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Conserved domains on  [gi|528519285|ref|XP_005162604|]
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histone-lysine N-methyltransferase 2C isoform X5 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4789-4941 8.11e-110

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: 346.72  E-value: 8.11e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4789 KSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDA 4868
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4869 TITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4424-4528 1.27e-71

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: 235.71  E-value: 1.27e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1672-1752 2.29e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called 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.


:

Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1672 QRSTLKWEKEETLGEMATVAPVLYTNMNFPNLQDEFPDWATRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQLS 1751
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 528519285 1752 N 1752
Cdd:cd22026    81 N 81
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 263-346 1.93e-44

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


The actual alignment was detected with superfamily member cd15696:

Pssm-ID: 473978  Cd Length: 90  Bit Score: 157.41  E-value: 1.93e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  263 GQCCAHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLL 342
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 528519285  343 CPDY 346
Cdd:cd15696    87 CPTH 90
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 973-1029 1.96e-36

PHD finger 4 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 fourth PHD finger.


:

Pssm-ID: 277071  Cd Length: 57  Bit Score: 133.22  E-value: 1.96e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  973 SFTLKQDMCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLECT 1029
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1030-1076 5.25e-30

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: 114.50  E-value: 5.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4640-4723 8.45e-27

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: 106.54  E-value: 8.45e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4640 PEFVIRVVEQgyDDLILTGSSPKGVWDKVLEPVAERRNETGFLRLFPVYLKGEDLFGLTVSAVTRIVESLPGVEACERYT 4719
Cdd:pfam05965    2 PLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNYK 79


                   ....
gi 528519285  4720 FRYG 4723
Cdd:pfam05965   80 FRYG 83
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1108-1157 9.91e-27

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


The actual alignment was detected with superfamily member cd15600:

Pssm-ID: 473978  Cd Length: 51  Bit Score: 105.40  E-value: 9.91e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1108 CPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENAADEGFDCTLC 1157
Cdd:cd15600     2 CPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 406-451 7.05e-26

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


:

Pssm-ID: 277069  Cd Length: 46  Bit Score: 102.71  E-value: 7.05e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 360-404 2.92e-22

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


:

Pssm-ID: 276984  Cd Length: 48  Bit Score: 92.37  E-value: 2.92e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLD--VTVTPLKRAGWQCPEC 404
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4582-4633 6.66e-18

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: 80.24  E-value: 6.66e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  4582 GSLVLHAVGQLLPQQMlAFHSMTAIFPVGYEASRIYWSMRHGNRRCHYVCSI 4633
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1883-2338 5.43e-14

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 79.98  E-value: 5.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1883 RPQPPPLSSTSKTPTQDTQYPQG---PSSQPQSPQMFSPESSGSRPSSPYDPYGKMVGTPRPP-------PSGSSTPRRG 1952
Cdd:PHA03247 2588 RPDAPPQSARPRAPVDDRGDPRGpapPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPErprddpaPGRVSRPRRA 2667

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1953 S-------VSDMQERCRPSSAHESFGSPTTTSTDPYAKPPDTPRPSdPFVKPMCTPRLGSLSEQQGRQL----------M 2015
Cdd:PHA03247 2668 RrlgraaqASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH-ALVSATPLPPGPAAARQASPALpaapappavpA 2746

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2016 GNVTPGDNFSRPG-QRSEAYQRMAHSRMVLSDPysRPLLTPVPGSNESGSVPVFKTPMPPSGLQQdSFNGGQQGMRRGSS 2094
Cdd:PHA03247 2747 GPATPGGPARPARpPTTAGPPAPAPPAAPAAGP--PRRLTRPAVASLSESRESLPSPWDPADPPA-AVLAPAAALPPAAS 2823

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2095 DTFPHVQHTDTYSNQPLTPHPSMADGINNEGRMM-------RPGQGSHFAQPLSMGRHPQRDPYSQAPSTPRQ------D 2161
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApggdvrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTEsfalppD 2903

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2162 YPQQMSDPYAQMPGTPRPHDPYAQMPG-TPRPNCDPYPLPPPTTRTEPIDKFSQSQPSS-------------RRQSPSHA 2227
Cdd:PHA03247 2904 QPERPPQPQAPPPPQPQPQPPPPPQPQpPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgrvavpRFRVPQPA 2983

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2228 idPYAQMPGTPRPSPGERYSKSPGSLRSSDPFSQPPgTPRPI--KNEIY--------------------DQQGTPMPILP 2285
Cdd:PHA03247 2984 --PSREAPASSTPPLTGHSLSRVSSWASSLALHEET-DPPPVslKQTLWppddtedsdadslfdsdserSDLEALDPLPP 3060

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 2286 DPYSQPPGTPRPGAgLEGFSRLNPRLNFithqtDPLGLQAQSRTQDPFSRSCG 2338
Cdd:PHA03247 3061 EPHDPFAHEPDPAT-PEAGARESPSSQF-----GPPPLSANAALSRRYVRSTG 3107
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2141-2552 5.41e-10

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 66.50  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2141 SMGRHPQRDPYSQAPSTPRQDypqqMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSR 2220
Cdd:PHA03247 2584 SRARRPDAPPQSARPRAPVDD----RGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPG 2659

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2221 RQSPSHAIDPYAQMPGTPRPSPGERYSKSP---GSLRSS-DPFSQPP-----------GTPRPIKNEIYDQQGTPMPILP 2285
Cdd:PHA03247 2660 RVSRPRRARRLGRAAQASSPPQRPRRRAARptvGSLTSLaDPPPPPPtpepaphalvsATPLPPGPAAARQASPALPAAP 2739

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2286 DPYSQPPGTPRPGAGLEGFSRLNPRLNFI-THQTDPLGLQAQSRTQDPFSRSCGTDSQTPKHPGISDENISIQQTIPNQT 2364
Cdd:PHA03247 2740 APPAVPAGPATPGGPARPARPPTTAGPPApAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2365 PIHDP----------FEQAPLTPCSQTGERSSQDVIVSTGNPSDSQNTMQPPLGETEEKIKQR-QRLRQLILKQQQEKSA 2433
Cdd:PHA03247 2820 PAASPagplppptsaQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPvRRLARPAVSRSTESFA 2899

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2434 IRKEkGLQEATASAAPGTPRHWSQDDSGPQSdifgRPPPPYPGTmrsspihagqrfPGTFLADQCGPMPNEPQCSRQPFP 2513
Cdd:PHA03247 2900 LPPD-QPERPPQPQAPPPPQPQPQPPPPPQP----QPPPPPPPR------------PQPPLAPTTDPAGAGEPSGAVPQP 2962

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 528519285 2514 RDLNNVGMRPQGQRFAFPPGAPNQEQFLRPPHQMQGGPL 2552
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 484-535 4.06e-05

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


The actual alignment was detected with superfamily member cd15511:

Pssm-ID: 473978  Cd Length: 52  Bit Score: 44.02  E-value: 4.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  484 LCLICGQSQDSGSPADKHTCCTCKRWVHVDCVRQEGTNPDTQLQDGYTCRAC 535
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
PRK00409 super family cl29770
recombination and DNA strand exchange inhibitor protein; Reviewed
 3179-3286 1.70e-04

recombination and DNA strand exchange inhibitor protein; Reviewed


The actual alignment was detected with superfamily member PRK00409:

Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 47.90  E-value: 1.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 3179 NESQKKQYEEWLQETQQLLQMQQKF---LEDQIGAHRKSKKALSAKQ-RTAKKAGREFPEEDAEQLKNVTEQQ-----SV 3249
Cdd:PRK00409  525 LEELERELEQKAEEAEALLKEAEKLkeeLEEKKEKLQEEEDKLLEEAeKEAQQAIKEAKKEADEIIKELRQLQkggyaSV 604

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 528519285 3250 VQKQLEQIRKQQKEHAELIEEYRVKQQQQQQRLQTGM 3286
Cdd:PRK00409  605 KAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGD 641
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3285-3597 3.15e-04

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 47.31  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3285 GMMGPMKTMPVMQGQPPGMmpvgppmAQPMMGSMLPMQHPhfGKPSRM-PSMPGWHPGTTGPISGPRMPP--HLPPQMAL 3361
Cdd:pfam09606  136 GAGFPSQMSRVGRMQPGGQ-------AGGMMQPSSGQPGS--GTPNQMgPNGGPGQGQAGGMNGGQQGPMggQMPPQMGV 206

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3362 PNPAQPLQAQ-----------PPAPIAPGGKP------GQSGTVAGGNGGGASSSAPHVKFDDNNPFSEGFQERERRERL 3424
Cdd:pfam09606  207 PGMPGPADAGaqmgqqaqangGMNPQQMGGAPnqvamqQQQPQQQGQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGP 286

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3425 REQQEKQRVQLMQEVERQRALQRLELEQQslglgpdnnGDSLAQMPfynSDLSQEFMQTPRPQQQQQQLGPLFPQQGNVP 3504
Cdd:pfam09606  287 PGQQPGAMPNVMSIGDQNNYQQQQTRQQQ---------QQQGGNHP---AAHQQQMNQSVGQGGQVVALGGLNHLETWNP 354

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3505 CDFVGQGSAFMQGGEHRPIPGNGSFGPEMGPNFQPKNPMMPGFSAGRPRP--PGFGGTRMpHHGGGEPSSFGMNSTTPLP 3582
Cdd:pfam09606  355 GNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSPQPSVPSPqgPGSQPPQS-HPGGMIPSPALIPSPSPQM 433

                          330
                   ....*....|....*
gi 528519285  3583 PNFPGSgQSLIQLYS 3597
Cdd:pfam09606  434 SQQPAQ-QRTIGQDS 447
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4789-4941 8.11e-110

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: 346.72  E-value: 8.11e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4789 KSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDA 4868
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4869 TITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4424-4528 1.27e-71

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: 235.71  E-value: 1.27e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1672-1752 2.29e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called 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.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1672 QRSTLKWEKEETLGEMATVAPVLYTNMNFPNLQDEFPDWATRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQLS 1751
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 528519285 1752 N 1752
Cdd:cd22026    81 N 81
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 263-346 1.93e-44

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: 157.41  E-value: 1.93e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  263 GQCCAHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLL 342
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 528519285  343 CPDY 346
Cdd:cd15696    87 CPTH 90
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 973-1029 1.96e-36

PHD finger 4 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 fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 133.22  E-value: 1.96e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  973 SFTLKQDMCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLECT 1029
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4801-4940 2.96e-36

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


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 135.47  E-value: 2.96e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRkekMYEAQNRG-VYMFRIDSEHVIDATITGGPARYIN 4879
Cdd:COG2940     5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAER---REPHKEPLhTYLFELDDDGVIDGALGGNPARFIN 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4880 HSCAPNCITEvvalERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHkiPCHCGavNCRKW 4940
Cdd:COG2940    82 HSCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4803-4924 1.72e-35

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: 132.84  E-value: 1.72e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   4803 NVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNR-GVYMFRIDSEHVIDATITGGPARYINHS 4881
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 528519285   4882 CAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDD 4924
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1030-1076 5.25e-30

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: 114.50  E-value: 5.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4813-4918 5.69e-28

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: 111.08  E-value: 5.69e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4813 GLGLYAARDIEKYTMVIEYIGT-IIRSEVANRKEKMYEAQNR----GVYMFRID--SEHVIDATIT--GGPARYINHSCA 4883
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 528519285  4884 PNCITEVVALERGHKIIISSNRRIQRGEELCYDYK 4918
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4640-4723 8.45e-27

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: 106.54  E-value: 8.45e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4640 PEFVIRVVEQgyDDLILTGSSPKGVWDKVLEPVAERRNETGFLRLFPVYLKGEDLFGLTVSAVTRIVESLPGVEACERYT 4719
Cdd:pfam05965    2 PLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNYK 79


                   ....
gi 528519285  4720 FRYG 4723
Cdd:pfam05965   80 FRYG 83
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1108-1157 9.91e-27

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: 105.40  E-value: 9.91e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1108 CPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENAADEGFDCTLC 1157
Cdd:cd15600     2 CPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 406-451 7.05e-26

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


Pssm-ID: 277069  Cd Length: 46  Bit Score: 102.71  E-value: 7.05e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4641-4728 2.44e-22

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: 93.90  E-value: 2.44e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   4641 EFVIRVVEqgYDDLILTGSSPKGVWDKVLEPVAERRNETGFLRLFPVYLKGEDLFGLTVSAVTRIVESLPGVEACERYTF 4720
Cdd:smart00542    1 LFRVEIES--DPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 528519285   4721 RYGRNPLM 4728
Cdd:smart00542   79 RYHRSPLL 86
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 360-404 2.92e-22

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 92.37  E-value: 2.92e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLD--VTVTPLKRAGWQCPEC 404
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4582-4633 6.66e-18

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: 80.24  E-value: 6.66e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  4582 GSLVLHAVGQLLPQQMlAFHSMTAIFPVGYEASRIYWSMRHGNRRCHYVCSI 4633
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4451-4528 1.32e-15

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: 1.32e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4451 HLNCALWSTEVYetQAGA------LINVELALRRGLSVRCAYC-QQTGATSGCHRLRCTNAYHFTCALKAQCTF-FKDKT 4522
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 528519285  4523 ----MLCHLH 4528
Cdd:pfam13771   79 gtfkSYCKKH 88
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1883-2338 5.43e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 79.98  E-value: 5.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1883 RPQPPPLSSTSKTPTQDTQYPQG---PSSQPQSPQMFSPESSGSRPSSPYDPYGKMVGTPRPP-------PSGSSTPRRG 1952
Cdd:PHA03247 2588 RPDAPPQSARPRAPVDDRGDPRGpapPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPErprddpaPGRVSRPRRA 2667

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1953 S-------VSDMQERCRPSSAHESFGSPTTTSTDPYAKPPDTPRPSdPFVKPMCTPRLGSLSEQQGRQL----------M 2015
Cdd:PHA03247 2668 RrlgraaqASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH-ALVSATPLPPGPAAARQASPALpaapappavpA 2746

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2016 GNVTPGDNFSRPG-QRSEAYQRMAHSRMVLSDPysRPLLTPVPGSNESGSVPVFKTPMPPSGLQQdSFNGGQQGMRRGSS 2094
Cdd:PHA03247 2747 GPATPGGPARPARpPTTAGPPAPAPPAAPAAGP--PRRLTRPAVASLSESRESLPSPWDPADPPA-AVLAPAAALPPAAS 2823

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2095 DTFPHVQHTDTYSNQPLTPHPSMADGINNEGRMM-------RPGQGSHFAQPLSMGRHPQRDPYSQAPSTPRQ------D 2161
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApggdvrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTEsfalppD 2903

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2162 YPQQMSDPYAQMPGTPRPHDPYAQMPG-TPRPNCDPYPLPPPTTRTEPIDKFSQSQPSS-------------RRQSPSHA 2227
Cdd:PHA03247 2904 QPERPPQPQAPPPPQPQPQPPPPPQPQpPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgrvavpRFRVPQPA 2983

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2228 idPYAQMPGTPRPSPGERYSKSPGSLRSSDPFSQPPgTPRPI--KNEIY--------------------DQQGTPMPILP 2285
Cdd:PHA03247 2984 --PSREAPASSTPPLTGHSLSRVSSWASSLALHEET-DPPPVslKQTLWppddtedsdadslfdsdserSDLEALDPLPP 3060

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 2286 DPYSQPPGTPRPGAgLEGFSRLNPRLNFithqtDPLGLQAQSRTQDPFSRSCG 2338
Cdd:PHA03247 3061 EPHDPFAHEPDPAT-PEAGARESPSSQF-----GPPPLSANAALSRRYVRSTG 3107
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4592-4635 8.14e-13

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: 65.38  E-value: 8.14e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 528519285   4592 LLPQQMLAFHSMTAIFPVGYEASRIYWSMRHGNRRCHYVCSINE 4635
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1030-1078 1.09e-12

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: 65.21  E-value: 1.09e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 528519285  1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQ--NVPKGSWKCKWCVLC 1078
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 268-344 1.44e-12

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: 66.20  E-value: 1.44e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   268 HLRCAAWSEGVCRGEGQSLLY----VDKAIDSGSTECCAYCK-RLGASIKCCEESCGRSFHYPCAAAAGTFQDIK----T 338
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSMGFpiedIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedngT 80


                   ....*.
gi 528519285   339 YTLLCP 344
Cdd:pfam13771   81 FKSYCK 86
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1030-1075 2.59e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.46  E-value: 2.59e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528519285   1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPL-QNVPKGSWKCKWC 1075
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLlEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 406-451 5.66e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 60.30  E-value: 5.66e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528519285    406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMET-IPTNGWRCKNC 451
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 981-1031 1.54e-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: 59.04  E-value: 1.54e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285   981 CVVCGsfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKG-WRCLECTVC 1031
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 980-1028 1.66e-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: 59.15  E-value: 1.66e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 528519285    980 MCVVCGsfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 406-454 2.78e-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: 58.66  E-value: 2.78e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 528519285   406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQP--IMETIPTNGWRCKNCRTC 454
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2141-2552 5.41e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 66.50  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2141 SMGRHPQRDPYSQAPSTPRQDypqqMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSR 2220
Cdd:PHA03247 2584 SRARRPDAPPQSARPRAPVDD----RGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPG 2659

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2221 RQSPSHAIDPYAQMPGTPRPSPGERYSKSP---GSLRSS-DPFSQPP-----------GTPRPIKNEIYDQQGTPMPILP 2285
Cdd:PHA03247 2660 RVSRPRRARRLGRAAQASSPPQRPRRRAARptvGSLTSLaDPPPPPPtpepaphalvsATPLPPGPAAARQASPALPAAP 2739

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2286 DPYSQPPGTPRPGAGLEGFSRLNPRLNFI-THQTDPLGLQAQSRTQDPFSRSCGTDSQTPKHPGISDENISIQQTIPNQT 2364
Cdd:PHA03247 2740 APPAVPAGPATPGGPARPARPPTTAGPPApAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2365 PIHDP----------FEQAPLTPCSQTGERSSQDVIVSTGNPSDSQNTMQPPLGETEEKIKQR-QRLRQLILKQQQEKSA 2433
Cdd:PHA03247 2820 PAASPagplppptsaQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPvRRLARPAVSRSTESFA 2899

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2434 IRKEkGLQEATASAAPGTPRHWSQDDSGPQSdifgRPPPPYPGTmrsspihagqrfPGTFLADQCGPMPNEPQCSRQPFP 2513
Cdd:PHA03247 2900 LPPD-QPERPPQPQAPPPPQPQPQPPPPPQP----QPPPPPPPR------------PQPPLAPTTDPAGAGEPSGAVPQP 2962

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 528519285 2514 RDLNNVGMRPQGQRFAFPPGAPNQEQFLRPPHQMQGGPL 2552
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1842-2233 1.28e-09

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 64.94  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1842 SPHTSSGgnsplqalTPKDSFAMTQMPGTASSGTSADDVFLRPQPPPLSSTSKTPTQDTQYPQGPSSQPQSPQMFSPESS 1921
Cdd:pfam05109  441 APNTTTG--------LPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSA 512

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1922 GSRPSSPYDPYGKMVGTPRPppsGSSTPRRGSVSDMQERCRPSSAHESfGSPTTTSTDPYAKPPDTPR--PSDPFVKPM- 1998
Cdd:pfam05109  513 VTTPTPNATSPTPAVTTPTP---NATSPTLGKTSPTSAVTTPTPNATS-PTPAVTTPTPNATIPTLGKtsPTSAVTTPTp 588

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1999 --CTPRLGSLSEQ---QGRQLMGNVTPGDNFSRPGQRSEAYQRMAH-------SRMVLSDPYSRPLLTPVPGSNESGSVP 2066
Cdd:pfam05109  589 naTSPTVGETSPQantTNHTLGGTSSTPVVTSPPKNATSAVTTGQHnitssstSSMSLRPSSISETLSPSTSDNSTSHMP 668

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2067 VFKTPMPpsglqqdsfNGGQQGMRRGSSDTFPHvqHTDTYSNQPLTPHPSMADGINNEGRMMRPGQGShfaqpLSMGRHP 2146
Cdd:pfam05109  669 LLTSAHP---------TGGENITQVTPASTSTH--HVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVN-----VTKGTPP 732

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2147 QRDPYSQAPSTPRQDYPQQMSDPYAQMPGT-------------PRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFS 2213
Cdd:pfam05109  733 KNATSPQAPSGQKTAVPTVTSTGGKANSTTggkhttghgartsTEPTTDYGGDSTTPRTRYNATTYLPPSTSSKLRPRWT 812

                          410       420
                   ....*....|....*....|
gi 528519285  2214 QSQPSSRRQSPSHAIDPYAQ 2233
Cdd:pfam05109  813 FTSPPVTTAQATVPVPPTSQ 832
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 360-407 8.03e-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: 54.42  E-value: 8.03e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 528519285   360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVT--PLKRAGWQCPECKVC 407
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 360-404 7.30e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 51.44  E-value: 7.30e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 528519285    360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVTP-LKRAGWQCPEC 404
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1107-1158 1.64e-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: 47.87  E-value: 1.64e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  1107 VCPVCtRSYREEELILQCRQCDRWVHGSCqgLNSDEDVENAADEGFDCTLCR 1158
Cdd:pfam00628    1 YCAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECK 49
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1107-1157 4.31e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 46.44  E-value: 4.31e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 528519285   1107 VCPVCTRSYREEELIlQCRQCDRWVHGSCQGLNSDEDVEnaaDEGFDCTLC 1157
Cdd:smart00249    1 YCSVCGKPDDGGELL-QCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
HMG smart00398
high mobility group;
1691-1744 1.13e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.15  E-value: 1.13e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285   1691 APVLYTNMNFPNLQDEFPD--WATRVKQIAKLWRKASSQERAPYVQKARDNRAALR 1744
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDlsNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 484-535 4.06e-05

PHD finger 3 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 third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 44.02  E-value: 4.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  484 LCLICGQSQDSGSPADKHTCCTCKRWVHVDCVRQEGTNPDTQLQDGYTCRAC 535
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 485-535 6.73e-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: 43.35  E-value: 6.73e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 528519285    485 CLICGQSQDSGspaDKHTCCTCKRWVHVDCVRQEGTNPDtqLQDGYTCRAC 535
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPPLLEEE--PDGKWYCPKC 47
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 3179-3286 1.70e-04

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 47.90  E-value: 1.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 3179 NESQKKQYEEWLQETQQLLQMQQKF---LEDQIGAHRKSKKALSAKQ-RTAKKAGREFPEEDAEQLKNVTEQQ-----SV 3249
Cdd:PRK00409  525 LEELERELEQKAEEAEALLKEAEKLkeeLEEKKEKLQEEEDKLLEEAeKEAQQAIKEAKKEADEIIKELRQLQkggyaSV 604

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 528519285 3250 VQKQLEQIRKQQKEHAELIEEYRVKQQQQQQRLQTGM 3286
Cdd:PRK00409  605 KAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGD 641
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4418-4544 2.16e-04

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 47.67  E-value: 2.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4418 PKDMRRCCFCHEEgDGLtdgparLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLS---VRCAYCQQTGATS 4494
Cdd:COG5141   244 EYQIRCCSFCPSS-DGA------FKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSrwkLGCLICKEFGGTC 316

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528519285 4495 -GCHRLRCTNAYHFTCALKAqCTFFK------------DKTMLCHLHRPRG-TSLIGGGLLGTE 4544
Cdd:COG5141   317 iQCSYFNCTRAYHVTCARRA-GYFDLniyshngisyciDHEPLCRKHYPLGyGRMNGLRYFGYE 379
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3285-3597 3.15e-04

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 47.31  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3285 GMMGPMKTMPVMQGQPPGMmpvgppmAQPMMGSMLPMQHPhfGKPSRM-PSMPGWHPGTTGPISGPRMPP--HLPPQMAL 3361
Cdd:pfam09606  136 GAGFPSQMSRVGRMQPGGQ-------AGGMMQPSSGQPGS--GTPNQMgPNGGPGQGQAGGMNGGQQGPMggQMPPQMGV 206

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3362 PNPAQPLQAQ-----------PPAPIAPGGKP------GQSGTVAGGNGGGASSSAPHVKFDDNNPFSEGFQERERRERL 3424
Cdd:pfam09606  207 PGMPGPADAGaqmgqqaqangGMNPQQMGGAPnqvamqQQQPQQQGQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGP 286

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3425 REQQEKQRVQLMQEVERQRALQRLELEQQslglgpdnnGDSLAQMPfynSDLSQEFMQTPRPQQQQQQLGPLFPQQGNVP 3504
Cdd:pfam09606  287 PGQQPGAMPNVMSIGDQNNYQQQQTRQQQ---------QQQGGNHP---AAHQQQMNQSVGQGGQVVALGGLNHLETWNP 354

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3505 CDFVGQGSAFMQGGEHRPIPGNGSFGPEMGPNFQPKNPMMPGFSAGRPRP--PGFGGTRMpHHGGGEPSSFGMNSTTPLP 3582
Cdd:pfam09606  355 GNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSPQPSVPSPqgPGSQPPQS-HPGGMIPSPALIPSPSPQM 433

                          330
                   ....*....|....*
gi 528519285  3583 PNFPGSgQSLIQLYS 3597
Cdd:pfam09606  434 SQQPAQ-QRTIGQDS 447
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3176-3274 3.80e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 47.09  E-value: 3.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3176 GFVNESQKK---------QYEEWLQETQQLLQMQQKfledqigahrkSKKALSAKQRT--AKKAG-REFPEEDAEQLKNV 3243
Cdd:pfam01576  447 SLLNEAEGKniklskdvsSLESQLQDTQELLQEETR-----------QKLNLSTRLRQleDERNSlQEQLEEEEEAKRNV 515

                           90       100       110
                   ....*....|....*....|....*....|....
gi 528519285  3244 TEQQSVVQKQLEQIRKQQKEHA---ELIEEYRVK 3274
Cdd:pfam01576  516 ERQLSTLQAQLSDMKKKLEEDAgtlEALEEGKKR 549
HMG_box pfam00505
HMG (high mobility group) box;
1693-1744 2.01e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 39.52  E-value: 2.01e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  1693 VLYTNMNFPNLQDEFPDWATR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1744
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
3180-3270 8.99e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.81  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 3180 ESQKKQYEEWLQETQQLLQMQQKFLEDQIGAHRKSKKALSAKQRTAKKAGREFpEEDAEQLKNVTEQQSVVQKQLEQIRK 3259
Cdd:COG4372    65 EEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEEL-EELQKERQDLEQQRKQLEAQIAELQS 143

                          90
                  ....*....|.
gi 528519285 3260 QQKEHAELIEE 3270
Cdd:COG4372   144 EIAEREEELKE 154
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4789-4941 8.11e-110

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: 346.72  E-value: 8.11e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4789 KSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDA 4868
Cdd:cd19171     1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4869 TITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19171    81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 4788-4941 1.00e-102

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: 326.58  E-value: 1.00e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4788 SKSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVID 4867
Cdd:cd19208     1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528519285 4868 ATITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19208    81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 4787-4941 3.44e-88

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: 285.05  E-value: 3.44e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4787 HSKSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVI 4866
Cdd:cd19209     1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528519285 4867 DATITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19209    81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4424-4528 1.27e-71

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: 235.71  E-value: 1.27e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15697     1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15697    81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 4790-4938 1.35e-69

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: 231.72  E-value: 1.35e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4790 SAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQN-RGVYMFRIDSEHVIDA 4868
Cdd:cd10518     2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4869 TITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQhKIPCHCGAVNCR 4938
Cdd:cd10518    82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4424-4528 4.98e-65

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: 216.78  E-value: 4.98e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15666     1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15666    81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4424-4529 4.16e-62

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: 208.37  E-value: 4.16e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15698     1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                          90       100
                  ....*....|....*....|....*.
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLHR 4529
Cdd:cd15698    81 VYHFACAIRAKCMFFKDKTMLCPMHK 106
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 4792-4942 3.03e-60

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: 204.93  E-value: 3.03e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4792 QYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDATIT 4871
Cdd:cd19170     4 RFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4872 GGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDqhKIPCHCGAVNCRKWMN 4942
Cdd:cd19170    84 GNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 4801-4938 1.83e-54

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: 188.31  E-value: 1.83e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRG-VYMFRIDSEHVIDATITGGPARYIN 4879
Cdd:cd19169    12 KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEAIGIGsSYLFRVDDDTIIDATKCGNLARFIN 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4880 HSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDqhKIPCHCGAVNCR 4938
Cdd:cd19169    92 HSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIEDE--KIPCLCGAPQCR 148
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1672-1752 2.29e-54

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called 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.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 185.37  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1672 QRSTLKWEKEETLGEMATVAPVLYTNMNFPNLQDEFPDWATRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQLS 1751
Cdd:cd22026     1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQMS 80


                  .
gi 528519285 1752 N 1752
Cdd:cd22026    81 N 81
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 4801-4938 3.26e-47

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: 167.60  E-value: 3.26e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRG-VYMFRIDSEHVIDATITGGPARYIN 4879
Cdd:cd20072    12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4880 HSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDqhKIPCHCGAVNCR 4938
Cdd:cd20072    92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 4792-4942 3.37e-47

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: 167.51  E-value: 3.37e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4792 QYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDATIT 4871
Cdd:cd19206     4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4872 GGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWMN 4942
Cdd:cd19206    84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 263-346 1.93e-44

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: 157.41  E-value: 1.93e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  263 GQCCAHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLL 342
Cdd:cd15696     7 GECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                  ....
gi 528519285  343 CPDY 346
Cdd:cd15696    87 CPTH 90
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 4790-4942 6.43e-44

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: 158.26  E-value: 6.43e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4790 SAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDAT 4869
Cdd:cd19207     2 AMRFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDAT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4870 ITGGPARYINHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWMN 4942
Cdd:cd19207    82 MHGNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 1677-1743 5.07e-39

high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins; This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) 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, and 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 called 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. All subfamily members contain one HMG-box domain.


Pssm-ID: 438813  Cd Length: 67  Bit Score: 140.96  E-value: 5.07e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 1677 KWEKEETLGEMATVAPVLYTNMNFPNLQDEFPDWATRVKQIAKLWRKASSQERAPYVQKARDNRAAL 1743
Cdd:cd21997     1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 263-346 1.64e-38

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: 140.15  E-value: 1.64e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  263 GQCCAHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLL 342
Cdd:cd15665     7 GEVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                  ....
gi 528519285  343 CPDY 346
Cdd:cd15665    87 CPEH 90
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1668-1749 1.79e-38

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called 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.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 139.84  E-value: 1.79e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1668 MSNAQRSTLKWEKEETLGEMATVAPVLYTNMNFPNLQDEFPDWATRVKQIAKLWRKASSQERAPYVQKARDNRAALRINK 1747
Cdd:cd22027     2 LSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRINK 81


                  ..
gi 528519285 1748 VQ 1749
Cdd:cd22027    82 VQ 83
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 4801-4942 1.05e-37

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: 140.54  E-value: 1.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGV-YMFRIDSEHVIDATITGGPARYIN 4879
Cdd:cd19204    13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4880 HSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDqhKIPCHCGAVNCRKWMN 4942
Cdd:cd19204    93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 973-1029 1.96e-36

PHD finger 4 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 fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 133.22  E-value: 1.96e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  973 SFTLKQDMCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLECT 1029
Cdd:cd15596     1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECT 57
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 4801-4942 2.22e-36

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: 136.72  E-value: 2.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGV-YMFRIDSEHVIDATITGGPARYIN 4879
Cdd:cd19205    13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4880 HSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDqhKIPCHCGAVNCRKWMN 4942
Cdd:cd19205    93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4801-4940 2.96e-36

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


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 135.47  E-value: 2.96e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRkekMYEAQNRG-VYMFRIDSEHVIDATITGGPARYIN 4879
Cdd:COG2940     5 HPRIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAER---REPHKEPLhTYLFELDDDGVIDGALGGNPARFIN 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4880 HSCAPNCITEvvalERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHkiPCHCGavNCRKW 4940
Cdd:COG2940    82 HSCDPNCEAD----EEDGRIFIVALRDIAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4803-4924 1.72e-35

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: 132.84  E-value: 1.72e-35
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   4803 NVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNR-GVYMFRIDSEHVIDATITGGPARYINHS 4881
Cdd:smart00317    2 KLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAkAFYLFDIDSDLCIDARRKGNLARFINHS 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 528519285   4882 CAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDD 4924
Cdd:smart00317   82 CEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 4424-4528 4.00e-35

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: 130.99  E-value: 4.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15664     1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15664    81 NYHFMCARKAECVFQDDKKVFCPAH 105
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 4422-4529 1.38e-32

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: 124.34  E-value: 1.38e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4422 RRCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRC 4501
Cdd:cd15693     1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                          90       100
                  ....*....|....*....|....*...
gi 528519285 4502 TNAYHFTCALKAQCTFFKDKTMLCHLHR 4529
Cdd:cd15693    81 TSNYHFMCSRAKNCVFLEDKKVYCQRHK 108
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 4802-4941 3.72e-30

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: 118.45  E-value: 3.72e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4802 SNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMF-RIDSEHVIDATITGGPARYINH 4880
Cdd:cd19172     2 AKVEVFRTEKKGWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYAREGNRHYYFmALKSDEIIDATKKGNLSRFINH 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528519285 4881 SCAPNCITE--VValeRGH-KIIISSNRRIQRGEELCYDYKFDLEDDQHKiPCHCGAVNCRKWM 4941
Cdd:cd19172    82 SCEPNCETQkwTV---NGElRVGFFAKRDIPAGEELTFDYQFERYGKEAQ-KCYCGSPNCRGYI 141
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4813-4941 3.87e-30

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: 122.02  E-value: 3.87e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRgVYMFRID-----SEHVIDATITGGPARYINHSCAPNCI 4887
Cdd:cd10542    99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNLA 177

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 4888 TEVVALE----RGHKIIISSNRRIQRGEELCYDYKFDLEDDQH----------KIPCHCGAVNCRKWM 4941
Cdd:cd10542   178 VYAVWINhldpRLPRIAFFAKRDIKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 4813-4941 4.33e-30

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: 118.29  E-value: 4.33e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVAnrKEKMYEAQNRG---VYMFRIDSEHVIDATITGGPARYINHSCAPNCITE 4889
Cdd:cd19175    11 GWGLVADEDINAGEFIIEYVGEVIDDKTC--EERLWDMKHKGeknFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQ 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4890 VVALERGHKIIISSNRRIQRGEELCYDYKF-DLEDDQHkipCHCGAVNCRKWM 4941
Cdd:cd19175    89 KWQVDGETRIGVFAIRDIKKGEELTYDYQFvQFGADQD---CHCGSKNCRGKL 138
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1030-1076 5.25e-30

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: 114.50  E-value: 5.25e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 4803-4938 1.57e-29

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: 116.20  E-value: 1.57e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4803 NVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRK-EKMYEAQNRGVYMFRIDSEHVIDATITGGPARYINHS 4881
Cdd:cd10531     1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERlDEYEELGKSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 4882 CAPNCITEVVALeRGHKII-ISSNRRIQRGEELCYDYKFDLEDDQhKIPCHCGAVNCR 4938
Cdd:cd10531    81 CEPNCETQKWIV-NGEYRIgIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 980-1028 3.20e-29

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 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, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 112.17  E-value: 3.20e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  980 MCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:cd15512     1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 4804-4917 3.70e-29

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: 114.65  E-value: 3.70e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4804 VYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGvYMFRIDSEHVIDATITGGPARYINHSCA 4883
Cdd:cd10519     3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 528519285 4884 PNCITEVVALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10519    82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDY 115
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 4813-4937 3.31e-28

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: 112.79  E-value: 3.31e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTII-RSEVANRKEKMYEAQNRGVYMFRIDSEHVIDATITGGPARYINHSCAPNCITEVV 4891
Cdd:cd19173    13 GWGLRTKRDIKKGDFVIEYVGELIdEEECRRRLKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 4892 ALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQhKIPCHCGAVNC 4937
Cdd:cd19173    93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4813-4918 5.69e-28

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: 111.08  E-value: 5.69e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4813 GLGLYAARDIEKYTMVIEYIGT-IIRSEVANRKEKMYEAQNR----GVYMFRID--SEHVIDATIT--GGPARYINHSCA 4883
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 528519285  4884 PNCITEVVALERGHKIIISSNRRIQRGEELCYDYK 4918
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDYG 115
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 4424-4528 2.14e-27

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: 108.97  E-value: 2.14e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15694     1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                          90       100
                  ....*....|....*....|....*
gi 528519285 4504 AYHFTCALKAQCTFFKDKTMLCHLH 4528
Cdd:cd15694    81 NFHFMCARASRCCFQDDKKVFCQKH 105
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 979-1028 2.68e-27

PHD finger 3 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 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 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 third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 107.04  E-value: 2.68e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  979 DMCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:cd15597     1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 50
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 263-346 6.32e-27

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: 107.31  E-value: 6.32e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  263 GQCCAHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLL 342
Cdd:cd15695     7 GECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                  ....
gi 528519285  343 CPDY 346
Cdd:cd15695    87 CPEH 90
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4640-4723 8.45e-27

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: 106.54  E-value: 8.45e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4640 PEFVIRVVEQgyDDLILTGSSPKGVWDKVLEPVAERRNETGFLRLFPVYLKGEDLFGLTVSAVTRIVESLPGVEACERYT 4719
Cdd:pfam05965    2 PLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNYK 79


                   ....
gi 528519285  4720 FRYG 4723
Cdd:pfam05965   80 FRYG 83
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1108-1157 9.91e-27

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: 105.40  E-value: 9.91e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1108 CPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENAADEGFDCTLC 1157
Cdd:cd15600     2 CPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 4424-4528 1.64e-26

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: 106.90  E-value: 1.64e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPArLLNLDLDLWVHLNCALWSTEVYETQAGAL--INVELALRRGLSVRCAYCQQT-GATSGCHRLR 4500
Cdd:cd15571     1 CALCPRSGGALKGGGA-LKTTSDGLWVHVVCALWSPEVYFDDGTLLevEGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 528519285 4501 CTNAYHFTCALKAQCTF-----FKDKTMLCHLH 4528
Cdd:cd15571    80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 406-451 7.05e-26

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


Pssm-ID: 277069  Cd Length: 46  Bit Score: 102.71  E-value: 7.05e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 4813-4942 1.55e-25

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: 105.07  E-value: 1.55e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTII-RSEVANRKEKMYEAqNRGVYMFRIDSEHVIDATITGGPARYINHSCAPNCITEVV 4891
Cdd:cd19174    11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQYHN-HSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNCEMQKW 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4892 ALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHCGAVNCRKWMN 4942
Cdd:cd19174    90 SVNGVYRIGLFALKDIPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1107-1157 1.28e-24

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: 99.28  E-value: 1.28e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285 1107 VCPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENAADEGFDCTLC 1157
Cdd:cd15514     1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 406-451 2.02e-22

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 92.88  E-value: 2.02e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4641-4728 2.44e-22

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: 93.90  E-value: 2.44e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   4641 EFVIRVVEqgYDDLILTGSSPKGVWDKVLEPVAERRNETGFLRLFPVYLKGEDLFGLTVSAVTRIVESLPGVEACERYTF 4720
Cdd:smart00542    1 LFRVEIES--DPGEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 528519285   4721 RYGRNPLM 4728
Cdd:smart00542   79 RYHRSPLL 86
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 360-404 2.92e-22

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 92.37  E-value: 2.92e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLD--VTVTPLKRAGWQCPEC 404
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 406-451 1.19e-21

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


Pssm-ID: 277070  Cd Length: 46  Bit Score: 90.83  E-value: 1.19e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 4800-4919 6.35e-21

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: 91.13  E-value: 6.35e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4800 WKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEaQNRGVYMFRIDSEHVIDATITGGPARYIN 4879
Cdd:cd19218     2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYD-KYMCSFLFNLNNDFVVDATRKGNKIRFAN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 528519285 4880 HSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKF 4919
Cdd:cd19218    81 HSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4808-4917 8.47e-20

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: 91.28  E-value: 8.47e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4808 RSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEaQNRGVYMFRIDS---------EHVIDATITGGPARYI 4878
Cdd:cd10538    95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIYD-KSGGSYLFDLDEfsdsdgdgeELCVDATFCGNVSRFI 173

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 528519285 4879 NHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10538   174 NHSCDPNLFPFNVVIDhddlRYPRIALFATRDILPGEELTFDY 216
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 4424-4528 9.49e-20

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: 87.36  E-value: 9.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFC--HEEGDGLTD--GPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLSVRCAYCQQTGATSGCHRL 4499
Cdd:cd15668     1 CVFCkrGPHYKGLGDlfGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 528519285 4500 RCTNAYHFTCALKAQCTFFKDK-TMLCHLH 4528
Cdd:cd15668    74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1108-1157 9.51e-20

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: 85.34  E-value: 9.51e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1108 CPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENAADEGFDCTLC 1157
Cdd:cd15601     2 CPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 4801-4923 1.05e-19

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: 88.20  E-value: 1.05e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEaQNRGVYMFRIDSEHVIDATITGGPARYINH 4880
Cdd:cd19217     5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYD-KYMSSFLFNLNNDFVVDATRKGNKIRFANH 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 528519285 4881 SCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLED 4923
Cdd:cd19217    84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 4810-4917 1.11e-19

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: 88.40  E-value: 1.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4810 RIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEA-QNRGVYM--FRIDSE-HVIDAT-ITGGPARYINHSC-A 4883
Cdd:cd10528    25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGKtYCVDATkESGRLGRLINHSKkK 104

                          90       100       110
                  ....*....|....*....|....*....|....
gi 528519285 4884 PNCITEVVALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10528   105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 4806-4937 1.42e-19

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: 88.12  E-value: 1.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4806 LARSRIQGLGLYAARDIEKYTMVIEYIGTII-RSEVANRKEKMYEAQNRGVYMFRIDSEHVIDATITGGPARYINHSCAP 4884
Cdd:cd19211     6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIdEEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4885 NCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIpCHCGAVNC 4937
Cdd:cd19211    86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTV-CRCGAPNC 137
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 4813-4917 2.11e-19

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: 87.01  E-value: 2.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNrgvYMFRIDSEH-VIDATITGGPARYINHSCAPNCITEVV 4891
Cdd:cd10522    14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                          90       100
                  ....*....|....*....|....*.
gi 528519285 4892 ALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10522    91 TLKGEQHIGFVAIRDIKPGEELFISY 116
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 4813-4941 1.35e-18

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: 88.89  E-value: 1.35e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKmyeAQNRGV--YMFRIdSEHV---------IDATITGGPARYINHS 4881
Cdd:cd10544   101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGDmnYIIVL-REHLssgkvletfVDPTYIGNIGRFLNHS 176

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285 4882 CAPNCItevVALERGH----KIIISSNRRIQRGEELCYDY------------KFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd10544   177 CEPNLF---MVPVRVDsmvpKLALFAARDIVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRGFL 249
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4582-4633 6.66e-18

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: 80.24  E-value: 6.66e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  4582 GSLVLHAVGQLLPQQMlAFHSMTAIFPVGYEASRIYWSMRHGNRRCHYVCSI 4633
Cdd:pfam05964    1 GSLTVLSLGEIVPDRP-AFHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 4812-4941 5.55e-17

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: 84.16  E-value: 5.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEaqNRGV-YMFRID-------SEHVIDATITGGPARYINHSCA 4883
Cdd:cd20073   103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFDLDlfedqvdEYYTVDAQYCGDVTRFINHSCD 180

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 4884 PNCITEVVALERGHKIIIS----SNRRIQRGEELCYDYKFDLEDDQ----------------HKIPCHCGAVNCRKWM 4941
Cdd:cd20073   181 PNLAIYSVLRDKSDSKIYDlaffAIKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 4813-4941 6.80e-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: 84.29  E-value: 6.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVAN-RKEKMYEAQNRGVYMFRID--------------SEHVIDATITGGPARY 4877
Cdd:cd19473   117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFALDkfsdpdsldprlrgDPYEIDGEFMSGPTRF 196

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 4878 INHSCAPNC-ITEVV---ALERGHKIIISSNRRIQRGEELCYDY----------KFDLEDDQHKIPCHCGAVNCRKWM 4941
Cdd:cd19473   197 INHSCDPNLrIFARVgdhADKHIHDLAFFAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGYL 274
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4424-4528 7.56e-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: 7.56e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCheegdgltdgparllNLDlDLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTN 4503
Cdd:cd15665     1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                          90       100
                  ....*....|....*....|....*..
gi 528519285 4504 AYHFTCALKAQCtF--FKDKTMLCHLH 4528
Cdd:cd15665    65 SFHFPCAAAAGC-FqdIKTLTLFCPEH 90
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 267-345 1.16e-16

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: 78.78  E-value: 1.16e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLY--VDKAIDSGSTECCAYC-KRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKT----Y 339
Cdd:cd15571    26 VHVVCALWSPEVYFDDGTLLEVegVSKIPKRRKKLKCSICgKRGGACIQCSYPGCPRSFHVSCAIRAGCLFEFEDgpgnF 105


                  ....*.
gi 528519285  340 TLLCPD 345
Cdd:cd15571   106 VVYCPK 111
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4812-4937 1.39e-16

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: 79.58  E-value: 1.39e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTIIRS-EVANRKEKMYEAQNRGVYMFRIDSEHVIDATITGGPARYINHSCAPNCITEV 4890
Cdd:cd19212    12 RGWGLRTKRSIKKGEFVNEYVGELIDEeECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 4891 VALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKIpCHCGAVNC 4937
Cdd:cd19212    92 WTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTE-CHCGADNC 137
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4812-4941 4.65e-16

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: 81.09  E-value: 4.65e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEaqNRGV-YMFRID---SEHVIDATITGGPARYINHSCAPNCI 4887
Cdd:cd10532    95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYD--SKGItYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQ 172

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4888 TEVVALE----RGHKIIISSNRRIQRGEELCYDYKF----DLEDD---------QHKIPCHCGAVNCRKWM 4941
Cdd:cd10532   173 VFNVFIDnldtRLPRIALFSTRTIKAGEELTFDYQMkgsgDLSSDsidnspakkRVRTVCKCGAVTCRGYL 243
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4451-4528 1.32e-15

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: 1.32e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4451 HLNCALWSTEVYetQAGA------LINVELALRRGLSVRCAYC-QQTGATSGCHRLRCTNAYHFTCALKAQCTF-FKDKT 4522
Cdd:pfam13771    1 HVVCALWSPELV--QRGNdsmgfpIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDN 78

                           90
                   ....*....|
gi 528519285  4523 ----MLCHLH 4528
Cdd:pfam13771   79 gtfkSYCKKH 88
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 1030-1075 2.25e-15

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 72.68  E-value: 2.25e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1030-1075 2.45e-15

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: 72.81  E-value: 2.45e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 4804-4917 2.71e-15

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: 75.30  E-value: 2.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4804 VYLARSRIQ-GLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRgVYMFRIDSEHVIDATITGGPARYINH-- 4880
Cdd:cd19168     3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 528519285 4881 --SCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd19168    82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNY 120
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4802-4937 2.81e-15

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: 75.73  E-value: 2.81e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4802 SNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVAnrKEKMYEAQNRGV---YMFRIDSEHVIDATITGGPARYI 4878
Cdd:cd19210     2 PEVEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIDEEEC--RARIRYAQEHDItnfYMLTLDKDRIIDAGPKGNYARFM 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4879 NHSCAPNCITEVVALERGHKIIISSNRRIQRGEELCYDYKFDLEDDQhKIPCHCGAVNC 4937
Cdd:cd19210    80 NHCCQPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYNLECLGNG-KTVCKCGAPNC 137
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 268-344 2.85e-15

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: 74.65  E-value: 2.85e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  268 HLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQdIKTYTLLCP 344
Cdd:cd15666    28 HLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGCMF-FKDKTMLCP 103
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1030-1075 3.00e-15

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 72.50  E-value: 3.00e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15519     1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 4803-4917 4.87e-15

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: 72.67  E-value: 4.87e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4803 NVYLARSRIQGLGLYAARDIEKytmvieyiGTIIrsevanrkekmyeaqnrgvymfridsehvidatitgGPARYINHSC 4882
Cdd:cd08161     1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 528519285 4883 APNCITEVVALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd08161    37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4812-4941 5.98e-15

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: 78.01  E-value: 5.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNrGVYMFRID---SEHVIDATITGGPARYINHSCAPNCIT 4888
Cdd:cd10525    97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDLDyveDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4889 EVVAL----ERGHKIIISSNRRIQRGEELCYDYKF-----DLEDDQH-----------------KIPCHCGAVNCRKWM 4941
Cdd:cd10525   176 YNVFIdnldERLPRIALFATRTIRAGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4801-4938 7.78e-15

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: 76.99  E-value: 7.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKmyeaqnrGVYMFRIDSE----HVIDATITGGPAR 4876
Cdd:cd10543    90 RYRLQLFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED-------DSYLFDLDNKdgetYCIDARRYGNISR 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 4877 YINHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDYKFDLEDDQHK-IPCHCGAVNCR 4938
Cdd:cd10543   163 FINHLCEPNLIPVRVFVEhqdlRFPRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4447-4528 2.97e-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: 71.13  E-value: 2.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4447 DLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTNAYHFTCALKAQcTF--FKDKTML 4524
Cdd:cd15696     8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAG-TFqdFSRRLLL 86


                  ....
gi 528519285 4525 CHLH 4528
Cdd:cd15696    87 CPTH 90
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1883-2338 5.43e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 79.98  E-value: 5.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1883 RPQPPPLSSTSKTPTQDTQYPQG---PSSQPQSPQMFSPESSGSRPSSPYDPYGKMVGTPRPP-------PSGSSTPRRG 1952
Cdd:PHA03247 2588 RPDAPPQSARPRAPVDDRGDPRGpapPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPErprddpaPGRVSRPRRA 2667

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1953 S-------VSDMQERCRPSSAHESFGSPTTTSTDPYAKPPDTPRPSdPFVKPMCTPRLGSLSEQQGRQL----------M 2015
Cdd:PHA03247 2668 RrlgraaqASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPH-ALVSATPLPPGPAAARQASPALpaapappavpA 2746

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2016 GNVTPGDNFSRPG-QRSEAYQRMAHSRMVLSDPysRPLLTPVPGSNESGSVPVFKTPMPPSGLQQdSFNGGQQGMRRGSS 2094
Cdd:PHA03247 2747 GPATPGGPARPARpPTTAGPPAPAPPAAPAAGP--PRRLTRPAVASLSESRESLPSPWDPADPPA-AVLAPAAALPPAAS 2823

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2095 DTFPHVQHTDTYSNQPLTPHPSMADGINNEGRMM-------RPGQGSHFAQPLSMGRHPQRDPYSQAPSTPRQ------D 2161
Cdd:PHA03247 2824 PAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVApggdvrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTEsfalppD 2903

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2162 YPQQMSDPYAQMPGTPRPHDPYAQMPG-TPRPNCDPYPLPPPTTRTEPIDKFSQSQPSS-------------RRQSPSHA 2227
Cdd:PHA03247 2904 QPERPPQPQAPPPPQPQPQPPPPPQPQpPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgrvavpRFRVPQPA 2983

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2228 idPYAQMPGTPRPSPGERYSKSPGSLRSSDPFSQPPgTPRPI--KNEIY--------------------DQQGTPMPILP 2285
Cdd:PHA03247 2984 --PSREAPASSTPPLTGHSLSRVSSWASSLALHEET-DPPPVslKQTLWppddtedsdadslfdsdserSDLEALDPLPP 3060

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 2286 DPYSQPPGTPRPGAgLEGFSRLNPRLNFithqtDPLGLQAQSRTQDPFSRSCG 2338
Cdd:PHA03247 3061 EPHDPFAHEPDPAT-PEAGARESPSSQF-----GPPPLSANAALSRRYVRSTG 3107
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1886-2298 5.57e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 79.60  E-value: 5.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1886 PPPLSSTSKTPTQDTQYPQGPSSQPQSPQMFSPESSgSRPSSPYDPYGKMVGT------------PRPPPSGsstprrgs 1953
Cdd:PHA03247 2560 PPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQS-ARPRAPVDDRGDPRGPappsplppdthaPDPPPPS-------- 2630

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1954 vsdmqercrPSSAHESFGSPTTTSTDPYAKPPDTPRPSdpfvkpmcTPRLGSLSEQQGRQLMGNVTPgdnfsrPGQRSEA 2033
Cdd:PHA03247 2631 ---------PSPAANEPDPHPPPTVPPPERPRDDPAPG--------RVSRPRRARRLGRAAQASSPP------QRPRRRA 2687

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2034 YQRMAHSRMVLSDPYSRPL--------------LTPVPGSNESGSVPVFKTPMPPSGLQQDSFNGGQQgmRRGSSDTfph 2099
Cdd:PHA03247 2688 ARPTVGSLTSLADPPPPPPtpepaphalvsatpLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPA--RPARPPT--- 2762

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2100 vqhtdtySNQPLTPHPSMADGINNEGRMMRPGqgshfAQPLSMGRhpqrdPYSQAPSTPrQDYPQQMSDPYAQMPGTPRP 2179
Cdd:PHA03247 2763 -------TAGPPAPAPPAAPAAGPPRRLTRPA-----VASLSESR-----ESLPSPWDP-ADPPAAVLAPAAALPPAASP 2824

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2180 HDPYAQmPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSRRQSPSHAidpyAQMPGTPRPSPGERYSKSPGSlRSSDPF 2259
Cdd:PHA03247 2825 AGPLPP-PTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP----AAKPAAPARPPVRRLARPAVS-RSTESF 2898

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 528519285 2260 SQPPGTPRPIKNEIYDQQGTPMPILPDPYSQPPGTPRPG 2298
Cdd:PHA03247 2899 ALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPP 2937
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1031-1075 5.77e-14

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: 68.84  E-value: 5.77e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4801-4938 6.29e-14

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: 74.58  E-value: 6.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4801 KSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKmyeaqnrGVYMFRIDSE----HVIDATITGGPAR 4876
Cdd:cd10535    90 RARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevYCIDARFYGNVSR 162

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 4877 YINHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKI-PCHCGAVNCR 4938
Cdd:cd10535   163 FINHHCEPNLVPVRVFMAhqdlRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1030-1075 1.08e-13

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 67.84  E-value: 1.08e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15510     1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1836-2300 1.10e-13

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 78.67  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1836 SGDASNSPHTSSGGnsplqaLTPKDSFAMTQMPGTASSGtsADDVFLRPQPPPLSSTSKTPTQDTQYPQGPSSQPQSPQM 1915
Cdd:PHA03307   28 PGDAADDLLSGSQG------QLVSDSAELAAVTVVAGAA--ACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPAS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1916 FSPESSGSRPSSPYDPygkmvGTPRPPPSGSSTPRRGSVSDMQERCRPSSAHESFGSPTTTSTDPYAKPPDTPRPSDPFV 1995
Cdd:PHA03307  100 PAREGSPTPPGPSSPD-----PPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAAL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1996 kpmctprLGSLSEQQGRQLmgnVTPGDnfSRPGQRSEAyqRMAHSRMVLSDPYSRPLLTPVPGSNESGSVPVFKTPMPPS 2075
Cdd:PHA03307  175 -------PLSSPEETARAP---SSPPA--EPPPSTPPA--AASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2076 GLQQDSFNGGQQGMRRGSSDtfphvqhtdtysnQPLTPHPSMADGINNEGRMMRPGQGSHFAQPLSMGRHPQR-DPYSQA 2154
Cdd:PHA03307  241 SSESSGCGWGPENECPLPRP-------------APITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPsSPGSGP 307

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2155 PSTPRQDYPQQMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPttrtepiDKFSQSQPSSRRQSPSHAIDPY-AQ 2233
Cdd:PHA03307  308 APSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSR-------PPPPADPSSPRKRPRPSRAPSSpAA 380

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 2234 MPGTPRPsPGERYSKSPGSLRSSDPFSQPPGTPRPIKNEIYDQQGTPMPILPDPYsqPPGTPRPGAG 2300
Cdd:PHA03307  381 SAGRPTR-RRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARYPLLT--PSGEPWPGSP 444
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1030-1076 1.17e-13

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: 68.05  E-value: 1.17e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCV 47
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 407-451 1.29e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 67.80  E-value: 1.29e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1030-1075 2.02e-13

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: 67.09  E-value: 2.02e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1030-1075 2.92e-13

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


Pssm-ID: 277069  Cd Length: 46  Bit Score: 66.89  E-value: 2.92e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15594     1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 4424-4528 3.02e-13

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: 68.79  E-value: 3.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGD----GLTDGPArllnldLDLWVHLNCALWSTEVYETqAGALINVELALRRGLSVRCAYCQQTGATSGCHRL 4499
Cdd:cd15699     1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLV-CGRLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 528519285 4500 RCTNAYHFTCALKAQCTFFKDK-TMLCHLH 4528
Cdd:cd15699    74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4447-4528 3.02e-13

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: 68.40  E-value: 3.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4447 DLWVHLNCALWSTEVYETQAGALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTNAYHFTCAlKAQCTFFKDKT--ML 4524
Cdd:cd15695     8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCA-AASGSFQSMKTllLL 86


                  ....
gi 528519285 4525 CHLH 4528
Cdd:cd15695    87 CPEH 90
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 1031-1075 3.38e-13

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 66.65  E-value: 3.38e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15627     2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 406-451 3.60e-13

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


Pssm-ID: 277004  Cd Length: 44  Bit Score: 66.56  E-value: 3.60e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQpiMETIPTNGWRCKNC 451
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4813-4939 4.57e-13

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: 73.09  E-value: 4.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMY--------------EAQNRGvymFRIDSE---HVIDATITGGPA 4875
Cdd:cd10517   140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievvEKLKEG---YESDVEehcYIIDAKSEGNLG 216

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4876 RYINHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDYKFDLEDDQHKI-PCHCGAVNCRK 4939
Cdd:cd10517   217 RYLNHSCSPNLFVQNVFVDthdlRFPWVAFFASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 4424-4517 5.77e-13

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: 67.98  E-value: 5.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEegdgltdgPARLLNL-DL------DLWVHLNCALWSTEVYETqAGALINVELALRRGLSVRCAYCQQTGATSGC 4496
Cdd:cd15700     1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                          90       100
                  ....*....|....*....|.
gi 528519285 4497 HRLRCTNAYHFTCALKAQCTF 4517
Cdd:cd15700    72 CHKGCTQSYHYICAVEAGCLF 92
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4592-4635 8.14e-13

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: 65.38  E-value: 8.14e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....
gi 528519285   4592 LLPQQMLAFHSMTAIFPVGYEASRIYWSMRHGNRRCHYVCSINE 4635
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVIDE 44
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1030-1075 9.62e-13

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: 65.25  E-value: 9.62e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1030-1078 1.09e-12

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: 65.21  E-value: 1.09e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 528519285  1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQ--NVPKGSWKCKWCVLC 1078
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4789-4938 1.19e-12

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: 70.82  E-value: 1.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4789 KSAQYRRMNAEWKSNVYLARSRIQGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKmyeaqnrGVYMFRIDSE----H 4864
Cdd:cd10533    78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4865 VIDATITGGPARYINHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDYKFDLEDDQHK-IPCHCGAVNCR 4938
Cdd:cd10533   151 CIDARYYGNISRFINHLCDPNIIPVRVFMLhqdlRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 268-344 1.44e-12

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: 66.20  E-value: 1.44e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285   268 HLRCAAWSEGVCRGEGQSLLY----VDKAIDSGSTECCAYCK-RLGASIKCCEESCGRSFHYPCAAAAGTFQDIK----T 338
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSMGFpiedIEKIPKRRWKLKCYLCKkKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedngT 80


                   ....*.
gi 528519285   339 YTLLCP 344
Cdd:pfam13771   81 FKSYCK 86
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
4422-4528 1.46e-12

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 66.98  E-value: 1.46e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  4422 RRCCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLSVRCAYCQQ-TGATSG 4495
Cdd:pfam13832    1 VRCCLCPLRGGALkqtSDG----------RWVHVLCAIFVPEVRfgNVATMEPIDVSRIPPERWKLKCVFCKKrSGACIQ 70

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 528519285  4496 CHRLRCTNAYHFTCALKAQCTF------FKDKTMLCHLH 4528
Cdd:pfam13832   71 CSKGRCTTAFHVTCAQAAGVYMepedwpNVVVIAYCQKH 109
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1030-1075 2.12e-12

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


Pssm-ID: 277070  Cd Length: 46  Bit Score: 64.25  E-value: 2.12e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15595     1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 406-451 2.28e-12

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: 64.42  E-value: 2.28e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15513     1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 1031-1075 2.47e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 63.97  E-value: 2.47e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1031-1075 2.77e-12

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: 63.97  E-value: 2.77e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 404-451 3.66e-12

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


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 63.48  E-value: 3.66e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  404 CKVCLSCKNpgdDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15545     2 CQICRSGDN---EDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 268-344 4.10e-12

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: 65.50  E-value: 4.10e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285  268 HLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCA-AAAGTFQDIKtyTLLCP 344
Cdd:cd15664    28 HINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCArKAECVFQDDK--KVFCP 103
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1031-1075 4.60e-12

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: 63.54  E-value: 4.60e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGS-WKCKWC 1075
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 266-345 4.93e-12

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: 65.35  E-value: 4.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  266 CAHLRCAAWSEGVC-RGEGQSLLY------VDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGT-FQDIK 337
Cdd:cd15669    24 CAHYFCLLFSSGLPqRGEDNEGIYgflpedIRKEVRRASRLRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFG 103


                  ....*...
gi 528519285  338 TYTLLCPD 345
Cdd:cd15669   104 EYRSFCWE 111
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 1031-1075 9.99e-12

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


Pssm-ID: 277005  Cd Length: 46  Bit Score: 62.40  E-value: 9.99e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1031-1075 1.30e-11

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: 62.29  E-value: 1.30e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVP-KGSWKCKWC 1075
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 4424-4528 2.18e-11

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: 63.95  E-value: 2.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGParLLNLDLDLWVHLNCALWSTEVYETQ-------AGALIN-VELALRRGLSVRCAYCQQTGATSG 4495
Cdd:cd15673     1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 528519285 4496 CHRLRCTNAYHFTCALKAQCTFFKDK-----TMLCHLH 4528
Cdd:cd15673    79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1030-1075 2.59e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 61.46  E-value: 2.59e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528519285   1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPL-QNVPKGSWKCKWC 1075
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLlEEEPDGKWYCPKC 47
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 4812-4939 2.81e-11

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: 66.80  E-value: 2.81e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTIIRSEVANRKEKMYEAQNRGVYMFRIDSEHVIDATITGGPARYINHSCAPNCITEVV 4891
Cdd:cd10541   102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4892 ALE----RGHKIIISSNRRIQRGEELCYDYKFDLED-DQHKIPCHCGAVNCRK 4939
Cdd:cd10541   182 FVDthdlRFPWVAFFASKRIKAGTELTWDYNYEVGSvEGKELLCCCGSNECRG 234
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 4814-4928 3.69e-11

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: 65.12  E-value: 3.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4814 LGLYAARDIEKYTMVIEYIGTI-IRSEVANRKEKMYE---AQNRGVYmFRIDSEHVIDATITGGPARYINHSCAPNCITE 4889
Cdd:cd19183    14 FGLFADRPIPAGDPIQELLGEIgLQSEYIADPENQYQilgAPKPHVF-FHPQSPLYIDTRRSGSVARFIRRSCRPNAELV 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 528519285 4890 VVALERGH--KIIISSNRRIQRGEELCYDYKFDLEDDQHKI 4928
Cdd:cd19183    93 TVASDSGSvlKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 407-451 3.70e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 60.89  E-value: 3.70e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15544     2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 1031-1075 5.43e-11

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


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 60.40  E-value: 5.43e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15545     2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 406-451 5.66e-11

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 60.30  E-value: 5.66e-11
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 528519285    406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMET-IPTNGWRCKNC 451
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 4815-4920 6.74e-11

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: 62.68  E-value: 6.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4815 GLYAARDIEKYTMVIEYIGTI-IRSEVAnRKEKMYEAQNRGVYMF--RIDSEHVIDATITGGPARYINHSCAPNC-ITEV 4890
Cdd:cd10529    18 GLVATEDISPGEPILEYKGEVsLRSEFK-EDNGFFKRPSPFVFFYdgFEGLPLCVDARKYGNEARFIRRSCRPNAeLRHV 96

                          90       100       110
                  ....*....|....*....|....*....|
gi 528519285 4891 VALERGHKIIISSNRRIQRGEELCYDYKFD 4920
Cdd:cd10529    97 VVSNGELRLFIFALKDIRKGTEITIPFDYD 126
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 406-451 7.08e-11

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: 60.10  E-value: 7.08e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15515     1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1031-1075 9.88e-11

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: 59.70  E-value: 9.88e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 267-346 1.16e-10

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: 61.43  E-value: 1.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  267 AHLRCAAWSEGVCRGEGQsLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIKTYTLLCPDY 346
Cdd:cd15700    26 VHEACAVWTTGVYLVAGK-LFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENFSLRCPKH 104
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 981-1031 1.54e-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: 59.04  E-value: 1.54e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285   981 CVVCGsfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKG-WRCLECTVC 1031
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 980-1028 1.66e-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: 59.15  E-value: 1.66e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 528519285    980 MCVVCGsfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 4812-4941 1.69e-10

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: 65.24  E-value: 1.69e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4812 QGLGLYAARDIEKYTMVIEYIGTI---IRSEVANRKEKMYEAQNRGVYMFRI-----------DSEHVIDATITGGPARY 4877
Cdd:cd10523   118 KGWGVRCLDDIDKGTFVCIYAGRVlsrARSPTEPLPPKLELPSENEVEVVTSwlilskkrklrENVCFLDASKEGNVGRF 197

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4878 INHSCAPNCITEVVALERGHK----IIISSNRRIQRGEELCYDYKFDLEDDQHK-IPCHCGAVNCRKWM 4941
Cdd:cd10523   198 LNHSCCPNLFVQNVFVDTHDKnfpwVAFFTNRVVKAGTELTWDYSYDAGTSPEQeIPCLCGVNKCQKKI 266
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 407-451 1.97e-10

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


Pssm-ID: 277099  Cd Length: 47  Bit Score: 58.71  E-value: 1.97e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1028-1075 2.15e-10

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: 58.45  E-value: 2.15e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1028 CTVCeacgqaSDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15532     2 CRVC------KDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1031-1075 2.25e-10

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: 58.81  E-value: 2.25e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGS-WKCKWC 1075
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEdWYCPSC 47
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 258-344 2.27e-10

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: 60.40  E-value: 2.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  258 LFDPTGQCCAHLRCAAWSEGVCRGEGQsLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQDIK 337
Cdd:cd15668    16 LFGPYYEVWVHEDCAVWAPGVYLVGGK-LYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEE 94


                  ....*..
gi 528519285  338 TYTLLCP 344
Cdd:cd15668    95 NFSLLCP 101
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 406-451 2.41e-10

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 58.42  E-value: 2.41e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15603     1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 406-454 2.78e-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: 58.66  E-value: 2.78e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 528519285   406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQP--IMETIPTNGWRCKNCRTC 454
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 407-451 4.11e-10

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: 57.66  E-value: 4.11e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15543     2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 1030-1075 4.64e-10

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


Pssm-ID: 277004  Cd Length: 44  Bit Score: 57.70  E-value: 4.64e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15529     1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 4424-4528 4.93e-10

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: 59.96  E-value: 4.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGlTDGPARLLNLDlDLWVHLNCALWSTEVYETQ------AGALIN-VELALRRGLSVRCAYCQQTGATSGC 4496
Cdd:cd15669     1 CVLCGRSDDD-PDKYGEKLQKD-GICAHYFCLLFSSGLPQRGednegiYGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 528519285 4497 HRLRCTNAYHFTCALKAQCT--FFKDKTMLCHLH 4528
Cdd:cd15669    79 AVKGCRRSFHFPCGLENGCVtqFFGEYRSFCWEH 112
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2141-2552 5.41e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 66.50  E-value: 5.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2141 SMGRHPQRDPYSQAPSTPRQDypqqMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSR 2220
Cdd:PHA03247 2584 SRARRPDAPPQSARPRAPVDD----RGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPG 2659

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2221 RQSPSHAIDPYAQMPGTPRPSPGERYSKSP---GSLRSS-DPFSQPP-----------GTPRPIKNEIYDQQGTPMPILP 2285
Cdd:PHA03247 2660 RVSRPRRARRLGRAAQASSPPQRPRRRAARptvGSLTSLaDPPPPPPtpepaphalvsATPLPPGPAAARQASPALPAAP 2739

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2286 DPYSQPPGTPRPGAGLEGFSRLNPRLNFI-THQTDPLGLQAQSRTQDPFSRSCGTDSQTPKHPGISDENISIQQTIPNQT 2364
Cdd:PHA03247 2740 APPAVPAGPATPGGPARPARPPTTAGPPApAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2365 PIHDP----------FEQAPLTPCSQTGERSSQDVIVSTGNPSDSQNTMQPPLGETEEKIKQR-QRLRQLILKQQQEKSA 2433
Cdd:PHA03247 2820 PAASPagplppptsaQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPvRRLARPAVSRSTESFA 2899

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2434 IRKEkGLQEATASAAPGTPRHWSQDDSGPQSdifgRPPPPYPGTmrsspihagqrfPGTFLADQCGPMPNEPQCSRQPFP 2513
Cdd:PHA03247 2900 LPPD-QPERPPQPQAPPPPQPQPQPPPPPQP----QPPPPPPPR------------PQPPLAPTTDPAGAGEPSGAVPQP 2962

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 528519285 2514 RDLNNVGMRPQGQRFAFPPGAPNQEQFLRPPHQMQGGPL 2552
Cdd:PHA03247 2963 WLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 1031-1075 6.97e-10

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


Pssm-ID: 277098  Cd Length: 46  Bit Score: 57.06  E-value: 6.97e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15628     2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 406-451 8.74e-10

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: 56.77  E-value: 8.74e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15604     1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 1031-1075 1.04e-09

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 56.69  E-value: 1.04e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGqasDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15539     2 CAVCG---DGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 406-451 1.21e-09

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: 56.50  E-value: 1.21e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15602     1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 407-451 1.22e-09

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: 56.62  E-value: 1.22e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15527     2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1842-2233 1.28e-09

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 64.94  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1842 SPHTSSGgnsplqalTPKDSFAMTQMPGTASSGTSADDVFLRPQPPPLSSTSKTPTQDTQYPQGPSSQPQSPQMFSPESS 1921
Cdd:pfam05109  441 APNTTTG--------LPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSA 512

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1922 GSRPSSPYDPYGKMVGTPRPppsGSSTPRRGSVSDMQERCRPSSAHESfGSPTTTSTDPYAKPPDTPR--PSDPFVKPM- 1998
Cdd:pfam05109  513 VTTPTPNATSPTPAVTTPTP---NATSPTLGKTSPTSAVTTPTPNATS-PTPAVTTPTPNATIPTLGKtsPTSAVTTPTp 588

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1999 --CTPRLGSLSEQ---QGRQLMGNVTPGDNFSRPGQRSEAYQRMAH-------SRMVLSDPYSRPLLTPVPGSNESGSVP 2066
Cdd:pfam05109  589 naTSPTVGETSPQantTNHTLGGTSSTPVVTSPPKNATSAVTTGQHnitssstSSMSLRPSSISETLSPSTSDNSTSHMP 668

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2067 VFKTPMPpsglqqdsfNGGQQGMRRGSSDTFPHvqHTDTYSNQPLTPHPSMADGINNEGRMMRPGQGShfaqpLSMGRHP 2146
Cdd:pfam05109  669 LLTSAHP---------TGGENITQVTPASTSTH--HVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVN-----VTKGTPP 732

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2147 QRDPYSQAPSTPRQDYPQQMSDPYAQMPGT-------------PRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFS 2213
Cdd:pfam05109  733 KNATSPQAPSGQKTAVPTVTSTGGKANSTTggkhttghgartsTEPTTDYGGDSTTPRTRYNATTYLPPSTSSKLRPRWT 812

                          410       420
                   ....*....|....*....|
gi 528519285  2214 QSQPSSRRQSPSHAIDPYAQ 2233
Cdd:pfam05109  813 FTSPPVTTAQATVPVPPTSQ 832
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1030-1078 1.51e-09

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: 56.26  E-value: 1.51e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKW-CVLC 1078
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTKNSGWqCSEC 50
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 1028-1075 1.64e-09

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 56.25  E-value: 1.64e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1028 CTVCEACGQasdpgrLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15523     2 CSVCRKSGE------LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 404-451 2.17e-09

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


Pssm-ID: 277098  Cd Length: 46  Bit Score: 55.91  E-value: 2.17e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  404 CKVClscKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15628     2 CKVC---RKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 4813-4917 2.32e-09

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: 58.16  E-value: 2.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4813 GLGLYAARDIEKytmvieyiGTIIRSE------VANRKEKMYEAQNRGVYMFRIdsehvidatitggpARYINHSCAPNC 4886
Cdd:cd20071    10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 528519285 4887 iteVVALERGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd20071    68 ---VVVFDGNGTLRVRALRDIKAGEELTISY 95
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 406-451 3.57e-09

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: 55.15  E-value: 3.57e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15605     1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 1030-1075 4.62e-09

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


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 54.67  E-value: 4.62e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1030 VCEACGQAsdpGRLLLCDDCDISYHTYCLDPPL--QNVPKGSWKCKWC 1075
Cdd:cd15533     1 YCDSCGEG---GDLLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 268-337 5.11e-09

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: 56.59  E-value: 5.11e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528519285  268 HLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAA-GTFQDIK 337
Cdd:cd15694    28 HVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCARASrCCFQDDK 98
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 360-407 8.03e-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: 54.42  E-value: 8.03e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 528519285   360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVT--PLKRAGWQCPECKVC 407
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 268-344 9.22e-09

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: 56.21  E-value: 9.22e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  268 HLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTFQdIKTYTLLCP 344
Cdd:cd15698    28 HLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIRAKCMF-FKDKTMLCP 103
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2025-2406 9.95e-09

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: 62.09  E-value: 9.95e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2025 SRPGQRSEAYQRMAHSRMVLSDPYSRPLLTPVPGSNESGSVPvfktpmPPSGLQQDSFNGGQQGMRRGSSdtfPHVQHTD 2104
Cdd:pfam03154  108 SRPNSPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSPSIP------SPQDNESDSDSSAQQQILQTQP---PVLQAQS 178

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2105 TYSNQPLTPHP---SMADGINNEGRMMRPGQGSHFAQPLSMGRHPQRDPYSQAPSTPrQDYPQQMsdpyaqmpgtPRPHD 2181
Cdd:pfam03154  179 GAASPPSPPPPgttQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTP-TLHPQRL----------PSPHP 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2182 PYAQMPGTPRP-NCDPYPLPPPTTRTEpidkfSQSQPSSRRQSPSHAIDPYAQMPGTPRPSPGERYSKSPGSLRSSDPFS 2260
Cdd:pfam03154  248 PLQPMTQPPPPsQVSPQPLPQPSLHGQ-----MPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQ 322

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2261 QPPGTPRPIKNEIYDQQGTPMPILPDPYSQ-----PPGTPRP----------------------GAGLEGFSRLNPRLNF 2313
Cdd:pfam03154  323 QRIHTPPSQSQLQSQQPPREQPLPPAPLSMphikpPPTTPIPqlpnpqshkhpphlsgpspfqmNSNLPPPPALKPLSSL 402

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2314 ITH-----QTDPLGLQAQSRTQDPFSRSCGTDSQTPKHP--GISDENISIQQTIPNQTpihdPFEQAPLTPCSQTGERSS 2386
Cdd:pfam03154  403 STHhppsaHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPppAASHPPTSGLHQVPSQS----PFPQHPFVPGGPPPITPP 478

                          410       420
                   ....*....|....*....|
gi 528519285  2387 QDVIVSTgnpSDSQNTMQPP 2406
Cdd:pfam03154  479 SGPPTST---SSAMPGIQPP 495
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 406-451 1.23e-08

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: 53.86  E-value: 1.23e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  406 VCLSCKNPGDD-SKMLVCDMCDKGYHTFCLQPIMET-IPTNGWRCKNC 451
Cdd:cd15489     1 SCIVCGKGGDLgGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1786-2292 1.75e-08

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: 61.32  E-value: 1.75e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1786 KESEQEQEWKFRQQMRQKSKQQAKIEATQKLEQVKNEQQQLQKQQQQLQYSGDASNSPHTSSGGNSPLQALTPKDSFAMT 1865
Cdd:pfam03154   67 KKIKEEAPSPLKSAKRQREKGASDTEEPERATAKKSKTQEISRPNSPSEGEGESSDGRSVNDEGSSDPKDIDQDNRSTSP 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1866 QMPG----TASSGTSADDVFLRPQPPPLSSTSKTPTQDTQYPQGPSsqpQSPQMFSPESSGSRPSSPYDPYGKMVGTPRP 1941
Cdd:pfam03154  147 SIPSpqdnESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTT---QAATAGPTPSAPSVPPQGSPATSQPPNQTQS 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  1942 PPSGSSTPRRGSVSDMQercRPSSAHesfgSPTTTSTDPYAKPPDTPRPSDPFVKPMCTPRLGSlSEQQGRQLMGNVTPG 2021
Cdd:pfam03154  224 TAAPHTLIQQTPTLHPQ---RLPSPH----PPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPH-SLQTGPSHMQHPVPP 295

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2022 DNFSRPGQRSEAyQRMAHSRMVLSDPYSRPLLTPVPGSNESGSVPVFKTPMPPSGLqqdsfnggqqgmrrgssdTFPHVQ 2101
Cdd:pfam03154  296 QPFPLTPQSSQS-QVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPL------------------SMPHIK 356

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2102 HTdtysnqPLTPHPSMadginnegrmmrPGQGSHfaqplsmgRHPqrdPYSQAPStPRQdYPQQMSDPYAQMPGT----- 2176
Cdd:pfam03154  357 PP------PTTPIPQL------------PNPQSH--------KHP---PHLSGPS-PFQ-MNSNLPPPPALKPLSslsth 405

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2177 --PRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSRRQSPSHAIDPYAQMPGTPRPSPG-ERYSKSPGSL 2253
Cdd:pfam03154  406 hpPSAHPPPLQLMPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPiTPPSGPPTST 485

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  2254 RSSDPFSQPPGT------------------PRPIKNEIYDQQGTPMPILPDPYSQPP 2292
Cdd:pfam03154  486 SSAMPGIQPPSSasvsssgpvpaavscplpPVQIKEEALDEAEEPESPPPPPRSPSP 542
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1030-1075 1.78e-08

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: 53.47  E-value: 1.78e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1030 VCEACGQA-SDPGRLLLCDDCDISYHTYCLDPPLQ-NVPKGSWKCKWC 1075
Cdd:cd15489     1 SCIVCGKGgDLGGELLQCDGCGKWFHADCLGPPLSsFVPNGKWICPVC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 980-1028 2.02e-08

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: 53.09  E-value: 2.02e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  980 MCVVCGSfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:cd15489     1 SCIVCGK-GGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 268-344 2.11e-08

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: 55.05  E-value: 2.11e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285  268 HLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAG-TFqdIKTYTLLCP 344
Cdd:cd15697    28 HLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTCAIKAQcMF--FKDKTMLCP 103
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 407-451 2.39e-08

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: 52.76  E-value: 2.39e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNG-WRCKNC 451
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 1031-1075 2.92e-08

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


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 52.42  E-value: 2.92e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1031 CEACGQasdPGRLLLCDDCDISYHTYCLDPPL--QNVPKGSWKCKWC 1075
Cdd:cd15535     2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 267-339 3.16e-08

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: 54.62  E-value: 3.16e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGT--FQDIKTY 339
Cdd:cd15693    29 THVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCvfLEDKKVY 103
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 407-451 3.41e-08

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: 52.42  E-value: 3.41e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15536     2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1031-1075 4.05e-08

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 52.22  E-value: 4.05e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQAsdpGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15531     2 CEVCQQG---GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 1031-1076 4.97e-08

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


Pssm-ID: 277099  Cd Length: 47  Bit Score: 52.16  E-value: 4.97e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 360-404 7.30e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 51.44  E-value: 7.30e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 528519285    360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVTP-LKRAGWQCPEC 404
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1027-1075 8.92e-08

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


Pssm-ID: 277038  Cd Length: 49  Bit Score: 51.24  E-value: 8.92e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285 1027 ECTVCEACGQASDpgrLLLCDDCDISYHTYCLDPPLQNVPKG---SWKCKWC 1075
Cdd:cd15563     1 ECCVCKQTGDNSQ---LVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 407-451 1.02e-07

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


Pssm-ID: 277005  Cd Length: 46  Bit Score: 51.23  E-value: 1.02e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15530     2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 265-343 1.20e-07

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: 53.16  E-value: 1.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  265 CCAHLRCAAWSEG-VCRG-------EGQSLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAA---AAGTF 333
Cdd:cd15673    23 IAAHHNCMLFSSGlVQYVspnendfGGFDIEDVKKEIKRGRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKkddAKIIE 102

                          90
                  ....*....|.
gi 528519285  334 QDIK-TYTLLC 343
Cdd:cd15673   103 RNSQgIYRVYC 113
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 404-451 1.20e-07

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: 50.74  E-value: 1.20e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  404 CKVClscknpGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15532     2 CRVC------KDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1108-1145 1.32e-07

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: 51.00  E-value: 1.32e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 528519285 1108 CPVCTRSYREEEL---ILQCRQCDRWVHGSCQGLnSDEDVE 1145
Cdd:cd15593     2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGL-SDELYE 41
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1107-1157 1.35e-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: 50.78  E-value: 1.35e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285 1107 VCPVCTRSYREEELILQCRQCDRWVHGSCQGLNSDEDVENaadEGFDCTLC 1157
Cdd:cd15489     1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPN---GKWICPVC 48
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2149-2551 1.42e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 1.42e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2149 DPYSQAPSTPRQDYPQQMSDPYAQMPGTPRP-------HDPYAQMPGTPRPNCDPYPLPPPTTRTEPidkfsQSQPSSRR 2221
Cdd:PHA03247 2503 PPDPDAPPAPSRLAPAILPDEPVGEPVHPRMltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVP-----PPRPAPRP 2577

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2222 QSPshAIDPYAQMPGTP----RP-SPGERYSKSPGSLRSSD------PFSQPPGTPRPIKNEIYDQQGTPMPILPDPYSQ 2290
Cdd:PHA03247 2578 SEP--AVTSRARRPDAPpqsaRPrAPVDDRGDPRGPAPPSPlppdthAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDD 2655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2291 PPG--------------TPRPGAGLEGFSR--LNPRLNFITHQTDPlglQAQSRTQDPfsRSCGTDSQTPKHPGISDENI 2354
Cdd:PHA03247 2656 PAPgrvsrprrarrlgrAAQASSPPQRPRRraARPTVGSLTSLADP---PPPPPTPEP--APHALVSATPLPPGPAAARQ 2730

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2355 SIQQtiPNQTPIHDPFEQAPLTPCSQTGERSSQdvivSTGNPSDSQNTMQPPLGetEEKIKQRQRLRQLILKQQQEKSAI 2434
Cdd:PHA03247 2731 ASPA--LPAAPAPPAVPAGPATPGGPARPARPP----TTAGPPAPAPPAAPAAG--PPRRLTRPAVASLSESRESLPSPW 2802

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2435 RKEKGLQEATASAAPGTPRHWSQDDSGPQSDIFGRPPPPYPGTMRSSPIHAGQRFPGTFLADQ--CGPMPNEPQCSRQPF 2512
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRppSRSPAAKPAAPARPP 2882

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 528519285 2513 PRDLNNVGMRPQGQRFAFPPGAPNQEQFLRPPHQMQGGP 2551
Cdd:PHA03247 2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQP 2921
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 1027-1075 1.65e-07

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 50.42  E-value: 1.65e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285 1027 ECTVCEacgqasDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15541     1 WCAVCQ------NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 404-451 1.72e-07

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


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 50.54  E-value: 1.72e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  404 CKVCLSCKNPGddsKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15519     2 CEVCGLDDNEG---EVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 254-346 1.85e-07

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: 52.23  E-value: 1.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  254 NVAFLFDPTGQCCAHLRCAAWSEGVCRGEGQsLLYVDKAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCAAAAGTF 333
Cdd:cd15699    12 NLGDLFGPFYEFWVHEGCILWANGIYLVCGR-LYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCL 90

                          90
                  ....*....|...
gi 528519285  334 QDIKTYTLLCPDY 346
Cdd:cd15699    91 LNEENFSVRCPKH 103
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 403-451 2.40e-07

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 49.76  E-value: 2.40e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  403 ECKVClscknpGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15539     1 ECAVC------GDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 4447-4512 3.56e-07

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: 51.82  E-value: 3.56e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528519285 4447 DLWVHLNCALWSTEVYETQAGALINVELA---------LRRGLSVRCAYCQQTGATSGCHRLRCTNAYHFTCALK 4512
Cdd:cd15712    20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALC 94
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1108-1157 5.82e-07

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: 49.37  E-value: 5.82e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 1108 CPVCTRSYRE---EELILQCRQCDRWVHGSCQGLnSDEDVENAAD----EGFDCTLC 1157
Cdd:cd15508     2 CPLCEKCYDDddyDSKMMQCSQCDHWVHAKCEGL-SDEMYEILSYlpesIEYTCSLC 57
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 360-404 9.15e-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: 48.47  E-value: 9.15e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  360 CLVCDSSGDLLDQ-LFCCTCGQHYHGTCLDVTVTPL-KRAGWQCPEC 404
Cdd:cd15489     2 CIVCGKGGDLGGElLQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 407-451 1.28e-06

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


Pssm-ID: 277100  Cd Length: 49  Bit Score: 48.05  E-value: 1.28e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 1031-1075 1.31e-06

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 47.80  E-value: 1.31e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDpgrLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1107-1158 1.64e-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: 47.87  E-value: 1.64e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  1107 VCPVCtRSYREEELILQCRQCDRWVHGSCqgLNSDEDVENAADEGFDCTLCR 1158
Cdd:pfam00628    1 YCAVC-GKSDDGGELVQCDGCDDWFHLAC--LGPPLDPAEIPSGEWLCPECK 49
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 1031-1076 1.65e-06

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


Pssm-ID: 277100  Cd Length: 49  Bit Score: 47.66  E-value: 1.65e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCV 1076
Cdd:cd15630     3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACI 48
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1028-1075 2.19e-06

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: 47.43  E-value: 2.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285 1028 CTVCEaCGQASDPGRLLLCDDCDISYHTYCLDPPLQN----VPKGSWKCKWC 1075
Cdd:cd15502     2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 4828-4917 3.27e-06

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: 51.64  E-value: 3.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4828 VIEYIGTIIRSEVANRKEKmyeaqnRGVYMFRID-------------------------------SEHVIDATITGGPAR 4876
Cdd:cd10545   112 ICEYVGELLDTSEADTRSG------NDDYLFDIDnrqtnrgwdggqrldvgmsdgerssaedeesSEFTIDAGSFGNVAR 185

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 4877 YINHSCAPNCITEVVALE----RGHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10545   186 FINHSCSPNLFVQCVLYDhndlRLPRVMLFAADNIPPLQELTYDY 230
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 407-451 3.46e-06

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: 46.88  E-value: 3.46e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPT-NGWRCKNC 451
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1107-1157 4.31e-06

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 46.44  E-value: 4.31e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 528519285   1107 VCPVCTRSYREEELIlQCRQCDRWVHGSCQGLNSDEDVEnaaDEGFDCTLC 1157
Cdd:smart00249    1 YCSVCGKPDDGGELL-QCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 994-1028 4.92e-06

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ 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 and 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) 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 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 lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 46.58  E-value: 4.92e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528519285  994 RLLSCSQCGQCYHPFCVNI--KITKVVLSKGWRCLEC 1028
Cdd:cd15526    20 ELISCADCGSSGHPSCLKFspGLTDAVKSYRWQCIEC 56
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 407-451 4.94e-06

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 46.53  E-value: 4.94e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPT--NGWRCKNC 451
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPLvrAGWQCPEC 48
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 1030-1072 5.28e-06

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


Pssm-ID: 277009  Cd Length: 47  Bit Score: 46.19  E-value: 5.28e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 528519285 1030 VCEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVP-KGSWKC 1072
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPaTGRWMC 44
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 1031-1075 5.29e-06

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


Pssm-ID: 276972  Cd Length: 48  Bit Score: 46.15  E-value: 5.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVP-KG-SWKCKWC 1075
Cdd:cd15497     2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPnRGfVWSCAPC 48
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 406-451 5.87e-06

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


Pssm-ID: 277038  Cd Length: 49  Bit Score: 46.23  E-value: 5.87e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTN---GWRCKNC 451
Cdd:cd15563     1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 267-346 8.73e-06

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: 47.97  E-value: 8.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLYVD---------KAIDSGSTECCAYCKRLGASIKCCEESCGRSFHYPCA----AAAGTF 333
Cdd:cd15712    23 AHQNCLLYSSGFVESEEYNPLNLDrrfdvesvlNEIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCAlcddAAIETD 102

                          90
                  ....*....|...
gi 528519285  334 QDIKTYTLLCPDY 346
Cdd:cd15712   103 EVRGIYRVFCQKH 115
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2175-2298 8.87e-06

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 52.48  E-value: 8.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2175 GTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSRRQSPSHAIDPYAQMPGTPRPSPGERYSKSPGSLR 2254
Cdd:PHA03307  773 ALLEPAEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSE 852

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 528519285 2255 SSDPFSQPPGTPRPIKNEIYDQQGTPMPILPDPYSQPPGTPRPG 2298
Cdd:PHA03307  853 SSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAP 896
PHA03379 PHA03379
EBNA-3A; Provisional
 1845-2310 1.10e-05

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 51.98  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1845 TSSGGNSPLQALTPkdsfamtQMPGTASSGTSADDVFLrPQPPPLSSTSKTPTQDT---------QYPQGPsSQPQSP-- 1913
Cdd:PHA03379  412 TYGTPRPPVEKPRP-------EVPQSLETATSHGSAQV-PEPPPVHDLEPGPLHDQhsmapcpvaQLPPGP-LQDLEPgd 482

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1914 QMFSPESSGS--------------RP--SSPYDPYGKMVGTPRPPP-SGSSTPRrgSVSDMQERCRPSSAHESFGSPTTT 1976
Cdd:PHA03379  483 QLPGVVQDGRpacapvpapagpivRPweASLSQVPGVAFAPVMPQPmPVEPVPV--PTVALERPVCPAPPLIAMQGPGET 560

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1977 S-----TDPYAKPPDTPRPSDPFVKPMCTPRLGSL-SEQQGRQLMGNVTPGDNFSRPGQRSEAYQRMAHSRMVLSDPYSR 2050
Cdd:PHA03379  561 SgivrvRERWRPAPWTPNPPRSPSQMSVRDRLARLrAEAQPYQASVEVQPPQLTQVSPQQPMEYPLEPEQQMFPGSPFSQ 640

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2051 plltpVPGSNESGSVPVFKTPMPPSGLQQDSFNGGQQGMRRGSSDTFPHV-QHTDTYSNQPLTPhpsmadginnegRMMR 2129
Cdd:PHA03379  641 -----VADVMRAGGVPAMQPQYFDLPLQQPISQGAPLAPLRASMGPVPPVpATQPQYFDIPLTE------------PINQ 703

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2130 PGQGSHF--AQPLSMGRHPQRDPYSQAPST----PRQDYPQQMSDPYAQ-----MPGTPRPHDPyaQMPGTPRPNCDPYP 2198
Cdd:PHA03379  704 GASAAHFlpQQPMEGPLVPERWMFQGATLSqsvrPGVAQSQYFDLPLTQpinhgAPAAHFLHQP--PMEGPWVPEQWMFQ 781

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2199 LPPPTTRTEPIdkfsQSQPSSRRQSPsHAIDPyaqmPGTPRPSPGERYSKSPGSLrsSDPFSQPPGTPRPIKNEIYDQ-- 2276
Cdd:PHA03379  782 GAPPSQGTDVV----QHQLDALGYVL-HVLNH----PGVPVSPAVNQYHVSQAAF--GLPIDEDESGEGSDTSEPCEAld 850

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 528519285 2277 ---QGTPMPILPDPYSQPPGTPRPGAGLEGFSRLNPR 2310
Cdd:PHA03379  851 lsiHGRPCPQAPEWPVQGEGGQDATEVLDLSIHGRPR 887
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 4800-4939 1.11e-05

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: 48.05  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4800 WKSNVYLARSRiQGLGLYAARDIEKYTMVIEYIGTIIRsevaNRKEKMYEAQNRG-----VYMFRIDSEHVIDatitgGP 4874
Cdd:cd10524     7 CPCNRYSLENH-YGAKIIATKPIKKGEKIHELCGCIAE----LSEEEEALLRPGGndfsvMYSSRKKCSQLWL-----GP 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285 4875 ARYINHSCAPNCitEVVALERGhKIIISSNRRIQRGEEL-CY---DYkFDLEDdqhkipCHCGAVNCRK 4939
Cdd:cd10524    77 AAFINHDCRPNC--KFVPTGKS-TACVKVLRDIEPGEEItVYygdNY-FGENN------EECECETCER 135
HMG smart00398
high mobility group;
1691-1744 1.13e-05

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.15  E-value: 1.13e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285   1691 APVLYTNMNFPNLQDEFPD--WATRVKQIAKLWRKASSQERAPYVQKARDNRAALR 1744
Cdd:smart00398    8 AFMLFSQENRAKIKAENPDlsNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1694-1741 1.19e-05

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 45.59  E-value: 1.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1694 LYTNMNFPNLQDEFPDW--ATRVKQIAKLWRKASSQERAPYVQKARDNRA 1741
Cdd:cd00084     8 LFSKEKRPKLKKENPDLsfTEISKLLGERWKELSEEEKQPYEEKAKEDKE 57
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1030-1081 1.34e-05

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: 45.18  E-value: 1.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285 1030 VCEACG--QASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKcKWcvLCTHC 1081
Cdd:cd15499     1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGDE-KW--FCSRC 51
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 981-1028 1.45e-05

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 44.99  E-value: 1.45e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  981 CVVCGSFGRGAEgrLLSCSQCGQCYHPFCVN--IKITKVVLSkGWRCLEC 1028
Cdd:cd15509     2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLDpaVRPTPLVRA-GWQCPEC 48
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
267-336 1.81e-05

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 46.57  E-value: 1.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285   267 AHLRCAAWSEGVCRGEGQSL--LYVDKAIDSGSTECCAYC-KRLGASIKCCEESCGRSFHYPCAAAAGTFQDI 336
Cdd:pfam13832   22 VHVLCAIFVPEVRFGNVATMepIDVSRIPPERWKLKCVFCkKRSGACIQCSKGRCTTAFHVTCAQAAGVYMEP 94
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 407-451 1.92e-05

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: 44.56  E-value: 1.92e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  407 CLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTN-GWRCKNC 451
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1107-1157 2.36e-05

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: 44.59  E-value: 2.36e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 1107 VCPVCTRSYREEEL---ILQCRQCDRWVHGSCQGLNSD--EDVENAADE-GFDCTLC 1157
Cdd:cd15592     1 FCPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENLSDEmyEILSNLPESvAYTCINC 57
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 2110-2551 2.63e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 50.85  E-value: 2.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2110 PLTPHPSMADGinNEGRMMRPgqgsHFAQPLSMGRHPQRDPYSQAPSTPRQDYPQQMSDP-YAQMPGTPRPHDPYAQMPG 2188
Cdd:PRK10263  366 PQTGEPVIAPA--PEGYPQQS----QYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPyYAPAPEQPAQQPYYAPAPE 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2189 TPRPNCDPYPLPP-PTTRTEPIDKFSQSQPSSRRQSPSHAIDPYAQMPGTPRPSPG------------------ERYSKS 2249
Cdd:PRK10263  440 QPVAGNAWQAEEQqSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVveetkparpplyyfeeveEKRARE 519

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2250 PGSLRSsdpFSQPpgTPRPIKNeiydqqgtPMPILPdpySQPPGTPRPGAGLEGFSRLNPRLNFITHQTDPLGlQAQSRT 2329
Cdd:PRK10263  520 REQLAA---WYQP--IPEPVKE--------PEPIKS---SLKAPSVAAVPPVEAAAAVSPLASGVKKATLATG-AAATVA 582

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2330 QDPFSRSCGTdsqTPKhPGISdENISIQQTIPNQTPIHDPFEQA------PLTPCSQTGERSSQDVIVSTGNP--SDSQN 2401
Cdd:PRK10263  583 APVFSLANSG---GPR-PQVK-EGIGPQLPRPKRIRVPTRRELAsygiklPSQRAAEEKAREAQRNQYDSGDQynDDEID 657

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2402 TMQ------------------------PPLGETEEKIKQRQRLRQLILKQQQEKSAiRKEKGLQEATASAAPGTPRHWSQ 2457
Cdd:PRK10263  658 AMQqdelarqfaqtqqqrygeqyqhdvPVNAEDADAAAEAELARQFAQTQQQRYSG-EQPAGANPFSLDDFEFSPMKALL 736

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2458 DDsGPQSDIFGrppppyPGTM-RSSPIHAGQRFPGTFLADQCGPMPNEPQCSRQPFPrdlnnvgmrPQGQRFAFPPGAPN 2536
Cdd:PRK10263  737 DD-GPHEPLFT------PIVEpVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVA---------PQPQYQQPQQPVAP 800

                         490
                  ....*....|....*
gi 528519285 2537 QEQFLRPPHQMQGGP 2551
Cdd:PRK10263  801 QPQYQQPQQPVAPQP 815
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 359-404 2.89e-05

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: 44.29  E-value: 2.89e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  359 KCLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVTPLKRAGWQCPEC 404
Cdd:cd15527     1 TCSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1836-2076 3.41e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 50.55  E-value: 3.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1836 SGDASNSPHTSSGGNSPLQALTPKDSFAMTQMPGTASSGTSAddvflRPQPPPLSSTSKTPTQDTQYPQGPSSQPQ---- 1911
Cdd:PHA03307  213 ISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENE-----CPLPRPAPITLPTRIWEASGWNGPSSRPGpass 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1912 --SPQMFSPESSGSRPSSPYDPYGKMVGTP--RPPPSGSSTPRRGSVSDMQERCRPSSAHESFGSPTTTSTDPYAKPPDT 1987
Cdd:PHA03307  288 ssSPRERSPSPSPSSPGSGPAPSSPRASSSssSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRK 367

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1988 PRPSDPFVKPMCTPRLGSLSEQQGRQLMGNVTPGD-NFSRPGQRSEAyqRMAHSRMVLSDPYSR-PLLTPvpgsneSGSv 2065
Cdd:PHA03307  368 RPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDaTGRFPAGRPRP--SPLDAGAASGAFYARyPLLTP------SGE- 438

                         250
                  ....*....|.
gi 528519285 2066 PVFKTPMPPSG 2076
Cdd:PHA03307  439 PWPGSPPPPPG 449
SET_SpSet7-like cd10540
SET domain found in Schizossacharomyces pombe Set7 and similar proteins; Schizosaccharomyces ...
 4804-4923 3.88e-05

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: 45.71  E-value: 3.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4804 VYLARSRIQGLGLYAARDIEKYTmVIEYIGTIIRSEVANRKEKMYEAQNrgvYMFRIDSEHVIDATITGGparYINHSCA 4883
Cdd:cd10540     2 LEVKPSTLKGRGVFATRPIKKGE-VIEEAPVIVLPKEEYQHLCKTVLDH---YVFSWGDGCLALALGYGS---MFNHSYT 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 528519285 4884 PNCitEVVALERGHKIIISSNRRIQRGEELCYDYKFDLED 4923
Cdd:cd10540    75 PNA--EYEIDFENQTIVFYALRDIEAGEELTINYGDDLWD 112
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 484-535 4.06e-05

PHD finger 3 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 third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 44.02  E-value: 4.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  484 LCLICGQSQDSGSPADKHTCCTCKRWVHVDCVRQEGTNPDTQLQDGYTCRAC 535
Cdd:cd15511     1 PCPACKKNLDPELQKDMLHCHVCKRWIHLECEKPNDNELLDQLKEDYICSLC 52
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1028-1078 4.07e-05

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: 44.00  E-value: 4.07e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285 1028 CTVCEACGQASDPgrLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWCVLC 1078
Cdd:cd15507     2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPTRKKKTWICSKC 50
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 4449-4528 4.23e-05

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: 45.82  E-value: 4.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4449 WVHLNCALWSTEVYETQAGALINVElALRRGLSVR----CAYCQQTG--ATSGCHRLRCTNAYHFTCALKA--------- 4513
Cdd:cd15703    19 WAHVVCAIWIPEVCFANTVFLEPVE-GVNNIPPARwkltCYLCKQKGrgAAIQCHKVNCYTAFHVTCAQRAglfmkiepv 97

                          90       100
                  ....*....|....*....|.
gi 528519285 4514 ------QCTFFKDKTMLCHLH 4528
Cdd:cd15703    98 retglnGTTFTVRKTAYCENH 118
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1693-1747 4.47e-05

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 44.23  E-value: 4.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 1693 VLYTNMNFPNLQDEFPDWATRV--KQIAKLWRKASSQERAPYVQKARD-NRAALRINK 1747
Cdd:cd21977     9 IMFCRLNRKNYIDKHPGLASTEltKELGQLWRELSAEEKKPYCVRARElSQLHNRKVK 66
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 1024-1075 4.59e-05

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


Pssm-ID: 276979  Cd Length: 53  Bit Score: 43.96  E-value: 4.59e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285 1024 RCLECTVceacGQASDPGRLLLCD-DCDISYHTYCLDPPL--QNVPKG--SWKCKWC 1075
Cdd:cd15504     1 FCAKCQS----GEASPDNDILLCDgGCNRAYHQKCLEPPLltEDIPPEdeGWLCPLC 53
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 404-451 4.89e-05

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: 43.64  E-value: 4.89e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285  404 CKVCLScKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNG---WRCKNC 451
Cdd:cd15499     2 CSICGG-AEARDGNEILICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 359-404 5.49e-05

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


Pssm-ID: 277037  Cd Length: 50  Bit Score: 43.55  E-value: 5.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  359 KCLVCDSSGD--LLDQlfCCTCGQHYHGTCLD--VTVTPLKRA--GWQCPEC 404
Cdd:cd15562     1 SCGICKKSNDqhLLAL--CDTCKLYYHLGCLDppLTRMPKKTKnsGWQCSEC 50
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 1031-1075 6.15e-05

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


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 43.34  E-value: 6.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQASDpgrLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15524     2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 407-451 6.33e-05

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


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 42.97  E-value: 6.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15531     2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4451-4514 6.72e-05

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: 45.34  E-value: 6.72e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528519285 4451 HLNCALWSTEVYETQAG-------ALINVELALRRGLSVRCAYCQQTGATSGCHRLRCTNAYHFTCAL--KAQ 4514
Cdd:cd15710    26 HHKCMLFSSALVSSHSDsenlggfSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCALhdKAQ 98
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 485-535 6.73e-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: 43.35  E-value: 6.73e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 528519285    485 CLICGQSQDSGspaDKHTCCTCKRWVHVDCVRQEGTNPDtqLQDGYTCRAC 535
Cdd:smart00249    2 CSVCGKPDDGG---ELLQCDGCDRWYHQTCLGPPLLEEE--PDGKWYCPKC 47
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 406-451 6.78e-05

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: 43.12  E-value: 6.78e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  406 VCLSCKNPGDDsKMLVCDMCDKGYHTFCLQPIMETIPTNG--WRCKNC 451
Cdd:cd15506     1 LCFLCGSAGLN-ELLYCSVCCEPYHTFCLEEAERPLNINKdnWCCRRC 47
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4424-4520 6.86e-05

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: 45.46  E-value: 6.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHE-EGDGLTDGPARLLNLDlDLWVHLNCALWST---EVYETQAGALINVELA-----LRRGLSVRCAYCQQTGATS 4494
Cdd:cd15711     1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                          90       100
                  ....*....|....*....|....*.
gi 528519285 4495 GCHRLRCTNAYHFTCALKAQCTFFKD 4520
Cdd:cd15711    80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 406-451 6.88e-05

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


Pssm-ID: 277037  Cd Length: 50  Bit Score: 43.16  E-value: 6.88e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIP----TNGWRCKNC 451
Cdd:cd15562     1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPkktkNSGWQCSEC 50
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 242-327 7.05e-05

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: 45.34  E-value: 7.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  242 DELGQIGLPDEINVAflfdptgqccAHLRCAAWSEGVCRGE-------GQSLLYVDKAIDSGSTECCAYCKRLGASIKCC 314
Cdd:cd15710    10 KECGQLLISENQKVA----------AHHKCMLFSSALVSSHsdsenlgGFSIEDVQKEIKRGTKLMCSLCHCPGATIGCD 79

                          90
                  ....*....|...
gi 528519285  315 EESCGRSFHYPCA 327
Cdd:cd15710    80 VKTCHRTYHYYCA 92
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 4424-4528 8.88e-05

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: 44.93  E-value: 8.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGL---TDgparllnldlDLWVHLNCALWSTEVYETQA--GALINVELALRRGLSVRCAYCQQT-----GAT 4493
Cdd:cd15714     1 CCLCNLRGGALqmtTD----------ERWVHVICAIAVPEARFLNVieRHPVDVSAIPEQRWKLKCVYCRKRmkkvsGAC 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 528519285 4494 SGCHRLRCTNAYHFTCALKAQCTFFKDK-----TMLCHLH 4528
Cdd:cd15714    71 IQCSYDHCSTSFHVTCAHAAGVVMEPDDwpyvvSITCFKH 110
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 360-404 1.00e-04

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


Pssm-ID: 277038  Cd Length: 49  Bit Score: 42.77  E-value: 1.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLD--VTVTPLKRA-GWQCPEC 404
Cdd:cd15563     2 CCVCKQTGDNSQLVRCDECKLCYHFGCLDppLKKSPKQRGyGWVCEEC 49
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1031-1075 1.01e-04

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


Pssm-ID: 276984  Cd Length: 48  Bit Score: 42.68  E-value: 1.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285 1031 CEACGQASDPGRLLLCDDCDISYHTYCLDPPLQNVP--KGSWKCKWC 1075
Cdd:cd15509     2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 980-1028 1.12e-04

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: 42.35  E-value: 1.12e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  980 MCVVCGSFGRGaegRLLSCSQCGQCYHPFCVNIKITKVVLSKG-WRCLEC 1028
Cdd:cd15506     1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 1031-1075 1.24e-04

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 42.10  E-value: 1.24e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQasdPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15623     2 CRVCQK---AGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 407-451 1.30e-04

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


Pssm-ID: 276972  Cd Length: 48  Bit Score: 42.30  E-value: 1.30e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  407 CLSCKN--PGDDSkmLVCDMCDKGYHTFCLQPIMETIPTNG--WRCKNC 451
Cdd:cd15497     2 CKVCKEwcASDDS--VRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 485-535 1.32e-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: 42.30  E-value: 1.32e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285  485 CLICGQSQDSGSPAdkHTCCTCKRWVHVDCVRQEGTNPDTqlQDGYTCRAC 535
Cdd:cd15489     2 CIVCGKGGDLGGEL--LQCDGCGKWFHADCLGPPLSSFVP--NGKWICPVC 48
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 4449-4528 1.36e-04

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: 44.25  E-value: 1.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4449 WVHLNCALWSTEVY--ETQAGALI-NVELALRRGLSVRCAYCQQ-TGATSGCHRLRCTNAYHFTCALKA----------- 4513
Cdd:cd15670    19 WAHVVCALWIPEVSfaNTVFLEPIdGIQNIPKARWKLTCYICKKrMGACIQCHKKNCYTAFHVTCAQQAglymkiepvkd 98

                          90
                  ....*....|....*...
gi 528519285 4514 ---QCTFFKDKTMLCHLH 4528
Cdd:cd15670    99 pgnGTSDSVRKEAYCDKH 116
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 4424-4517 1.50e-04

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: 44.27  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGL---TDGparllnldldLWVHLNCALWSTEVY--ETQAGALINVELALRRGLSVRCAYCQQ-------TG 4491
Cdd:cd15675     1 CCLCCLRGGALkptTDG----------RWAHVVCAIAIPEVRfsNVPERGPIDISKIPPARLKLKCIYCSKitksmshMG 70

                          90       100
                  ....*....|....*....|....*.
gi 528519285 4492 ATSGCHRLRCTNAYHFTCALKAQCTF 4517
Cdd:cd15675    71 ACIQCSTGKCTTSFHVTCAHAAGVQM 96
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 406-451 1.52e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 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, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 42.06  E-value: 1.52e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  406 VCLSCKNPG--DDSKMLVCDMCDKGYHTFCLQ-PIMETIPTNGWRCKNC 451
Cdd:cd15512     1 MCVSCGSFGrgAEGRLIACSQCGQCYHPYCVNvKVTKVILSKGWRCLDC 49
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 1027-1074 1.63e-04

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


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 41.93  E-value: 1.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1027 ECTVCEacgqasDPGRLLLCD--DCDISYHTYCLDppLQNVPKGSWKCKW 1074
Cdd:cd15568     1 ECFRCG------DGGDLVLCDfkGCPKVYHLSCLG--LEKPPGGKWICPW 42
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 3179-3286 1.70e-04

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 47.90  E-value: 1.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 3179 NESQKKQYEEWLQETQQLLQMQQKF---LEDQIGAHRKSKKALSAKQ-RTAKKAGREFPEEDAEQLKNVTEQQ-----SV 3249
Cdd:PRK00409  525 LEELERELEQKAEEAEALLKEAEKLkeeLEEKKEKLQEEEDKLLEEAeKEAQQAIKEAKKEADEIIKELRQLQkggyaSV 604

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 528519285 3250 VQKQLEQIRKQQKEHAELIEEYRVKQQQQQQRLQTGM 3286
Cdd:PRK00409  605 KAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGD 641
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 267-337 1.76e-04

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: 44.28  E-value: 1.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLYVD--KAIDSGSTE-CCAYCKR--LGASIKCCEESCGRSFHYPCAAAAGTFQDIK 337
Cdd:cd15703    20 AHVVCAIWIPEVCFANTVFLEPVEgvNNIPPARWKlTCYLCKQkgRGAAIQCHKVNCYTAFHVTCAQRAGLFMKIE 95
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
4418-4544 2.16e-04

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


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 47.67  E-value: 2.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4418 PKDMRRCCFCHEEgDGLtdgparLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLS---VRCAYCQQTGATS 4494
Cdd:COG5141   244 EYQIRCCSFCPSS-DGA------FKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSrwkLGCLICKEFGGTC 316

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528519285 4495 -GCHRLRCTNAYHFTCALKAqCTFFK------------DKTMLCHLHRPRG-TSLIGGGLLGTE 4544
Cdd:COG5141   317 iQCSYFNCTRAYHVTCARRA-GYFDLniyshngisyciDHEPLCRKHYPLGyGRMNGLRYFGYE 379
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1868-2299 2.40e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.67  E-value: 2.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1868 PGTASSGTSADDvflRPQPPPLSSTSKTPTQDTQYPQGPSSQPQSPQMFSPESSGSRPSSPYDPYGKMVGTPRPPPSGSS 1947
Cdd:PRK07764  400 SAAAAAPAAAPA---PAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEP 476

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1948 TPRRGSvsdmqercRPSSAHESFGS---PTTTSTDPYAKPPDTPRPSDPFVKPMCTPRLGS----------LSEQQGRQL 2014
Cdd:PRK07764  477 TAAPAP--------APPAAPAPAAApaaPAAPAAPAGADDAATLRERWPEILAAVPKRSRKtwaillpeatVLGVRGDTL 548

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2015 -MGNVTPGD--NFSRPGQR---SEAYQRMAHSRM----VLSDPYSRPLLTPVPGSNESGSVPVFKTPMPPSGlqqdsfng 2084
Cdd:PRK07764  549 vLGFSTGGLarRFASPGNAevlVTALAEELGGDWqveaVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAA-------- 620

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2085 gqqgmrrgssdtfphvqhtdtySNQPLTPHPSMADGInnegrmmrPGQGSHFAQPLSMGRHPQRDPySQAPSTPRQDYPQ 2164
Cdd:PRK07764  621 ----------------------PAAPAAPAPAGAAAA--------PAEASAAPAPGVAAPEHHPKH-VAVPDASDGGDGW 669

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2165 QMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKFSQSQPSSRRQSPSHAIDPYAQMPGTPRPSPGE 2244
Cdd:PRK07764  670 PAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 528519285 2245 RYSKSPGSLRSSDPFSQPPGTPRPikNEIYDQQGTPMPILPDPYSQPPGTPRPGA 2299
Cdd:PRK07764  750 DPAGAPAQPPPPPAPAPAAAPAAA--PPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 406-451 2.57e-04

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 41.23  E-value: 2.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15523     1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 4449-4530 2.61e-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: 43.91  E-value: 2.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4449 WVHLNCALWSTEVYETQAGALINVElALRRGLSVR----CAYCQQ--TGATSGCHRLRCTNAYHFTCALKAQ-------- 4514
Cdd:cd15701    19 WAHVVCALWIPEVCFANTVFLEPID-SIEHIPPARwkltCYICKQrgSGACIQCHKANCYTAFHVTCAQQAGlymkmepv 97

                          90       100
                  ....*....|....*....|...
gi 528519285 4515 -------CTFFKDKTMLCHLHRP 4530
Cdd:cd15701    98 retgangTSFSVRKTAYCDIHTP 120
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 1034-1074 2.76e-04

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


Pssm-ID: 277131  Cd Length: 43  Bit Score: 41.49  E-value: 2.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528519285 1034 CGQASDPGRLLLCD--DCDISYHTYCLDppLQNVPKGSWKCKW 1074
Cdd:cd15661     2 CFQCGDGGELVMCDkkDCPKAYHLLCLN--LTQPPYGKWECPW 42
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 4449-4512 2.85e-04

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: 43.59  E-value: 2.85e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528519285 4449 WVHLNCALWSTEV-------YEtqagALINVELALRRGLSVRCAYCQ-QTGATSGCHRLRCTNAYHFTCALK 4512
Cdd:cd15671    20 WVHVSCALWIPEVsigcpekME----PITKISHIPMSRWALVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQ 87
PHA03377 PHA03377
EBNA-3C; Provisional
 1898-2334 2.96e-04

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 47.35  E-value: 2.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1898 QDTQYPQGPSSQPQSPQMFSPESSGsRPSSPYDPYGKMVGTPRPPPSGSSTPRRGSVSDMQERcrpSSAHESFGSPTTTs 1977
Cdd:PHA03377  537 QDGFQRSGRRQKRATPPKVSPSDRG-PPKASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPR---QQAKCKDGPPASG- 611

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1978 tdPYAKPPDTPRPSD---PFVKPMCTPRLGSLSEQQGRQLMGNVTPGDNFSRPgQRSEAYQRMAHSRMVLSDPYSRP--- 2051
Cdd:PHA03377  612 --PHEKQPPSSAPRDmapSVVRMFLRERLLEQSTGPKPKSFWEMRAGRDGSGI-QQEPSSRRQPATQSTPPRPSWLPsvf 688

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2052 LLTPVPGSNESGSVPVFKTPM----PPSGLQQDSFNGGQQGMRRGSS-DTFPHVQHTDTYSNQPLTPHPSMADGINNEGR 2126
Cdd:PHA03377  689 VLPSVDAGRAQPSEESHLSSMsptqPISHEEQPRYEDPDDPLDLSLHpDQAPPPSHQAPYSGHEEPQAQQAPYPGYWEPR 768

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2127 MMR-PGQGshFAQPLSMGRHPQRDPYSQAPSTPRQDYPQQMSD--PYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPT 2203
Cdd:PHA03377  769 PPQaPYLG--YQEPQAQGVQVSSYPGYAGPWGLRAQHPRYRHSwaYWSQYPGHGHPQGPWAPRPPHLPPQWDGSAGHGQD 846

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2204 TRTEPIDKFSQSQPSSRRQSPSHAIdPYAQMPGT----PRPSPGERYSKSPGSLRSSDPfsqppgtPRPIKNEIY---DQ 2276
Cdd:PHA03377  847 QVSQFPHLQSETGPPRLQLSQVPQL-PYSQTLVSssapSWSSPQPRAPIRPIPTRFPPP-------PMPLQDSMAvgcDS 918

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2277 QGTPMPILP--DPYSQPPGTPrpgAGLEGFSRLNPRLNFiTHQTDPLGLQAQSRTQDPFS 2334
Cdd:PHA03377  919 SGTACPSMPfaSDYSQGAFTP---LDINAQTPKRPRVEE-SSHGPARCSQATTEAQEILS 974
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 980-1028 3.10e-04

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 41.63  E-value: 3.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  980 MCVVC---GSFGRGAEGRLLSCSQCGQCYHPFCVNI--KITKVVLSKGWRCLEC 1028
Cdd:cd15528     1 VCGICekgGKSNKGEPEELIHCSQCGNSGHPSCLEMsdEMVAVIKTYPWQCMEC 54
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3285-3597 3.15e-04

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 47.31  E-value: 3.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3285 GMMGPMKTMPVMQGQPPGMmpvgppmAQPMMGSMLPMQHPhfGKPSRM-PSMPGWHPGTTGPISGPRMPP--HLPPQMAL 3361
Cdd:pfam09606  136 GAGFPSQMSRVGRMQPGGQ-------AGGMMQPSSGQPGS--GTPNQMgPNGGPGQGQAGGMNGGQQGPMggQMPPQMGV 206

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3362 PNPAQPLQAQ-----------PPAPIAPGGKP------GQSGTVAGGNGGGASSSAPHVKFDDNNPFSEGFQERERRERL 3424
Cdd:pfam09606  207 PGMPGPADAGaqmgqqaqangGMNPQQMGGAPnqvamqQQQPQQQGQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGP 286

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3425 REQQEKQRVQLMQEVERQRALQRLELEQQslglgpdnnGDSLAQMPfynSDLSQEFMQTPRPQQQQQQLGPLFPQQGNVP 3504
Cdd:pfam09606  287 PGQQPGAMPNVMSIGDQNNYQQQQTRQQQ---------QQQGGNHP---AAHQQQMNQSVGQGGQVVALGGLNHLETWNP 354

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3505 CDFVGQGSAFMQGGEHRPIPGNGSFGPEMGPNFQPKNPMMPGFSAGRPRP--PGFGGTRMpHHGGGEPSSFGMNSTTPLP 3582
Cdd:pfam09606  355 GNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSPQPSVPSPqgPGSQPPQS-HPGGMIPSPALIPSPSPQM 433

                          330
                   ....*....|....*
gi 528519285  3583 PNFPGSgQSLIQLYS 3597
Cdd:pfam09606  434 SQQPAQ-QRTIGQDS 447
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 360-404 3.35e-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: 41.11  E-value: 3.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  360 CLVCDSSGDLLdqlFCCTCGQHYHGTCLDVTVTPLKRAGWQCPEC 404
Cdd:cd15532     2 CRVCKDGGELL---CCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 360-404 3.38e-04

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


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 41.23  E-value: 3.38e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  360 CLVCDSSGDLLdqlFCCTCGQHYHGTCLDVTVTPLKRAGWQCPEC 404
Cdd:cd15523     2 CSVCRKSGELL---MCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 360-404 3.56e-04

PHD finger 4 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 fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 41.54  E-value: 3.56e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  360 CLVCDSSGDLLDQ--LFCCTCGQHYHGTCLDVTVTP-LKRAGWQCPEC 404
Cdd:cd15596     9 CVVCGSFGQGAEGrlLACSQCGQCYHPYCVSIKITKvVLSKGWRCLEC 56
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
4926-4942 3.58e-04

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 40.47  E-value: 3.58e-04
                            10
                    ....*....|....*..
gi 528519285   4926 HKIPCHCGAVNCRKWMN 4942
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 981-1028 3.74e-04

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: 41.08  E-value: 3.74e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  981 CVVCGSFGRGAEgRLLSCSQCGQCYHPFCV--NIKITKVVLSKGWRCLEC 1028
Cdd:cd15591     2 CHVCGRKNKESK-PLLECERCRNCYHPACLgpNYPKPANRKKRPWICSAC 50
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 3176-3274 3.80e-04

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 47.09  E-value: 3.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3176 GFVNESQKK---------QYEEWLQETQQLLQMQQKfledqigahrkSKKALSAKQRT--AKKAG-REFPEEDAEQLKNV 3243
Cdd:pfam01576  447 SLLNEAEGKniklskdvsSLESQLQDTQELLQEETR-----------QKLNLSTRLRQleDERNSlQEQLEEEEEAKRNV 515

                           90       100       110
                   ....*....|....*....|....*....|....
gi 528519285  3244 TEQQSVVQKQLEQIRKQQKEHA---ELIEEYRVK 3274
Cdd:pfam01576  516 ERQLSTLQAQLSDMKKKLEEDAgtlEALEEGKKR 549
dnaA PRK14086
chromosomal replication initiator protein DnaA;
2168-2300 4.29e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 46.74  E-value: 4.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2168 DPYAQMPGTPRPHDPYAQMPGTPRPNCDPYP-------------LPPPTTRTEPIDKFSQSQPSSRRQSPSHAIDPYAQM 2234
Cdd:PRK14086   89 DPSAGEPAPPPPHARRTSEPELPRPGRRPYEgyggpraddrppgLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDYGWQ 168

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 2235 PGTPRPSPGERYSKSPGSLRSSDPFSQPPGTPRPIKNEIYDQQGTPMP--ILPDPYSQPPGTPRPGAG 2300
Cdd:PRK14086  169 QQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPdwDRPRRDRTDRPEPPPGAG 236
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 267-336 4.31e-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: 42.85  E-value: 4.31e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLYVDkAIDSGSTE----CCAYCK-RLGASIKCCEESCGRSFHYPCAAAAGTFQDI 336
Cdd:cd15662    20 AHLACAIWIPETCLLDVKTMEPVD-GINAISKErwelSCTICKqRYGACIQCSNNSCRVAYHPLCARAAGLCMEV 93
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 4424-4528 4.61e-04

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


Pssm-ID: 277172  Cd Length: 118  Bit Score: 43.11  E-value: 4.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTdgparllNLDLDLWVHLNCALWSTEVYETQAGALINVElALRRGLSVR----CAYCQQ--TGATSGCH 4497
Cdd:cd15702     1 CVLCPNKGGAFK-------KTDDDRWGHVVCALWIPEVGFANTVFIEPID-GVRNIPPARwkltCYLCKQkgVGACIQCH 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285 4498 RLRCTNAYHFTCALKA---------------QCTFFKDKTMLCHLH 4528
Cdd:cd15702    73 KANCYTAFHVTCAQKAglymkmepvkevtggGTTFSVRKTAYCDAH 118
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 992-1028 5.02e-04

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


Pssm-ID: 277013  Cd Length: 41  Bit Score: 40.39  E-value: 5.02e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528519285  992 EGRLLSCSQCGQCYHPFCVNIKITkvvLSKGWRCLEC 1028
Cdd:cd15538     8 EGQVLCCSLCPRVYHKKCLKLTSE---PDEDWVCPEC 41
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 359-404 5.48e-04

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 40.86  E-value: 5.48e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  359 KCLVCDSSGD----LLDQLFCC-TCGQHYHGTCLDVT---VTPLKRAGWQCPEC 404
Cdd:cd15528     1 VCGICEKGGKsnkgEPEELIHCsQCGNSGHPSCLEMSdemVAVIKTYPWQCMEC 54
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1884-2057 5.49e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 46.07  E-value: 5.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1884 PQPPPLSSTSKTPTQDTQ-YPQGPSSQPQSPQMFSPESSgSRPSSPYDPYGKMvgtpRPPPSGSSTPRRGSVSDMQErcr 1962
Cdd:PLN03209  396 ASSKSVDAVAKPAEPDVVpSPGSASNVPEVEPAQVEAKK-TRPLSPYARYEDL----KPPTSPSPTAPTGVSPSVSS--- 467

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1963 PSSAHESFGSPTTTS-TDPYAKPPDTPRPSDPF-----VKPMCTPRLGSLSEQQGRQLMGNVTPGDNFSRPGQRSEAYQR 2036
Cdd:PLN03209  468 TSSVPAVPDTAPATAaTDAAAPPPANMRPLSPYavyddLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHH 547

                         170       180
                  ....*....|....*....|....*.
gi 528519285 2037 MAHSRMVLSdPYSR-----PLLTPVP 2057
Cdd:PLN03209  548 AQPKPRPLS-PYTMyedlkPPTSPTP 572
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 2137-2269 5.52e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 46.62  E-value: 5.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2137 AQPLSMGRHPQRDPYSQAPSTPRQDYpQQMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPP---PTTRTEPIDKFS 2213
Cdd:PRK10263  753 QQPQQPVAPQQQYQQPQQPVAPQPQY-QQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQyqqPQQPVAPQPQYQ 831

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285 2214 QSQPSSRRQSPSHAIDPYAQMPGTPRPspgerYSKSPGSLRSSDPFSQPPGTPRPI 2269
Cdd:PRK10263  832 QPQQPVAPQPQDTLLHPLLMRNGDSRP-----LHKPTTPLPSLDLLTPPPSEVEPV 882
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1885-2119 6.40e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 46.07  E-value: 6.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1885 QPPPLSSTSKTP-----TQDTQYPQGPSSQPQSPQmfsPESSGSRPSSPYDPYG--KMVGTPRPPPSGSSTPRRGSVSDM 1957
Cdd:PLN03209  328 VPPKESDAADGPkpvptKPVTPEAPSPPIEEEPPQ---PKAVVPRPLSPYTAYEdlKPPTSPIPTPPSSSPASSKSVDAV 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1958 QERCRPSSAHESFGSPTTTSTDPYAKPPDTPRPSDPFV-----KPMCTPRLGSLSEQQGRQLMGNVTPGDNFSRPGQRSE 2032
Cdd:PLN03209  405 AKPAEPDVVPSPGSASNVPEVEPAQVEAKKTRPLSPYAryedlKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAAT 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2033 AYQRMAHSRMVLSDPYSRPLLTPVPGSnesgsvpvfKTPMPPSGLQQDSFNGGQQGMRRGSSDTFP-HVQHTDTYSNQPL 2111
Cdd:PLN03209  485 DAAAPPPANMRPLSPYAVYDDLKPPTS---------PSPAAPVGKVAPSSTNEVVKVGNSAPPTALaDEQHHAQPKPRPL 555


                  ....*...
gi 528519285 2112 TPHPSMAD 2119
Cdd:PLN03209  556 SPYTMYED 563
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3127-3385 7.10e-04

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 46.15  E-value: 7.10e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3127 GMPPMVMNRMQQVP----ASHAPDTPAFSQPFFG----PDGKLPPQIARPTPP----------NFGPGFVNESQKKQYEE 3188
Cdd:pfam09606  158 MMQPSSGQPGSGTPnqmgPNGGPGQGQAGGMNGGqqgpMGGQMPPQMGVPGMPgpadagaqmgQQAQANGGMNPQQMGGA 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3189 WLQETQQLLQMQQKFLEDQIGAHRKSKKALSAKQRTAKKAG-----REFPEEDAEQLKNV--TEQQSVVQKQLEQIRKQQ 3261
Cdd:pfam09606  238 PNQVAMQQQQPQQQGQQSQLGMGINQMQQMPQGVGGGAGQGgpgqpMGPPGQQPGAMPNVmsIGDQNNYQQQQTRQQQQQ 317

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3262 KE-HAELIEEYRVKQQQQQQRLQTGMMGPMKTMPVMQGQPPGMMPVGPPMAQP-MMGSMLP--------MQHPHFGKPSR 3331
Cdd:pfam09606  318 QGgNHPAAHQQQMNQSVGQGGQVVALGGLNHLETWNPGNFGGLGANPMQRGQPgMMSSPSPvpgqqvrqVTPNQFMRQSP 397

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528519285  3332 MPSMPGW-HPGTTGP---ISGPRMPPHL----PPQMAlPNPAQPLQAQPPAPIAPGGKPGQS 3385
Cdd:pfam09606  398 QPSVPSPqGPGSQPPqshPGGMIPSPALipspSPQMS-QQPAQQRTIGQDSPGGSLNTPGQS 458
SET_SETD7 cd10530
SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins; SETD7 (EC 2. ...
 4804-4917 7.43e-04

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: 42.67  E-value: 7.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4804 VYLARSRIQ--GLGLYAARDIEKYTMVIEYIGT-IIRSEVANRKEKMYEaqnrgvYMFRIDSEHVIDAtitggPARY--- 4877
Cdd:cd10530     9 VYVAESLIPsaGEGLFAKVAVGPNTVMSFYNGVrITHQEVDSRDWSLNG------NTISLDEETVIDV-----PEPYnsv 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285 4878 ----------INHSCAPNCITEVVALER-GHKIIISSNRRIQRGEELCYDY 4917
Cdd:cd10530    78 skycaslghkANHSFTPNCIYDPFVHPRfGPIKCIRTLRAVEAGEELTVAY 128
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 404-451 7.65e-04

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: 40.50  E-value: 7.65e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285  404 CKVClSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMET----IPTNGWRCKNC 451
Cdd:cd15502     2 CIVC-QRGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1107-1157 8.39e-04

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: 40.22  E-value: 8.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285 1107 VCPVCTRSYRE-EELILQCRQCDRWVHGSCQGLNSDedvENAADEGFDCTLC 1157
Cdd:cd15517     1 VCGICNLETAAvDELWVQCDGCDKWFHQFCLGLSNE---RYADEDKFKCPNC 49
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 484-535 8.88e-04

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: 40.16  E-value: 8.88e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528519285  484 LCLICGQSQDSGSPADKH--TCCTCKRWVHVDCVRQEGTNPDTQLQDG---YTCRAC 535
Cdd:cd15615     1 FCILCGQVYEENEGDEKEwvQCDSCSEWVHFECDGRTGLGAFKYAKSDglqYVCPRC 57
dnaA PRK14086
chromosomal replication initiator protein DnaA;
2109-2315 9.44e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 45.59  E-value: 9.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2109 QPLTPHPSMADG--INNEGRMMRPGQGSHFAQPlsmgRHPQRDPYSQAPsTPRQDYPQQM-------------------- 2166
Cdd:PRK14086   96 APPPPHARRTSEpeLPRPGRRPYEGYGGPRADD----RPPGLPRQDQLP-TARPAYPAYQqrpepgawpraaddygwqqq 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2167 ------SDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEpidkfsQSQPSSRRQSpshaidpyaqmpgTPRP 2240
Cdd:PRK14086  171 rlgfppRAPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPD------WDRPRRDRTD-------------RPEP 231

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528519285 2241 SPGeryskSPGSLRSSDPFSQPPGTPRPiknEIYDQQGTPMPilpdpySQPPGTPRPGaglEGFSRLNPRLNFIT 2315
Cdd:PRK14086  232 PPG-----AGHVHRGGPGPPERDDAPVV---PIRPSAPGPLA------AQPAPAPGPG---EPTARLNPKYTFDT 289
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 1031-1075 9.76e-04

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


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 39.54  E-value: 9.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQAsdpGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15567     2 CFICSEG---GSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 1030-1075 9.86e-04

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


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 39.91  E-value: 9.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1030 VCEACGQAS--DPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15492     1 VCDVCLDGEseDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 4816-4937 9.99e-04

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: 42.69  E-value: 9.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4816 LYAARDIEKYTMVIEYIGTII---RSEVANRKEK------MYEAQNRGVYMfridsehVIDATITGGPARYINHSCAPNC 4886
Cdd:cd19181    21 LRAARDLALDTLIIEYRGKVMlrqQFEVNGHFFKrpypfvLFYSKFNGVEM-------CVDARTFGNDARFIRRSCTPNA 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285 4887 -ITEVVALERGHkIIISSNRRIQRGEELCYDYKFDLEDDQHKIPCHC--GAVNC 4937
Cdd:cd19181    94 eVRHMIADGMIH-LCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
 1034-1074 1.12e-03

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 39.53  E-value: 1.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 528519285 1034 CGQASDPGRLLLCDD--CDISYHTYCLDppLQNVPKGSWKCKW 1074
Cdd:cd15660     2 CFRCGDGGQLVLCDRksCTKAYHLSCLG--LTKRPFGKWECPW 42
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 406-451 1.16e-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: 39.58  E-value: 1.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15522     1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 484-535 1.18e-03

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: 39.84  E-value: 1.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 528519285  484 LCLICGQSQdsGSPADKHTCC-TCKRWVHVDCVRQEGTNPDTQLQdgYTCRAC 535
Cdd:cd15517     1 VCGICNLET--AAVDELWVQCdGCDKWFHQFCLGLSNERYADEDK--FKCPNC 49
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 404-451 1.33e-03

PHD finger 4 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 fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 40.00  E-value: 1.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  404 CKVCLSCKNpGDDSKMLVCDMCDKGYHTFCLQ-PIMETIPTNGWRCKNC 451
Cdd:cd15596     9 CVVCGSFGQ-GAEGRLLACSQCGQCYHPYCVSiKITKVVLSKGWRCLEC 56
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
 981-1028 1.39e-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: 39.64  E-value: 1.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528519285  981 CVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLS---KGWRCLEC 1028
Cdd:cd15501     2 CVVCKQMDVTSGNQLVECQECHNLYHQECHKPPVTDKDVNdprLVWYCSRC 52
PHA03378 PHA03378
EBNA-3B; Provisional
 1893-2298 1.44e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 45.06  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1893 SKTPTQDTQYPQGPSSQPQSPQMFSPESSGSRPSSPydpygKMVGTPRPPPSGSSTPrrgsvSDMQERCRPSSAHESFGS 1972
Cdd:PHA03378  555 STEPVHDQLLPAPGLGPLQIQPLTSPTTSQLASSAP-----SYAQTPWPVPHPSQTP-----EPPTTQSHIPETSAPRQW 624

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 1973 PTTTSTDPYAKPPDTPRPSDPFVKPmcTPRLGSLSEQQGRQlmgnvtpgDNFSRPGQRSEAYQRMAHSRMVLSDPYSRPL 2052
Cdd:PHA03378  625 PMPLRPIPMRPLRMQPITFNVLVFP--TPHQPPQVEITPYK--------PTWTQIGHIPYQPSPTGANTMLPIQWAPGTM 694

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2053 LTPvpgsnesgsvPVFKTPMPPSGLQQdsfngGQQGMRRGSSDTFPHVQHTDTYSNQPLTPHPSMADGINNEGRMMRPGQ 2132
Cdd:PHA03378  695 QPP----------PRAPTPMRPPAAPP-----GRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAA 759

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2133 GSHFAQPlsmgrhPQRDPYSQAPSTPRQDYPQQMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPIDKF 2212
Cdd:PHA03378  760 APGRARP------PAAAPGAPTPQPPPQAPPAPQQRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLLTGGV 833

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 2213 SQSQPSSRRQSPSHaidpyAQMPGTPRPSPGerySKSPGSLRSSDPFSQPPGTPrpikNEIYDQQGTPMPILPDPYSQPP 2292
Cdd:PHA03378  834 KRGRPSLKKPAALE-----RQAAAGPTPSPG---SGTSDKIVQAPVFYPPVLQP----IQVMRQLGSVRAAAASTVTQAP 901


                  ....*.
gi 528519285 2293 gTPRPG 2298
Cdd:PHA03378  902 -TEYTG 906
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1028-1076 1.45e-03

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


Pssm-ID: 277053  Cd Length: 53  Bit Score: 39.68  E-value: 1.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285 1028 CTVCEAcGQASDPGRLLLCDDCDISYHTYCLDPPLQNV---PKGSWKCKWCV 1076
Cdd:cd15578     2 CTVCQD-GSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCV 52
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 301-331 1.50e-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: 41.46  E-value: 1.50e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 528519285  301 CAYCKR-----LGASIKCCEESCGRSFHYPCAAAAG 331
Cdd:cd15714    56 CVYCRKrmkkvSGACIQCSYDHCSTSFHVTCAHAAG 91
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
 1030-1075 1.59e-03

PHD finger found in protein Jade-2 and similar proteins; 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 Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 39.22  E-value: 1.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1030 VCEAC--GQASDPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15680     1 VCDVCrsPEGEDGNEMVFCDKCNVCVHQACYG--ILKVPTGSWLCRTC 46
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 4424-4513 1.67e-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: 41.10  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGPArllnldlDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLSVRCAYCQQ-----TGATSG 4495
Cdd:cd15715     1 CCLCNLRGGALKQTSD-------DKWAHVMCAVALPEVRFINVVERTPIDISripLQR-LKLKCIFCRNrikrvSGACIQ 72

                          90
                  ....*....|....*...
gi 528519285 4496 CHRLRCTNAYHFTCALKA 4513
Cdd:cd15715    73 CSYGRCPASFHVTCAHAA 90
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 360-404 1.77e-03

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 39.16  E-value: 1.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  360 CLVCDSSGDLLDQLFCCTCGQHYHGTCLDVTVTPLKRAGWQCPEC 404
Cdd:cd15603     2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 360-404 1.80e-03

PHD finger 3 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 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 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 third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 39.25  E-value: 1.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  360 CLVCDSSGDLLDQ--LFCCTCGQHYHGTCLDVTVTPLK-RAGWQCPEC 404
Cdd:cd15597     3 CVVCGSFGRGSEGhlLACSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 404-451 1.83e-03

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


Pssm-ID: 276979  Cd Length: 53  Bit Score: 39.34  E-value: 1.83e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  404 CKVCLSCK-NPGDDskMLVCD-MCDKGYHTFCLQPIMETI----PTNGWRCKNC 451
Cdd:cd15504     2 CAKCQSGEaSPDND--ILLCDgGCNRAYHQKCLEPPLLTEdippEDEGWLCPLC 53
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 1028-1075 1.88e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 38.90  E-value: 1.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1028 CTVCEAcGQASDPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15679     2 CDVCQS-PDGEDGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
PHD1_DPF3 cd15692
PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed ...
 979-1028 1.93e-03

PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277162  Cd Length: 57  Bit Score: 39.28  E-value: 1.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  979 DMCVVCGSFGR--GAEGRLLSCSQCGQCYHPFCVN--IKITKVVLSKGWRCLEC 1028
Cdd:cd15692     3 DFCLGGSNMNKksGRPEELVSCADCGRSGHPTCLQftVNMTEAVKTYQWQCIEC 56
HMG_box pfam00505
HMG (high mobility group) box;
1693-1744 2.01e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 39.52  E-value: 2.01e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  1693 VLYTNMNFPNLQDEFPDWATR--VKQIAKLWRKASSQERAPYVQKARDNRAALR 1744
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
 1034-1075 2.16e-03

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277092  Cd Length: 43  Bit Score: 38.89  E-value: 2.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 528519285 1034 CGQASDPGRLLLCDDCDISYHTYCLDPPLQNVPKGSWKCKWC 1075
Cdd:cd15622     2 CAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 267-331 2.45e-03

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: 40.89  E-value: 2.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528519285  267 AHLRCAAWSEGVCRGEGQSLLYVDKAIDSGSTE---CCAYCK-RLGASIKCCEESCGRSFHYPCAAAAG 331
Cdd:cd15671    21 VHVSCALWIPEVSIGCPEKMEPITKISHIPMSRwalVCVLCKeKTGACIQCSVKSCKTAFHVTCAFQHG 89
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
 1108-1135 2.70e-03

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


Pssm-ID: 277085  Cd Length: 51  Bit Score: 38.63  E-value: 2.70e-03
                          10        20
                  ....*....|....*....|....*...
gi 528519285 1108 CPVCTRSYREEELILQCRQCDRWVHGSC 1135
Cdd:cd15613     2 CGSCGGNYTADEFWICCDVCEKWYHGKC 29
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 990-1028 2.74e-03

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


Pssm-ID: 276985  Cd Length: 46  Bit Score: 38.57  E-value: 2.74e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 528519285  990 GAEGRLLSCSQCGQCYHPFCVNIKITKVVlSKGWRCLEC 1028
Cdd:cd15510     9 GDDTKMLVCETCDKGYHTSCLRPVMSSIP-KYGWKCKNC 46
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 406-451 2.99e-03

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 38.48  E-value: 2.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15541     1 WCAVCQNGGE---LLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 404-451 3.03e-03

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 38.25  E-value: 3.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  404 CKVCLsckNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15623     2 CRVCQ---KAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 1030-1076 3.08e-03

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 38.84  E-value: 3.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285 1030 VCEAC--GQASDPGRLLLCDDCDISYHTYCLDPPlqNVPKGSWKCKWCV 1076
Cdd:cd15677     3 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHCL 49
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 980-1028 3.33e-03

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: 38.30  E-value: 3.33e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  980 MCVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:cd15517     1 VCGICNLETAAVDELWVQCDGCDKWFHQFCLGLSNERYADEDKFKCPNC 49
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 360-404 3.37e-03

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: 38.49  E-value: 3.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  360 CLVCDSSGdLLDQLFCCTCGQHYHGTCLDVTVTPLKRAG--WQCPEC 404
Cdd:cd15506     2 CFLCGSAG-LNELLYCSVCCEPYHTFCLEEAERPLNINKdnWCCRRC 47
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 4424-4513 3.53e-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: 40.34  E-value: 3.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTDGparllnlDLDLWVHLNCALWSTEVYETQAGALINVELA---LRRgLSVRCAYCQQ-----TGATSG 4495
Cdd:cd15713     1 CCLCSLRGGALQRA-------NDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQR-FKLKCIFCKKrrkrtAGCCVQ 72

                          90
                  ....*....|....*...
gi 528519285 4496 CHRLRCTNAYHFTCALKA 4513
Cdd:cd15713    73 CSHGRCPTSFHASCAQAA 90
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 4424-4511 3.54e-03

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: 40.46  E-value: 3.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4424 CCFCHEEGDGLTdgPARllnlDLDLWVHLNCALWSTEVY-----ETQAGALINVELALRRGLSvrCAYCQQ-TGATSGCH 4497
Cdd:cd15705     1 CLLCPKRGGALK--PTR----SGTKWVHVSCALWIPEVSigcpeKMEPITKISHIPASRWALS--CSLCKEcTGTCIQCS 72

                          90
                  ....*....|....
gi 528519285 4498 RLRCTNAYHFTCAL 4511
Cdd:cd15705    73 MPSCITAFHVTCAF 86
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 407-451 3.57e-03

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


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 38.17  E-value: 3.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285  407 CLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNC 451
Cdd:cd15559     2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
 1028-1077 3.76e-03

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), 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-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 Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 38.41  E-value: 3.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285 1028 CTVCEAcGQASDPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWCVL 1077
Cdd:cd15681     2 CDVCRS-PDSEEGNDMVFCDKCNICVHQACYG--ILKVPEGSWLCRTCVL 48
PHD2_Snt2p_like cd15498
PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 981-1028 4.01e-03

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


Pssm-ID: 276973  Cd Length: 55  Bit Score: 38.22  E-value: 4.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 528519285  981 CVVCGSFGRGAEGRLLSCSQCGQCYHPFCVNIKITKVV------LSKGWRCLEC 1028
Cdd:cd15498     2 CSVCSEQFASNFNTSLSCYNCGLNVHASCYGITVPGKMnkvknlKSYKWLCDPC 55
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 4816-4920 4.04e-03

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: 40.65  E-value: 4.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 4816 LYAARDIEKYTMVIEYIGTIIRSEvanrkekMYEAQN---RGVYMFRI------DSEHVIDATITGGPARYINHSCAPNC 4886
Cdd:cd19182    21 LKAAKDLPPDTLIIEYRGKFMLRE-------QFEANGyffKRPYPFVLfyskfhGLEMCVDARTFGNEARFIRRSCTPNA 93

                          90       100       110
                  ....*....|....*....|....*....|....
gi 528519285 4887 ITEVVALERGHKIIISSNRRIQRGEELCYDYKFD 4920
Cdd:cd19182    94 EVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDFD 127
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 407-452 4.38e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 38.10  E-value: 4.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  407 CLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNCR 452
Cdd:cd15624     2 CAVCQNGGD---LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCR 44
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 406-450 4.43e-03

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


Pssm-ID: 277009  Cd Length: 47  Bit Score: 38.10  E-value: 4.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  406 VCLSCKNPGDDSKMLVCDMCDKGYHTFCLQPIMETIPTNG-WRCKN 450
Cdd:cd15534     1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMCPN 46
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 360-404 4.64e-03

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


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 37.82  E-value: 4.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528519285  360 CLVCDSSGDLLdqlfCCT-CGQHYHGTCLDVTVTPLKRAGWQCPEC 404
Cdd:cd15539     2 CAVCGDGGELL----CCDgCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_KDM2B cd15644
PHD finger found in Lysine-specific demethylase 2B (KDM2B); KDM2B, also termed Ndy1, or ...
 980-1028 5.43e-03

PHD finger found in Lysine-specific demethylase 2B (KDM2B); KDM2B, also termed Ndy1, or CXXC-type zinc finger protein 2, or F-box and leucine-rich (LRR) repeat protein 10 (FBXL10), or F-box protein FBL10, or JmjC domain-containing histone demethylation protein 1B (Jhdm1b), or Jumonji domain-containing EMSY-interactor methyltransferase motif protein (Protein JEMMA), or [Histone-H3]-lysine-36 demethylase 1B, is a ubiquitously expressed histone H3 lysine 4 (H3K4me2) or histone H3 lysine 36 (H3K36me2) demethylase that functions as a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. It regulates the differentiation of Mesenchymal Stem Cells (MSCs) and has been implicated in cell cycle regulation by de-repressing cyclin-dependent kinase inhibitor 2B (CDKN2B or p15INK4B). It also plays a role in recruiting polycomb repressive complex 1 (PRC1) to CpG islands (CGIs) of developmental genes and regulates lysine 119 monoubiquitylation on H2A (H2AK119ub1) in embryonic stem cells (ESCs). Moreover, it acts as an oncogene that plays a critical role in leukemia development and maintenance. KDM2B consists of two Jumonji C (JmjC) domains, and FBXHA and FBXHB domains. A CXXC zinc-finger domain, followed by a plant homeodomain (PHD) finger, is located within the FBXHA domain, and an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain, is located within the FBXHB domain.


Pssm-ID: 277114  Cd Length: 62  Bit Score: 38.42  E-value: 5.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528519285  980 MCVVCGSFGR-----GAEGR----LLSCSQCGQCYHPFCVNIKITKVV----LSKGWRCLEC 1028
Cdd:cd15644     1 VCLVCGEAGKedtveEEEGKfnlmLMECSICNEIIHPGCLKVKESDGVvndeLPNCWECPKC 62
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 404-451 5.48e-03

PHD finger 3 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 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 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 third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 38.09  E-value: 5.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  404 CKVCLSCKNpGDDSKMLVCDMCDKGYHTFCLQP-IMETIPTNGWRCKNC 451
Cdd:cd15597     3 CVVCGSFGR-GSEGHLLACSQCSQCYHPYCVNSkITKVMLLKGWRCVEC 50
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 1028-1075 5.92e-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: 5.92e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1028 CTVCeacgqaSDPGRLLLCDDCDISYHTYCLDPPLqnvPKGSWKCKWC 1075
Cdd:cd15658     2 CFVC------ARGGRLLCCESCPASFHPECLSIEM---PEGCWNCNEC 40
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 1110-1157 6.16e-03

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


Pssm-ID: 277029  Cd Length: 47  Bit Score: 37.75  E-value: 6.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285 1110 VCTRSYREEELILQCRQCDRWVHGSCQGLnsdeDVENAAD-EGFDCTLC 1157
Cdd:cd15554     3 ICRQPYDVTRFMIECDVCKDWFHGSCVGV----EEHQANDiERYHCPNC 47
CCDC34 pfam13904
Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several ...
 3178-3269 6.33e-03

Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.


Pssm-ID: 464032 [Multi-domain]  Cd Length: 221  Bit Score: 41.61  E-value: 6.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3178 VNESQKKQYEEWLQ------ETQQLLQMQQKFLEDQIGAHRK-------------------SKKALSAKQRTAKKAG--- 3229
Cdd:pfam13904   49 LERQPLEAYENWLAakqrqrQKELQAQKEEREKEEQEAELRKrlakekyqewlqrkarqqtKKREESHKQKAAESASksl 128

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 528519285  3230 ----REFPEEDA-----EQLKNVTEQQSvvQKQLEQIRKQQKEHAELIE 3269
Cdd:pfam13904  129 akpeRKVSQEEAkevlqEWERKKLEQQQ--RKREEEQREQLKKEEEEQE 175
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1108-1157 6.88e-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: 37.84  E-value: 6.88e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528519285 1108 CPVCTRSYREEELI----LQCRQCDRWVHGSCQGLNSDEDVENAADEG--FDCTLC 1157
Cdd:cd15615     2 CILCGQVYEENEGDekewVQCDSCSEWVHFECDGRTGLGAFKYAKSDGlqYVCPRC 57
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
 407-453 7.23e-03

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


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 37.63  E-value: 7.23e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528519285  407 CLSCKNPGDdskMLVCDMCDKGYHTFCLQPIMETIPTNGWRCKNCRT 453
Cdd:cd15625     5 CAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCRN 48
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 980-1028 7.25e-03

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


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 37.40  E-value: 7.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  980 MCVVCGsfgrgAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKG-WRCLEC 1028
Cdd:cd15535     1 FCSACG-----GYGSFLCCDGCPRSFHFSCLDPPLEEDNLPDDeWFCNEC 45
Gag_spuma pfam03276
Spumavirus gag protein;
2147-2296 7.80e-03

Spumavirus gag protein;


Pssm-ID: 460872 [Multi-domain]  Cd Length: 614  Bit Score: 42.43  E-value: 7.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2147 QRDPYSQAPSTPRQDYPQQMSDPYAQMPGTPRPHDPYAQMPGTPRPNCDPYPLPPPTTRTEPidkfsqsqPSSRRQSPSH 2226
Cdd:pfam03276  177 EISPGAQGGIPPGASFSGLPSLPAIGGIHLPAIPGIHARAPPGNIARSLGDDIMPSLGDAGM--------PQPRFAFHPG 248

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  2227 aiDPYAQMPGTP-RPSPGERYSKSPGSLRSSDPFSQPPGTPRPIKNEIYDQQGTPMPI----------LPDPYSQPPGTP 2295
Cdd:pfam03276  249 --NPFAEAEGHPfAEAEGERPRDIPRAPRIDAPSAPAIPAIQPIAPPMIPPIGAPIPIphgasipgehIRNPREEPIRLG 326


                   .
gi 528519285  2296 R 2296
Cdd:pfam03276  327 R 327
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
 1031-1075 7.84e-03

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


Pssm-ID: 277096  Cd Length: 42  Bit Score: 37.02  E-value: 7.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 528519285 1031 CEACGQAsdpGRLLLCDDCDISYHTYCLDPPLQnVPKGSWKCKWC 1075
Cdd:cd15626     2 CEVCGQE---GKLFCCCTCSRVFHEDCHIPPVE-AQRSPWSCTFC 42
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 406-451 8.00e-03

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: 37.53  E-value: 8.00e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 528519285  406 VCLSCKNPGDDSKML--VCDMCDKGYHTFC--LQPIMETIPTNgWRCKNC 451
Cdd:cd15517     1 VCGICNLETAAVDELwvQCDGCDKWFHQFClgLSNERYADEDK-FKCPNC 49
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
 1028-1075 8.25e-03

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which 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. 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 Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 37.39  E-value: 8.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285 1028 CTVCEAcGQASDPGRLLLCDDCDISYHTYCLDppLQNVPKGSWKCKWC 1075
Cdd:cd15573     2 CDVCRS-PDSEEGNEMVFCDKCNICVHQACYG--IQKIPEGSWLCRTC 46
PHD3_KMT2C cd15511
PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1108-1157 8.49e-03

PHD finger 3 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 third PHD finger.


Pssm-ID: 276986  Cd Length: 52  Bit Score: 37.47  E-value: 8.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 528519285 1108 CPVCTRSYREEEL--ILQCRQCDRWVHGSCQGLNsDEDVENAADEGFDCTLC 1157
Cdd:cd15511     2 CPACKKNLDPELQkdMLHCHVCKRWIHLECEKPN-DNELLDQLKEDYICSLC 52
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 981-1028 8.53e-03

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: 37.35  E-value: 8.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528519285  981 CVVCGsfGRGAEGRLLSCSQCGQCYHPFCVNIKITKVVLSKGWRCLEC 1028
Cdd:cd15525     2 CHVCG--GKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDEWYCPDC 47
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 301-331 8.54e-03

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: 39.27  E-value: 8.54e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 528519285  301 CAYCKRL-------GASIKCCEESCGRSFHYPCAAAAG 331
Cdd:cd15675    56 CIYCSKItksmshmGACIQCSTGKCTTSFHVTCAHAAG 93
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 4449-4512 8.64e-03

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: 39.32  E-value: 8.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528519285 4449 WVHLNCALWSTEVY---ETQAGALINVELALRRGLSVRCAYCQ-QTGATSGCHRLRCTNAYHFTCALK 4512
Cdd:cd15706    20 WAHVSCALWIPEVSiacPERMEPITKVSHIPPSRWALVCSLCKlKTGACIQCSVKSCITAFHVTCAFE 87
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
3180-3270 8.99e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.81  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285 3180 ESQKKQYEEWLQETQQLLQMQQKFLEDQIGAHRKSKKALSAKQRTAKKAGREFpEEDAEQLKNVTEQQSVVQKQLEQIRK 3259
Cdd:COG4372    65 EEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEEL-EELQKERQDLEQQRKQLEAQIAELQS 143

                          90
                  ....*....|.
gi 528519285 3260 QQKEHAELIEE 3270
Cdd:COG4372   144 EIAEREEELKE 154
ERM_helical pfam20492
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ...
 3180-3284 9.56e-03

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.


Pssm-ID: 466641 [Multi-domain]  Cd Length: 120  Bit Score: 39.13  E-value: 9.56e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528519285  3180 ESQKKQYEEWLQETQ-QLLQMQQKFLEDQIGAHR---KSKKALSAKQRTAKKAgREFpEEDAEQLKNVTEQQSVVQKQLE 3255
Cdd:pfam20492    5 EREKQELEERLKQYEeETKKAQEELEESEETAEEleeERRQAEEEAERLEQKR-QEA-EEEKERLEESAEMEAEEKEQLE 82

                           90       100
                   ....*....|....*....|....*....
gi 528519285  3256 QIRKQQKEHAELIEEYRVKQQQQQQRLQT 3284
Cdd:pfam20492   83 AELAEAQEEIARLEEEVERKEEEARRLQE 111
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 1028-1076 9.77e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 37.21  E-value: 9.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285 1028 CTVCEAcGQASDPGRLLLCDDCDISYHTYCLDPPLqnVPKGSWKCKWCV 1076
Cdd:cd15572     4 CCICLD-GECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRRCL 49
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 980-1025 9.81e-03

PHD finger 2 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 second PHD finger.


Pssm-ID: 277040  Cd Length: 51  Bit Score: 37.02  E-value: 9.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528519285  980 MCVVCGSFGRGAEGrLLSCSQ--CGQCYHPFCVN-IKITKVVLSKGWRC 1025
Cdd:cd15565     1 SCFVCKKLGSVGGE-VFKCSVasCGKFYHEECLKkWPLTTISDSKKFRC 48
 
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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