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Conserved domains on  [gi|1370477523|ref|XP_024308618|]
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sp110 nuclear body protein isoform X5 [Homo sapiens]

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 ...
14-112 3.60e-58

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: 189.67  E-value: 3.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523  14 MEEALFQHFMHQKLGIAYAIHKPFPFFEGLLDNSIITKRMYMESLEACRNLIPVSRVVHNILTQLERTFNLSLLVTLFSQ 93
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1370477523  94 INLREYPNLVTIYRSFKRV 112
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
414-488 2.04e-33

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: 121.92  E-value: 2.04e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370477523 414 DFHCSKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDgTWLTPNEFEVEGKGRNAKNWKRNIRCEGMTLGELLKRK 488
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNED-SWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKG 74
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
492-533 7.65e-23

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: 91.33  E-value: 7.65e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 492 ECEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRMLWSCTFC 533
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
Bromodomain super family cl02556
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
524-586 3.67e-11

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: 60.13  E-value: 3.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523 524 KRMLWSCTFCRMKRSSGSQQCHHVSKTLERQMQPQD---------------------------------------QLASD 564
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGikepmwlnkvkerlnervyhtvegfvrdmrlifhnhklfYKDDD 80
                          90       100
                  ....*....|....*....|..
gi 1370477523 565 FGQVGLDLEAEFEKDLKDVLGF 586
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
14-112 3.60e-58

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: 189.67  E-value: 3.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523  14 MEEALFQHFMHQKLGIAYAIHKPFPFFEGLLDNSIITKRMYMESLEACRNLIPVSRVVHNILTQLERTFNLSLLVTLFSQ 93
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1370477523  94 INLREYPNLVTIYRSFKRV 112
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
414-488 2.04e-33

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: 121.92  E-value: 2.04e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370477523 414 DFHCSKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDgTWLTPNEFEVEGKGRNAKNWKRNIRCEGMTLGELLKRK 488
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNED-SWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKG 74
SAND smart00258
SAND domain;
418-488 8.89e-29

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 108.97  E-value: 8.89e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370477523  418 SKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDgTWLTPNEFEVEGKGRNAKNWKRNIRCEGMTLGELLKRK 488
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYED-KWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENG 70
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
492-533 7.65e-23

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: 91.33  E-value: 7.65e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 492 ECEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRMLWSCTFC 533
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
524-586 3.67e-11

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: 60.13  E-value: 3.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523 524 KRMLWSCTFCRMKRSSGSQQCHHVSKTLERQMQPQD---------------------------------------QLASD 564
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGikepmwlnkvkerlnervyhtvegfvrdmrlifhnhklfYKDDD 80
                          90       100
                  ....*....|....*....|..
gi 1370477523 565 FGQVGLDLEAEFEKDLKDVLGF 586
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
493-536 7.10e-08

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 49.03  E-value: 7.10e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370477523 493 CEVC---CQGGQLLCCGTCPRVFHEDCHIPPVEAKRML---WSCTFCRMK 536
Cdd:pfam00628   2 CAVCgksDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
493-533 1.09e-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: 45.67  E-value: 1.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1370477523  493 CEVC---CQGGQLLCCGTCPRVFHEDCHIPP--VEAKRMLWSCTFC 533
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 ...
14-112 3.60e-58

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: 189.67  E-value: 3.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523  14 MEEALFQHFMHQKLGIAYAIHKPFPFFEGLLDNSIITKRMYMESLEACRNLIPVSRVVHNILTQLERTFNLSLLVTLFSQ 93
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSD 80
                          90
                  ....*....|....*....
gi 1370477523  94 INLREYPNLVTIYRSFKRV 112
Cdd:pfam03172  81 VNLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
414-488 2.04e-33

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: 121.92  E-value: 2.04e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370477523 414 DFHCSKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDgTWLTPNEFEVEGKGRNAKNWKRNIRCEGMTLGELLKRK 488
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQNED-SWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKG 74
SAND smart00258
SAND domain;
418-488 8.89e-29

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 108.97  E-value: 8.89e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370477523  418 SKLPVTCGEAKGILYKKKMKHGSSVKCIRNEDgTWLTPNEFEVEGKGRNAKNWKRNIRCEGMTLGELLKRK 488
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYED-KWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENG 70
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
492-533 7.65e-23

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: 91.33  E-value: 7.65e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 492 ECEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRMLWSCTFC 533
Cdd:cd15626     1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEAQRSPWSCTFC 42
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
492-533 1.06e-16

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: 73.92  E-value: 1.06e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370477523 492 ECEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAK-RMLWSCTFC 533
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFpSGEWSCSLC 43
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
524-586 3.67e-11

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: 60.13  E-value: 3.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370477523 524 KRMLWSCTFCRMKRSSGSQQCHHVSKTLERQMQPQD---------------------------------------QLASD 564
Cdd:cd05501     1 PEELLKCEFLLLKVYCMSKSGFFISKPYYIRDYCQGikepmwlnkvkerlnervyhtvegfvrdmrlifhnhklfYKDDD 80
                          90       100
                  ....*....|....*....|..
gi 1370477523 565 FGQVGLDLEAEFEKDLKDVLGF 586
Cdd:cd05501    81 FGQVGITLEKKFEKNFKEVFAI 102
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
489-534 4.38e-11

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 58.05  E-value: 4.38e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370477523 489 NSDECEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRM-LWSCTFCR 534
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVgEWVCTLCR 47
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
492-533 1.50e-09

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 53.61  E-value: 1.50e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370477523 492 ECEVCCQGGQLLCCGTCPRVFHEDCHIPPV-EAKRMLWSCTFC 533
Cdd:cd15539     1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLtLIPSGTWRCSSC 43
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
493-533 3.45e-09

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: 52.76  E-value: 3.45e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVEA-KRMLWSCTFC 533
Cdd:cd15622     2 CAVCQNGGELLCCEKCPKVFHLSCHVPTLMNfPSGEWICTFC 43
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
493-534 3.45e-09

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: 52.74  E-value: 3.45e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVEA-KRMLWSCTFCR 534
Cdd:cd15624     2 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSfPSGDWICTFCR 44
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
493-533 9.09e-09

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


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 51.59  E-value: 9.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRML---WSCTFC 533
Cdd:cd15533     2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLDEEDLPpgeWLCHRC 45
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
493-533 3.11e-08

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: 49.97  E-value: 3.11e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPV-EAKRMLWSCTFC 533
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLaEIPDGDWFCPRC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
493-533 3.72e-08

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 49.52  E-value: 3.72e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVE-AKRMLWSCTFC 533
Cdd:cd15531     2 CEVCQQGGEIILCDTCPRAYHLVCLDPELEkAPEGKWSCPHC 43
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
493-536 7.10e-08

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 49.03  E-value: 7.10e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370477523 493 CEVC---CQGGQLLCCGTCPRVFHEDCHIPPVEAKRML---WSCTFCRMK 536
Cdd:pfam00628   2 CAVCgksDDGGELVQCDGCDDWFHLACLGPPLDPAEIPsgeWLCPECKPK 51
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
493-533 1.08e-07

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 48.16  E-value: 1.08e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPV-EAKRMLWSCTFC 533
Cdd:cd15523     2 CSVCRKSGELLMCDTCSLVYHLDCLDPPLkTIPKGMWICPKC 43
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
493-533 1.10e-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: 48.26  E-value: 1.10e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPV-EAKRMLWSCTFC 533
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALqEVPGEDWKCLLC 43
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
493-516 2.91e-07

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 46.86  E-value: 2.91e-07
                          10        20
                  ....*....|....*....|....
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDC 516
Cdd:cd15567     2 CFICSEGGSLICCESCPASFHPEC 25
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
475-534 3.23e-07

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: 48.84  E-value: 3.23e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370477523 475 RCEgMTLGELLKRKNSD----ECEVCCQGGQLLCCGTCPRVFHEDC---HIPPVEAKRML----WSCTFCR 534
Cdd:cd11726    32 SCL-KFYNSGEFSKDEDgsdeYCRWCGQGGDLICCDFCPNVFCKKCikrNLGRAELSRIEesdkWKCFVCD 101
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
493-533 6.37e-07

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: 46.26  E-value: 6.37e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVEAKRML---WSCTFC 533
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEEDNLPddeWFCNEC 45
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
493-533 1.09e-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: 45.67  E-value: 1.09e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1370477523  493 CEVC---CQGGQLLCCGTCPRVFHEDCHIPP--VEAKRMLWSCTFC 533
Cdd:smart00249   2 CSVCgkpDDGGELLQCDGCDRWYHQTCLGPPllEEEPDGKWYCPKC 47
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
493-533 2.53e-06

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


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 44.50  E-value: 2.53e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPPVE-AKRMLWSCTFC 533
Cdd:cd15524     2 CAACKRGGNLQPCGTCPRAYHLDCLDPPLKtAPKGVWVCPKC 43
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
493-533 2.73e-06

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 44.33  E-value: 2.73e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHIPP-VEAKRMLWSCTFC 533
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPlEEVPEEDWQCEVC 43
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
493-533 4.86e-06

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: 43.75  E-value: 4.86e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHipPVEAKRMLWSCTFC 533
Cdd:cd15658     2 CFVCARGGRLLCCESCPASFHPECL--SIEMPEGCWNCNEC 40
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
493-533 1.25e-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: 42.69  E-value: 1.25e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1370477523 493 CEVCCQGGQ----LLCCGTCPRVFHEDCHIPPVE--AKRMLWSCTFC 533
Cdd:cd15489     2 CIVCGKGGDlggeLLQCDGCGKWFHADCLGPPLSsfVPNGKWICPVC 48
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
493-534 1.50e-05

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: 42.30  E-value: 1.50e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDCHipPVEAKRMLWSCTFCR 534
Cdd:cd15657     2 CFVCSKGGSLLCCESCPAAFHPDCL--NIEMPDGSWFCNDCR 41
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
493-533 5.05e-05

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: 40.79  E-value: 5.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDC----HIPPVEAKrmlWSCTFC 533
Cdd:cd15537     2 CFECHAPGEVLPCSGCFRVYHSDClsedFRPDSTSH---WTCPVC 43
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
493-516 1.72e-04

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 39.23  E-value: 1.72e-04
                          10        20
                  ....*....|....*....|....
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDC 516
Cdd:cd15656     2 CFVCSEGGSLLCCESCPAAFHREC 25
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
495-533 2.58e-04

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 38.96  E-value: 2.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370477523 495 VCCQGGQ-------LLCCGTCPRVFHEDCHIPPVEAKRML-----WSCTFC 533
Cdd:cd15504     3 AKCQSGEaspdndiLLCDGGCNRAYHQKCLEPPLLTEDIPpedegWLCPLC 53
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
493-533 5.24e-04

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


Pssm-ID: 277002  Cd Length: 46  Bit Score: 38.13  E-value: 5.24e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370477523 493 CEVCCQGGQ---LLCCGTCPRVFHEDCHIPPVEAKRML-WSCTFC 533
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMPKGkWVCQIC 46
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
493-533 6.07e-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: 38.09  E-value: 6.07e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1370477523 493 CEVCCQ-----GGQLLCCGTCPRVFHEDCHIPPVEAK-----RMLWSCTFC 533
Cdd:cd15501     2 CVVCKQmdvtsGNQLVECQECHNLYHQECHKPPVTDKdvndpRLVWYCSRC 52
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
493-533 6.19e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 37.69  E-value: 6.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370477523 493 CEVCCQGGQLLCCGTCPRVFHEDChippVEAKRML---WSCTFC 533
Cdd:cd15538     2 CWRCHKEGQVLCCSLCPRVYHKKC----LKLTSEPdedWVCPEC 41
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
492-533 6.75e-04

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 37.67  E-value: 6.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370477523 492 ECEVCCQGG---QLLCCGTCPRVFHEDCHIPPVEA---KRMLWSCTFC 533
Cdd:cd15509     1 NCAVCDSPGdlsDLLFCTSCGQHYHGSCLDPAVRPtplVRAGWQCPEC 48
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
493-533 1.13e-03

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 37.06  E-value: 1.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370477523 493 CEVCCQG---GQLLCCGTCPRVFHEDCHIPPV-EAKRMLWSCTFC 533
Cdd:cd15519     2 CEVCGLDdneGEVLLCDGCDAEYHTSCLDPPLgEIPPGTWFCPSC 46
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
492-516 5.17e-03

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 35.00  E-value: 5.17e-03
                          10        20
                  ....*....|....*....|....*..
gi 1370477523 492 ECEVCCQGGQLLCC--GTCPRVFHEDC 516
Cdd:cd15568     1 ECFRCGDGGDLVLCdfKGCPKVYHLSC 27
ADDz cd11672
ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is ...
493-533 5.68e-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: 36.77  E-value: 5.68e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1370477523 493 CEVCCQGGQLLCCGT--CPRVFHEDC---HIPPVEAKRML----WSCTFC 533
Cdd:cd11672    48 CRICCEGGNLLCCGNnfCHRCFCKECvdrLVGPGELSTMDennqWYCYIC 97
 
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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