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Conserved domains on  [gi|1958798715|ref|XP_038938275|]
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histone-lysine N-methyltransferase 2A isoform X3 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 3832-3985 2.13e-115

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


:

Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 362.48  E-value: 2.13e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDA 3911
Cdd:cd19170      1 MAMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCRKFLN 3985
Cdd:cd19170     81 TMHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIED--VKIPCTCGSKKCRKYLN 152
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 1891-2003 1.40e-82

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: 266.87  E-value: 1.40e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1891 RQCALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 1970
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958798715 1971 TSNYHFMCSRAKNCVFLDDKKVYCQRHRDLIKG 2003
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKDLIKG 113
Bromo_ALL-1 cd05493
Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and ...
 1667-1797 5.05e-52

Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


:

Pssm-ID: 99925  Cd Length: 131  Bit Score: 180.32  E-value: 5.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1667 VLTALLNSRTTSHLLRYRqaAKPPDLNPETEESIPSRSSPEGPDPPV--LTEVSKQDEQQPLDLEGVKKKMDQGNYVSVL 1744
Cdd:cd05493      1 ELEELLDSRTKSHLLRCG--PKPPALLPETEESLPGRKSPVTPEVLQglLSSEVKQEELPPLDLEAVGKKLEAGFYTSVL 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958798715 1745 EFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFW 1797
Cdd:cd05493     79 DFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSEDPKLW 131
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1585-1644 3.97e-36

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


:

Pssm-ID: 277067  Cd Length: 57  Bit Score: 132.03  E-value: 3.97e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1585 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNLPESVAYTCVNC 1644
Cdd:cd15592      1 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLS---DEMYEILSNLPESVAYTCINC 57
PHD1_KMT2A cd15588
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1451-1497 4.56e-33

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


:

Pssm-ID: 277063  Cd Length: 47  Bit Score: 123.14  E-value: 4.56e-33
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1451 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1497
Cdd:cd15588      1 VCFLCASSGHVEFVYCQVCCEPFHKFCLEEAERPLEDQLENWCCRRC 47
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 3685-3768 1.64e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 1.64e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  3685 LVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLSGAKHCRNYKFRFH 3764
Cdd:smart00542    2 FRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWFRYH 81


                    ....
gi 1958798715  3765 KPEE 3768
Cdd:smart00542   82 RSPL 85
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1499-1547 1.42e-29

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


:

Pssm-ID: 277065  Cd Length: 50  Bit Score: 113.20  E-value: 1.42e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQATK-LLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15590      1 FCHVCGRQHQATKqLLECNKCRNSYHPECLGPNYPTKPTKKKRVWICTKC 50
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 1145-1192 6.07e-21

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


:

Pssm-ID: 366873  Cd Length: 48  Bit Score: 88.57  E-value: 6.07e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1145 KKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKC 1192
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 2044-2091 4.58e-16

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


:

Pssm-ID: 461787  Cd Length: 51  Bit Score: 74.46  E-value: 4.58e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 2044 GSMTIDCLGIL---NDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKI 2091
Cdd:pfam05964    1 GSLTVLSLGEIvpdRPAFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2958-3354 4.22e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.68  E-value: 4.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 2958 SQNSSRLAVISDSGEKRVTITEKSVTSTEGDPALLSPGVDPAPEGHMTPDHFIQGHMDADHISSPPCGSVEQGHGNNQDl 3037
Cdd:pfam03154   79 SAKRQREKGASDTEEPERATAKKSKTQEISRPNSPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESD- 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3038 TRNSSTPGLQVPVSPTVPIQNQKYVPNSTDSPGPSQISNAA----VQTTPPHLKPATEKLIVVNQN-MQPLYVLQTLPNG 3112
Cdd:pfam03154  158 SDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGptpsAPSVPPQGSPATSQPPNQTQStAAPHTLIQQTPTL 237

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3113 VTQKI--------QLTSP-----VSSTPNVMETNTSVLGPMGSGLTLTTGLNP-SLPP---------SQSLFPPASKGLL 3169
Cdd:pfam03154  238 HPQRLpsphpplqPMTQPpppsqVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPqpfpltpqsSQSQVPPGPSPAA 317

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3170 SMPHHQHLHSFP--AAAQSSFPPNISS-PPSGL-LIGVQPPPD---PQLLGSEANQRTDLTTTVT--------TPSSGLK 3234
Cdd:pfam03154  318 PGQSQQRIHTPPsqSQLQSQQPPREQPlPPAPLsMPHIKPPPTtpiPQLPNPQSHKHPPHLSGPSpfqmnsnlPPPPALK 397

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3235 krPISRLHTRKnkklAPSSAPsniAPSDVVSNMTLINFTPSQ---LSNHPSLLDLGSLNP--SSHRTVPNIIKRSKSGIM 3309
Cdd:pfam03154  398 --PLSSLSTHH----PPSAHP---PPLQLMPQSQQLPPPPAQppvLTQSQSLPPPAASHPptSGLHQVPSQSPFPQHPFV 468

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*
gi 1958798715 3310 YFEQAPLLPPQSVGGTTATGAGSSTISQDTSHLTSGPVSALASGS 3354
Cdd:pfam03154  469 PGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCP 513
 
Name Accession Description Interval E-value
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 3832-3985 2.13e-115

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 362.48  E-value: 2.13e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDA 3911
Cdd:cd19170      1 MAMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCRKFLN 3985
Cdd:cd19170     81 TMHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIED--VKIPCTCGSKKCRKYLN 152
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 1891-2003 1.40e-82

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: 266.87  E-value: 1.40e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1891 RQCALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 1970
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958798715 1971 TSNYHFMCSRAKNCVFLDDKKVYCQRHRDLIKG 2003
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKDLIKG 113
Bromo_ALL-1 cd05493
Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and ...
 1667-1797 5.05e-52

Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99925  Cd Length: 131  Bit Score: 180.32  E-value: 5.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1667 VLTALLNSRTTSHLLRYRqaAKPPDLNPETEESIPSRSSPEGPDPPV--LTEVSKQDEQQPLDLEGVKKKMDQGNYVSVL 1744
Cdd:cd05493      1 ELEELLDSRTKSHLLRCG--PKPPALLPETEESLPGRKSPVTPEVLQglLSSEVKQEELPPLDLEAVGKKLEAGFYTSVL 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958798715 1745 EFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFW 1797
Cdd:cd05493     79 DFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSEDPKLW 131
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 3847-3967 1.89e-45

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 160.96  E-value: 1.89e-45
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVDATMHGNAARFINHSC 3925
Cdd:smart00317    3 LEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHSC 82

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 1958798715  3926 EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDA 3967
Cdd:smart00317   83 EPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
3832-3982 1.41e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 142.02  E-value: 1.41e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKktskeavgVYRSPIHGRGLFCKRNIDAGEMVIEYAGnviRSIQTDKREKYYDSKGIGC-YMFRIDDSEVVD 3910
Cdd:COG2940      1 MAMLHPRIE--------VRPSPIHGRGVFATRDIPKGTLIGEYPG---EVITWAEAERREPHKEPLHtYLFELDDDGVID 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 3911 ATMHGNAARFINHSCEPNCYSRVINidgqKHIVIFAMRKIYRGEELTYDYKFPIEDAsnKLPCNCgaKKCRK 3982
Cdd:COG2940     70 GALGGNPARFINHSCDPNCEADEED----GRIFIVALRDIAAGEELTYDYGLDYDEE--EYPCRC--PNCRG 133
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1585-1644 3.97e-36

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 132.03  E-value: 3.97e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1585 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNLPESVAYTCVNC 1644
Cdd:cd15592      1 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLS---DEMYEILSNLPESVAYTCINC 57
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 3856-3961 3.56e-33

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 125.71  E-value: 3.56e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGN-VIRSIQTDKREKYYDSKGI----GCYMFRIDDSE--VVDAT--MHGNAARFINHSCE 3926
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDSeyCIDARalYYGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958798715 3927 PNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYK 3961
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
PHD1_KMT2A cd15588
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1451-1497 4.56e-33

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 277063  Cd Length: 47  Bit Score: 123.14  E-value: 4.56e-33
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1451 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1497
Cdd:cd15588      1 VCFLCASSGHVEFVYCQVCCEPFHKFCLEEAERPLEDQLENWCCRRC 47
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 3685-3768 1.64e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 1.64e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  3685 LVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLSGAKHCRNYKFRFH 3764
Cdd:smart00542    2 FRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWFRYH 81


                    ....
gi 1958798715  3765 KPEE 3768
Cdd:smart00542   82 RSPL 85
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1499-1547 1.42e-29

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 113.20  E-value: 1.42e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQATK-LLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15590      1 FCHVCGRQHQATKqLLECNKCRNSYHPECLGPNYPTKPTKKKRVWICTKC 50
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 3680-3764 2.66e-24

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 99.22  E-value: 2.66e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3680 KPKkgLVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLSGAKHCRNY 3759
Cdd:pfam05965    1 GPL--FRVTVEEDPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1958798715 3760 KFRFH 3764
Cdd:pfam05965   79 KFRYG 83
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 1145-1192 6.07e-21

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 88.57  E-value: 6.07e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1145 KKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKC 1192
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 2044-2091 4.58e-16

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 74.46  E-value: 4.58e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 2044 GSMTIDCLGIL---NDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKI 2091
Cdd:pfam05964    1 GSLTVLSLGEIvpdRPAFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 1920-1997 9.42e-16

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: 75.06  E-value: 9.42e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1920 HVNCALWSAEVFEDDDGS----LKNVHMAVIRGKQLRCEFC-QKPGATVGCCLTSCTSNYHFMCSRAKNCVF-----LDD 1989
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqfdedNGT 80


                   ....*...
gi 1958798715 1990 KKVYCQRH 1997
Cdd:pfam13771   81 FKSYCKKH 88
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 2050-2093 1.34e-15

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 73.09  E-value: 1.34e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1958798715  2050 CLGILNDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKIME 2093
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
BROMO smart00297
bromo domain;
1653-1785 2.94e-11

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 63.07  E-value: 2.94e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  1653 RLALEKELQASLKQVLTALLNSRTTSHLLryrqaaKPPDLNpeteesipsrsspEGPDppvltevSKQDEQQPLDLEGVK 1732
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFL------KPVSRK-------------EAPD-------YYDIIKKPMDLKTIK 54

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1958798715  1733 KKMDQGNYVSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERV 1785
Cdd:smart00297   55 KKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1499-1547 4.00e-10

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: 57.61  E-value: 4.00e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1958798715  1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1451-1500 8.71e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 56.73  E-value: 8.71e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 1451 VCFLCASSG-HVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRCKFC 1500
Cdd:pfam00628    1 YCAVCGKSDdGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1499-1550 2.34e-09

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: 55.58  E-value: 2.34e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNyPTKPTKKKKVWICTKCVRC 1550
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPP-LDPAEIPSGEWLCPECKPK 51
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1599-1647 9.06e-06

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: 45.56  E-value: 9.06e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNlpesvAYTCVNCTER 1647
Cdd:pfam00628   11 GGELVQCDGCDDWFHLACLGPP---LDPAEIPSG-----EWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1451-1497 9.69e-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: 42.58  E-value: 9.69e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1958798715  1451 VCFLCASSGH-VEFVYCQVCCEPFHKFCLEENERPlEDQLENWCCRRC 1497
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1599-1644 1.13e-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: 42.20  E-value: 1.13e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1958798715  1599 ESKMMQCGKCDRWVHSKCEGLSGTEDemyeilsnlPESVAYTCVNC 1644
Cdd:smart00249   11 GGELLQCDGCDRWYHQTCLGPPLLEE---------EPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1952-1997 1.30e-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: 42.20  E-value: 1.30e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1958798715  1952 RCEFCQKP---GATVGCCltSCTSNYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:smart00249    1 YCSVCGKPddgGELLQCD--GCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2958-3354 4.22e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.68  E-value: 4.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 2958 SQNSSRLAVISDSGEKRVTITEKSVTSTEGDPALLSPGVDPAPEGHMTPDHFIQGHMDADHISSPPCGSVEQGHGNNQDl 3037
Cdd:pfam03154   79 SAKRQREKGASDTEEPERATAKKSKTQEISRPNSPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESD- 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3038 TRNSSTPGLQVPVSPTVPIQNQKYVPNSTDSPGPSQISNAA----VQTTPPHLKPATEKLIVVNQN-MQPLYVLQTLPNG 3112
Cdd:pfam03154  158 SDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGptpsAPSVPPQGSPATSQPPNQTQStAAPHTLIQQTPTL 237

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3113 VTQKI--------QLTSP-----VSSTPNVMETNTSVLGPMGSGLTLTTGLNP-SLPP---------SQSLFPPASKGLL 3169
Cdd:pfam03154  238 HPQRLpsphpplqPMTQPpppsqVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPqpfpltpqsSQSQVPPGPSPAA 317

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3170 SMPHHQHLHSFP--AAAQSSFPPNISS-PPSGL-LIGVQPPPD---PQLLGSEANQRTDLTTTVT--------TPSSGLK 3234
Cdd:pfam03154  318 PGQSQQRIHTPPsqSQLQSQQPPREQPlPPAPLsMPHIKPPPTtpiPQLPNPQSHKHPPHLSGPSpfqmnsnlPPPPALK 397

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3235 krPISRLHTRKnkklAPSSAPsniAPSDVVSNMTLINFTPSQ---LSNHPSLLDLGSLNP--SSHRTVPNIIKRSKSGIM 3309
Cdd:pfam03154  398 --PLSSLSTHH----PPSAHP---PPLQLMPQSQQLPPPPAQppvLTQSQSLPPPAASHPptSGLHQVPSQSPFPQHPFV 468

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*
gi 1958798715 3310 YFEQAPLLPPQSVGGTTATGAGSSTISQDTSHLTSGPVSALASGS 3354
Cdd:pfam03154  469 PGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCP 513
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
1916-1993 3.47e-03

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 43.43  E-value: 3.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1916 NEWTHVNCALWSAEVfedddgSLKNVH-MAVIRGKQ--------LRCEFCQKPGAT-VGCCLTSCTSNYHFMCSRAKnCV 1985
Cdd:COG5141    266 GRWGHVICAMFNPEL------SFGHLLsKDPIDNIAsvsssrwkLGCLICKEFGGTcIQCSYFNCTRAYHVTCARRA-GY 338


                   ....*...
gi 1958798715 1986 FldDKKVY 1993
Cdd:COG5141    339 F--DLNIY 344
 
Name Accession Description Interval E-value
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 3832-3985 2.13e-115

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 362.48  E-value: 2.13e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDA 3911
Cdd:cd19170      1 MAMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCRKFLN 3985
Cdd:cd19170     81 TMHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIED--VKIPCTCGSKKCRKYLN 152
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 3832-3985 1.51e-111

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac).


Pssm-ID: 380983 [Multi-domain]  Cd Length: 154  Bit Score: 351.63  E-value: 1.51e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDA 3911
Cdd:cd19206      1 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 3985
Cdd:cd19206     81 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 3832-3985 8.04e-94

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation.


Pssm-ID: 380984 [Multi-domain]  Cd Length: 154  Bit Score: 300.79  E-value: 8.04e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDA 3911
Cdd:cd19207      1 MAMRFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 3985
Cdd:cd19207     81 TMHGNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 3832-3981 2.21e-90

SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380916  Cd Length: 150  Bit Score: 290.65  E-value: 2.21e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVD 3910
Cdd:cd10518      1 MSKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGGgGTYMFRIDEDLVID 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 3911 ATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDAsNKLPCNCGAKKCR 3981
Cdd:cd10518     81 ATKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDE-EKIPCLCGAPNCR 150
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 1891-2003 1.40e-82

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: 266.87  E-value: 1.40e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1891 RQCALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 1970
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958798715 1971 TSNYHFMCSRAKNCVFLDDKKVYCQRHRDLIKG 2003
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKDLIKG 113
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 1893-1997 4.16e-72

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: 236.53  E-value: 4.16e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1972
Cdd:cd15664      1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                           90       100
                   ....*....|....*....|....*
gi 1958798715 1973 NYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:cd15664     81 NYHFMCARKAECVFQDDKKVFCPAH 105
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 1893-1997 1.14e-63

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: 212.59  E-value: 1.14e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1972
Cdd:cd15694      1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                           90       100
                   ....*....|....*....|....*
gi 1958798715 1973 NYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:cd15694     81 NFHFMCARASRCCFQDDKKVFCQKH 105
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 3834-3981 1.29e-63

SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated.


Pssm-ID: 380946  Cd Length: 148  Bit Score: 214.12  E-value: 1.29e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3834 MRFRHLKkTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIG-CYMFRIDDSEVVDAT 3912
Cdd:cd19169      3 LKFNQLK-FRKKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEAIGIGsSYLFRVDDDTIIDAT 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958798715 3913 MHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCR 3981
Cdd:cd19169     82 KCGNLARFINHSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIED--EKIPCLCGAPQCR 148
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 3836-3984 6.69e-61

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 206.51  E-value: 6.69e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3836 FRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHG 3915
Cdd:cd19171      5 YRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDATMTG 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958798715 3916 NAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd19171     85 GPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 3833-3981 2.33e-58

SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3).


Pssm-ID: 380998  Cd Length: 148  Bit Score: 199.19  E-value: 2.33e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3833 PMRFRHLKKTSKEaVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIG-CYMFRIDDSEVVDA 3911
Cdd:cd20072      2 LLRFNQLKKRKKQ-LKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCR 3981
Cdd:cd20072     81 TKKGNIARFINHCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREE--DKIPCLCGAPNCR 148
Bromo_ALL-1 cd05493
Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and ...
 1667-1797 5.05e-52

Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99925  Cd Length: 131  Bit Score: 180.32  E-value: 5.05e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1667 VLTALLNSRTTSHLLRYRqaAKPPDLNPETEESIPSRSSPEGPDPPV--LTEVSKQDEQQPLDLEGVKKKMDQGNYVSVL 1744
Cdd:cd05493      1 ELEELLDSRTKSHLLRCG--PKPPALLPETEESLPGRKSPVTPEVLQglLSSEVKQEELPPLDLEAVGKKLEAGFYTSVL 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958798715 1745 EFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFW 1797
Cdd:cd05493     79 DFSDDIVKIIQAALNSEGGQPEIKKANSMAKSFFIKLMESVFPWFNSEDPKLW 131
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 3841-3985 5.31e-47

SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression.


Pssm-ID: 380981 [Multi-domain]  Cd Length: 153  Bit Score: 166.74  E-value: 5.31e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3841 KTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGC-YMFRIDDSEVVDATMHGNAAR 3919
Cdd:cd19204     10 KFRKKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLAR 89

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958798715 3920 FINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCRKFLN 3985
Cdd:cd19204     90 FINHCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIED--NKIPCLCGTENCRGTLN 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 3835-3984 8.65e-46

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival.


Pssm-ID: 380985 [Multi-domain]  Cd Length: 154  Bit Score: 163.26  E-value: 8.65e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3835 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 3914
Cdd:cd19208      5 QYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVIDATLT 84

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3915 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd19208     85 GGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 3834-3985 1.75e-45

SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.


Pssm-ID: 380982 [Multi-domain]  Cd Length: 153  Bit Score: 162.53  E-value: 1.75e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3834 MRFRHLKkTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGC-YMFRIDDSEVVDAT 3912
Cdd:cd19205      4 LKFNQLK-FRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDAT 82

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958798715 3913 MHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDasNKLPCNCGAKKCRKFLN 3985
Cdd:cd19205     83 KCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIED--VKIPCLCGSENCRGTLN 153
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 3847-3967 1.89e-45

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 160.96  E-value: 1.89e-45
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVDATMHGNAARFINHSC 3925
Cdd:smart00317    3 LEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHSC 82

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 1958798715  3926 EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDA 3967
Cdd:smart00317   83 EPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 3835-3984 1.64e-43

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 156.78  E-value: 1.64e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3835 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 3914
Cdd:cd19209      6 QYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 85

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3915 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd19209     86 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
3832-3982 1.41e-38

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 142.02  E-value: 1.41e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3832 MPMRFRHLKktskeavgVYRSPIHGRGLFCKRNIDAGEMVIEYAGnviRSIQTDKREKYYDSKGIGC-YMFRIDDSEVVD 3910
Cdd:COG2940      1 MAMLHPRIE--------VRPSPIHGRGVFATRDIPKGTLIGEYPG---EVITWAEAERREPHKEPLHtYLFELDDDGVID 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 3911 ATMHGNAARFINHSCEPNCYSRVINidgqKHIVIFAMRKIYRGEELTYDYKFPIEDAsnKLPCNCgaKKCRK 3982
Cdd:COG2940     70 GALGGNPARFINHSCDPNCEADEED----GRIFIVALRDIAAGEELTYDYGLDYDEE--EYPCRC--PNCRG 133
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 3856-3981 1.46e-38

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins.


Pssm-ID: 380929  Cd Length: 136  Bit Score: 142.01  E-value: 1.46e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGC-YMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVI 3934
Cdd:cd10531     11 GWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERLDEYEELGKSNfYILSLSDDVVIDATRKGNLSRFINHSCEPNCETQKW 90

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 3935 NIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLpCNCGAKKCR 3981
Cdd:cd10531     91 IVNGEYRIGIFALRDIPAGEELTFDYNFVNYNEAKQV-CLCGAQNCR 136
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 1893-1997 3.27e-36

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: 133.97  E-value: 3.27e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1972
Cdd:cd15666      1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                           90       100
                   ....*....|....*....|....*
gi 1958798715 1973 NYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:cd15666     81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1585-1644 3.97e-36

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 132.03  E-value: 3.97e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1585 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNLPESVAYTCVNC 1644
Cdd:cd15592      1 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLS---DEMYEILSNLPESVAYTCINC 57
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 3856-3984 7.08e-36

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).


Pssm-ID: 380952 [Multi-domain]  Cd Length: 139  Bit Score: 134.47  E-value: 7.08e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKG-IGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVI 3934
Cdd:cd19175     11 GWGLVADEDINAGEFIIEYVGEVIDDKTCEERLWDMKHKGeKNFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQKW 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3935 NIDGQKHIVIFAMRKIYRGEELTYDYKFpiEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd19175     91 QVDGETRIGVFAIRDIKKGEELTYDYQF--VQFGADQDCHCGSKNCRGKL 138
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 3847-3984 7.48e-36

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.


Pssm-ID: 380949 [Multi-domain]  Cd Length: 142  Bit Score: 134.25  E-value: 7.48e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMF-RIDDSEVVDATMHGNAARFINHSC 3925
Cdd:cd19172      4 VEVFRTEKKGWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYAREGNRHYYFmALKSDEIIDATKKGNLSRFINHSC 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958798715 3926 EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKlPCNCGAKKCRKFL 3984
Cdd:cd19172     84 EPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFERYGKEAQ-KCYCGSPNCRGYI 141
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 3849-3985 3.91e-35

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).


Pssm-ID: 380951 [Multi-domain]  Cd Length: 141  Bit Score: 132.42  E-value: 3.91e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKR--EKYYDSKGIgcYMFRIDDSEVVDATMHGNAARFINHSCE 3926
Cdd:cd19174      4 RFRTEDKGWGVRTKEPIKAGQFIIEYVGEVVSEQEFRRRmiEQYHNHSHH--YCLNLDSGMVIDGYRMGNEARFVNHSCD 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958798715 3927 PNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 3985
Cdd:cd19174     82 PNCEMQKWSVNGVYRIGLFALKDIPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 3856-3961 3.56e-33

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 125.71  E-value: 3.56e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGN-VIRSIQTDKREKYYDSKGI----GCYMFRIDDSE--VVDAT--MHGNAARFINHSCE 3926
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDEDSeyCIDARalYYGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958798715 3927 PNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYK 3961
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
PHD1_KMT2A cd15588
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1451-1497 4.56e-33

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 277063  Cd Length: 47  Bit Score: 123.14  E-value: 4.56e-33
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1451 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1497
Cdd:cd15588      1 VCFLCASSGHVEFVYCQVCCEPFHKFCLEEAERPLEDQLENWCCRRC 47
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 3845-3960 1.06e-32

SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380917  Cd Length: 117  Bit Score: 124.28  E-value: 1.06e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3845 EAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGcYMFRIDDSEVVDATMHGNAARFINHS 3924
Cdd:cd10519      1 KRLLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHS 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958798715 3925 CEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10519     80 SNPNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDY 115
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 3685-3768 1.64e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 122.79  E-value: 1.64e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  3685 LVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLSGAKHCRNYKFRFH 3764
Cdd:smart00542    2 FRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWFRYH 81


                    ....
gi 1958798715  3765 KPEE 3768
Cdd:smart00542   82 RSPL 85
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 3856-3984 5.61e-32

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.


Pssm-ID: 380940 [Multi-domain]  Cd Length: 245  Bit Score: 127.02  E-value: 5.61e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIgCYMFRID----DSE-VVDATMHGNAARFINHSCEPN-- 3928
Cdd:cd10542     99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDynddDCEyTVDAAYYGNISHFINHSCDPNla 177

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958798715 3929 CYSRVIN-IDGQK-HIVIFAMRKIYRGEELTYDYKFPIEDASN----------KLPCNCGAKKCRKFL 3984
Cdd:cd10542    178 VYAVWINhLDPRLpRIAFFAKRDIKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 1893-1997 4.92e-30

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: 116.53  E-value: 4.92e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANdAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLK--NVHMAVIRGKQLRCEFCQKP-GATVGCCLTS 1969
Cdd:cd15571      1 CALCPRSGGALKG-GGALKTTSDGLWVHVVCALWSPEVYFDDGTLLEveGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1958798715 1970 CTSNYHFMCSRAKNCVFL-----DDKKVYCQRH 1997
Cdd:cd15571     80 CPRSFHVSCAIRAGCLFEfedgpGNFVVYCPKH 112
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1499-1547 1.42e-29

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), 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 H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 113.20  E-value: 1.42e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQATK-LLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15590      1 FCHVCGRQHQATKqLLECNKCRNSYHPECLGPNYPTKPTKKKRVWICTKC 50
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 3849-3984 1.95e-29

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.


Pssm-ID: 380950 [Multi-domain]  Cd Length: 142  Bit Score: 116.26  E-value: 1.95e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVDATMHGNAARFINHSCEP 3927
Cdd:cd19173      6 PFKTGDRGWGLRTKRDIKKGDFVIEYVGELIDEEECRRRLKKAHENNItNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQP 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958798715 3928 NCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFpiEDASN-KLPCNCGAKKCRKFL 3984
Cdd:cd19173     86 NCETQKWTVNGDTRVGLFAVRDIPAGEELTFNYNL--DCLGNeKKVCRCGAPNCSGFL 141
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 1893-1997 1.22e-28

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 112.45  E-value: 1.22e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1972
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1958798715 1973 NYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 3837-3960 1.23e-27

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 113.62  E-value: 1.23e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3837 RHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGiGCYMFRIDDSE--------- 3907
Cdd:cd10538     81 RVVQRGLQARLQVFRTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIYDKSG-GSYLFDLDEFSdsdgdgeel 159

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958798715 3908 VVDATMHGNAARFINHSCEPNCYSRVINIDGQKH----IVIFAMRKIYRGEELTYDY 3960
Cdd:cd10538    160 CVDATFCGNVSRFINHSCDPNLFPFNVVIDHDDLryprIALFATRDILPGEELTFDY 216
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 1893-1998 2.04e-26

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 106.29  E-value: 2.04e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTS 1972
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*.
gi 1958798715 1973 NYHFMCSRAKNCVFLDDKKVYCQRHR 1998
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHK 106
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 3856-3960 2.67e-26

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.


Pssm-ID: 380920 [Multi-domain]  Cd Length: 122  Bit Score: 106.27  E-value: 2.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKgigCYMFRIDDSE-VVDATMHGNAARFINHSCEPNCYSRVI 3934
Cdd:cd10522     14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDP---LYPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                           90       100
                   ....*....|....*....|....*.
gi 1958798715 3935 NIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10522     91 TLKGEQHIGFVAIRDIKPGEELFISY 116
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1451-1497 2.68e-26

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 103.59  E-value: 2.68e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1451 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1497
Cdd:cd15506      1 LCFLCGSAGLNELLYCSVCCEPYHTFCLEEAERPLNINKDNWCCRRC 47
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 3847-3984 2.47e-25

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation.


Pssm-ID: 380987 [Multi-domain]  Cd Length: 142  Bit Score: 104.24  E-value: 2.47e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVDATMHGNAARFINHSC 3925
Cdd:cd19210      4 VEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIDEEECRARIRYAQEHDItNFYMLTLDKDRIIDAGPKGNYARFMNHCC 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3926 EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKfpIEDASN-KLPCNCGAKKCRKFL 3984
Cdd:cd19210     84 QPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYN--LECLGNgKTVCKCGAPNCSGFL 141
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 3849-3960 2.53e-25

SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes.


Pssm-ID: 380926 [Multi-domain]  Cd Length: 141  Bit Score: 104.20  E-value: 2.53e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKRE-KYYDSKGIGCYM--FRIDDSEV-VDATMH-GNAARFINH 3923
Cdd:cd10528     21 VIEIDGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREaLYAKDPSTGCYMyyFQYKGKTYcVDATKEsGRLGRLINH 100

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1958798715 3924 SC-EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10528    101 SKkKPNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 3852-3962 8.70e-25

SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380995  Cd Length: 120  Bit Score: 101.91  E-value: 8.70e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3852 SPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDsKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYS 3931
Cdd:cd19218     11 SDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYD-KYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYA 89

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958798715 3932 RVINIDGQKHIVIFAMRKIYRGEELTYDYKF 3962
Cdd:cd19218     90 KVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 3852-3967 1.00e-24

SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380994  Cd Length: 136  Bit Score: 102.45  E-value: 1.00e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3852 SPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDsKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYS 3931
Cdd:cd19217     13 SDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD-KYMSSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYA 91

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958798715 3932 RVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDA 3967
Cdd:cd19217     92 KVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQADA 127
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 3680-3764 2.66e-24

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 99.22  E-value: 2.66e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3680 KPKkgLVFEISSDDGFQICAESIEDAWKSLTDKVQEARSNARLKQLSFAGVNGLRMLGILHDAVVFLIEQLSGAKHCRNY 3759
Cdd:pfam05965    1 GPL--FRVTVEEDPDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1958798715 3760 KFRFH 3764
Cdd:pfam05965   79 KFRYG 83
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 3849-3984 2.87e-24

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.


Pssm-ID: 380942 [Multi-domain]  Cd Length: 254  Bit Score: 105.07  E-value: 2.87e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIrSIQTDKREKYYDSKGIGCYMF----RIDDSEV----VDATMHGNAARF 3920
Cdd:cd10544     94 VFKTPKKGWGLRTLEFIPKGRFVCEYAGEVI-GFEEARRRTKSQTKGDMNYIIvlreHLSSGKVletfVDPTYIGNIGRF 172

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958798715 3921 INHSCEPNCYSRVINIDGQ-KHIVIFAMRKIYRGEELTYDY------------KFPIEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd10544    173 LNHSCEPNLFMVPVRVDSMvPKLALFAARDIVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRGFL 249
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1585-1644 1.04e-23

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


Pssm-ID: 276983  Cd Length: 57  Bit Score: 96.75  E-value: 1.04e-23
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1585 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNLPESVAYTCVNC 1644
Cdd:cd15508      1 YCPLCEKCYDDDDYDSKMMQCSQCDHWVHAKCEGLS---DEMYEILSYLPESIEYTCSLC 57
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 3849-3984 1.37e-23

SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS).


Pssm-ID: 380988 [Multi-domain]  Cd Length: 142  Bit Score: 99.29  E-value: 1.37e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIG-CYMFRIDDSEVVDATMHGNAARFINHSCEP 3927
Cdd:cd19211      6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIDEEECMARIKHAHENDIThFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958798715 3928 NCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEdASNKLPCNCGAKKCRKFL 3984
Cdd:cd19211     86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCL-GNEKTVCRCGAPNCSGFL 141
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 3849-3984 1.97e-23

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.


Pssm-ID: 380999 [Multi-domain]  Cd Length: 259  Bit Score: 102.65  E-value: 1.97e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIgCYMFRID--DSEV-----VDATMHGNAARFI 3921
Cdd:cd20073     97 IFKTKHKGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYDNVGV-TYLFDLDlfEDQVdeyytVDAQYCGDVTRFI 175

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3922 NHSCEPN--CYSRVINIDGQK--HIVIFAMRKIYRGEELTYDYKFPIED----------------ASNKLPCNCGAKKCR 3981
Cdd:cd20073    176 NHSCDPNlaIYSVLRDKSDSKiyDLAFFAIKDIPALEELTFDYSGRNNFdqlgfignrsnskyinLKNKRPCYCGSANCR 255


                   ...
gi 1958798715 3982 KFL 3984
Cdd:cd20073    256 GWL 258
PHD1_KMT2B cd15589
PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1451-1497 4.61e-23

PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 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 through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 277064  Cd Length: 47  Bit Score: 94.54  E-value: 4.61e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1451 VCFLCASSGHVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRC 1497
Cdd:cd15589      1 VCLLCASKGQHELLFCQVCCEPFHRFCLEESERPLPEQEENWCCRRC 47
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 3856-3984 2.45e-21

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy.


Pssm-ID: 380989 [Multi-domain]  Cd Length: 142  Bit Score: 93.07  E-value: 2.45e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGI-GCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVI 3934
Cdd:cd19212     13 GWGLRTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSVtNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQKW 92

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3935 NIDGQKHIVIFAMRKIYRGEELTYDYKFPIEdASNKLPCNCGAKKCRKFL 3984
Cdd:cd19212     93 TVNGDVRVGLFALCDIPAGMELTFNYNLDCL-GNGRTECHCGADNCSGFL 141
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 1145-1192 6.07e-21

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 88.57  E-value: 6.07e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1145 KKGRRSRRCGQCPGCQVPEDCGVCTNCLDKPKFGGRNIKKQCCKMRKC 1192
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1585-1644 2.82e-20

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


Pssm-ID: 277068  Cd Length: 57  Bit Score: 86.83  E-value: 2.82e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1585 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNLPESVAYTCVNC 1644
Cdd:cd15593      1 YCPICLKCYEDNDYESKMMQCAKCDHWVHAKCEGLS---DELYEILSSLPDSVVYSCAPC 57
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 3837-3984 2.94e-20

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380930 [Multi-domain]  Cd Length: 243  Bit Score: 93.03  E-value: 2.94e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3837 RHLKKTSKEAVGVYRSPiHGRGLFCK--RNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIgCYMFRID---DSEVVDA 3911
Cdd:cd10532     76 RVVQKGTQYSLCIFRTS-NGRGWGVKtlQKIKKNSFVMEYVGEVITSEEAERRGQFYDSKGI-TYLFDLDyesDEFTVDA 153

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3912 TMHGNAARFINHSCEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDYKF------PIEDASN-------KLPCN 3974
Cdd:cd10532    154 ARYGNVSHFVNHSCDPNLQVFNVFIDNLDtrlpRIALFSTRTIKAGEELTFDYQMkgsgdlSSDSIDNspakkrvRTVCK 233

                          170
                   ....*....|
gi 1958798715 3975 CGAKKCRKFL 3984
Cdd:cd10532    234 CGAVTCRGYL 243
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 3856-3984 4.78e-19

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380923 [Multi-domain]  Cd Length: 255  Bit Score: 89.95  E-value: 4.78e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIgCYMFRID---DSEVVDATMHGNAARFINHSCEPN--CY 3930
Cdd:cd10525     98 GWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQGA-TYLFDLDyveDVYTVDAAYYGNISHFVNHSCDPNlqVY 176

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958798715 3931 SRVI-NIDGQ-KHIVIFAMRKIYRGEELTYDYKF---PIEDASNKL-------------------PCNCGAKKCRKFL 3984
Cdd:cd10525    177 NVFIdNLDERlPRIALFATRTIRAGEELTFDYNMqvdPVDAESTKMdsnfglaglpgspkkrvriECKCGVRSCRKYL 254
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 3847-3960 5.26e-19

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


Pssm-ID: 380914 [Multi-domain]  Cd Length: 72  Bit Score: 83.84  E-value: 5.26e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEyagnvirsiqtdkrekyydskgigcymfriddsevvdatmhgnaARFINHSCE 3926
Cdd:cd08161      2 IRPSTIPGAGFGLFATRDIPKGEVIGL--------------------------------------------ARFINHSCE 37

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1958798715 3927 PNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd08161     38 PNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 3857-3960 8.06e-19

SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380927  Cd Length: 127  Bit Score: 85.02  E-value: 8.06e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3857 RGLFCKRNIDAGEMVIEYAGNVirSIQTDKREKYYDSKGIGCYMF---RIDDSEV-VDATMHGNAARFINHSCEPNCYSR 3932
Cdd:cd10529     17 KGLVATEDISPGEPILEYKGEV--SLRSEFKEDNGFFKRPSPFVFfydGFEGLPLcVDARKYGNEARFIRRSCRPNAELR 94

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958798715 3933 -VINIDGQKHIVIFAMRKIYRGEELT--YDY 3960
Cdd:cd10529     95 hVVVSNGELRLFIFALKDIRKGTEITipFDY 125
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1499-1547 4.32e-18

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


Pssm-ID: 276982  Cd Length: 50  Bit Score: 80.20  E-value: 4.32e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQATK-LLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15507      1 FCHVCGRKGQAQKqLLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 1893-1997 1.34e-17

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: 81.28  E-value: 1.34e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALClmYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVF------EDDDGS--LKNVHMAVIRGKQLRCEFCQKPGATVG 1964
Cdd:cd15673      1 CGFC--KSGEENKETGGKLASGEKIAAHHNCMLFSSGLVqyvspnENDFGGfdIEDVKKEIKRGRKLKCNLCKKTGATIG 78

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1958798715 1965 CCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1997
Cdd:cd15673     79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 3856-3984 1.78e-17

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.


Pssm-ID: 380996 [Multi-domain]  Cd Length: 274  Bit Score: 85.83  E-value: 1.78e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTD-KREKYYDSKGIGCYMFRID---DSEVVDATMHGNA-----------ARF 3920
Cdd:cd19473    117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFALDkfsDPDSLDPRLRGDPyeidgefmsgpTRF 196

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958798715 3921 INHSCEPN--CYSRVINIdGQKHI---VIFAMRKIYRGEELTYDY----------KFPIEDASNKLPCNCGAKKCRKFL 3984
Cdd:cd19473    197 INHSCDPNlrIFARVGDH-ADKHIhdlAFFAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGYL 274
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 3849-3981 3.72e-17

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380933 [Multi-domain]  Cd Length: 231  Bit Score: 83.83  E-value: 3.72e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKyyDSkgigcYMFRID--DSEV--VDATMHGNAARFINHS 3924
Cdd:cd10535     95 LYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE--DS-----YLFDLDnkDGEVycIDARFYGNVSRFINHH 167

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 3925 CEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDYKFPIEDASNKL-PCNCGAKKCR 3981
Cdd:cd10535    168 CEPNLVPVRVFMAHQDlrfpRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 1918-1997 3.85e-17

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: 79.66  E-value: 3.85e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1918 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1996
Cdd:cd15668     24 WVHEDCAVWAPGVYLVG-GKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENfSLLCPK 102


                   .
gi 1958798715 1997 H 1997
Cdd:cd15668    103 H 103
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 3845-3960 3.89e-17

SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380945  Cd Length: 124  Bit Score: 80.31  E-value: 3.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3845 EAVGVYRSPIH-GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGiGCYMFRIDDSEVVDATMHGNAARFINH 3923
Cdd:cd19168      1 KAVVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVS-YLYLFEEQEGIWVDAAIYGNLSRYINH 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1958798715 3924 SCEP----NCYSRVINIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd19168     80 ATDKvktgNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNY 120
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 1918-1997 5.69e-17

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: 78.52  E-value: 5.69e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1918 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCvFLDDKK--VYCQ 1995
Cdd:cd15665     10 YAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGC-FQDIKTltLFCP 88


                   ..
gi 1958798715 1996 RH 1997
Cdd:cd15665     89 EH 90
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 3849-3981 1.15e-16

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380941 [Multi-domain]  Cd Length: 231  Bit Score: 82.39  E-value: 1.15e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKyyDSkgigcYMFRIDDSEV----VDATMHGNAARFINHS 3924
Cdd:cd10543     95 LFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED--DS-----YLFDLDNKDGetycIDARRYGNISRFINHL 167

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3925 CEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDY--KF-PIEdaSNKLPCNCGAKKCR 3981
Cdd:cd10543    168 CEPNLIPVRVFVEHQDlrfpRIAFFASRDIKAGEELGFDYgeKFwRIK--GKYFTCRCGSPKCK 229
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 3849-3981 2.30e-16

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380931 [Multi-domain]  Cd Length: 239  Bit Score: 81.60  E-value: 2.30e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKyyDSkgigcYMFRID--DSEV--VDATMHGNAARFINHS 3924
Cdd:cd10533     95 LYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED--DS-----YLFDLDnkDGEVycIDARYYGNISRFINHL 167

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 3925 CEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDYKFPIEDASNK-LPCNCGAKKCR 3981
Cdd:cd10533    168 CDPNIIPVRVFMLHQDlrfpRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 2044-2091 4.58e-16

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 74.46  E-value: 4.58e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 2044 GSMTIDCLGIL---NDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKI 2091
Cdd:pfam05964    1 GSLTVLSLGEIvpdRPAFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 1893-1997 5.15e-16

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: 76.52  E-value: 5.15e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMyGDDSANDAGRLLYIGqNEWTHVNCALWSAEVF---EDDDG----SLKNVHMAVIRGKQLRCEFCQKPGATVGC 1965
Cdd:cd15669      1 CVLCGR-SDDDPDKYGEKLQKD-GICAHYFCLLFSSGLPqrgEDNEGiygfLPEDIRKEVRRASRLRCFYCKKKGASIGC 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1958798715 1966 CLTSCTSNYHFMCSRAKNCV--FLDDKKVYCQRH 1997
Cdd:cd15669     79 AVKGCRRSFHFPCGLENGCVtqFFGEYRSFCWEH 112
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 1920-1997 9.42e-16

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: 75.06  E-value: 9.42e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1920 HVNCALWSAEVFEDDDGS----LKNVHMAVIRGKQLRCEFC-QKPGATVGCCLTSCTSNYHFMCSRAKNCVF-----LDD 1989
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqfdedNGT 80


                   ....*...
gi 1958798715 1990 KKVYCQRH 1997
Cdd:pfam13771   81 FKSYCKKH 88
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 2050-2093 1.34e-15

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 73.09  E-value: 1.34e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 1958798715  2050 CLGILNDLSDCEDKLFPIGYQCSRVYWSTTDARKRCVYTCKIME 2093
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1499-1547 1.37e-15

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


Pssm-ID: 277066  Cd Length: 50  Bit Score: 73.43  E-value: 1.37e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQATK-LLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15591      1 FCHVCGRKNKESKpLLECERCRNCYHPACLGPNYPKPANRKKRPWICSAC 50
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 3849-3984 3.82e-15

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380939 [Multi-domain]  Cd Length: 236  Bit Score: 77.97  E-value: 3.82e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKrEKYYDSKGIGCYMFRIDDS-EVVDATMHGNAARFINHSCEP 3927
Cdd:cd10541     96 LFKTQNKGWGIRCLDDIAKGTFVCIYAGKILTDDFADK-EGLEMGDEYFANLDHIEEScYIIDAKLEGNLGRYLNHSCSP 174

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 3928 NCYSRVINIDGQKH----IVIFAMRKIYRGEELTYDYKFPIEDASNK-LPCNCGAKKCRKFL 3984
Cdd:cd10541    175 NLFVQNVFVDTHDLrfpwVAFFASKRIKAGTELTWDYNYEVGSVEGKeLLCCCGSNECRGRL 236
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 1893-1997 4.02e-15

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: 74.16  E-value: 4.02e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALClmygddSANDAGRLLYIG--QNEWTHVNCALWSAEVFEDDDGSLKN---------VHMAVIRGKQLRCEFCQKPGA 1961
Cdd:cd15712      1 CAFC------PKGEEYSIMYFAqeQNIAAHQNCLLYSSGFVESEEYNPLNldrrfdvesVLNEIKRGKRLKCNFCRKKGA 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1958798715 1962 TVGCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1997
Cdd:cd15712     75 TVGCEERACRRSYHYFCALCDDAAIETDEvrgiyRVFCQKH 115
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 3856-3984 1.99e-14

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 76.94  E-value: 1.99e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3856 GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREK-----Y----------------YDSKG-IGCYmfriddseVVDATM 3913
Cdd:cd10517    140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLqygdeYfaeldyievveklkegYESDVeEHCY--------IIDAKS 211

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958798715 3914 HGNAARFINHSCEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDYKFPIEDASNK-LPCNCGAKKCRKFL 3984
Cdd:cd10517    212 EGNLGRYLNHSCSPNLFVQNVFVDTHDlrfpWVAFFASRYIRAGTELTWDYNYEVGSVPGKvLYCYCGSSNCRGRL 287
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 3849-3984 5.56e-14

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380921 [Multi-domain]  Cd Length: 266  Bit Score: 75.25  E-value: 5.56e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQT---------DKREKYYDSKGIGCYMFRI-----DDSEVVDATMH 3914
Cdd:cd10523    112 VFKTEKKGWGVRCLDDIDKGTFVCIYAGRVLSRARSpteplppklELPSENEVEVVTSWLILSKkrklrENVCFLDASKE 191

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958798715 3915 GNAARFINHSCEPNCYSRVINIDGQKH----IVIFAMRKIYRGEELTYDYKFPIEDASNK-LPCNCGAKKCRKFL 3984
Cdd:cd10523    192 GNVGRFLNHSCCPNLFVQNVFVDTHDKnfpwVAFFTNRVVKAGTELTWDYSYDAGTSPEQeIPCLCGVNKCQKKI 266
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 1918-1981 6.04e-14

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 69.97  E-value: 6.04e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 1918 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRA 1981
Cdd:cd15696     10 WAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAG 73
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 1918-1981 1.58e-12

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 66.09  E-value: 1.58e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 1918 WTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRA 1981
Cdd:cd15695     10 WVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAA 73
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 1918-1997 1.74e-12

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. 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. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 66.44  E-value: 1.74e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1918 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1996
Cdd:cd15700     25 WVHEACAVWTTGVYLVA-GKLFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENfSLRCPK 103


                   .
gi 1958798715 1997 H 1997
Cdd:cd15700    104 H 104
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 3855-3960 1.80e-12

SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions.


Pssm-ID: 380997 [Multi-domain]  Cd Length: 122  Bit Score: 67.02  E-value: 1.80e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3855 HGRGLFCKRNIDAGEMVI-EYAgnvIRSIQTDKREKYYDSKGIGCYMFRIddsevvdatmhgnaARFINHSCEPNCysrV 3933
Cdd:cd20071      9 KGRGLVATRDIEPGELILvEKP---LVSVPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA---V 68

                           90       100
                   ....*....|....*....|....*..
gi 1958798715 3934 INIDGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd20071     69 VVFDGNGTLRVRALRDIKAGEELTISY 95
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 3858-3964 3.21e-12

SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression.


Pssm-ID: 380960  Cd Length: 173  Bit Score: 67.81  E-value: 3.21e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3858 GLFCKRNIDAGEMVIEYAGNVIR--SIQTDKREKYYDSKGIGCYMFRIDDSE-VVDATMHGNAARFINHSCEPNC--YSR 3932
Cdd:cd19183     15 GLFADRPIPAGDPIQELLGEIGLqsEYIADPENQYQILGAPKPHVFFHPQSPlYIDTRRSGSVARFIRRSCRPNAelVTV 94

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1958798715 3933 VINIDGQKHIVIFAMRKIYRGEELTYDYKFPI 3964
Cdd:cd19183     95 ASDSGSVLKFVLYASRDISPGEEITIGWDWDN 126
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 3849-3960 1.84e-11

SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380943 [Multi-domain]  Cd Length: 232  Bit Score: 67.04  E-value: 1.84e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREK----------YYDSKGIGCYMFRIDDSE----------- 3907
Cdd:cd10545     90 VFKTAERGWGVRSWDSIPAGSFICEYVGELLDTSEADTRSGnddylfdidnRQTNRGWDGGQRLDVGMSdgerssaedee 169

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 3908 ----VVDATMHGNAARFINHSCEPNCYSRVINIDGQK----HIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10545    170 ssefTIDAGSFGNVARFINHSCSPNLFVQCVLYDHNDlrlpRVMLFAADNIPPLQELTYDY 230
BROMO smart00297
bromo domain;
1653-1785 2.94e-11

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 63.07  E-value: 2.94e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715  1653 RLALEKELQASLKQVLTALLNSRTTSHLLryrqaaKPPDLNpeteesipsrsspEGPDppvltevSKQDEQQPLDLEGVK 1732
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFL------KPVSRK-------------EAPD-------YYDIIKKPMDLKTIK 54

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1958798715  1733 KKMDQGNYVSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERV 1785
Cdd:smart00297   55 KKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1499-1547 4.00e-10

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: 57.61  E-value: 4.00e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1958798715  1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGK--WYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1451-1500 8.71e-10

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


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 56.73  E-value: 8.71e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 1451 VCFLCASSG-HVEFVYCQVCCEPFHKFCLEENERPLEDQLENWCCRRCKFC 1500
Cdd:pfam00628    1 YCAVCGKSDdGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 1893-1997 1.14e-09

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. 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.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 58.94  E-value: 1.14e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMyGDDSANDAGRL-LYIGQNEWTHVNCALWSAEVF--------EDDDGSLKNVHMAVIRGKQLRCEFCQKPGATV 1963
Cdd:cd15711      1 CGFCHA-GEEENETRGKLhIFNAKKAAAHYKCMLFSSGTVqltttsraEFGDFDIKTVIQEIKRGKRMKCTLCSQLGATI 79

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1958798715 1964 GCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1997
Cdd:cd15711     80 GCEIKACVKTYHYHCGVQDKAKYIENMsrgiyKLYCKNH 118
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 3849-3980 2.11e-09

SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression.


Pssm-ID: 380958  Cd Length: 150  Bit Score: 58.87  E-value: 2.11e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYdSKGIGCYMFRIDDSEV---VDATMHGNAARFINHSC 3925
Cdd:cd19181     11 VTRVQKHRKILRAARDLALDTLIIEYRGKVMLRQQFEVNGHFF-KRPYPFVLFYSKFNGVemcVDARTFGNDARFIRRSC 89

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958798715 3926 EPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNC--GAKKC 3980
Cdd:cd19181     90 TPNAEVRHMIADGMIHLCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1499-1550 2.34e-09

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: 55.58  E-value: 2.34e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNyPTKPTKKKKVWICTKCVRC 1550
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPP-LDPAEIPSGEWLCPECKPK 51
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 1918-1997 2.37e-09

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. 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). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 57.23  E-value: 2.37e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1918 WTHVNCALWSAEVFEDDdGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCVFLDDK-KVYCQR 1996
Cdd:cd15699     24 WVHEGCILWANGIYLVC-GRLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCLLNEENfSVRCPK 102


                   .
gi 1958798715 1997 H 1997
Cdd:cd15699    103 H 103
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
1891-1997 4.34e-09

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 56.58  E-value: 4.34e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1891 RQCALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNV---HMAVIRGKqLRCEFCQKP-GATVGCC 1966
Cdd:pfam13832    1 VRCCLCPLRG-------GALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPIdvsRIPPERWK-LKCVFCKKRsGACIQCS 72

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1958798715 1967 LTSCTSNYHFMCSRAKNCVF-LDD-----KKVYCQRH 1997
Cdd:pfam13832   73 KGRCTTAFHVTCAQAAGVYMePEDwpnvvVIAYCQKH 109
SET_SpSet7-like cd10540
SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces ...
 3849-3960 1.28e-08

SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces pombe Set7 is a novel histone-lysine N-methyltransferase. The family also includes a viral histone H3 lysine 27 methyltransferase from Paramecium bursaria Chlorella virus 1 (PBCV-1).


Pssm-ID: 380938  Cd Length: 112  Bit Score: 55.34  E-value: 1.28e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3849 VYRSPIHGRGLFCKRNIDAGEmVIEYAGNVIRSIqtdkrEKYYDSKG--IGCYMFRIDDSEVVDATMHGNAArfiNHSCE 3926
Cdd:cd10540      4 VKPSTLKGRGVFATRPIKKGE-VIEEAPVIVLPK-----EEYQHLCKtvLDHYVFSWGDGCLALALGYGSMF---NHSYT 74

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1958798715 3927 PNCYsRVINIDGQKhIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10540     75 PNAE-YEIDFENQT-IVFYALRDIEAGEELTINY 106
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 1893-1997 1.64e-08

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. 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. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 55.35  E-value: 1.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDDsanDAGRLLyIGQNE--WTHVNCALWS-AEVFEDDDG------SLKNVHMAVIRGKQLRCEFCQKPGATV 1963
Cdd:cd15710      1 CGFCRSNREK---ECGQLL-ISENQkvAAHHKCMLFSsALVSSHSDSenlggfSIEDVQKEIKRGTKLMCSLCHCPGATI 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1958798715 1964 GCCLTSCTSNYHFMCSrakncvfLDDKK------------VYCQRH 1997
Cdd:cd15710     77 GCDVKTCHRTYHYYCA-------LHDKAqirenpsqgiymIYCRKH 115
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1499-1547 2.15e-07

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 50.01  E-value: 2.15e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1499 FCHVCGRQHQAT-KLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:cd15489      1 SCIVCGKGGDLGgELLQCDGCGKWFHADCLGPPLSSFVPNGK--WICPVC 48
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 3909-3962 4.64e-07

SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide.


Pssm-ID: 380959  Cd Length: 129  Bit Score: 51.43  E-value: 4.64e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958798715 3909 VDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKF 3962
Cdd:cd19182     73 VDARTFGNEARFIRRSCTPNAEVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDF 126
SET_ATXR5_6-like cd10539
SET domain found in fungal protein lysine methyltransferase SET5 and similar protein; The ...
 3863-3966 1.26e-06

SET domain found in fungal protein lysine methyltransferase SET5 and similar protein; The family includes Arabidopsis thaliana ATXR5 and ATXR6. Both ATXR5 (also termed protein SET DOMAIN GROUP 15, or TRX-related protein 5) and ATXR6 (also termed protein SET DOMAIN GROUP 34, or TRX-related protein 6) function as histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). They are required for chromatin structure and gene silencing.


Pssm-ID: 380937  Cd Length: 138  Bit Score: 50.49  E-value: 1.26e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3863 RNIDAGEMVIEYAGNVirsiQTDKREKYYDSKGIGCYMFRIDDSE--VVDATMHGNAARFI----NHSCE----PNCYSR 3932
Cdd:cd10539     22 GFIKDLTIIAEYTGDV----DYIRNREFDDNDSIMTLLLAGDPSKslVICPDKRGNIARFIsginNHTKDgkkkQNCKCV 97

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1958798715 3933 VINIDGQKHIVIFAMRKIYRGEELTYDY-----KFPIED 3966
Cdd:cd10539     98 RYSINGEARVLLVATRDIAKGERLYYDYngyehEYPTEH 136
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 3855-3960 1.35e-06

SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions.


Pssm-ID: 380922 [Multi-domain]  Cd Length: 141  Bit Score: 50.74  E-value: 1.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3855 HGRGLFCKRNIDAGEmVIEYAGNVIRSIQTDkrEKYYDSKGIGCYMFRIDDSEVVDATMHGnAARFINHSCEPNCysRVI 3934
Cdd:cd10524     18 YGAKIIATKPIKKGE-KIHELCGCIAELSEE--EEALLRPGGNDFSVMYSSRKKCSQLWLG-PAAFINHDCRPNC--KFV 91

                           90       100
                   ....*....|....*....|....*.
gi 1958798715 3935 NIdGQKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10524     92 PT-GKSTACVKVLRDIEPGEEITVYY 116
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 1893-1997 1.72e-06

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: 49.36  E-value: 1.72e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGDD-SANDAGRllyigqnEWTHVNCALWSAEV-FEDDDG--SLKNV-HMAVIRgKQLRCEFCQ-KPGATVGCC 1966
Cdd:cd15671      1 CVLCPKKGGAmKSTKSGT-------KWVHVSCALWIPEVsIGCPEKmePITKIsHIPMSR-WALVCVLCKeKTGACIQCS 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1958798715 1967 LTSCTSNYHFMCS-----RAKNCVFLDDKKV----YCQRH 1997
Cdd:cd15671     73 VKSCKTAFHVTCAfqhglEMKTILEDEDDEVkfksYCPKH 112
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1599-1647 9.06e-06

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: 45.56  E-value: 9.06e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSgteDEMYEILSNlpesvAYTCVNCTER 1647
Cdd:pfam00628   11 GGELVQCDGCDDWFHLACLGPP---LDPAEIPSG-----EWLCPECKPK 51
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 1893-1997 2.17e-05

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: 46.20  E-value: 2.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGK--QLRCEFCQK-------PGATV 1963
Cdd:cd15675      1 CCLCCLRG-------GALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPIDISKIPPArlKLKCIYCSKitksmshMGACI 73

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1958798715 1964 GCCLTSCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1997
Cdd:cd15675     74 QCSTGKCTTSFHVTCAHAAGVQMEPDDwpypvYVTCTKH 112
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 1916-1997 2.42e-05

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: 46.17  E-value: 2.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1916 NEWTHVNCALWSAEVfedddgSLKN-VHMAVIRGKQ--------LRCEFC-QKPGATVGCCLTSCTSNYHFMC------- 1978
Cdd:cd15670     17 GRWAHVVCALWIPEV------SFANtVFLEPIDGIQnipkarwkLTCYICkKRMGACIQCHKKNCYTAFHVTCaqqagly 90

                           90       100
                   ....*....|....*....|....*.
gi 1958798715 1979 -----SRAKNCVFLDD--KKVYCQRH 1997
Cdd:cd15670     91 mkiepVKDPGNGTSDSvrKEAYCDKH 116
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1603-1644 9.55e-05

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 42.54  E-value: 9.55e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958798715 1603 MQCGKCDRWVHSKCEGLSGTEDEMYEIlsnlpesvaYTCVNC 1644
Cdd:cd15517     17 VQCDGCDKWFHQFCLGLSNERYADEDK---------FKCPNC 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1451-1497 9.69e-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: 42.58  E-value: 9.69e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1958798715  1451 VCFLCASSGH-VEFVYCQVCCEPFHKFCLEENERPlEDQLENWCCRRC 1497
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDGCDRWYHQTCLGPPLLE-EEPDGKWYCPKC 47
SET_SMYD4 cd10536
SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing ...
 3920-3960 1.01e-04

SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins; SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. In zebrafish, SMYD4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart; mutants show a strong defect in cardiomyocyte proliferation, which lead to a severe cardiac malformation.


Pssm-ID: 380934 [Multi-domain]  Cd Length: 218  Bit Score: 46.52  E-value: 1.01e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1958798715 3920 FINHSCEPNCysrVINIDGQKhIVIFAMRKIYRGEELTYDY 3960
Cdd:cd10536    153 LLNHSCDPNT---IRSFYGNT-IVVRATRPIKKGEEITICY 189
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1599-1644 1.13e-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: 42.20  E-value: 1.13e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1958798715  1599 ESKMMQCGKCDRWVHSKCEGLSGTEDemyeilsnlPESVAYTCVNC 1644
Cdd:smart00249   11 GGELLQCDGCDRWYHQTCLGPPLLEE---------EPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1952-1997 1.30e-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: 42.20  E-value: 1.30e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1958798715  1952 RCEFCQKP---GATVGCCltSCTSNYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:smart00249    1 YCSVCGKPddgGELLQCD--GCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 1917-1997 2.00e-04

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: 43.56  E-value: 2.00e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1917 EWTHVNCALWSAEVF----EDDDGSLKNVHMAVIRGkQLRCEFCQ-KPGATVGCCLTSCTSNYHFMCSRAKNC---VFLD 1988
Cdd:cd15706     19 KWAHVSCALWIPEVSiacpERMEPITKVSHIPPSRW-ALVCSLCKlKTGACIQCSVKSCITAFHVTCAFEHSLemkTILD 97

                           90
                   ....*....|....
gi 1958798715 1989 DK-----KVYCQRH 1997
Cdd:cd15706     98 EGdevkfKSYCLKH 111
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1601-1644 2.35e-04

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


Pssm-ID: 276989  Cd Length: 51  Bit Score: 41.50  E-value: 2.35e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958798715 1601 KMMQCGKCDRWVHSKCEGLSgTEDEMyEILSNlpesVAYTCVNC 1644
Cdd:cd15514     14 LIIQCSQCERWLHGACDSLR-TEEEA-ERAAD----NGYRCLLC 51
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1499-1547 3.56e-04

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


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 40.73  E-value: 3.56e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1499 FCHVCGrqhQATKLLECNKCRNSYHPECLGPNyptKPTKKKKVWICTKC 1547
Cdd:cd15532      1 FCRVCK---DGGELLCCDGCPSSYHLHCLNPP---LAEIPDGDWFCPRC 43
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2958-3354 4.22e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.68  E-value: 4.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 2958 SQNSSRLAVISDSGEKRVTITEKSVTSTEGDPALLSPGVDPAPEGHMTPDHFIQGHMDADHISSPPCGSVEQGHGNNQDl 3037
Cdd:pfam03154   79 SAKRQREKGASDTEEPERATAKKSKTQEISRPNSPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIPSPQDNESD- 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3038 TRNSSTPGLQVPVSPTVPIQNQKYVPNSTDSPGPSQISNAA----VQTTPPHLKPATEKLIVVNQN-MQPLYVLQTLPNG 3112
Cdd:pfam03154  158 SDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGptpsAPSVPPQGSPATSQPPNQTQStAAPHTLIQQTPTL 237

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3113 VTQKI--------QLTSP-----VSSTPNVMETNTSVLGPMGSGLTLTTGLNP-SLPP---------SQSLFPPASKGLL 3169
Cdd:pfam03154  238 HPQRLpsphpplqPMTQPpppsqVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQhPVPPqpfpltpqsSQSQVPPGPSPAA 317

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3170 SMPHHQHLHSFP--AAAQSSFPPNISS-PPSGL-LIGVQPPPD---PQLLGSEANQRTDLTTTVT--------TPSSGLK 3234
Cdd:pfam03154  318 PGQSQQRIHTPPsqSQLQSQQPPREQPlPPAPLsMPHIKPPPTtpiPQLPNPQSHKHPPHLSGPSpfqmnsnlPPPPALK 397

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3235 krPISRLHTRKnkklAPSSAPsniAPSDVVSNMTLINFTPSQ---LSNHPSLLDLGSLNP--SSHRTVPNIIKRSKSGIM 3309
Cdd:pfam03154  398 --PLSSLSTHH----PPSAHP---PPLQLMPQSQQLPPPPAQppvLTQSQSLPPPAASHPptSGLHQVPSQSPFPQHPFV 468

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*
gi 1958798715 3310 YFEQAPLLPPQSVGGTTATGAGSSTISQDTSHLTSGPVSALASGS 3354
Cdd:pfam03154  469 PGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCP 513
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 1893-1980 4.51e-04

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: 42.76  E-value: 4.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALClmygddsANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNV----HMAVIRGKqLRCEFCQK--PGATVGCC 1966
Cdd:cd15701      1 CALC-------PNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIdsieHIPPARWK-LTCYICKQrgSGACIQCH 72

                           90
                   ....*....|....
gi 1958798715 1967 LTSCTSNYHFMCSR 1980
Cdd:cd15701     73 KANCYTAFHVTCAQ 86
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 1893-1997 4.54e-04

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: 42.46  E-value: 4.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMavIRGKQ-----LRCEFCQKP-GATVGCC 1966
Cdd:cd15662      1 CCLCPVVG-------GALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDG--INAISkerweLSCTICKQRyGACIQCS 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1958798715 1967 LTSCTSNYHFMCSRAKN-CVFLDDKKV------------YCQRH 1997
Cdd:cd15662     72 NNSCRVAYHPLCARAAGlCMEVADEGGedpgdqglrllsYCPRH 115
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1500-1547 4.96e-04

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


Pssm-ID: 277000  Cd Length: 47  Bit Score: 40.43  E-value: 4.96e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDE--WYCPDC 47
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1499-1547 4.98e-04

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


Pssm-ID: 277011  Cd Length: 46  Bit Score: 40.48  E-value: 4.98e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKC 1547
Cdd:cd15536      1 YCEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEE---WFCPEC 46
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 1723-1777 5.38e-04

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


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 41.97  E-value: 5.38e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958798715 1723 QQPLDLEGVKKKMDQGNYVSVLEFSDDIVKIIQAAINSDGGQPEI-KKANSMVKSF 1777
Cdd:cd04369     40 KNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIyKDAKKLEKLF 95
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1599-1644 5.53e-04

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


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 40.38  E-value: 5.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSGTEdemyeilsnLPESVAYTCVNC 1644
Cdd:cd15489     12 GGELLQCDGCGKWFHADCLGPPLSS---------FVPNGKWICPVC 48
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
 1918-1997 6.03e-04

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: 42.12  E-value: 6.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1918 WTHVNCALWSAEV-FEDDDG-----SLKNVHMAVIRGKqlrCEFC-QKPGATVGCCltSCTSNYHFMC-SRA-------- 1981
Cdd:cd15663     20 WVHVTCAWFRPEVcFKNEEKmepavGLLRIPLSTFLKA---CVICkQIHGSCTQCC--KCATYFHAMCaSRAgyhmelhc 94

                           90
                   ....*....|....*...
gi 1958798715 1982 --KNCVFLDDKKVYCQRH 1997
Cdd:cd15663     95 leKNGVQITRMVSYCSFH 112
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 1917-1997 6.99e-04

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: 42.00  E-value: 6.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1917 EWTHVNCALWSAEVF----EDDDGSLKNVHMAVIRGKqLRCEFCQK-PGATVGCCLTSCTSNYHFMCSRAKN----CVFL 1987
Cdd:cd15705     19 KWVHVSCALWIPEVSigcpEKMEPITKISHIPASRWA-LSCSLCKEcTGTCIQCSMPSCITAFHVTCAFDHGlemrTTLA 97

                           90
                   ....*....|....
gi 1958798715 1988 DDKKV----YCQRH 1997
Cdd:cd15705     98 DNDEVkfksFCLEH 111
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1500-1547 9.03e-04

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


Pssm-ID: 277002  Cd Length: 46  Bit Score: 39.67  E-value: 9.03e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKC 1547
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGK---WVCQIC 46
SET_SMYD3 cd19203
SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 ...
 3896-3960 9.64e-04

SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins; SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. It is overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers.


Pssm-ID: 380980 [Multi-domain]  Cd Length: 210  Bit Score: 43.51  E-value: 9.64e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958798715 3896 IGCYMFRIDDSEVVDAT--MHGNAARFiNHSCEPNCysrVINIDGqKHIVIFAMRKIYRGEELTYDY 3960
Cdd:cd19203    120 VTCNSFTICDAEMQEVGvgLYPSASLL-NHSCDPNC---VIVFNG-PHLLLRAIREIEVGEELTISY 181
PHD_Hop1p_like cd15558
PHD finger found in Schizosaccharomyces pombe meiosis-specific protein hop1 (Hop1p) and ...
 1599-1641 1.10e-03

PHD finger found in Schizosaccharomyces pombe meiosis-specific protein hop1 (Hop1p) and similar proteins; Fission yeast Hop1p, also termed linear element-associated protein hop1, is an S. pombe homolog of the synaptonemal complex (SC)-associated protein Hop1 in Saccharomyces cerevisiae. In contrast to S. cerevisiae, S. pombe forms thin threads, known as linear elements (LinEs), in meiotic nuclei, instead of a canonical synaptonemal complex. LinEs contain Rec10 protein and are evolutionary relics of SC axial elements. Fission yeast Hop1p is a linear element (LinE)-associated protein. It also associates with Rec10, which plays a role in recruiting the recombination machinery to chromatin. Hop1p contains an N-terminal HORMA (for Hop1p, Rev7p, and MAD2) domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277033  Cd Length: 47  Bit Score: 39.35  E-value: 1.10e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSGTEDEmyeilsNLPES-VAYTC 1641
Cdd:cd15558     10 DGAMIQCAFCDTWQHLLCYGFESAKDP------RIPDIhVCYRC 47
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 1893-1997 1.18e-03

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: 41.43  E-value: 1.18e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddSANDAGRllyiGQNEWTHVNCALWSAEV----FEDDDGSLKNVHMAVIRGkQLRCEFC-QKPGATVGCCL 1967
Cdd:cd15707      1 CILCPNKG--GAMKSTR----SGTKWAHVSCALWIPEVsigcVEKMEPITKISSIPASRW-ALICVLCrERTGACIQCSV 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1958798715 1968 TSCTSNYHFMCSRAKNC---VFLDDK-------KVYCQRH 1997
Cdd:cd15707     74 KTCKTAYHVTCGFQHGLemkTILDEEsedgvklRSYCQKH 113
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1585-1644 1.21e-03

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 39.77  E-value: 1.21e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 1585 FCPLCDKCYDDDDYESK-MMQCGKCDRWVHSKCEGLSGTEDEMYeilsNLPESVAYTCVNC 1644
Cdd:cd15615      1 FCILCGQVYEENEGDEKeWVQCDSCSEWVHFECDGRTGLGAFKY----AKSDGLQYVCPRC 57
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
 1500-1547 1.33e-03

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


Pssm-ID: 276976  Cd Length: 52  Bit Score: 39.25  E-value: 1.33e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 1500 CHVCGRQHQATK--LLECNKCRNSYHPECLGPNYPTKPTK-KKKVWICTKC 1547
Cdd:cd15501      2 CVVCKQMDVTSGnqLVECQECHNLYHQECHKPPVTDKDVNdPRLVWYCSRC 52
SET_SETD7 cd10530
SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2. ...
 3847-3960 1.59e-03

SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2.1.1.43; also termed histone H3-K4 methyltransferase SETD7, H3-K4-HMTase SETD7, lysine N-methyltransferase 7 (KMT7) or SET7/9) is a histone-lysine N-methyltransferase that specifically monomethylates 'Lys-4' of histone H3. It plays a central role in the transcriptional activation of genes such as collagenase or insulin. Set7/9 also methylates non-histone proteins, including estrogen receptor alpha (ERa), suggesting it has a role in diverse biological processes. ERa methylation by Set7/9 stabilizes ERa and activates its transcriptional activities, which are involved in the carcinogenesis of breast cancer. In a high-throughput screen, treatment of human breast cancer cells (MCF7 cells) with cyproheptadine, a Set7/9 inhibitor, decreased the expression and transcriptional activity of ERa, thereby inhibiting estrogen-dependent cell growth.


Pssm-ID: 380928  Cd Length: 130  Bit Score: 41.52  E-value: 1.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3847 VGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGcymfrIDDSEVVDATMHGNAARF------ 3920
Cdd:cd10530     11 VAESLIPSAGEGLFAKVAVGPNTVMSFYNGVRITHQEVDSRDWSLNGNTIS-----LDEETVIDVPEPYNSVSKycaslg 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 3921 --INHSCEPNC------YSRVINIDgqkhiVIFAMRKIYRGEELTYDY 3960
Cdd:cd10530     86 hkANHSFTPNCiydpfvHPRFGPIK-----CIRTLRAVEAGEELTVAY 128
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 1499-1547 1.63e-03

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


Pssm-ID: 277013  Cd Length: 41  Bit Score: 38.85  E-value: 1.63e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1499 FCHVCgrqHQATKLLECNKCRNSYHPECLGPNyptkpTKKKKVWICTKC 1547
Cdd:cd15538      1 FCWRC---HKEGQVLCCSLCPRVYHKKCLKLT-----SEPDEDWVCPEC 41
PHD1_PHF1 cd15500
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ...
 1500-1547 1.79e-03

PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger.


Pssm-ID: 276975  Cd Length: 51  Bit Score: 39.04  E-value: 1.79e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1500 CHVCGRQ--HQATKLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKC 1547
Cdd:cd15500      2 CCVCDSEtvSPKNPLVNCEKCHHAYHQECHVPRVPLESAGDGDSWMCRQC 51
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
 1602-1644 1.79e-03

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


Pssm-ID: 277027  Cd Length: 50  Bit Score: 38.92  E-value: 1.79e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958798715 1602 MMQCGKCDRWVHSKCEGLSGTEDEMYEilsnlPESVAYTCVNC 1644
Cdd:cd15552     13 MICCDRCEEWFHGDCVGITEAQGKEME-----ENIEEYVCPKC 50
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1500-1548 1.83e-03

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


Pssm-ID: 276988  Cd Length: 47  Bit Score: 39.00  E-value: 1.83e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKCV 1548
Cdd:cd15513      2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGG---WKCKWCV 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1451-1497 1.99e-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: 38.84  E-value: 1.99e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1451 VCFLCASSGHV--EFVYCQVCCEPFHKFCLEENErPLEDQLENWCCRRC 1497
Cdd:cd15489      1 SCIVCGKGGDLggELLQCDGCGKWFHADCLGPPL-SSFVPNGKWICPVC 48
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1500-1547 2.00e-03

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


Pssm-ID: 277077  Cd Length: 46  Bit Score: 38.67  E-value: 2.00e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPnypTKPTKKKKVWICTKC 1547
Cdd:cd15604      2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLP---PLPEPPKGIWRCPKC 46
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 1893-1997 2.20e-03

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: 40.81  E-value: 2.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALClmygddsANDAGRLLYIGQNEWTHVNCALWSAE------VFEDDDGSLKNVHMAviRGKqLRCEFCQKP--GATVG 1964
Cdd:cd15703      1 CVLC-------PNKGGAFKQTSDGRWAHVVCAIWIPEvcfantVFLEPVEGVNNIPPA--RWK-LTCYLCKQKgrGAAIQ 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1965 CCLTSCTSNYHFMCS-RA--------------KNCVFLDDKKVYCQRH 1997
Cdd:cd15703     71 CHKVNCYTAFHVTCAqRAglfmkiepvretglNGTTFTVRKTAYCENH 118
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
3969-3985 2.24e-03

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 37.77  E-value: 2.24e-03
                            10
                    ....*....|....*..
gi 1958798715  3969 NKLPCNCGAKKCRKFLN 3985
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1500-1547 2.29e-03

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


Pssm-ID: 277089  Cd Length: 47  Bit Score: 38.78  E-value: 2.29e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDED--WYCPSC 47
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
 1602-1644 2.44e-03

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


Pssm-ID: 277108  Cd Length: 51  Bit Score: 38.75  E-value: 2.44e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1958798715 1602 MMQCGKCDRWVHSKCEGLSGTEDEMYEilsnlPESVAYTCVNC 1644
Cdd:cd15638     14 MVGCGRCDDWFHGDCVGLSLSQAQQME-----EEDKEYVCVKC 51
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1500-1548 2.91e-03

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 38.39  E-value: 2.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKCV 1548
Cdd:cd15602      2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGD---WRCPKCV 47
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1952-1997 3.19e-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: 38.07  E-value: 3.19e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1952 RCEFCQKPGATVGCCL--TSCTSNYHFMCSRAKNCVFLDDKKVYCQRH 1997
Cdd:cd15489      1 SCIVCGKGGDLGGELLqcDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
1916-1993 3.47e-03

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 43.43  E-value: 3.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1916 NEWTHVNCALWSAEVfedddgSLKNVH-MAVIRGKQ--------LRCEFCQKPGAT-VGCCLTSCTSNYHFMCSRAKnCV 1985
Cdd:COG5141    266 GRWGHVICAMFNPEL------SFGHLLsKDPIDNIAsvsssrwkLGCLICKEFGGTcIQCSYFNCTRAYHVTCARRA-GY 338


                   ....*...
gi 1958798715 1986 FldDKKVY 1993
Cdd:COG5141    339 F--DLNIY 344
SET_SMYD1_2_3-like cd19167
SET domain (including post-SET domain) found in SET and MYND domain-containing proteins, SMYD1, ...
 3896-3982 3.78e-03

SET domain (including post-SET domain) found in SET and MYND domain-containing proteins, SMYD1, SMYD2, SMYD3 and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1, SMYD2 and SMYD3. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex.


Pssm-ID: 380944 [Multi-domain]  Cd Length: 205  Bit Score: 41.64  E-value: 3.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 3896 IGCYMFRIDDSEV--VDATMHGNAArFINHSCEPNCysrvINIDGQKHIVIFAMRKIYRGEELTYDY---KFPIEDASNK 3970
Cdd:cd19167    115 VNCNGFTISDEELqhVGVGIYPQAA-LLNHSCCPNC----IVTFNGPNIEVRAVQEIEPGEEVFHSYidlLYPTEERRDQ 189

                           90
                   ....*....|....*...
gi 1958798715 3971 L------PCNCgaKKCRK 3982
Cdd:cd19167    190 LrdqyffLCQC--ADCQT 205
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 1893-1997 3.98e-03

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: 39.94  E-value: 3.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVI--RGKQLRCEFCQK-----PGATVGC 1965
Cdd:cd15715      1 CCLCNLRG-------GALKQTSDDKWAHVMCAVALPEVRFINVVERTPIDISRIplQRLKLKCIFCRNrikrvSGACIQC 73

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1958798715 1966 CLTSCTSNYHFMCSRAKNCVFLDDKKVY-----CQRH 1997
Cdd:cd15715     74 SYGRCPASFHVTCAHAAGVLMEPDDWPYvvfitCFRH 110
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1500-1547 4.94e-03

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


Pssm-ID: 277088  Cd Length: 47  Bit Score: 37.64  E-value: 4.94e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKkvWICTKC 1547
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDDED--WYCPEC 47
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 1499-1547 5.06e-03

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 37.59  E-value: 5.06e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1499 FCHVCGRqhqATKLLECNKCRNSYHPECLgpnyptKPTKKKKVWICTKC 1547
Cdd:cd15658      1 FCFVCAR---GGRLLCCESCPASFHPECL------SIEMPEGCWNCNEC 40
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1599-1644 5.18e-03

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 37.58  E-value: 5.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSgTEDEMYEILSNlpesvAYTCVNC 1644
Cdd:cd15601     12 EDLLIQCRHCDRWVHAVCESLF-TEDEVEQAADE-----GFDCSSC 51
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1499-1547 5.33e-03

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


Pssm-ID: 276977  Cd Length: 52  Bit Score: 37.80  E-value: 5.33e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1958798715 1499 FCHVCGRQHQATK--LLECNKCRNSYHPECLGPN-YPTKPTKKKKVWICTKC 1547
Cdd:cd15502      1 VCIVCQRGHSPKSnrIVFCDGCNTPYHQLCHDPSiDDEVVEDPDAEWFCKKC 52
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1500-1547 5.58e-03

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 37.43  E-value: 5.58e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKC 1547
Cdd:cd15605      2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGD---WRCPKC 46
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1497-1529 6.11e-03

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


Pssm-ID: 277037  Cd Length: 50  Bit Score: 37.39  E-value: 6.11e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1958798715 1497 CKFCHVCGRQHQatkLLECNKCRNSYHPECLGP 1529
Cdd:cd15562      2 CGICKKSNDQHL---LALCDTCKLYYHLGCLDP 31
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1599-1645 6.14e-03

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 37.60  E-value: 6.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958798715 1599 ESKMMQCGKCDRWVHSKCEGLSgTEDEMyeilsnlpESVAYTCVNCT 1645
Cdd:cd15600     12 EELILQCRQCDRWMHASCQNLN-TEEEV--------ENAADNGFDCT 49
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 1893-1997 6.75e-03

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: 39.15  E-value: 6.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddsandaGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVI--RGKQLRCEFCQKP-----GATVGC 1965
Cdd:cd15714      1 CCLCNLRG-------GALQMTTDERWVHVICAIAVPEARFLNVIERHPVDVSAIpeQRWKLKCVYCRKRmkkvsGACIQC 73

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1958798715 1966 CLTSCTSNYHFMCSRAKNCVFLDDKKVY-----CQRH 1997
Cdd:cd15714     74 SYDHCSTSFHVTCAHAAGVVMEPDDWPYvvsitCFKH 110
PHD_HAC_like cd15614
PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar ...
 1604-1644 7.03e-03

PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar proteins; This family includes A. thaliana HACs (HAC1/2/4/5/12), which are histone acetyltransferases of the p300/CREB-binding protein (CBP) co-activator family. CBP-type HAT proteins are also found in animals, but absent in fungi. The domain architecture of CBP-type HAT proteins differs between plants and animals. Members in this family contain an N-terminal partially conserved KIX domain, a Zf-TAZ domain, a Cysteine rich CBP-type HAT domain that harbors a plant homeodomain (PHD) finger, a Zf-ZZ domain, and a Zf-TAZ domain. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277086  Cd Length: 73  Bit Score: 38.10  E-value: 7.03e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1958798715 1604 QCGKCDRWVHSKCeGLsgtedemYEILSNLPESVAYTCVNC 1644
Cdd:cd15614     41 QCDKCERWQHQIC-GL-------YNGRRNADETAEYVCPLC 73
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 1499-1547 7.46e-03

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


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 36.88  E-value: 7.46e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1958798715 1499 FCHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKC 1547
Cdd:cd15522      1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDD---WFCPKC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1500-1529 7.55e-03

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


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 36.86  E-value: 7.55e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGP 1529
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRP 31
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 1499-1529 7.69e-03

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


Pssm-ID: 277041  Cd Length: 48  Bit Score: 37.02  E-value: 7.69e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1958798715 1499 FCHVCGRQH--QATKLLECNKCRNSYHPECLGP 1529
Cdd:cd15566      1 TCATCEASGdgSSGKLVRCIRCPRAYHAGCIPA 33
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 1893-1997 8.00e-03

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: 38.80  E-value: 8.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958798715 1893 CALCLMYGddsandaGRLLYIGQNEWTHVNCA--LWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQK-PGATVGCCLT- 1968
Cdd:cd15713      1 CCLCSLRG-------GALQRANDDKWVHVMCAvaVLEARFVNIAERSPVDVSKIPLQRFKLKCIFCKKrRKRTAGCCVQc 73

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1958798715 1969 ---SCTSNYHFMCSRAKNCVFLDDK-----KVYCQRH 1997
Cdd:cd15713     74 shgRCPTSFHASCAQAAGVMMQPDDwpfvvFITCFRH 110
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1500-1547 8.78e-03

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 36.99  E-value: 8.78e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958798715 1500 CHVCGRQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKkkvWICTKC 1547
Cdd:cd15515      2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGD---WRCPKC 46
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1500-1548 9.64e-03

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 37.09  E-value: 9.64e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958798715 1500 CHVCG--RQHQATKLLECNKCRNSYHPECLGPNYPTKPTKKKKVWICTKCV 1548
Cdd:cd15499      2 CSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDEKWFCSRCV 52
 
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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