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Conserved domains on  [gi|942180996|ref|XP_014348180|]
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PREDICTED: autoimmune regulator, partial [Latimeria chalumnae]

Protein Classification

HSR and PHD1_AIRE domain-containing protein (domain architecture ID 11141070)

protein containing domains HSR, SAND, and PHD1_AIRE

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 ...
8-108 7.55e-43

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


:

Pssm-ID: 397335  Cd Length: 99  Bit Score: 143.06  E-value: 7.55e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996    8 CDADFRQILKMNRTEISMAVDDTFPFLHGLLDHDVVTEEMFKETLNMK-EREGSHKAVYFLLTWLLKRDQsilQDFWKIS 86
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEAL 77
                          90       100
                  ....*....|....*....|..
gi 942180996   87 FKEYNLERYPKLKPVYNSFPKD 108
Cdd:pfam03172  78 FSDVNLKEYPDLIEILRSFPNV 99
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
289-327 1.18e-22

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


:

Pssm-ID: 277014  Cd Length: 43  Bit Score: 88.66  E-value: 1.18e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 289 ECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15539    1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWR 39
SAND super family cl02536
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
197-256 1.13e-20

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


The actual alignment was detected with superfamily member smart00258:

Pssm-ID: 413362  Cd Length: 73  Bit Score: 84.32  E-value: 1.13e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996   197 TDIPVSCGAVEGILIKQVFESGSSKKCIKVGGEFYAPGKFEDLGGKNKSRNLKTNIRMKG 256
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRCGG 60
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
8-108 7.55e-43

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


Pssm-ID: 397335  Cd Length: 99  Bit Score: 143.06  E-value: 7.55e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996    8 CDADFRQILKMNRTEISMAVDDTFPFLHGLLDHDVVTEEMFKETLNMK-EREGSHKAVYFLLTWLLKRDQsilQDFWKIS 86
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEAL 77
                          90       100
                  ....*....|....*....|..
gi 942180996   87 FKEYNLERYPKLKPVYNSFPKD 108
Cdd:pfam03172  78 FSDVNLKEYPDLIEILRSFPNV 99
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
289-327 1.18e-22

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


Pssm-ID: 277014  Cd Length: 43  Bit Score: 88.66  E-value: 1.18e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 289 ECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15539    1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWR 39
SAND smart00258
SAND domain;
197-256 1.13e-20

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 84.32  E-value: 1.13e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996   197 TDIPVSCGAVEGILIKQVFESGSSKKCIKVGGEFYAPGKFEDLGGKNKSRNLKTNIRMKG 256
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRCGG 60
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
199-256 6.14e-14

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


Pssm-ID: 396076  Cd Length: 75  Bit Score: 66.05  E-value: 6.14e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 942180996  199 IPVSCGAVEGILIKQVFESGSSKKCIKVGGEFYAPGKFEDLGGKNKSRNLKTNIRMKG 256
Cdd:pfam01342   6 LPVTCGEAKGILHKEKFKQGISGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGG 63
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
290-327 1.67e-10

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


Pssm-ID: 395503  Cd Length: 51  Bit Score: 55.57  E-value: 1.67e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 942180996  290 CTVCR---DGGELICCDGCPKAFHLNCLIPPLTA--IPSGTWR 327
Cdd:pfam00628   2 CSVCGksdDDGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWL 44
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
290-327 6.11e-09

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: 51.06  E-value: 6.11e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 942180996   290 CTVCR---DGGELICCDGCPKAFHLNCLIPPLT-AIPSGTWR 327
Cdd:smart00249   2 CSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWY 43
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
8-108 7.55e-43

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


Pssm-ID: 397335  Cd Length: 99  Bit Score: 143.06  E-value: 7.55e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996    8 CDADFRQILKMNRTEISMAVDDTFPFLHGLLDHDVVTEEMFKETLNMK-EREGSHKAVYFLLTWLLKRDQsilQDFWKIS 86
Cdd:pfam03172   1 LEEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACrNLVPVQRVVYNVLSELEKTFS---LSLLEAL 77
                          90       100
                  ....*....|....*....|..
gi 942180996   87 FKEYNLERYPKLKPVYNSFPKD 108
Cdd:pfam03172  78 FSDVNLKEYPDLIEILRSFPNV 99
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
289-327 1.18e-22

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


Pssm-ID: 277014  Cd Length: 43  Bit Score: 88.66  E-value: 1.18e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 289 ECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15539    1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWR 39
SAND smart00258
SAND domain;
197-256 1.13e-20

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 84.32  E-value: 1.13e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 942180996   197 TDIPVSCGAVEGILIKQVFESGSSKKCIKVGGEFYAPGKFEDLGGKNKSRNLKTNIRMKG 256
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRCGG 60
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
290-327 3.02e-17

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


Pssm-ID: 277007  Cd Length: 43  Bit Score: 73.85  E-value: 3.02e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15532    2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWF 39
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
289-327 2.81e-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  Cd Length: 43  Bit Score: 71.22  E-value: 2.81e-16
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 289 ECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15541    1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWS 39
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
199-256 6.14e-14

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


Pssm-ID: 396076  Cd Length: 75  Bit Score: 66.05  E-value: 6.14e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 942180996  199 IPVSCGAVEGILIKQVFESGSSKKCIKVGGEFYAPGKFEDLGGKNKSRNLKTNIRMKG 256
Cdd:pfam01342   6 LPVTCGEAKGILHKEKFKQGISGKCIQTEDSWLTPKEFEIEGGKAKSKDWKRSIRCGG 63
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
286-326 7.54e-14

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


Pssm-ID: 277095  Cd Length: 49  Bit Score: 64.98  E-value: 7.54e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 286 NDDECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15625    1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEW 41
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
290-326 8.05e-14

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


Pssm-ID: 277008  Cd Length: 45  Bit Score: 64.69  E-value: 8.05e-14
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTA--IPSGTW 326
Cdd:cd15533    2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLDEedLPPGEW 40
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
290-326 3.26e-13

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: 63.16  E-value: 3.26e-13
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15622    2 CAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEW 38
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
290-326 1.21e-12

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  Cd Length: 43  Bit Score: 61.26  E-value: 1.21e-12
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15523    2 CSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMW 38
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
290-326 1.50e-12

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


Pssm-ID: 277010  Cd Length: 45  Bit Score: 61.28  E-value: 1.50e-12
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLT--AIPSGTW 326
Cdd:cd15535    2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEedNLPDDEW 40
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
290-326 8.36e-12

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: 59.29  E-value: 8.36e-12
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15624    2 CAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDW 38
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
290-326 1.05e-11

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


Pssm-ID: 277006  Cd Length: 43  Bit Score: 58.77  E-value: 1.05e-11
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15531    2 CEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKW 38
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
290-326 1.10e-11

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  Cd Length: 46  Bit Score: 58.63  E-value: 1.10e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15519    2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTW 41
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
290-327 1.67e-10

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


Pssm-ID: 395503  Cd Length: 51  Bit Score: 55.57  E-value: 1.67e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 942180996  290 CTVCR---DGGELICCDGCPKAFHLNCLIPPLTA--IPSGTWR 327
Cdd:pfam00628   2 CSVCGksdDDGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWL 44
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
290-326 1.67e-10

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  Cd Length: 43  Bit Score: 55.28  E-value: 1.67e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15524    2 CAACKRGGNLQPCGTCPRAYHLDCLDPPLKTAPKGVW 38
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
290-326 3.31e-10

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: 54.69  E-value: 3.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15527    2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMPKGKW 41
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
290-326 5.23e-10

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


Pssm-ID: 277042  Cd Length: 41  Bit Score: 53.79  E-value: 5.23e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15567    2 CFICSEGGSLICCESCPASFHPECL--GLEPPPEGKF 36
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
289-326 6.85e-10

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


Pssm-ID: 277043  Cd Length: 43  Bit Score: 53.87  E-value: 6.85e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 289 ECTVCRDGGELICCD--GCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15568    1 ECFRCGDGGDLVLCDfkGCPKVYHLSCL--GLEKPPGGKW 38
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
289-327 9.40e-10

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.


Pssm-ID: 277096  Cd Length: 42  Bit Score: 53.20  E-value: 9.40e-10
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 289 ECTVCRDGGELICCDGCPKAFHLNCLIPPLTAiPSGTWR 327
Cdd:cd15626    1 KCEVCGQEGKLFCCCTCSRVFHEDCHIPPVEA-QRSPWS 38
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
290-327 1.07e-09

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C 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 is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), 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. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family 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 or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 53.17  E-value: 1.07e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15515    2 CQVCGRGDDedkLLLCDGCDDSYHTFCLIPPLPDIPPGDWR 42
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
290-326 1.17e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); 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. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097  Cd Length: 46  Bit Score: 53.17  E-value: 1.17e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15627    2 CRICRRKGDaekMLLCDGCDRGHHMYCLRPPLKKVPEGDW 41
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
290-326 1.51e-09

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: 52.80  E-value: 1.51e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCR---DGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15544    2 CKVCRkkgDPDNMILCDGCDKAFHLYCLRPALREVPSGDW 41
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
290-326 4.24e-09

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


Pssm-ID: 277034  Cd Length: 43  Bit Score: 51.65  E-value: 4.24e-09
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15559    2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDW 38
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
290-327 4.97e-09

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: 51.38  E-value: 4.97e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15604    2 CRMCSRGDEddkLLLCDGCDDNYHTFCLLPPLPEPPKGIWR 42
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
290-327 6.11e-09

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: 51.06  E-value: 6.11e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 942180996   290 CTVCR---DGGELICCDGCPKAFHLNCLIPPLT-AIPSGTWR 327
Cdd:smart00249   2 CSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWY 43
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
290-327 6.74e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 50.90  E-value: 6.74e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15628    2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPDGEWM 42
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
290-327 1.31e-08

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: 50.34  E-value: 1.31e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15603    2 CLVCGSGNDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWR 42
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
290-327 1.90e-08

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid 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 of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 49.76  E-value: 1.90e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVC-RDGGE--LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15605    2 CHTCgRGDGEesMLLCDGCDDSYHTFCLLPPLSEVPKGDWR 42
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
290-327 9.43e-08

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A 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: 277075  Cd Length: 49  Bit Score: 48.02  E-value: 9.43e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGG---ELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15602    2 CLFCGRGNnedKLLLCDGCDDSYHTFCLIPPLPDVPKGDWR 42
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
290-326 9.48e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020  Cd Length: 46  Bit Score: 47.69  E-value: 9.48e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDG---GELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15545    2 CQICRSGdneDQLLLCDGCDRGYHTYCFKPKMTNVPEGDW 41
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
290-326 1.68e-07

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  Cd Length: 46  Bit Score: 46.88  E-value: 1.68e-07
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                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCR--DGGELIC-CDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15543    2 CRKCGlsDHPEWILlCDRCDAGYHTACLRPPLMIIPDGNW 41
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
290-326 1.76e-07

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: 46.83  E-value: 1.76e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLippLTAIPSGTW 326
Cdd:cd15658    2 CFVCARGGRLLCCESCPASFHPECL---SIEMPEGCW 35
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
290-327 2.26e-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: 46.72  E-value: 2.26e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15623    2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGEDWK 39
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
290-327 2.60e-07

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 46.57  E-value: 2.60e-07
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                 ....*....|....*....|....*....|....*....|..
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIP-SGTWR 327
Cdd:cd15534    2 CFKCNRSCRvapLIQCDYCPLLFHLDCLDPPLTHPPaTGRWM 43
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
290-326 2.93e-07

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 46.50  E-value: 2.93e-07
                         10        20        30
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gi 942180996 290 CTVCRDGGELICCD--GCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15661    2 CFQCGDGGELVMCDkkDCPKAYHLLCL--NLTQPPYGKW 38
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
290-327 3.60e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966  Cd Length: 48  Bit Score: 46.16  E-value: 3.60e-07
                         10        20        30        40
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gi 942180996 290 CTVCRDGG----ELICCDGCPKAFHLNCLIPPL-TAIPSGTWR 327
Cdd:cd15489    2 CIVCGKGGdlggELLQCDGCGKWFHADCLGPPLsSFVPNGKWI 44
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
290-326 3.68e-07

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: 46.16  E-value: 3.68e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIpplTAIPSGTW 326
Cdd:cd15656    2 CFVCSEGGSLLCCESCPAAFHRECLN---IDMPEGSW 35
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
290-327 4.94e-07

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: 45.40  E-value: 4.94e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLipPLTAIPSGTWR 327
Cdd:cd15538    2 CWRCHKEGQVLCCSLCPRVYHKKCL--KLTSEPDEDWV 37
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
290-326 5.28e-07

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: 45.38  E-value: 5.28e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCLIpplTAIPSGTW 326
Cdd:cd15657    2 CFVCSKGGSLLCCESCPAAFHPDCLN---IEMPDGSW 35
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
289-326 7.72e-07

PHD finger 5 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 fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 45.32  E-value: 7.72e-07
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gi 942180996 289 ECTVCRDGGELICCD--GCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15659    1 ECFSCGDGGQLVSCKkpGCPKVYHADCL--NLTKRPAGKW 38
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
289-326 1.72e-06

PHD finger 5 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 fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 44.15  E-value: 1.72e-06
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gi 942180996 289 ECTVCRDGGELICCD--GCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15660    1 ECFRCGDGGQLVLCDrkSCTKAYHLSCL--GLTKRPFGKW 38
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
290-323 2.58e-06

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 43.90  E-value: 2.58e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIPS 323
Cdd:cd15525    2 CHVCggkQDPEKQLLCDECDMAYHLYCLDPPLTSLPD 38
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
290-327 4.49e-06

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: 43.23  E-value: 4.49e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15513    2 CEGCgkaSDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWK 42
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
290-327 4.52e-06

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 43.06  E-value: 4.52e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15595    2 CQTCRKPGEdskMLVCEACDKGYHTFCLKPAMESLPTDSWK 42
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
290-323 4.95e-06

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 43.07  E-value: 4.95e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVCRD---GGELICCDGCPKAFHLNCLIPPLTAIPS 323
Cdd:cd15497    2 CKVCKEwcaSDDSVRCDECKVSYHLLCVDPPLTKKPN 38
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
287-314 5.05e-06

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: 44.60  E-value: 5.05e-06
                         10        20
                 ....*....|....*....|....*...
gi 942180996 287 DDECTVCRDGGELICCDGCPKAFHLNCL 314
Cdd:cd11726   50 DEYCRWCGQGGDLICCDFCPNVFCKKCI 77
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
290-327 6.01e-06

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 42.81  E-value: 6.01e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15510    2 CQACRQPGDdtkMLVCETCDKGYHTSCLRPVMSSIPKYGWK 42
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
290-326 9.49e-06

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 42.15  E-value: 9.49e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15629    2 CLVCRKGDNdeyLLLCDGCDRGCHMYCHRPKMLQVPEGDW 41
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
290-326 9.81e-06

PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the third PHD finger.


Pssm-ID: 277041  Cd Length: 48  Bit Score: 42.03  E-value: 9.81e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 942180996 290 CTVCRDG-----GELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15566    2 CATCEASgdgssGKLVRCIRCPRAYHAGCIPAGSKLLNKKLI 43
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
288-325 1.04e-05

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 42.01  E-value: 1.04e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 942180996 288 DECTVCRDGGELICCDGCPKAFHLNCLIPPLTAIPSGT 325
Cdd:cd15562    3 GICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKT 40
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
290-323 1.15e-05

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 41.88  E-value: 1.15e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIPS 323
Cdd:cd15616    2 CHVCggkQDPDKQLMCDECDMAFHIYCLNPPLSSIPD 38
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
290-327 1.75e-05

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); 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. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 41.46  E-value: 1.75e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTWR 327
Cdd:cd15594    2 CQTCRQPGDdnkMLVCDTCDKGYHTFCLQPVMTTIPKNGWK 42
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
290-326 2.16e-05

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 41.25  E-value: 2.16e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVC--RDGGE-LICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15536    2 CEVCgrSDREDrLLLCDGCDAGYHMECLTPPLDEVPIEEW 41
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
290-326 7.33e-05

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 39.57  E-value: 7.33e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDGGE---LICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15630    3 CQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPEGDW 42
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
290-320 1.69e-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: 1.69e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 942180996 290 CTVC-----RDGGELICCDG-CPKAFHLNCLIPPLTA 320
Cdd:cd15504    2 CAKCqsgeaSPDNDILLCDGgCNRAYHQKCLEPPLLT 38
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
290-327 1.94e-04

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; 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). 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). Both NSD1 and NSD2 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). In addition, NSD2 harbors a high mobility group (HMG) box. 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 first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 38.22  E-value: 1.94e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 942180996 290 CTVCRDGGELICCDG-CPKAFHLNCLipPLTAIPSGTWR 327
Cdd:cd15648    2 CQVCEKPGELLLCEGqCCGAFHLDCI--GLSEMPSGKFI 38
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
290-326 2.06e-04

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 38.52  E-value: 2.06e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIPSGTW 326
Cdd:cd15530    2 CSLCgtsENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSW 41
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
290-314 2.14e-04

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: 38.09  E-value: 2.14e-04
                         10        20
                 ....*....|....*....|....*
gi 942180996 290 CTVCRDGGELICCDGCPKAFHLNCL 314
Cdd:cd15537    2 CFECHAPGEVLPCSGCFRVYHSDCL 26
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
290-322 2.33e-04

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 38.40  E-value: 2.33e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 942180996 290 CTVC---RDGGELICCDGCPKAFHLNCLIPPLTAIP 322
Cdd:cd15617    2 CYVCggkQDAHMQLLCDECNMAYHIYCLNPPLDKIP 37
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
290-322 5.69e-04

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: 5.69e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 942180996 290 CTVC-----RDGGELICCDGCPKAFHLNCLIPPLTAIP 322
Cdd:cd15499    2 CSICggaeaRDGNEILICDKCDKGYHQLCHSPKVRTSP 39
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
289-325 1.13e-03

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 36.22  E-value: 1.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 289 ECTVCR---DGGELICCDGCPKAFHLNCLIPPLTAIPSGT 325
Cdd:cd15563    1 ECCVCKqtgDNSQLVRCDECKLCYHFGCLDPPLKKSPKQR 40
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
290-326 1.87e-03

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 35.87  E-value: 1.87e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 942180996 290 CTVCRDG-----GELICCDGCPKAFHLNCLIPPLT----AIPSGTW 326
Cdd:cd15502    2 CIVCQRGhspksNRIVFCDGCNTPYHQLCHDPSIDdevvEDPDAEW 47
PHD2_AIRE cd15540
PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
289-319 2.40e-03

PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the second PHD finger that may play a critical role in the activation of gene transcription.


Pssm-ID: 277015  Cd Length: 42  Bit Score: 35.26  E-value: 2.40e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 942180996 289 ECTVCRDG-GELICCDGCPKAFHLNCLIPPLT 319
Cdd:cd15540    1 RCGVCRGGrGDLLRCPQCLQAFHWHCHFPSGS 32
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
290-314 2.93e-03

PHD finger 1 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 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 first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 35.00  E-value: 2.93e-03
                         10        20
                 ....*....|....*....|....*.
gi 942180996 290 CTVCRDGGELICCDG-CPKAFHLNCL 314
Cdd:cd15564    2 CQICEKPGKLLTCEGpCCGHFHLDCL 27
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
290-326 4.63e-03

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 34.59  E-value: 4.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 942180996 290 CTVCRDGG---ELICCDGCPKAFHLNCLipPLTAIPSGTW 326
Cdd:cd15529    2 CTKCGDPHdedKMMFCDQCDRGYHTFCV--GLRSIPDGRW 39
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
290-318 5.25e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 34.68  E-value: 5.25e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 942180996 290 CTVCRDG-----GELICCDGCPKAFHLNCLIPPL 318
Cdd:cd15578    2 CTVCQDGssespNEIVLCDKCGQGYHQLCHNPKI 35
ADDz_Dnmt3 cd11725
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de ...
290-314 6.63e-03

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


Pssm-ID: 277251 [Multi-domain]  Cd Length: 108  Bit Score: 35.83  E-value: 6.63e-03
                         10        20
                 ....*....|....*....|....*..
gi 942180996 290 CTVCRDGGELICCD--GCPKAFHLNCL 314
Cdd:cd11725   50 CTICGGGGEVVLCDnpDCTRVYCTECL 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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