803196  719 KFYK--SRFKNLGVIVGNKFEKTFK 741
Cdd:smart00297  81 TYNGpdSEVYKDAKKLEKFFEKKLR 105
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
648-744 1.43e-10

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: 58.54  E-value: 1.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 648 EQLKCELLLLTIYCC--PKSGFFIRKPKKRkeDFPD----LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFY 721
Cdd:cd04369     1 LKKKLRSLLDALKKLkrDLSEPFLEPVDPK--EAPDyyevIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYN 78
                          90       100
                  ....*....|....*....|...
gi 1958803196 722 KSrfKNLGVIVGNKFEKTFKSVF 744
Cdd:cd04369    79 GP--GSPIYKDAKKLEKLFEKLL 99
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
644-722 2.37e-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 [Multi-domain]  Cd Length: 109  Bit Score: 55.37  E-value: 2.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 644 MSPEEQLKCELLLLTIYCCPKSGFFIRKPKKRKEDFPDLQEH-MWLNKIKHRLNKKA---YHSVQHFVGDMRLIFQNHSK 719
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPVSPSVPNYYKIIKTpMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYK 80

                  ...
gi 1958803196 720 FYK 722
Cdd:cd05502    81 FNE 83
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
579-619 4.95e-08

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


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 49.65  E-value: 4.95e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15541     2 CAVCQNGGELLCCDKCPRVFHLDCHIPPIpEFPSGEWSCSLC 43
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
579-619 1.77e-07

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: 47.88  E-value: 1.77e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALqEVPGEDWKCLLC 43
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
634-745 1.39e-06

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 51.34  E-value: 1.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 634 HKESEVLKRKMS-------PEEQLKCELL---LLTIYCCPKSGFFIRKPKKRkeDFPDL----QEHMWLNKIKHRLNKKA 699
Cdd:COG5076   125 HLKTSVKKRKTPkiedellYADNKAIAKFkkqLFLRDGRFLSSIFLGLPSKR--EYPDYyeiiKSPMDLLTIQKKLKNGR 202
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1958803196 700 YHSVQHFVGDMRLIFQNhskFYKSRFKNLGVIV-GNKFEKTFKSVFS 745
Cdd:COG5076   203 YKSFEEFVSDLNLMFDN---CKLYNGPDSSVYVdAKELEKYFLKLIE 246
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
676-741 1.51e-05

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


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 44.47  E-value: 1.51e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958803196 676 KEDFPDLQEH----MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQN-------HSKFYKSrfknlgvivGNKFEKTFK 741
Cdd:cd05509    28 KEEAPDYYDVikkpMDLSTMEEKLENGYYVTLEEFVADLKLIFDNcrlyngpDTEYYKC---------ANKLEKFFW 95
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
677-720 1.73e-05

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: 44.19  E-value: 1.73e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958803196 677 EDFPDLQEH-MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKF 720
Cdd:cd05498    36 HDYHDIIKHpMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKY 80
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
633-722 3.00e-05

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


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 43.86  E-value: 3.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 633 CHKESEVLKRKMSPEEQLKCELllltiyccpksgfFIRKPKKRKEdfPD----LQEHMWLNKIKHRLNKKAYHSVQHFVG 708
Cdd:cd05524     7 CQELYDTIRNYKSEDGRILCES-------------FIRVPKRRNE--PEyyevVSNPIDLLKIQQKLKTEEYDDVDDLTA 71
                          90
                  ....*....|....
gi 1958803196 709 DMRLIFQNHSKFYK 722
Cdd:cd05524    72 DFELLINNAKAYYK 85
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
665-720 4.04e-05

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


Pssm-ID: 99946  Cd Length: 105  Bit Score: 43.06  E-value: 4.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 665 SGFFIRKPKKrkEDFPD----LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKF 720
Cdd:cd05515    24 SLIFMRLPSK--SEYPDyydvIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKY 81
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
591-619 6.01e-05

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


Pssm-ID: 277002  Cd Length: 46  Bit Score: 40.82  E-value: 6.01e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1958803196 591 CATCRKCYHKNCHIPPVEVQ-SGPWHCAFC 619
Cdd:cd15527    17 CDACDKGFHMECHDPPLTRMpKGKWVCQIC 46
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
668-725 8.11e-05

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 41.92  E-value: 8.11e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 668 FIRKPKKR-KEDFPDLQEH-MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYKSRF 725
Cdd:pfam00439  17 FLEPVDPDeYPDYYSVIKKpMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGS 76
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
579-619 8.24e-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 [Multi-domain]  Cd Length: 48  Bit Score: 40.76  E-value: 8.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958803196 579 CKVCGQRRRVRP----CATCRKCYHKNCHIPPVE--VQSGPWHCAFC 619
Cdd:cd15489     2 CIVCGKGGDLGGellqCDGCGKWFHADCLGPPLSsfVPNGKWICPVC 48
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
579-619 1.31e-04

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


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 39.88  E-value: 1.31e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPVEVQ-SGPWHCAFC 619
Cdd:cd15524     2 CAACKRGGNLQPCGTCPRAYHLDCLDPPLKTApKGVWVCPKC 43
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
663-744 3.39e-04

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: 40.40  E-value: 3.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 663 PKSGFFIRKPKKRkeDFPD----LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNhSKFYKSRfknlGVIV---GNK 735
Cdd:cd05519    22 KLSELFLEKPSKK--LYPDyyviIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFAN-ARTYNQE----GSIVyedAVE 94

                  ....*....
gi 1958803196 736 FEKTFKSVF 744
Cdd:cd05519    95 MEKAFKKKY 103
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
652-722 6.78e-04

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: 40.07  E-value: 6.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958803196 652 CELLLLTIYCCPKSGFFIRkPKKRKE--DFPD-LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQN-------HSKFY 721
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLR-PVSKIEvpDYYDiIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNcflynpeHTSVY 95

                  .
gi 1958803196 722 K 722
Cdd:cd05504    96 K 96
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
676-723 8.09e-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 [Multi-domain]  Cd Length: 104  Bit Score: 39.53  E-value: 8.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958803196 676 KEDFPD----LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFYKS 723
Cdd:cd05522    34 KAREPEyyqeISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEN 85
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
578-619 9.01e-04

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.


Pssm-ID: 276976  Cd Length: 52  Bit Score: 37.71  E-value: 9.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958803196 578 ACKVCGQ-----RRRVRPCATCRKCYHKNCHIPPV--EVQSGP---WHCAFC 619
Cdd:cd15501     1 SCVVCKQmdvtsGNQLVECQECHNLYHQECHKPPVtdKDVNDPrlvWYCSRC 52
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
579-619 9.06e-04

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 37.43  E-value: 9.06e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15539     2 CAVCGDGGELLCCDGCPRAFHLACLVPPLtLIPSGTWRCSSC 43
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
579-619 9.53e-04

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 37.45  E-value: 9.53e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958803196 579 CKVCGQRRR---VRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15519     2 CEVCGLDDNegeVLLCDGCDAEYHTSCLDPPLgEIPPGTWFCPSC 46
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
579-619 1.02e-03

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: 37.35  E-value: 1.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15622     2 CAVCQNGGELLCCEKCPKVFHLSCHVPTLmNFPSGEWICTFC 43
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
579-619 1.18e-03

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: 37.48  E-value: 1.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958803196 579 CKVCGQRRRVRP-----CATCRKCYHKNCHIPPVEVQ----SGPWHCAFC 619
Cdd:cd15499     2 CSICGGAEARDGneiliCDKCDKGYHQLCHSPKVRTSplegDEKWFCSRC 51
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
579-620 1.24e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 37.33  E-value: 1.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPP-VEVQSGPWHCAFCK 620
Cdd:cd15624     2 CAVCQNGGDLLCCEKCPKVFHLTCHVPTlLSFPSGDWICTFCR 44
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
678-720 1.53e-03

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: 38.83  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958803196 678 DFPDL-QEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKF 720
Cdd:cd05500    38 HYPTIiKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTF 81
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
579-619 1.53e-03

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


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 37.19  E-value: 1.53e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958803196  579 CKVCGQRRRVRP---CATCRKCYHKNCHIPP--VEVQSGPWHCAFC 619
Cdd:smart00249   2 CSVCGKPDDGGEllqCDGCDRWYHQTCLGPPllEEEPDGKWYCPKC 47
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
666-716 1.87e-03

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


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 38.58  E-value: 1.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958803196 666 GFFIRKPKKRkeDFPD----LQEHMWLNKIKHRLNKKAYHSVQHFVGDMRLIFQN 716
Cdd:cd05518    25 DLFMEKPSKK--DYPDyykiILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRN 77
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
578-619 2.32e-03

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


Pssm-ID: 277076  Cd Length: 46  Bit Score: 36.47  E-value: 2.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1958803196 578 ACKVCGQ---RRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15603     1 VCLVCGSgndEDRLLLCDGCDDSYHTFCLIPPLhDVPKGDWRCPKC 46
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
670-721 2.48e-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: 37.90  E-value: 2.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958803196 670 RKPKKRKE--DFPDLQEH-MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFY 721
Cdd:cd05505    22 REPVTADEaeDYKKVITNpMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
579-619 2.81e-03

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


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 36.10  E-value: 2.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLaEIPDGDWFCPRC 43
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
578-619 3.49e-03

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


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 36.09  E-value: 3.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1958803196 578 ACKVCGQR---RRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15543     1 PCRKCGLSdhpEWILLCDRCDAGYHTACLRPPLmIIPDGNWFCPPC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
579-619 4.21e-03

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


Pssm-ID: 276988  Cd Length: 47  Bit Score: 35.91  E-value: 4.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958803196 579 CKVCGQRR---RVRPCATCRKCYHKNCHIPPVE-VQSGPWHCAFC 619
Cdd:cd15513     2 CEGCGKASdesRLLLCDDCDISYHTYCLDPPLQtVPKGGWKCKWC 46
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
579-619 5.03e-03

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


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 35.47  E-value: 5.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPVEVQSGP---WHCAFC 619
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEEDNLPddeWFCNEC 45
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
579-619 5.06e-03

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


Pssm-ID: 277066  Cd Length: 50  Bit Score: 35.68  E-value: 5.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958803196 579 CKVCGQRRRVRP----CATCRKCYHKNCHIP----PVEVQSGPWHCAFC 619
Cdd:cd15591     2 CHVCGRKNKESKplleCERCRNCYHPACLGPnypkPANRKKRPWICSAC 50
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
578-619 6.18e-03

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 35.06  E-value: 6.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958803196 578 ACKVCGQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15523     1 FCSVCRKSGELLMCDTCSLVYHLDCLDPPLkTIPKGMWICPKC 43
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
579-619 6.66e-03

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 35.08  E-value: 6.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPP-VEVQSGPWHCAFC 619
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPlEEVPEEDWQCEVC 43
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
578-619 7.77e-03

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


Pssm-ID: 277019  Cd Length: 46  Bit Score: 35.08  E-value: 7.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1958803196 578 ACKVC---GQRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15544     1 RCKVCrkkGDPDNMILCDGCDKAFHLYCLRPALrEVPSGDWFCPAC 46
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
579-619 8.19e-03

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 34.89  E-value: 8.19e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958803196 579 CKVCGQRRRVRPCATCRKCYHKNCHIPPVE-VQSGPWHCAFC 619
Cdd:cd15531     2 CEVCQQGGEIILCDTCPRAYHLVCLDPELEkAPEGKWSCPHC 43
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
579-619 8.60e-03

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


Pssm-ID: 277077  Cd Length: 46  Bit Score: 34.82  E-value: 8.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958803196 579 CKVCG---QRRRVRPCATCRKCYHKNCHIPPV-EVQSGPWHCAFC 619
Cdd:cd15604     2 CRMCSrgdEDDKLLLCDGCDDNYHTFCLLPPLpEPPKGIWRCPKC 46
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
668-721 9.70e-03

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 36.60  E-value: 9.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958803196 668 FIRKPKKRKEdfPDLQEH----MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKFY 721
Cdd:cd05525    29 FINLPSKKKN--PDYYERitdpVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
686-720 9.79e-03

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: 36.49  E-value: 9.79e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958803196 686 MWLNKIKHRLNKKAYHSVQHFVGDMRLIFQNHSKF 720
Cdd:cd05499    46 MDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTF 80
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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