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Conserved domains on  [gi|1034673826|ref|XP_016884850|]
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histone lysine demethylase PHF8 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
JHD pfam17811
Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain ...
338-441 7.11e-62

Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain pfam02373.


:

Pssm-ID: 436061  Cd Length: 104  Bit Score: 205.29  E-value: 7.11e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  338 LNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHE 417
Cdd:pfam17811    1 LNIEMQLRAYEIEKRLKTPDLFKFPNFETICWYVAKHLLETLRELREEGRRPAEYLVRGVKALLVALKSWTRKEALTEHE 80
                           90       100
                   ....*....|....*....|....
gi 1034673826  418 DEIPETVRTVQLIKDLAREIRLVE 441
Cdd:pfam17811   81 DEIPETIKPVQLIKDLSKEIRHVE 104
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
6-57 1.62e-33

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.


:

Pssm-ID: 277112  Cd Length: 52  Bit Score: 122.82  E-value: 1.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1034673826    6 VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLH 57
Cdd:cd15642      1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVTH 52
cupin_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
234-334 1.97e-15

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


The actual alignment was detected with superfamily member pfam02373:

Pssm-ID: 454753  Cd Length: 114  Bit Score: 73.10  E-value: 1.97e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  234 YCLMSVRDSYTDFHIDFGGT-SVWYHVLKGEKIFYLIrPTNANLTLFECWSSSSNQN----EMFFGDQVD---------K 299
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLySINYLHFGAPKVWYII-PPEYAEKFEKVLSDHFGGEqpddLLHLNTIISpkqlrengiP 79
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1034673826  300 CYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNF 334
Cdd:pfam02373   80 VYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
199-262 2.60e-12

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


:

Pssm-ID: 214721  Cd Length: 58  Bit Score: 62.65  E-value: 2.60e-12
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034673826   199 RLSNLVETPKivrKLSWVENLWPEecvFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKG 262
Cdd:smart00558    1 QLWNLAKLPF---KLNLLSDLPED---IPGPDVGPYLYMGMAGSTTPWHIDDYDLVNYLHQGAG 58
 
Name Accession Description Interval E-value
JHD pfam17811
Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain ...
338-441 7.11e-62

Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain pfam02373.


Pssm-ID: 436061  Cd Length: 104  Bit Score: 205.29  E-value: 7.11e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  338 LNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHE 417
Cdd:pfam17811    1 LNIEMQLRAYEIEKRLKTPDLFKFPNFETICWYVAKHLLETLRELREEGRRPAEYLVRGVKALLVALKSWTRKEALTEHE 80
                           90       100
                   ....*....|....*....|....
gi 1034673826  418 DEIPETVRTVQLIKDLAREIRLVE 441
Cdd:pfam17811   81 DEIPETIKPVQLIKDLSKEIRHVE 104
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
6-57 1.62e-33

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.


Pssm-ID: 277112  Cd Length: 52  Bit Score: 122.82  E-value: 1.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1034673826    6 VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLH 57
Cdd:cd15642      1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVTH 52
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
234-334 1.97e-15

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 73.10  E-value: 1.97e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  234 YCLMSVRDSYTDFHIDFGGT-SVWYHVLKGEKIFYLIrPTNANLTLFECWSSSSNQN----EMFFGDQVD---------K 299
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLySINYLHFGAPKVWYII-PPEYAEKFEKVLSDHFGGEqpddLLHLNTIISpkqlrengiP 79
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1034673826  300 CYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNF 334
Cdd:pfam02373   80 VYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
199-262 2.60e-12

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 62.65  E-value: 2.60e-12
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034673826   199 RLSNLVETPKivrKLSWVENLWPEecvFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKG 262
Cdd:smart00558    1 QLWNLAKLPF---KLNLLSDLPED---IPGPDVGPYLYMGMAGSTTPWHIDDYDLVNYLHQGAG 58
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
7-53 4.57e-11

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: 58.76  E-value: 4.57e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1034673826     7 YC-LCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:smart00249    1 YCsVCGKPDD-GGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
7-53 7.22e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 46.72  E-value: 7.22e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1034673826    7 YC-LCRLPyDVTRFMIECDMCQDWFHGSCVGVEEEKAADID-LYHCPNC 53
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPEC 48
 
Name Accession Description Interval E-value
JHD pfam17811
Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain ...
338-441 7.11e-62

Jumonji helical domain; This 4-helix bundle domain is associated with the Jumonji domain pfam02373.


Pssm-ID: 436061  Cd Length: 104  Bit Score: 205.29  E-value: 7.11e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  338 LNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHE 417
Cdd:pfam17811    1 LNIEMQLRAYEIEKRLKTPDLFKFPNFETICWYVAKHLLETLRELREEGRRPAEYLVRGVKALLVALKSWTRKEALTEHE 80
                           90       100
                   ....*....|....*....|....
gi 1034673826  418 DEIPETVRTVQLIKDLAREIRLVE 441
Cdd:pfam17811   81 DEIPETIKPVQLIKDLSKEIRHVE 104
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
6-57 1.62e-33

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.


Pssm-ID: 277112  Cd Length: 52  Bit Score: 122.82  E-value: 1.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1034673826    6 VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLH 57
Cdd:cd15642      1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVTH 52
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
7-53 4.29e-33

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 121.34  E-value: 4.29e-33
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15554      1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
7-56 2.31e-31

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 116.63  E-value: 2.31e-31
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVL 56
Cdd:cd15640      1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCEVL 50
PHD_PHF2 cd15641
PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger ...
7-54 6.12e-28

PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. It contains a plant homeodomain (PHD) finger and a JmjC domain and plays an important role in adipogenesis. The PHD finger domain can recognize trimethylated histone H3 lysine 4 (H3K4me3). PHF2 also has dimethylated histone H3 lysine 9(H3K9me2) demethylase activity and acts as a coactivator of several metabolism-related transcription factors. Moreover, it can demethylate ARID5B and further forms a complex with demethylated ARD5B to bind the promoter regions of target genes. The overexpression of PHF2 is involved in the progression of esophageal squamous cell carcinoma (ESCC).


Pssm-ID: 277111  Cd Length: 50  Bit Score: 106.64  E-value: 6.12e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCE 54
Cdd:cd15641      1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCE 48
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
7-53 2.40e-24

PHD finger 2 and 3 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 second and third PHD fingers.


Pssm-ID: 277035  Cd Length: 47  Bit Score: 96.26  E-value: 2.40e-24
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15560      1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
7-53 2.19e-17

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 76.67  E-value: 2.19e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1034673826    7 YCLCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEK----AADIDLYHCPNC 53
Cdd:cd15552      1 YCICRKPHN-NRFMICCDRCEEWFHGDCVGITEAQgkemEENIEEYVCPKC 50
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
7-53 8.48e-17

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 74.72  E-value: 8.48e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YCLCRLPyDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15553      1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
234-334 1.97e-15

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalyzing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 73.10  E-value: 1.97e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  234 YCLMSVRDSYTDFHIDFGGT-SVWYHVLKGEKIFYLIrPTNANLTLFECWSSSSNQN----EMFFGDQVD---------K 299
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLySINYLHFGAPKVWYII-PPEYAEKFEKVLSDHFGGEqpddLLHLNTIISpkqlrengiP 79
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1034673826  300 CYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNF 334
Cdd:pfam02373   80 VYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
6-53 1.00e-12

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.


Pssm-ID: 277109  Cd Length: 54  Bit Score: 63.45  E-value: 1.00e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1034673826    6 VYCLCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADIDL----YHCPNC 53
Cdd:cd15639      4 LYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLERngedYICPNC 54
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
199-262 2.60e-12

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 62.65  E-value: 2.60e-12
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034673826   199 RLSNLVETPKivrKLSWVENLWPEecvFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKG 262
Cdd:smart00558    1 QLWNLAKLPF---KLNLLSDLPED---IPGPDVGPYLYMGMAGSTTPWHIDDYDLVNYLHQGAG 58
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
7-53 4.25e-12

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 61.56  E-value: 4.25e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1034673826    7 YC-LCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15489      1 SCiVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
10-53 1.09e-11

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. 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 interaction 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. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 60.64  E-value: 1.09e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1034673826   10 CRLP-YDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15517      5 CNLEtAAVDELWVQCDGCDKWFHQFCLGLSNERYADEDKFKCPNC 49
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
7-53 2.57e-11

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 59.41  E-value: 2.57e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YCLCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd16039      1 YCICQKPDD-GRWMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
7-53 2.61e-11

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. 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 includes the second PHD finger of Lid2p.


Pssm-ID: 276993  Cd Length: 45  Bit Score: 59.28  E-value: 2.61e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YCLCRLPYDVTrfMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15518      1 YCFCRQGEGGT--MIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
7-53 4.57e-11

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: 58.76  E-value: 4.57e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1034673826     7 YC-LCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:smart00249    1 YCsVCGKPDD-GGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
7-53 4.30e-09

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 53.06  E-value: 4.30e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1034673826    7 YC-LCRLPYDVtRFMIECDMCQDWFHGSCVGVEEEkAADIDLYHCPNC 53
Cdd:cd15522      1 ICpICKKPDDG-SPMIGCDECDDWYHWECVGITDE-PPEEDDWFCPKC 46
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
10-53 1.86e-08

PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed nuclear proteins existing only in plants. They are involved in chromatin regulation by binding to tri- and dimethylated histone H3 at lysine 4 (H3K4me3/2), the active histone markers, through their plant homeodomain (PHD) fingers.


Pssm-ID: 277085  Cd Length: 51  Bit Score: 51.34  E-value: 1.86e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1034673826   10 CRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15613      5 CGGNYTADEFWICCDVCEKWYHGKCVKITPAKAEHIKQYKCPSC 48
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
7-36 1.95e-08

PHD finger 2 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 second PHD finger.


Pssm-ID: 277079  Cd Length: 56  Bit Score: 51.28  E-value: 1.95e-08
                           10        20        30
                   ....*....|....*....|....*....|
gi 1034673826    7 YCLCRLPydVTRFMIECDMCQDWFHGSCVG 36
Cdd:cd15606      1 YCICRKP--FSGFMLQCELCKDWFHSSCVP 28
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
7-53 3.95e-08

PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear.


Pssm-ID: 277017  Cd Length: 54  Bit Score: 50.44  E-value: 3.95e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034673826    7 YCLCRLPY-----DVTRFMIECDMCQDWFHGSCVGV------EEEKAADIdlyhCPNC 53
Cdd:cd15542      1 YCTCDRPYpdpedEVEDEMIQCVLCEDWFHGRHLGLtppepdPDEFDEMI----CSGC 54
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
9-53 5.60e-08

PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain.


Pssm-ID: 277108  Cd Length: 51  Bit Score: 49.92  E-value: 5.60e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1034673826    9 LCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADIDL----YHCPNC 53
Cdd:cd15638      4 FCKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEedkeYVCVKC 51
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
23-53 6.42e-08

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or 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 the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), 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. 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 asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that 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. 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 three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 49.63  E-value: 6.42e-08
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1034673826   23 CDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15610     20 CDGCEEWFHLLCVGLSPEEVAEDEDYICPSC 50
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
8-53 6.87e-08

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 49.62  E-value: 6.87e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYDVtRFMIECDMCQDWFHGSCVGVEEEKAADIdlYHCPNC 53
Cdd:cd15550      2 CICGFEHDD-GFMICCDKCSVWQHGDCMGIDRENIPDS--YLCEQC 44
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
8-53 1.27e-07

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 48.91  E-value: 1.27e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADiDLYHCPNC 53
Cdd:cd15556      2 CSCGTRDDDGERMIACDVCEVWQHTRCVGIADNEEPP-DHFLCRRC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
7-53 7.22e-07

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 46.72  E-value: 7.22e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1034673826    7 YC-LCRLPyDVTRFMIECDMCQDWFHGSCVGVEEEKAADID-LYHCPNC 53
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPEC 48
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
7-37 1.23e-06

PHD finger 2 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 (H3K4me3 and H3K4me2), 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. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that 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. 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 second PHD finger.


Pssm-ID: 276991  Cd Length: 53  Bit Score: 46.15  E-value: 1.23e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1034673826    7 YCLCRlpYDVTRFMIECDMCQDWFHGSCVGV 37
Cdd:cd15516      1 ICLCG--KALAAGMLQCELCQDWFHGSCVAV 29
PHD_TCF19 cd15609
PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed ...
10-51 5.31e-06

PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed transcription factor SC1, was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It also functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. TCF-19 contains an N-terminal fork head association domain (FHA), a proline rich region, and a C-terminal plant homeodomain (PHD) finger. The FHA domain may serve as a nuclear signaling domain or as a phosphoprotein binding domain. The proline rich region is a common characteristic of trans-activating factors. The PHD finger may allow TCF-19 to interact with chromatin via methylated histone H3.


Pssm-ID: 277082  Cd Length: 50  Bit Score: 44.38  E-value: 5.31e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1034673826   10 CRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDL-YHCP 51
Cdd:cd15609      7 CCLPQDETVSWVQCDDCDQWYHVACVGCDYNAVKDPDAdFHCG 49
PHD_PHF20_like cd15549
PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 ...
8-53 1.83e-05

PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 (P20L1); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. Both PHF20 and PHF20L1 contain an N-terminal MBT domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277024  Cd Length: 45  Bit Score: 42.85  E-value: 1.83e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYDvTRFMIECDMCQDWFHGSCVGVEEEKAADiDLYHCPNC 53
Cdd:cd15549      2 CICGVNEE-NGLMIQCELCLCWQHGVCMGIEEEESVP-ERYVCYVC 45
PHD_PHF23 cd15631
PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein ...
8-53 2.23e-05

PHD finger found in PHD finger protein 23 (PHF23); PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a plant homeodomain (PHD) finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277101  Cd Length: 44  Bit Score: 42.60  E-value: 2.23e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYdVTRFMIECDMCQDWFHGSCVGVEEEKAADIdlYHCPNC 53
Cdd:cd15631      2 CYCGKPF-AGRPMIECSQCGTWIHLSCAKIKKSNVPDF--FYCQKC 44
PHD3_Lid2p_like cd15520
PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
8-53 2.71e-05

PHD finger 3 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. The family corresponds to the third PHD finger.


Pssm-ID: 276995  Cd Length: 47  Bit Score: 42.20  E-value: 2.71e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNC 53
Cdd:cd15520      2 CGCGEGFNIADRMIFCDRCERTVHLDCVGLSDRIVDSPSEFFCPEC 47
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
7-53 3.58e-05

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980  Cd Length: 45  Bit Score: 41.90  E-value: 3.58e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1034673826    7 YCLCRLPYDVTrfMIECD--MCQ-DWFHGSCVGVeeeKAADIDLYHCPNC 53
Cdd:cd15505      1 YCICNQVSYGE--MVACDnpNCPiEWFHFECVGL---TAKPKGKWYCPEC 45
PHD_PHF20 cd15634
PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen ...
8-53 4.79e-05

PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.


Pssm-ID: 277104  Cd Length: 44  Bit Score: 41.47  E-value: 4.79e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPyDVTRFMIECDMCQDWFHGSCVGVEEEKAAdiDLYHCPNC 53
Cdd:cd15634      2 CICEVQ-EENDFMIQCEECLCWQHGVCMGLLEDNVP--EKYTCYIC 44
PHD2_KDM5C_5D cd15608
PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
8-37 6.47e-05

PHD finger 2 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/ARIDdomain-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 and H3K4me2), 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 second PHD finger.


Pssm-ID: 277081  Cd Length: 58  Bit Score: 41.71  E-value: 6.47e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 1034673826    8 CLCRLPYDVTrfMIECDMCQDWFHGSCVGV 37
Cdd:cd15608      2 CVCGQPPRPG--MLRCHLCQDWFHGGCVSF 29
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
8-53 1.04e-04

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 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, 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 sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 40.73  E-value: 1.04e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1034673826    8 CLCRLPYDVTRFMIECDMCQDWFHGSCVGV--EE--EKAADIDlYHCPNC 53
Cdd:cd15514      3 PVCSRSYNEGELIIQCSQCERWLHGACDSLrtEEeaERAADNG-YRCLLC 51
PHD_PHF13_like cd15546
PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival ...
8-53 1.54e-04

PHD finger found in PHD finger proteins PHF13 and PHF23; PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a PHD finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML).


Pssm-ID: 277021  Cd Length: 44  Bit Score: 40.12  E-value: 1.54e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYdVTRFMIECDMCQDWFHGSCVGVEEEKAADIdlYHCPNC 53
Cdd:cd15546      2 CFCGKPF-AGRPMIECSECLTWIHLSCAKIRKNNVPEV--FICQKC 44
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
6-53 1.86e-04

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 40.02  E-value: 1.86e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1034673826    6 VYCLCRLPYdVTRFMIECDMCQDWFHGSCVGVEEEKAADIdlYHCPNC 53
Cdd:cd15632      2 VTCFCMKPF-AGRPMIECNECHTWIHLSCAKIRKSNVPEV--YVCQKC 46
PHD_ASH1L cd15548
PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like ...
6-53 1.91e-04

PHD finger found in histone-lysine N-methyltransferase ASH1L; ASH1L, also termed ASH1-like protein, or absent small and homeotic disks protein 1 homolog, or lysine N-methyltransferase 2H, is a protein belonging to the Trithorax family. It methylates Lys36 of histone H3 independently of transcriptional elongation to promote the establishment of Hox gene expression by counteracting Polycomb silencing. It can suppress interleukin-6 (IL-6), and tumor necrosis factor (TNF) production in Toll-like receptor (TLR)-triggered macrophages, and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. ASH1L contains an associated with SET domain (AWS), a SET domain, a post-SET domain, a bromodomain, a bromo-adjacent homology domain (BAH), and a plant homeodomain (PHD) finger.


Pssm-ID: 277023  Cd Length: 43  Bit Score: 39.76  E-value: 1.91e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1034673826    6 VYCLCRLpYDVTRFMIECDMCQDWFHGSCVGVEeekaADIDLYHCPNC 53
Cdd:cd15548      1 IRCICGL-YKDEGLMIQCEKCMVWQHCDCMGVN----DDVEHYLCEQC 43
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
7-53 5.57e-04

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 38.97  E-value: 5.57e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1034673826    7 YC-LCRLPYDVTRF---MIECDMCQDWFHGSCVGVEEEK------AADIDLYHCPNC 53
Cdd:cd15508      1 YCpLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGLSDEMyeilsyLPESIEYTCSLC 57
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
21-53 6.79e-04

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 38.55  E-value: 6.79e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1034673826   21 IECDMCQDWFHGSCVGVEEEkAADIDLYHCPNC 53
Cdd:cd15547     16 VQCLKCGLWQHAECVNYDEE-SDKREPYLCPHC 47
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
169-321 1.12e-03

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


Pssm-ID: 433355  Cd Length: 251  Bit Score: 41.97  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  169 KMKLGDFVKYYYSGKREKVLNVISLEFSDTR--LSNLVETPKIVrklswvenlWPEECvFERPNVQKYCLMSVRDSYTDF 246
Cdd:pfam13621   76 RMPFGEFLDRLEAGSDTDTAPYAYLQSDNLRseFPELLEDNDLP---------FATEA-FGGEPDAVNLWMGNGRSVTSL 145
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034673826  247 HIDfggtsvWYH----VLKGEKIFYLIRPT-NANLTLFECWSSSSNQN-----------EMF--FGDqVDKCYKCSVKQG 308
Cdd:pfam13621  146 HYD------HYEnlycVVRGRKRFTLFPPSdVPNLYPGPLEPTPEGQVfslvdplapdlERFprFRD-AARPLVVTLNPG 218
                          170
                   ....*....|...
gi 1034673826  309 QTLFIPTGWIHAV 321
Cdd:pfam13621  219 DVLYLPALWWHHV 231
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
21-53 1.62e-03

PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or 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 the pregnant female 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 third PHD finger.


Pssm-ID: 277157  Cd Length: 50  Bit Score: 37.23  E-value: 1.62e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1034673826   21 IECD-MCQDWFHGSCVGVEEEKAADIDlYHCPNC 53
Cdd:cd15687     18 VQCDgSCNRWFHQVCVGVSAEMAEKED-YICVSC 50
PHD2_MTF2 cd15580
PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
7-35 2.45e-03

PHD finger 2 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 plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. This model corresponds to the second PHD finger.


Pssm-ID: 277055  Cd Length: 52  Bit Score: 36.80  E-value: 2.45e-03
                           10        20
                   ....*....|....*....|....*....
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCV 35
Cdd:cd15580      1 YCYCGGPGDWYLKMLQCCKCKQWFHEACV 29
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
8-53 2.71e-03

PHD finger 2 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), retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), or PLU-1) 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 the pregnant female 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 second PHD finger.


Pssm-ID: 277080  Cd Length: 44  Bit Score: 36.74  E-value: 2.71e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1034673826    8 CLCRLPYDVTrfMIECDMCQDWFHGSCVGVEEEkAADIDLYHCPNC 53
Cdd:cd15607      2 CVCQKAPMAP--MIQCELCRDAFHSGCVTAPSD-PQGPQAWLCPQC 44
PHD2_MTF2_PHF19_like cd15503
PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
7-35 2.95e-03

PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The PCL family includes PHD finger protein1 (PHF1) and its homologs metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. PCL proteins 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 finger 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 second PHD finger.


Pssm-ID: 276978  Cd Length: 52  Bit Score: 36.61  E-value: 2.95e-03
                           10        20
                   ....*....|....*....|....*....
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCV 35
Cdd:cd15503      1 YCYCGGPGEWNLKMLQCCKCRQWFHEACL 29
PHD_OBE1_like cd15612
PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins ...
21-53 3.37e-03

PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins mainly found in plants; Included in this family are OBERON 1 (OBE1, or potyvirus VPg-interacting protein 2) and OBERON 2 (OBE2, or potyvirus VPg-interacting protein 1), which have been involved in the maintenance and/or establishment of the meristems in Arabidopsis. They interact with potyvirus VPg-interacting proteins (PVIP1 and 2) and act as central regulators in auxin-mediated control of development. Both OBE1and OBE2 contain a plant homeodomain (PHD) finger. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277084  Cd Length: 60  Bit Score: 36.83  E-value: 3.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1034673826   21 IECDMCQDWFHGSC----------VGVEEEKAADIDLYHCPNC 53
Cdd:cd15612     18 IGCDVCSHWTHTDCairsgeismgVSLKGVEGSTEMEFHCRAC 60
PHD3_KDM5A cd15686
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone ...
10-53 3.38e-03

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone demethylase JARID1A, or 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 third PHD finger.


Pssm-ID: 277156  Cd Length: 52  Bit Score: 36.59  E-value: 3.38e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1034673826   10 CRLPYDVTRFMIECDM-CQDWFHGSCVGVEEEKAADIDlYHCPNC 53
Cdd:cd15686      8 CQRPCKDKVDWVQCDGgCDEWFHQVCVGVSPEMAENED-YICINC 51
PHD_Yng1p_like cd15587
PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the ...
7-55 7.28e-03

PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger.


Pssm-ID: 277062  Cd Length: 47  Bit Score: 35.47  E-value: 7.28e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1034673826    7 YCLC-RLPYDVtrfMIECD--MCQ-DWFHGSCVGVEEEKAADidlYHCPNCEV 55
Cdd:cd15587      1 YCYCrRVSFGE---MVACDnpDCKiEWFHFECVGLTETPKGK---WYCSDCKV 47
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
7-53 8.23e-03

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060  Cd Length: 45  Bit Score: 35.12  E-value: 8.23e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1034673826    7 YCLCR-LPYDVtrfMIECD--MCQ-DWFHGSCVGVEEEKAADidlYHCPNC 53
Cdd:cd15585      1 YCICNqVSYGE---MVGCDndDCPiEWFHYGCVGLTEAPKGK---WYCPQC 45
PHD_ash2p_like cd15583
PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and ...
7-53 8.70e-03

PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins; spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity.


Pssm-ID: 277058  Cd Length: 50  Bit Score: 35.40  E-value: 8.70e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1034673826    7 YCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDL---YHCPNC 53
Cdd:cd15583      1 YCYCGKDRNLGEVELQCSICLKWFHAKCVSIDNGSCLPFMTnyqFVCKRC 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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