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Conserved domains on  [gi|1039753045|ref|XP_017172843|]
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lysine-specific demethylase 4B isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 795-904 4.21e-75

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.


The actual alignment was detected with superfamily member cd15714:

Pssm-ID: 473978  Cd Length: 110  Bit Score: 242.54  E-value: 4.21e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCST 874
Cdd:cd15714      1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKLKCVYCRKRMKKVSGACIQCSYDHCST 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039753045  875 SFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15714     81 SFHVTCAHAAGVVMEPDDWPYVVSITCFKH 110
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 176-292 2.27e-52

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 catalysing hydroxylation.


:

Pssm-ID: 396791  Cd Length: 114  Bit Score: 179.03  E-value: 2.27e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1039753045  256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 652-786 4.54e-49

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.


The actual alignment was detected with superfamily member cd15576:

Pssm-ID: 473978  Cd Length: 99  Bit Score: 168.93  E-value: 4.54e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  652 YCAICTLFYPYSQvsclsglptlmapTVTCPTQPQCSLAycgpalsavtlqsvqterdsavqPPSKSGQRTRPLIPEMCF 731
Cdd:cd15576      1 YCAICTLFYPYTQ-------------SLQDPKEISDMSG-----------------------LVSKVGQKTRPLIPEMCF 44

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  732 TSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15576     45 TAGGENTEPLPSNSYIGDDGTSVLLSCAKCCLQVHASCYGVNPDLVNEGWTCSRC 99
Tudor_JMJD2B_rpt1 cd20464
first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; ...
 917-970 3.63e-34

first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410535  Cd Length: 54  Bit Score: 124.54  E-value: 3.63e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCL 970
Cdd:cd20464      1 VSLGQVVITKNRNGLYYRCRVIGTATQTFYEVNFDDGSYSDNVYPESITSRDCL 54
Tudor_SF super family cl02573
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 974-1029 4.45e-30

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


The actual alignment was detected with superfamily member cd20467:

Pssm-ID: 470623  Cd Length: 56  Bit Score: 112.99  E-value: 4.45e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP 1029
Cdd:cd20467      1 PPSEGELVELRWTDGNIYKAKFISAHLSHIYQVEFEDGSQLTVKRGEIFTLEEELP 56
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 1.14e-13

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


:

Pssm-ID: 128818  Cd Length: 42  Bit Score: 66.13  E-value: 1.14e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1039753045    15 IMTFRPTMDEFRDFNRYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545    2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
 
Name Accession Description Interval E-value
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 795-904 4.21e-75

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 242.54  E-value: 4.21e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCST 874
Cdd:cd15714      1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKLKCVYCRKRMKKVSGACIQCSYDHCST 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039753045  875 SFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15714     81 SFHVTCAHAAGVVMEPDDWPYVVSITCFKH 110
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
793-904 8.28e-57

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 191.40  E-value: 8.28e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  793 AECCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHC 872
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKLKCVFCKKRS----GACIQCSKGRC 76

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1039753045  873 STSFHVTCAHAAGVLMEPDDWP-YVVSITCLKH 904
Cdd:pfam13832   77 TTAFHVTCAQAAGVYMEPEDWPnVVVIAYCQKH 109
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 176-292 2.27e-52

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 catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 179.03  E-value: 2.27e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1039753045  256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD_JMJD2B cd15576
PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed ...
 652-786 4.54e-49

PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277051  Cd Length: 99  Bit Score: 168.93  E-value: 4.54e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  652 YCAICTLFYPYSQvsclsglptlmapTVTCPTQPQCSLAycgpalsavtlqsvqterdsavqPPSKSGQRTRPLIPEMCF 731
Cdd:cd15576      1 YCAICTLFYPYTQ-------------SLQDPKEISDMSG-----------------------LVSKVGQKTRPLIPEMCF 44

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  732 TSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15576     45 TAGGENTEPLPSNSYIGDDGTSVLLSCAKCCLQVHASCYGVNPDLVNEGWTCSRC 99
Tudor_JMJD2B_rpt1 cd20464
first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; ...
 917-970 3.63e-34

first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410535  Cd Length: 54  Bit Score: 124.54  E-value: 3.63e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCL 970
Cdd:cd20464      1 VSLGQVVITKNRNGLYYRCRVIGTATQTFYEVNFDDGSYSDNVYPESITSRDCL 54
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
750-888 3.71e-31

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 131.26  E-value: 3.71e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  750 DGTSPLISCAHCCLQVHASCYGVrPELAKEGWTCSRCAAHAWTAECCL-CNLRGGALQRTTEHRWIHVICAIAVPEVRFL 828
Cdd:COG5141    205 ENSNAIVFCDGCEICVHQSCYGI-QFLPEGFWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPELSFG 283

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039753045  829 NVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHCSTSFHVTCAHAAGVLM 888
Cdd:COG5141    284 HLLSKDPIDnIASVSSSRWKLGCLICKEFG----GTCIQCSYFNCTRAYHVTCARRAGYFD 340
Tudor_JMJD2B_rpt2 cd20467
second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar ...
 974-1029 4.45e-30

second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410538  Cd Length: 56  Bit Score: 112.99  E-value: 4.45e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP 1029
Cdd:cd20467      1 PPSEGELVELRWTDGNIYKAKFISAHLSHIYQVEFEDGSQLTVKRGEIFTLEEELP 56
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 1.14e-13

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 66.13  E-value: 1.14e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1039753045    15 IMTFRPTMDEFRDFNRYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545    2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 752-786 1.88e-13

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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 65.05  E-value: 1.88e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  752 TSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 920-954 5.32e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 63.98  E-value: 5.32e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  920 GQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGS 954
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 978-1012 6.16e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 63.59  E-value: 6.16e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  978 GELVELRWTDGNLYRARFISMATSLIYQVEFEDGS 1012
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 149-206 6.55e-13

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: 64.20  E-value: 6.55e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039753045   149 WNIGNLRTILDMVeRECGTIIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 206
Cdd:smart00558    3 WNLAKLPFKLNLL-SDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN pfam02375
jmjN domain;
16-50 1.10e-11

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 60.00  E-value: 1.10e-11
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045   16 MTFRPTMDEFRDFNRYVAYIESQGAhRAGLAKIIP 50
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 919-969 1.08e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.97  E-value: 1.08e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1039753045   919 LGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDC 969
Cdd:smart00333    5 VGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPE 55
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 973-1028 3.29e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 53.82  E-value: 3.29e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039753045   973 GPPPEGELVELRWTDGNLYRARFISMATSLIYQVEFED-GSQLTVKRGDIFTLEEEL 1028
Cdd:smart00333    1 PTFKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDyGNEEVVPPSDLRQLPEEL 57
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 748-786 7.32e-05

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: 41.04  E-value: 7.32e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 1039753045   748 GEDGTSPLISCAHCCLQVHASCYGVRPELA--KEGWTCSRC 786
Cdd:smart00249    7 KPDDGGELLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 850-892 2.31e-04

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: 39.89  E-value: 2.31e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 1039753045   850 CIYCRKRMKrvSGACIQCsyEHCSTSFHVTCAHAAGVLMEPDD 892
Cdd:smart00249    2 CSVCGKPDD--GGELLQC--DGCDRWYHQTCLGPPLLEEEPDG 40
 
Name Accession Description Interval E-value
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 795-904 4.21e-75

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277184  Cd Length: 110  Bit Score: 242.54  E-value: 4.21e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCST 874
Cdd:cd15714      1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIPEQRWKLKCVYCRKRMKKVSGACIQCSYDHCST 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039753045  875 SFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15714     81 SFHVTCAHAAGVVMEPDDWPYVVSITCFKH 110
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 795-904 2.20e-68

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 224.16  E-value: 2.20e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMK--RVSGACIQCSYEHC 872
Cdd:cd15675      1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPARLKLKCIYCSKITKsmSHMGACIQCSTGKC 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1039753045  873 STSFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15675     81 TTSFHVTCAHAAGVQMEPDDWPYPVYVTCTKH 112
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 795-904 4.03e-65

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 214.82  E-value: 4.03e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCST 874
Cdd:cd15715      1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIPLQRLKLKCIFCRNRIKRVSGACIQCSYGRCPA 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039753045  875 SFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15715     81 SFHVTCAHAAGVLMEPDDWPYVVFITCFRH 110
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
793-904 8.28e-57

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 191.40  E-value: 8.28e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  793 AECCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHC 872
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIDVSRIPPERWKLKCVFCKKRS----GACIQCSKGRC 76

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1039753045  873 STSFHVTCAHAAGVLMEPDDWP-YVVSITCLKH 904
Cdd:pfam13832   77 TTAFHVTCAQAAGVYMEPEDWPnVVVIAYCQKH 109
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 795-904 9.15e-56

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 188.26  E-value: 9.15e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCST 874
Cdd:cd15713      1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSKIPLQRFKLKCIFCKKRRKRTAGCCVQCSHGRCPT 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1039753045  875 SFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15713     81 SFHASCAQAAGVMMQPDDWPFVVFITCFRH 110
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 176-292 2.27e-52

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 catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 179.03  E-value: 2.27e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1039753045  256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
PHD_JMJD2B cd15576
PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed ...
 652-786 4.54e-49

PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277051  Cd Length: 99  Bit Score: 168.93  E-value: 4.54e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  652 YCAICTLFYPYSQvsclsglptlmapTVTCPTQPQCSLAycgpalsavtlqsvqterdsavqPPSKSGQRTRPLIPEMCF 731
Cdd:cd15576      1 YCAICTLFYPYTQ-------------SLQDPKEISDMSG-----------------------LVSKVGQKTRPLIPEMCF 44

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  732 TSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15576     45 TAGGENTEPLPSNSYIGDDGTSVLLSCAKCCLQVHASCYGVNPDLVNEGWTCSRC 99
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 795-889 2.24e-34

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 127.45  E-value: 2.24e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHCS 873
Cdd:cd15670      1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDgIQNIPKARWKLTCYICKKRM----GACIQCHKKNCY 76

                           90
                   ....*....|....*.
gi 1039753045  874 TSFHVTCAHAAGVLME 889
Cdd:cd15670     77 TAFHVTCAQQAGLYMK 92
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 795-904 2.55e-34

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has 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.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 127.32  E-value: 2.55e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGAL------QRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRmkrvSGACIQCS 868
Cdd:cd15571      1 CALCPRSGGALkgggalKTTSDGLWVHVVCALWSPEVYFDDGTLLEVEGVSKIPKRRKKLKCSICGKR----GGACIQCS 76

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1039753045  869 YEHCSTSFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15571     77 YPGCPRSFHVSCAIRAGCLFEFEDGPGNFVVYCPKH 112
Tudor_JMJD2B_rpt1 cd20464
first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; ...
 917-970 3.63e-34

first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410535  Cd Length: 54  Bit Score: 124.54  E-value: 3.63e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCL 970
Cdd:cd20464      1 VSLGQVVITKNRNGLYYRCRVIGTATQTFYEVNFDDGSYSDNVYPESITSRDCL 54
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
750-888 3.71e-31

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 131.26  E-value: 3.71e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  750 DGTSPLISCAHCCLQVHASCYGVrPELAKEGWTCSRCAAHAWTAECCL-CNLRGGALQRTTEHRWIHVICAIAVPEVRFL 828
Cdd:COG5141    205 ENSNAIVFCDGCEICVHQSCYGI-QFLPEGFWLCRKCIYGEYQIRCCSfCPSSDGAFKQTSDGRWGHVICAMFNPELSFG 283

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039753045  829 NVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHCSTSFHVTCAHAAGVLM 888
Cdd:COG5141    284 HLLSKDPIDnIASVSSSRWKLGCLICKEFG----GTCIQCSYFNCTRAYHVTCARRAGYFD 340
Tudor_JMJD2B_rpt2 cd20467
second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar ...
 974-1029 4.45e-30

second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins; JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410538  Cd Length: 56  Bit Score: 112.99  E-value: 4.45e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP 1029
Cdd:cd20467      1 PPSEGELVELRWTDGNIYKAKFISAHLSHIYQVEFEDGSQLTVKRGEIFTLEEELP 56
PHD_JMJD2C cd15577
PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed ...
 652-786 6.07e-30

PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications through modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277052  Cd Length: 104  Bit Score: 114.54  E-value: 6.07e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  652 YCAICTLFYPYSQVsclsglptlmaptvtcptqpqcslaycgPALSAVTlqSVQTERDsAVQPPSKSGQRTRPLIPEMCF 731
Cdd:cd15577      1 HCAICTLFMPYYKP----------------------------DALNEEN--SAQWEME-LPAAPCISMRKTKPLIPEMCF 49

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  732 TSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15577     50 IYREENCEPSPPNALLQEDGTSLLISCAKCCVQVHASCYGVPSHEIHDGWLCARC 104
PHD_JMJD2A cd15575
PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed ...
 652-786 5.21e-28

PHD finger found in Jumonji domain-containing protein 2A (JMJD2A); JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277050  Cd Length: 100  Bit Score: 108.84  E-value: 5.21e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  652 YCAICTLFYPYSQVSCLSGLPTlmaptvtcptqpqcslayCGPALSAVTLQsvqterdsavqppsksgQRTRPLIPEMCF 731
Cdd:cd15575      1 HCAVCMLFQTYQVDCWGGHNSS------------------SGVAASEARIK-----------------KKTKPLIPEMCF 45

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  732 TSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15575     46 TSTGCNTDLNLSTPYLEEDGTSILVTCKKCCVCVHASCYGVSPEKAAEDWMCSRC 100
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 795-889 7.70e-27

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 106.32  E-value: 7.70e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvSGACIQCSYEHCS 873
Cdd:cd15701      1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDsIEHIPPARWKLTCYICKQRG---SGACIQCHKANCY 77

                           90
                   ....*....|....*.
gi 1039753045  874 TSFHVTCAHAAGVLME 889
Cdd:cd15701     78 TAFHVTCAQQAGLYMK 93
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 795-891 1.82e-26

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 105.14  E-value: 1.82e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRMKrvsGACIQCSYEHCS 873
Cdd:cd15703      1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEgVNNIPPARWKLTCYLCKQKGR---GAAIQCHKVNCY 77

                           90
                   ....*....|....*...
gi 1039753045  874 TSFHVTCAHAAGVLMEPD 891
Cdd:cd15703     78 TAFHVTCAQRAGLFMKIE 95
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 795-904 4.04e-26

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 103.68  E-value: 4.04e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHR-WIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRmkrvSGACIQCSYEHC 872
Cdd:cd15671      1 CVLCPKKGGAMKSTKSGTkWVHVSCALWIPEVSIGCPEKMEPITkISHIPMSRWALVCVLCKEK----TGACIQCSVKSC 76

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1039753045  873 STSFHVTCAHAAG-----VLMEPDDWPYVVSItCLKH 904
Cdd:cd15671     77 KTAFHVTCAFQHGlemktILEDEDDEVKFKSY-CPKH 112
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 795-889 5.07e-26

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277172  Cd Length: 118  Bit Score: 103.97  E-value: 5.07e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvSGACIQCSYEHCS 873
Cdd:cd15702      1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCKQKG---VGACIQCHKANCY 77

                           90
                   ....*....|....*.
gi 1039753045  874 TSFHVTCAHAAGVLME 889
Cdd:cd15702     78 TAFHVTCAQKAGLYMK 93
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 795-889 2.76e-25

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 101.40  E-value: 2.76e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVD-VSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHCS 873
Cdd:cd15662      1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDgINAISKERWELSCTICKQRY----GACIQCSNNSCR 76

                           90
                   ....*....|....*.
gi 1039753045  874 TSFHVTCAHAAGVLME 889
Cdd:cd15662     77 VAYHPLCARAAGLCME 92
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 815-904 8.44e-25

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 99.33  E-value: 8.44e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  815 HVICAIAVPEVRFLNVIERN--PVDVSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHCSTSFHVTCAHAAGVLMEPDD 892
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSMGfpIEDIEKIPKRRWKLKCYLCKKKG----GACIQCSKKNCRRAFHVTCALEAGLLMQFDE 76

                           90
                   ....*....|..
gi 1039753045  893 WPYVVSITCLKH 904
Cdd:pfam13771   77 DNGTFKSYCKKH 88
ePHD_AF10_like cd15672
Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) ...
 795-889 9.73e-24

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.


Pssm-ID: 277142  Cd Length: 116  Bit Score: 97.15  E-value: 9.73e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYC---RKRMKRVSGACIQCSYEH 871
Cdd:cd15672      1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPIILQDVPQDRFNKTCYICeeqGRESKASTGACMQCNKSG 80

                           90
                   ....*....|....*...
gi 1039753045  872 CSTSFHVTCAHAAGVLME 889
Cdd:cd15672     81 CKQSFHVTCAQMAGLLCE 98
Tudor_JMJD2_rpt1 cd20391
first Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 917-969 1.06e-23

first Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also called lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 410462  Cd Length: 53  Bit Score: 94.97  E-value: 1.06e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDC 969
Cdd:cd20391      1 ISVGQRVIAKHKNGRYYEAEVVDLTTQTFYEVNFDDGSFSDDLPPEDIVSYNC 53
Tudor_JMJD2C_rpt1 cd20465
first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins; ...
 917-970 1.82e-23

first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins; JMJD2C, also called lysine-specific demethylase 4C (KDM4C), gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410536  Cd Length: 54  Bit Score: 94.15  E-value: 1.82e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCL 970
Cdd:cd20465      1 ISVGQTVISKHRNTRYYSCRVTEVTSQTFYEVMFDDGSFSRDTFPEDIVSRDCL 54
Tudor_JMJD2A_rpt1 cd20463
first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; ...
 917-971 2.66e-23

first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; JMJD2A, also called lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor corepressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER), and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410534  Cd Length: 55  Bit Score: 93.80  E-value: 2.66e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1039753045  917 VSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCLR 971
Cdd:cd20463      1 ITAGQKVISKHKNGRFYQCEVVRLTKETFYEVNFDDGSFSDNLYPEDIVSQDCLQ 55
Tudor_JMJD2_rpt2 cd20392
second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 974-1029 4.21e-23

second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also called lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 410463  Cd Length: 56  Bit Score: 93.09  E-value: 4.21e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP 1029
Cdd:cd20392      1 PPEVGDPVKVKWTDGELYDAKFVGSSIVIMYTVEFEDGSVLTLKREDVYTLDEELP 56
Tudor_JMJD2C_rpt2 cd20468
second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar ...
 974-1033 1.34e-22

second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins; JMJD2C, also called lysine-specific demethylase 4C (KDM4C), gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410539  Cd Length: 60  Bit Score: 91.88  E-value: 1.34e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELPKRVR 1033
Cdd:cd20468      1 PPAEGEVVQVKWPDGLLYGAKYLGSNIAHMYQVEFEDGSQIVMKREDIYTLDEELPKKVK 60
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 795-889 6.88e-22

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 91.89  E-value: 6.88e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRT-TEHRWIHVICAIAVPEVRFLNVIERNPV-DVSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEHC 872
Cdd:cd15707      1 CILCPNKGGAMKSTrSGTKWAHVSCALWIPEVSIGCVEKMEPItKISSIPASRWALICVLCRERT----GACIQCSVKTC 76

                           90
                   ....*....|....*..
gi 1039753045  873 STSFHVTCAHAAGVLME 889
Cdd:cd15707     77 KTAYHVTCGFQHGLEMK 93
Tudor_JMJD2A_rpt2 cd20466
second Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar ...
 974-1029 7.12e-22

second Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins; JMJD2A, also called lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor corepressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER), and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410537  Cd Length: 56  Bit Score: 89.59  E-value: 7.12e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  974 PPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP 1029
Cdd:cd20466      1 PPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 56
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 795-892 1.02e-20

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. 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 this non-canonical ePHD finger. It can interact with histones through its PHD fingers.


Pssm-ID: 277144  Cd Length: 114  Bit Score: 88.59  E-value: 1.02e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLK-CIYCR-KRMKRVsGACIQCSYEHC 872
Cdd:cd15674      1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVTLTEMNYSKWGAReCSLCEdPRFART-GVCISCDAGMC 79

                           90       100
                   ....*....|....*....|
gi 1039753045  873 STSFHVTCAHAAGVLMEPDD 892
Cdd:cd15674     80 KSYFHVTCAQREGLLSEATD 99
ePHD_AF10 cd15708
Extended PHD finger found in protein AF-10 and similar proteins; The extended plant ...
 795-889 1.05e-20

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.


Pssm-ID: 277178  Cd Length: 129  Bit Score: 88.98  E-value: 1.05e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCR---KRMKRVSGACIQCSYEH 871
Cdd:cd15708      5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPIVLQSVPHERYNKTCYICDeqgRESKAATGACMTCNKHG 84

                           90
                   ....*....|....*...
gi 1039753045  872 CSTSFHVTCAHAAGVLME 889
Cdd:cd15708     85 CRQAFHVTCAQLAGLLCE 102
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 795-888 1.91e-19

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277175  Cd Length: 111  Bit Score: 84.76  E-value: 1.91e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRT-TEHRWIHVICAIAVPEVRFLNVIERNPV-DVSAIPEQRWKLKCIYCRKrmkrVSGACIQCSYEHC 872
Cdd:cd15705      1 CLLCPKRGGALKPTrSGTKWVHVSCALWIPEVSIGCPEKMEPItKISHIPASRWALSCSLCKE----CTGTCIQCSMPSC 76

                           90
                   ....*....|....*.
gi 1039753045  873 STSFHVTCAHAAGVLM 888
Cdd:cd15705     77 ITAFHVTCAFDHGLEM 92
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 795-904 2.71e-19

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 84.39  E-value: 2.71e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRT-TEHRWIHVICAIAVPEVRFLNVIERNPV-DVSAIPEQRWKLKCIYCRKRmkrvSGACIQCSYEHC 872
Cdd:cd15706      1 CLLCPKTGGAMKATrTGTKWAHVSCALWIPEVSIACPERMEPItKVSHIPPSRWALVCSLCKLK----TGACIQCSVKSC 76

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1039753045  873 STSFHVTCAHAAGVLM-----EPDDWPYvvSITCLKH 904
Cdd:cd15706     77 ITAFHVTCAFEHSLEMktildEGDEVKF--KSYCLKH 111
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
 795-889 3.53e-19

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.


Pssm-ID: 277133  Cd Length: 112  Bit Score: 84.10  E-value: 3.53e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRT-TEHRWIHVICAIAVPEVRFLNVIERNP-VDVSAIPEQRWKLKCIYCrkrmKRVSGACIQCSyeHC 872
Cdd:cd15663      1 CCLCPVKGGALKPTdVEGLWVHVTCAWFRPEVCFKNEEKMEPaVGLLRIPLSTFLKACVIC----KQIHGSCTQCC--KC 74

                           90
                   ....*....|....*..
gi 1039753045  873 STSFHVTCAHAAGVLME 889
Cdd:cd15663     75 ATYFHAMCASRAGYHME 91
ePHD_AF17 cd15709
Extended PHD finger found in protein AF-17 and similar proteins; The extended plant ...
 795-891 5.56e-19

Extended PHD finger found in protein AF-17 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger.


Pssm-ID: 277179  Cd Length: 125  Bit Score: 83.96  E-value: 5.56e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCR---KRMKRVSGACIQCSYEH 871
Cdd:cd15709      5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPIVLQYVPHDRFNKTCYICEeqgRESKAASGACMTCNRHG 84

                           90       100
                   ....*....|....*....|
gi 1039753045  872 CSTSFHVTCAHAAGVLMEPD 891
Cdd:cd15709     85 CRQAFHVTCAQMAGLLCEEE 104
ePHD_JADE1 cd15704
Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant ...
 794-889 2.25e-17

Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the Serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation and ASA transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277174  Cd Length: 118  Bit Score: 78.96  E-value: 2.25e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  794 ECCLCNLRGGALQRT-TEHRWIHVICAIAVPEVRFLNVIERNPV-DVSAIPEQRWKLKCIYCRKRMkrvsGACIQCSYEH 871
Cdd:cd15704      3 KCLLCPKKGGAMKPTrSGTKWVHVSCALWIPEVSIGSPEKMEPItKVSHIPSSRWALVCSLCNEKV----GASIQCSVKN 78

                           90
                   ....*....|....*...
gi 1039753045  872 CSTSFHVTCAHAAGVLME 889
Cdd:cd15704     79 CRTAFHVTCAFDRGLEMK 96
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 1.14e-13

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 66.13  E-value: 1.14e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1039753045    15 IMTFRPTMDEFRDFNRYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545    2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 752-786 1.88e-13

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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 65.05  E-value: 1.88e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  752 TSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGDGWKCRRC 35
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 920-954 5.32e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 63.98  E-value: 5.32e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  920 GQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGS 954
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
Tudor_2 pfam18104
Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone ...
 978-1012 6.16e-13

Jumonji domain-containing protein 2A Tudor domain; This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD).


Pssm-ID: 465651  Cd Length: 35  Bit Score: 63.59  E-value: 6.16e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045  978 GELVELRWTDGNLYRARFISMATSLIYQVEFEDGS 1012
Cdd:pfam18104    1 GQDVIARWTDGRYYLGKFIGIHTQTFYEVEFEDGS 35
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 149-206 6.55e-13

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: 64.20  E-value: 6.55e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039753045   149 WNIGNLRTILDMVeRECGTIIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 206
Cdd:smart00558    3 WNLAKLPFKLNLL-SDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN pfam02375
jmjN domain;
16-50 1.10e-11

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 60.00  E-value: 1.10e-11
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1039753045   16 MTFRPTMDEFRDFNRYVAYIESQGAhRAGLAKIIP 50
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
PHD_JMJD2 cd15493
PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; ...
 754-786 1.71e-10

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. This model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276968  Cd Length: 42  Bit Score: 56.94  E-value: 1.71e-10
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1039753045  754 PLISCAHCCLQVHASCYGVRPEL-AKEGWTCSRC 786
Cdd:cd15493      9 RLLVCSRCCVCVHASCYGVPDIPgDGEGWKCDRC 42
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 919-969 1.08e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.97  E-value: 1.08e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1039753045   919 LGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDC 969
Cdd:smart00333    5 VGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPE 55
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 973-1028 3.29e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 53.82  E-value: 3.29e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039753045   973 GPPPEGELVELRWTDGNLYRARFISMATSLIYQVEFED-GSQLTVKRGDIFTLEEEL 1028
Cdd:smart00333    1 PTFKVGDKVAARWEDGEWYRARIVKVDGEQLYEVFFIDyGNEEVVPPSDLRQLPEEL 57
ePHD_Snt2p_like cd15667
Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) ...
 795-881 1.35e-07

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 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 PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.


Pssm-ID: 277137  Cd Length: 141  Bit Score: 51.61  E-value: 1.35e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRGG---------------ALQRTTEHRWIHVICAIAVPEVRFLNVIERNP-VDVSAIPEQRWKLKCIYCRKrmk 858
Cdd:cd15667      1 CSLCNAKESnyelakkqsprtrpdALKCTSNGTWCHVLCALFNEDIKFGNSKSLQPiLNTESVLLKGSRQKCEICKV--- 77

                           90       100
                   ....*....|....*....|...
gi 1039753045  859 rVSGACIQCsyEHCSTSFHVTCA 881
Cdd:cd15667     78 -SGGGLVKC--EVCDDRFHVSCA 97
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 795-904 1.47e-06

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of 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 by 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 PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 47.79  E-value: 1.47e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRG-------GALQRTTEHRWIHVICAIAVPEV------RFLNViernpvdVSAIPEQRwKLKCIYCRKRmkrvs 861
Cdd:cd15664      1 CALCGVYGddepndaGRLLYCGQDEWVHINCALWSAEVfeeddgSLQNV-------HSAVSRGR-MMKCELCGKP----- 67

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1039753045  862 GACIQCSYEHCSTSFHVTCAHAAGVLMEPDDwpyvvSITCLKH 904
Cdd:cd15664     68 GATVGCCLKSCPANYHFMCARKAECVFQDDK-----KVFCPAH 105
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 795-885 9.56e-06

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. 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 PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 45.00  E-value: 9.56e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLrgGALqrttehrWIHVICAI------AVPEVRFLNVierNPVDVSAIPEqrwklKCIYCRKrmkrvSGACIQCS 868
Cdd:cd15665      1 CALCNL--GEV-------YAHHCCAAwsegvcQTEDGALENV---DKAVAKALSQ-----KCSFCLR-----YGASISCR 58

                           90
                   ....*....|....*..
gi 1039753045  869 YEHCSTSFHVTCAHAAG 885
Cdd:cd15665     59 MPSCSKSFHFPCAAAAG 75
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
 748-786 1.74e-05

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 43.13  E-value: 1.74e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1039753045  748 GEDGTS-PLISCAHCCLQVHASCYGVRPELAKEGWTCSRC 786
Cdd:cd15495      8 GEDDDNnPLITCNRCQISVHQKCYGIREVDPDGSWVCRAC 47
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 978-1021 4.43e-05

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 41.80  E-value: 4.43e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1039753045  978 GELVELRWT-DGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDI 1021
Cdd:cd04508      1 GDRVEAKWSdDGQWYPATVVAVNDDGKYTVLFDDGNEEEVSEDDI 45
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 748-786 7.32e-05

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: 41.04  E-value: 7.32e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 1039753045   748 GEDGTSPLISCAHCCLQVHASCYGVRPELA--KEGWTCSRC 786
Cdd:smart00249    7 KPDDGGELLQCDGCDRWYHQTCLGPPLLEEepDGKWYCPKC 47
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 795-881 7.50e-05

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and 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 PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 43.06  E-value: 7.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRG-------GALQRTTEHRWIHVICAIAVPEV------RFLNViernpvdVSAIpEQRWKLKCIYCRKRmkrvs 861
Cdd:cd15666      1 CVLCGGEGdgdtdgpGRLLNLDVDKWVHLNCALWSYEVyetqngALMNV-------EEAL-RRALTTTCSHCGRT----- 67

                           90       100
                   ....*....|....*....|
gi 1039753045  862 GACIQCSYEHCSTSFHVTCA 881
Cdd:cd15666     68 GATVPCFKPRCANVYHLPCA 87
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 850-892 2.31e-04

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: 39.89  E-value: 2.31e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 1039753045   850 CIYCRKRMKrvSGACIQCsyEHCSTSFHVTCAHAAGVLMEPDD 892
Cdd:smart00249    2 CSVCGKPDD--GGELLQC--DGCDRWYHQTCLGPPLLEEEPDG 40
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 795-904 2.99e-04

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


Pssm-ID: 277164  Cd Length: 105  Bit Score: 41.18  E-value: 2.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  795 CCLCNLRG-------GALQRTTEHRWIHVICAIAVPEVrflnvIERNP---VDVSAIPEQRWKLKCIYCRKrmkrvSGAC 864
Cdd:cd15694      1 CALCLKYGdadskdaGRLLYIGQNEWTHVNCAIWSAEV-----FEENDgslKNVHAAVARGRQMRCEHCQK-----IGAT 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1039753045  865 IQCSYEHCSTSFHVTCAHAAGVLMEPDDwpyvvSITCLKH 904
Cdd:cd15694     71 VGCCLSACLSNFHFMCARASRCCFQDDK-----KVFCQKH 105
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 835-881 3.93e-04

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 41.08  E-value: 3.93e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1039753045  835 PVDVSAIPEQRWKLKCIYCRKRmkrvsGACIQCSYEHCSTSFHVTCA 881
Cdd:cd15669     51 PEDIRKEVRRASRLRCFYCKKK-----GASIGCAVKGCRRSFHFPCG 92
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 847-904 4.27e-04

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 41.22  E-value: 4.27e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039753045  847 KLKCIYCRKRmkrvsGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15673     64 KLKCNLCKKT-----GATIGCDVKQCKKTYHYHCAKKDDAKIIERNSQGIYRVYCKNH 116
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 748-786 1.66e-03

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: 37.30  E-value: 1.66e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1039753045  748 GEDGTSPLISCAHCCLQVHASCYGVRPELA--KEGWTCSRC 786
Cdd:cd15489      8 GGDLGGELLQCDGCGKWFHADCLGPPLSSFvpNGKWICPVC 48
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 847-904 1.98e-03

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 39.11  E-value: 1.98e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039753045  847 KLKCIYCRKRmkrvsGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWPYVVSITCLKH 904
Cdd:cd15712     63 RLKCNFCRKK-----GATVGCEERACRRSYHYFCALCDDAAIETDEVRGIYRVFCQKH 115
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 754-786 2.61e-03

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 36.83  E-value: 2.61e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1039753045  754 PLISCAHCCLQVHASCYGVrPELAKEGWTCSRC 786
Cdd:cd15492     15 EIVFCDGCNVAVHQSCYGI-PLIPEGDWFCRKC 46
PHD2_Snt2p_like cd15498
PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 747-774 2.77e-03

PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; This group corresponds to 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 second canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276973  Cd Length: 55  Bit Score: 37.07  E-value: 2.77e-03
                           10        20
                   ....*....|....*....|....*...
gi 1039753045  747 VGEDGTSPLISCAHCCLQVHASCYGVRP 774
Cdd:cd15498      8 QFASNFNTSLSCYNCGLNVHASCYGITV 35
Tudor_PHF20L1 cd20454
Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins; ...
 977-1027 4.03e-03

Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins; PHF20L1 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. In addition to the MBT domain, PHF20L1 also contains a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410525  Cd Length: 59  Bit Score: 36.87  E-value: 4.03e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1039753045  977 EGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEE 1027
Cdd:cd20454      4 AGEEVLARWTDCRYYPAKIEAINKEGTYTVQFYDGVIRCLKRMHIKSMPED 54
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 748-786 5.33e-03

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: 35.93  E-value: 5.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1039753045  748 GEDGTSPLISCAHCCLQVHASCYGV---RPELAKEGWTCSRC 786
Cdd:pfam00628    7 KSDDGGELVQCDGCDDWFHLACLGPpldPAEIPSGEWLCPEC 48
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 847-904 6.63e-03

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 37.29  E-value: 6.63e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039753045  847 KLKCIYCRKRmkrvsGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWpyvvSITCLKH 904
Cdd:cd15668     55 QSVCSSCQQT-----GATIGCLHKGCKAKYHYPCAVESGCQLDEENF----SLLCPKH 103
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 794-905 7.00e-03

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It 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, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 37.67  E-value: 7.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039753045  794 ECCLCNLRG-------GALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQrwKLKCIYCRKrmkrvSGACIQ 866
Cdd:cd15693      2 QCALCLKYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGK--QLRCEFCQK-----PGATVG 74

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1039753045  867 CSYEHCSTSFHVTCAHAAGVLMEPDDWPYvvsitCLKHR 905
Cdd:cd15693     75 CCLTSCTSNYHFMCSRAKNCVFLEDKKVY-----CQRHK 108
Tudor_TDRD15_rpt6 cd20441
sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 978-1037 7.36e-03

sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410512  Cd Length: 108  Bit Score: 37.41  E-value: 7.36e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039753045  978 GELVELRWT-DGNLYRARFISMATSLIYQVEFED-GSQLTVKRGDIFTLEEE---LPK-RVRSRLS 1037
Cdd:cd20441     41 GDLVAAEYDeDLALYRAVITAVLPGKSFKVEFIDyGNTAVVDKSNIYTLQEKflsLPRlSIPCSLS 106
Tudor_PHF20-like cd20386
Tudor domain found in PHD finger protein 20 (PHF20), PHF20-like protein 1 (PHF20L1), and ...
 978-1021 8.77e-03

Tudor domain found in PHD finger protein 20 (PHF20), PHF20-like protein 1 (PHF20L1), and similar proteins; PHF20, also called Glioma-expressed antigen 2, hepatocellular carcinoma-associated antigen 58, 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 to 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. PHF20L1 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. Both PHF20 and PHF20L1 contain an N-terminal malignant brain tumor (MBT) domain, a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410457 [Multi-domain]  Cd Length: 50  Bit Score: 35.26  E-value: 8.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1039753045  978 GELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDI 1021
Cdd:cd20386      4 GEEVLARWSDCKFYPAKILKVLDNGTYEVLFYDGFKKTVKASNL 47
Tudor_ARID4_rpt2 cd20390
second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The ...
 978-1021 9.26e-03

second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family; The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410461  Cd Length: 53  Bit Score: 35.33  E-value: 9.26e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1039753045  978 GELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDI 1021
Cdd:cd20390      2 GATVEVKTPDGQFAEAVITKLTDASTYTVVFDDGDEKTLRRTSL 45
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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