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Conserved domains on  [gi|2462578048|ref|XP_054200301|]
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nuclear receptor coactivator 1 isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 259-370 3.50e-40

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


:

Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 144.36  E-value: 3.50e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  259 VESFMTKQDTTGKIISIDTsslRAAGRTGWED--LVRKCIYAFFQPQGrePSYARQLFQEVM-TRGTASSPSYRFILNDG 335
Cdd:pfam14598    1 TEQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2462578048  336 TMLSAHTKCKLCYPQSPDMQPFIMGIHIIDREHSG 370
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 27-87 9.93e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 (NCoA-1) and similar proteins; NCoA-1, also termed Class E basic helix-loop-helix protein 74 (bHLHe74), or protein Hin-2, or RIP160, or renal carcinoma antigen NY-REN-52, or steroid receptor coactivator 1 (SRC-1), is a bHLH-PAS nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion.


:

Pssm-ID: 381518  Cd Length: 61  Bit Score: 129.71  E-value: 9.93e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462578048   27 LASSTEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEK 87
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVDQIQQMKRLEQEK 61
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 629-708 1.93e-24

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


:

Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 98.62  E-value: 1.93e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  629 TSH-KLVQLLTTTAEQQ-----LRHADIDTSCKDVLSCTGTSNSASANSSGGSCPSSHSSLTERHKILHRLLQEG-SPSD 701
Cdd:pfam08832    1 KGHkKLLQLLTTPTEQLgpsplRSHADADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDD 80


                   ....*..
gi 2462578048  702 ITTLSVE 708
Cdd:pfam08832   81 VAKLTAE 87
NCOA_u2 pfam16665
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 468-590 1.43e-21

Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.


:

Pssm-ID: 465223 [Multi-domain]  Cd Length: 119  Bit Score: 91.34  E-value: 1.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  468 SLNLNNSPMEGTGISLAQ---FMSPRRQvtsglaTRPRMPNNSFPPNIStLSSPVGMTSSAC--NNNNRSYSNIPVTSLQ 542
Cdd:pfam16665    2 GLNMNSPPQGSPGMTPPQqnlMMSPRHR------GSPKMPANQFSPGMG-LHSPMGSVSSGGsgGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2462578048  543 GMNEGPNNSVGFSASSPVLRQMSSQNSPSRlniQPAKAESKDNKEIAS 590
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSPNINST---QQKKEGSSDSKSPSS 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 924-969 2.06e-16

Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.


:

Pssm-ID: 462608 [Multi-domain]  Cd Length: 47  Bit Score: 74.36  E-value: 2.06e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2462578048  924 EGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLDVL 969
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLDPD 47
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1149-1205 2.31e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


:

Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.31e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1149 GLPVQMGNPRLPQGAPQQFPYPPNYGTNPGTPPASTSPFSQLAA-NPEASLANRNSMV 1205
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNYGMSQQPDPAFTSALSPQSPmMSPRMGPSQSPMM 58
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1212-1268 2.92e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


:

Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.92e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1212 NIGGQFGTGINPQMQQNVFQYPGA-GMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLL 1268
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 120-213 2.46e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


:

Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 61.88  E-value: 2.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  120 LDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFvKNLLPKSLVNGVPWPQEAT--RRNSHTFNC 197
Cdd:cd00130      1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL-RERLENLLSGGEPVTLEVRlrRKDGSVIWV 79

                           90
                   ....*....|....*.
gi 2462578048  198 RMLIHPPDEPGTENQE 213
Cdd:cd00130     80 LVSLTPIRDEGGEVIG 95
DUF4927 super family cl24752
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 741-818 4.35e-08

Domain of unknown function (DUF4927); This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown.


The actual alignment was detected with superfamily member pfam16279:

Pssm-ID: 465083  Cd Length: 87  Bit Score: 52.11  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  741 KESKDHQLLRYLLDKDE-KDLRSTpnlsldDVKVKVEKKE-QMDPCNTNPTPMTKPTPEEIKLEAQSQFTADLDQFDQLL 818
Cdd:pfam16279    8 KKKKNNALLRYLLDKDDsKDPLSK------DIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELSLDNLDAIL 81
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 974-1287 3.66e-05

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: 48.47  E-value: 3.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  974 PPQQATPPLIMEERPNLYSQPySSPSPTANLPSPFQGMVRQKPSLGTMPVQvtpPRGAFSPGMGMQPRQTLNRPPAAPNQ 1053
Cdd:pfam09606  110 MGQQMGGPGTASNLLASLGRP-QMPMGGAGFPSQMSRVGRMQPGGQAGGMM---QPSSGQPGSGTPNQMGPNGGPGQGQA 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1054 LRLQLQQRLQGQQQLIHQnrqailnQFAATAPVGINMRSGMQQQITPQPPLNAQMLA----QRQRELYSQQHRQRQLIQQ 1129
Cdd:pfam09606  186 GGMNGGQQGPMGGQMPPQ-------MGVPGMPGPADAGAQMGQQAQANGGMNPQQMGgapnQVAMQQQQPQQQGQQSQLG 258

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1130 QRAMLMRQQSFGNNLPPSSGLPVQMGNPrlPQGAPQQFPY------PPNYGTNPGTPPASTSPFSQLAANP--------E 1195
Cdd:pfam09606  259 MGINQMQQMPQGVGGGAGQGGPGQPMGP--PGQQPGAMPNvmsigdQNNYQQQQTRQQQQQQGGNHPAAHQqqmnqsvgQ 336

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1196 ASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSL----SPGSSMVPMPIPP----PQSSL 1267
Cdd:pfam09606  337 GGQVVALGGLNHLETWNPGNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNqfmrQSPQPSVPSPQGPgsqpPQSHP 416

                          330       340
                   ....*....|....*....|
gi 2462578048 1268 LQQTPPASGYQSPDMKAWQQ 1287
Cdd:pfam09606  417 GGMIPSPALIPSPSPQMSQQ 436
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 259-370 3.50e-40

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 144.36  E-value: 3.50e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  259 VESFMTKQDTTGKIISIDTsslRAAGRTGWED--LVRKCIYAFFQPQGrePSYARQLFQEVM-TRGTASSPSYRFILNDG 335
Cdd:pfam14598    1 TEQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2462578048  336 TMLSAHTKCKLCYPQSPDMQPFIMGIHIIDREHSG 370
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 27-87 9.93e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 (NCoA-1) and similar proteins; NCoA-1, also termed Class E basic helix-loop-helix protein 74 (bHLHe74), or protein Hin-2, or RIP160, or renal carcinoma antigen NY-REN-52, or steroid receptor coactivator 1 (SRC-1), is a bHLH-PAS nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion.


Pssm-ID: 381518  Cd Length: 61  Bit Score: 129.71  E-value: 9.93e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462578048   27 LASSTEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEK 87
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVDQIQQMKRLEQEK 61
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 629-708 1.93e-24

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 98.62  E-value: 1.93e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  629 TSH-KLVQLLTTTAEQQ-----LRHADIDTSCKDVLSCTGTSNSASANSSGGSCPSSHSSLTERHKILHRLLQEG-SPSD 701
Cdd:pfam08832    1 KGHkKLLQLLTTPTEQLgpsplRSHADADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDD 80


                   ....*..
gi 2462578048  702 ITTLSVE 708
Cdd:pfam08832   81 VAKLTAE 87
NCOA_u2 pfam16665
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 468-590 1.43e-21

Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.


Pssm-ID: 465223 [Multi-domain]  Cd Length: 119  Bit Score: 91.34  E-value: 1.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  468 SLNLNNSPMEGTGISLAQ---FMSPRRQvtsglaTRPRMPNNSFPPNIStLSSPVGMTSSAC--NNNNRSYSNIPVTSLQ 542
Cdd:pfam16665    2 GLNMNSPPQGSPGMTPPQqnlMMSPRHR------GSPKMPANQFSPGMG-LHSPMGSVSSGGsgGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2462578048  543 GMNEGPNNSVGFSASSPVLRQMSSQNSPSRlniQPAKAESKDNKEIAS 590
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSPNINST---QQKKEGSSDSKSPSS 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 924-969 2.06e-16

Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.


Pssm-ID: 462608 [Multi-domain]  Cd Length: 47  Bit Score: 74.36  E-value: 2.06e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2462578048  924 EGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLDVL 969
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLDPD 47
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1149-1205 2.31e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.31e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1149 GLPVQMGNPRLPQGAPQQFPYPPNYGTNPGTPPASTSPFSQLAA-NPEASLANRNSMV 1205
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNYGMSQQPDPAFTSALSPQSPmMSPRMGPSQSPMM 58
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1212-1268 2.92e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.92e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1212 NIGGQFGTGINPQMQQNVFQYPGA-GMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLL 1268
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 120-213 2.46e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 61.88  E-value: 2.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  120 LDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFvKNLLPKSLVNGVPWPQEAT--RRNSHTFNC 197
Cdd:cd00130      1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL-RERLENLLSGGEPVTLEVRlrRKDGSVIWV 79

                           90
                   ....*....|....*.
gi 2462578048  198 RMLIHPPDEPGTENQE 213
Cdd:cd00130     80 LVSLTPIRDEGGEVIG 95
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 115-172 6.49e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 59.34  E-value: 6.49e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048   115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNL 172
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
HLH smart00353
helix loop helix domain;
32-86 7.91e-09

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 52.99  E-value: 7.91e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2462578048    32 EKRRREQENKYLEELAELLSANISDidslsVKPDKCKILKKTVDQIQLMKRMEQE 86
Cdd:smart00353    4 ERRRRRKINEAFDELRSLLPTLPKN-----KKLSKAEILRLAIEYIKSLQEELQK 53
DUF4927 pfam16279
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 741-818 4.35e-08

Domain of unknown function (DUF4927); This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown.


Pssm-ID: 465083  Cd Length: 87  Bit Score: 52.11  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  741 KESKDHQLLRYLLDKDE-KDLRSTpnlsldDVKVKVEKKE-QMDPCNTNPTPMTKPTPEEIKLEAQSQFTADLDQFDQLL 818
Cdd:pfam16279    8 KKKKNNALLRYLLDKDDsKDPLSK------DIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELSLDNLDAIL 81
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 116-173 5.31e-07

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 49.72  E-value: 5.31e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048  116 LLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNLL 173
Cdd:pfam00989    6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 115-172 4.30e-06

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 51.27  E-value: 4.30e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048  115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNL 172
Cdd:COG5805    161 TLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 974-1287 3.66e-05

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: 48.47  E-value: 3.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  974 PPQQATPPLIMEERPNLYSQPySSPSPTANLPSPFQGMVRQKPSLGTMPVQvtpPRGAFSPGMGMQPRQTLNRPPAAPNQ 1053
Cdd:pfam09606  110 MGQQMGGPGTASNLLASLGRP-QMPMGGAGFPSQMSRVGRMQPGGQAGGMM---QPSSGQPGSGTPNQMGPNGGPGQGQA 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1054 LRLQLQQRLQGQQQLIHQnrqailnQFAATAPVGINMRSGMQQQITPQPPLNAQMLA----QRQRELYSQQHRQRQLIQQ 1129
Cdd:pfam09606  186 GGMNGGQQGPMGGQMPPQ-------MGVPGMPGPADAGAQMGQQAQANGGMNPQQMGgapnQVAMQQQQPQQQGQQSQLG 258

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1130 QRAMLMRQQSFGNNLPPSSGLPVQMGNPrlPQGAPQQFPY------PPNYGTNPGTPPASTSPFSQLAANP--------E 1195
Cdd:pfam09606  259 MGINQMQQMPQGVGGGAGQGGPGQPMGP--PGQQPGAMPNvmsigdQNNYQQQQTRQQQQQQGGNHPAAHQqqmnqsvgQ 336

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1196 ASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSL----SPGSSMVPMPIPP----PQSSL 1267
Cdd:pfam09606  337 GGQVVALGGLNHLETWNPGNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNqfmrQSPQPSVPSPQGPgsqpPQSHP 416

                          330       340
                   ....*....|....*....|
gi 2462578048 1268 LQQTPPASGYQSPDMKAWQQ 1287
Cdd:pfam09606  417 GGMIPSPALIPSPSPQMSQQ 436
PHA03247 PHA03247
large tegument protein UL36; Provisional
 974-1309 6.36e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 6.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  974 PPQQATPPlimeERPNLYSQPYSSPSPTANLPSPFQGMVRQKPSLGTMPVQVTPPrGAFSPGMGMQPRQTLNRPPAAPNQ 1053
Cdd:PHA03247  2673 AAQASSPP----QRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPP-GPAAARQASPALPAAPAPPAVPAG 2747

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1054 LRLQLQQRLQGQqqlihqnRQAILNQFAATAPVGinmRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAM 1133
Cdd:PHA03247  2748 PATPGGPARPAR-------PPTTAGPPAPAPPAA---PAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1134 LMRQQSFGNNL-PPSSGLPVQmgnPRLPQGaPQQFPYPPNYGTNPGTPPASTSPFSQLAANPEASLANRNSMVSRgmtgn 1212
Cdd:PHA03247  2818 LPPAASPAGPLpPPTSAQPTA---PPPPPG-PPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLAR----- 2888

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1213 iggqfgtginPQMQQNVFQYP----GAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLLQQTPPA-------SGYQSPD 1281
Cdd:PHA03247  2889 ----------PAVSRSTESFAlppdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLApttdpagAGEPSGA 2958

                          330       340       350
                   ....*....|....*....|....*....|....
gi 2462578048 1282 MKAWQQGAIGNNNV------FSQAVQNQPTPAQP 1309
Cdd:PHA03247  2959 VPQPWLGALVPGRVavprfrVPQPAPSREAPASS 2992
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 1153-1272 1.21e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 43.26  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1153 QMGNPRLPQGAPQQ--FPYPPNYGTNPGtppastspfSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVF 1230
Cdd:TIGR01628  379 QPRMRQLPMGSPMGgaMGQPPYYGQGPQ---------QQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2462578048 1231 QYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLLQQTP 1272
Cdd:TIGR01628  450 AQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNK 491
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 259-370 3.50e-40

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 144.36  E-value: 3.50e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  259 VESFMTKQDTTGKIISIDTsslRAAGRTGWED--LVRKCIYAFFQPQGrePSYARQLFQEVM-TRGTASSPSYRFILNDG 335
Cdd:pfam14598    1 TEQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDG 75

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2462578048  336 TMLSAHTKCKLCYPQSPDMQPFIMGIHIIDREHSG 370
Cdd:pfam14598   76 DFLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 27-87 9.93e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 (NCoA-1) and similar proteins; NCoA-1, also termed Class E basic helix-loop-helix protein 74 (bHLHe74), or protein Hin-2, or RIP160, or renal carcinoma antigen NY-REN-52, or steroid receptor coactivator 1 (SRC-1), is a bHLH-PAS nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion.


Pssm-ID: 381518  Cd Length: 61  Bit Score: 129.71  E-value: 9.93e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462578048   27 LASSTEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEK 87
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVDQIQQMKRLEQEK 61
bHLH-PAS_NCoA3_SRC3 cd18949
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 3 ...
 30-100 1.14e-29

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 3 (NCoA-3) and similar proteins; NCoA-3, also termed ACTR, or amplified in breast cancer 1 protein (AIB-1), or CBP-interacting protein (pCIP), or Class E basic helix-loop-helix protein 42 (bHLHe42), or receptor-associated coactivator 3 (RAC-3), or steroid receptor coactivator protein 3 (SRC-3), or thyroid hormone receptor activator molecule 1 (TRAM-1), is a bHLH-PAS steroid/nuclear receptor-associated coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. It also plays a central role in creating a multisubunit coactivator complex, which probably acts via remodeling of chromatin.


Pssm-ID: 381519  Cd Length: 73  Bit Score: 112.83  E-value: 1.14e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462578048   30 STEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKrmEQEK-STTDDDVQKSDIS 100
Cdd:cd18949      4 SGEKRRREQESKYIEELAELISANLSDIDNFNVKPDKCAILKETVRQIRQIK--EQGKsSSNDDDVQKADVS 73
bHLH-PAS_SRC cd11439
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator ...
 27-84 9.85e-29

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator (SRC) family; The SRC family of coactivators includes SRC-1 (NcoA-1/p160), SRC-2(TIF2/GRIP1/NcoA-2) and SRC-3(NcoA-3/pCIP/RAC3/ACTR/pCIP/AIB1/TRAM1), which are critical mediators of steroid receptor action. They contain bHLH-PAS domain at the N-terminal that is followed by receptor interacting domain and C-terminal transcriptional activation domain. SRC coactivators interact with nuclear receptors in a ligand-dependent manner and enhance transcriptional activation by the receptor via histone acetylation/methylation.


Pssm-ID: 381445  Cd Length: 58  Bit Score: 109.82  E-value: 9.85e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048   27 LASSTEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKRME 84
Cdd:cd11439      1 NKCLNEKRRREQENKYIEELAELISASISDMDSLSVKPDKCAILQETVKQIRQIKEQE 58
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 629-708 1.93e-24

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 98.62  E-value: 1.93e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  629 TSH-KLVQLLTTTAEQQ-----LRHADIDTSCKDVLSCTGTSNSASANSSGGSCPSSHSSLTERHKILHRLLQEG-SPSD 701
Cdd:pfam08832    1 KGHkKLLQLLTTPTEQLgpsplRSHADADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDD 80


                   ....*..
gi 2462578048  702 ITTLSVE 708
Cdd:pfam08832   81 VAKLTAE 87
bHLH-PAS_NCoA2_SRC2 cd18950
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 2 ...
 30-88 2.08e-23

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 2 (NCoA-2) and similar proteins; NCoA-2, also termed Class E basic helix-loop-helix protein 75 (bHLHe75), or transcriptional intermediary factor 2 (TIF2), or steroid receptor coactivator 2 (SRC-2), or glucocorticoid receptor interacting protein-1 (GRIP1), is a bHLH-PAS transcriptional coactivator for steroid receptors and nuclear receptors. It is required with NCoA-1 to control energy balance between white and brown adipose tissues.


Pssm-ID: 381520  Cd Length: 64  Bit Score: 94.76  E-value: 2.08e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462578048   30 STEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKrmEQEKS 88
Cdd:cd18950      6 STEKRNREQENKYIEELAELIFANFNDIDNFNVKPDKCAILKETVKQIRQIK--EQEKA 62
NCOA_u2 pfam16665
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 468-590 1.43e-21

Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known.


Pssm-ID: 465223 [Multi-domain]  Cd Length: 119  Bit Score: 91.34  E-value: 1.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  468 SLNLNNSPMEGTGISLAQ---FMSPRRQvtsglaTRPRMPNNSFPPNIStLSSPVGMTSSAC--NNNNRSYSNIPVTSLQ 542
Cdd:pfam16665    2 GLNMNSPPQGSPGMTPPQqnlMMSPRHR------GSPKMPANQFSPGMG-LHSPMGSVSSGGsgGGGSRTYSSSSLNALQ 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2462578048  543 GMNEGPNNSVGFSASSPVLRQMSSQNSPSRlniQPAKAESKDNKEIAS 590
Cdd:pfam16665   75 AISEGVGNSLGSSLTSPVPKQDSSPNINST---QQKKEGSSDSKSPSS 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 924-969 2.06e-16

Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.


Pssm-ID: 462608 [Multi-domain]  Cd Length: 47  Bit Score: 74.36  E-value: 2.06e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2462578048  924 EGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLDVL 969
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLDPD 47
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1149-1205 2.31e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.31e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1149 GLPVQMGNPRLPQGAPQQFPYPPNYGTNPGTPPASTSPFSQLAA-NPEASLANRNSMV 1205
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNYGMSQQPDPAFTSALSPQSPmMSPRMGPSQSPMM 58
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1212-1268 2.92e-14

Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.


Pssm-ID: 462174  Cd Length: 58  Bit Score: 68.64  E-value: 2.92e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048 1212 NIGGQFGTGINPQMQQNVFQYPGA-GMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLL 1268
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 120-213 2.46e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 61.88  E-value: 2.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  120 LDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFvKNLLPKSLVNGVPWPQEAT--RRNSHTFNC 197
Cdd:cd00130      1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL-RERLENLLSGGEPVTLEVRlrRKDGSVIWV 79

                           90
                   ....*....|....*.
gi 2462578048  198 RMLIHPPDEPGTENQE 213
Cdd:cd00130     80 LVSLTPIRDEGGEVIG 95
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 115-172 6.49e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 59.34  E-value: 6.49e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048   115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNL 172
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
HLH smart00353
helix loop helix domain;
32-86 7.91e-09

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 52.99  E-value: 7.91e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2462578048    32 EKRRREQENKYLEELAELLSANISDidslsVKPDKCKILKKTVDQIQLMKRMEQE 86
Cdd:smart00353    4 ERRRRRKINEAFDELRSLLPTLPKN-----KKLSKAEILRLAIEYIKSLQEELQK 53
DUF4927 pfam16279
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 741-818 4.35e-08

Domain of unknown function (DUF4927); This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown.


Pssm-ID: 465083  Cd Length: 87  Bit Score: 52.11  E-value: 4.35e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  741 KESKDHQLLRYLLDKDE-KDLRSTpnlsldDVKVKVEKKE-QMDPCNTNPTPMTKPTPEEIKLEAQSQFTADLDQFDQLL 818
Cdd:pfam16279    8 KKKKNNALLRYLLDKDDsKDPLSK------DIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELSLDNLDAIL 81
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 32-82 1.77e-07

basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis.


Pssm-ID: 381392 [Multi-domain]  Cd Length: 46  Bit Score: 48.67  E-value: 1.77e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462578048   32 EKRRREQENKYLEELAELLSANisdidSLSVKPDKCKILKKTVDQIQLMKR 82
Cdd:cd00083      1 ERRRRDKINDAFEELKRLLPEL-----PDSKKLSKASILQKAVEYIRELQS 46
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 116-173 5.31e-07

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 49.72  E-value: 5.31e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048  116 LLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNLL 173
Cdd:pfam00989    6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 115-172 4.30e-06

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 51.27  E-value: 4.30e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462578048  115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNL 172
Cdd:COG5805    161 TLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 32-79 2.68e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA.


Pssm-ID: 381397 [Multi-domain]  Cd Length: 55  Bit Score: 42.95  E-value: 2.68e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462578048   32 EKRRREQENKYLEELAELLSANiSDIDSlsvKPDKCKILKKTVDQIQL 79
Cdd:cd11391      8 AKKRRDKENAEISELASLLPLP-PAVGS---KLDKLSVLRLAVAYLRL 51
bHLHzip_scCBP1 cd11398
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae ...
 15-90 2.97e-05

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.


Pssm-ID: 381404 [Multi-domain]  Cd Length: 89  Bit Score: 43.87  E-value: 2.97e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462578048   15 DSHKRkgspcdtlassTEKRRREQENKYLEELAELLSANisdidslSVKPDKCKILKKTVDQIQLMKRME---QEKSTT 90
Cdd:cd11398      9 DNHKE-----------VERRRRENINEGINELAALVPGN-------AREKNKGAILARAVEYIQELQETEaknIEKWTL 69
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 974-1287 3.66e-05

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: 48.47  E-value: 3.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  974 PPQQATPPLIMEERPNLYSQPySSPSPTANLPSPFQGMVRQKPSLGTMPVQvtpPRGAFSPGMGMQPRQTLNRPPAAPNQ 1053
Cdd:pfam09606  110 MGQQMGGPGTASNLLASLGRP-QMPMGGAGFPSQMSRVGRMQPGGQAGGMM---QPSSGQPGSGTPNQMGPNGGPGQGQA 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1054 LRLQLQQRLQGQQQLIHQnrqailnQFAATAPVGINMRSGMQQQITPQPPLNAQMLA----QRQRELYSQQHRQRQLIQQ 1129
Cdd:pfam09606  186 GGMNGGQQGPMGGQMPPQ-------MGVPGMPGPADAGAQMGQQAQANGGMNPQQMGgapnQVAMQQQQPQQQGQQSQLG 258

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1130 QRAMLMRQQSFGNNLPPSSGLPVQMGNPrlPQGAPQQFPY------PPNYGTNPGTPPASTSPFSQLAANP--------E 1195
Cdd:pfam09606  259 MGINQMQQMPQGVGGGAGQGGPGQPMGP--PGQQPGAMPNvmsigdQNNYQQQQTRQQQQQQGGNHPAAHQqqmnqsvgQ 336

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1196 ASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSL----SPGSSMVPMPIPP----PQSSL 1267
Cdd:pfam09606  337 GGQVVALGGLNHLETWNPGNFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNqfmrQSPQPSVPSPQGPgsqpPQSHP 416

                          330       340
                   ....*....|....*....|
gi 2462578048 1268 LQQTPPASGYQSPDMKAWQQ 1287
Cdd:pfam09606  417 GGMIPSPALIPSPSPQMSQQ 436
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 29-82 5.07e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) family; The ARNT family of bHLH-PAS transcription regulators includes ARNT, ARNT-like proteins (ARNTL and ARNTL2), and Drosophila melanogaster protein cycle. They act as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.


Pssm-ID: 381443  Cd Length: 58  Bit Score: 42.41  E-value: 5.07e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462578048   29 SSTEKRRREQENKYLEELAELLSAnisdIDSLSVKPDKCKILKKTVDQIQLMKR 82
Cdd:cd11437      6 SEIEKRRRDKMNAYIQELSALVPA----CNAMSRKLDKLTVLRMAVQHLKSLRG 55
bHLHzip_USF_MITF cd11387
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream ...
 32-86 6.10e-05

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements. The MITF (also known as microphthalmia-TFE, or MiT) subfamily comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.


Pssm-ID: 381393 [Multi-domain]  Cd Length: 58  Bit Score: 42.24  E-value: 6.10e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2462578048   32 EKRRREQENKYLEELAELLSAniSDIDSLSVKPDKCKILKKTVDQIQLMKRMEQE 86
Cdd:cd11387      6 ERRRRDNINEKIQELGSLVPP--SRLETKDLKPNKGSILSKAVEYIRELQNQNQE 58
PHA03247 PHA03247
large tegument protein UL36; Provisional
 974-1309 6.36e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 6.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  974 PPQQATPPlimeERPNLYSQPYSSPSPTANLPSPFQGMVRQKPSLGTMPVQVTPPrGAFSPGMGMQPRQTLNRPPAAPNQ 1053
Cdd:PHA03247  2673 AAQASSPP----QRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPP-GPAAARQASPALPAAPAPPAVPAG 2747

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1054 LRLQLQQRLQGQqqlihqnRQAILNQFAATAPVGinmRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAM 1133
Cdd:PHA03247  2748 PATPGGPARPAR-------PPTTAGPPAPAPPAA---PAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAA 2817

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1134 LMRQQSFGNNL-PPSSGLPVQmgnPRLPQGaPQQFPYPPNYGTNPGTPPASTSPFSQLAANPEASLANRNSMVSRgmtgn 1212
Cdd:PHA03247  2818 LPPAASPAGPLpPPTSAQPTA---PPPPPG-PPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLAR----- 2888

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1213 iggqfgtginPQMQQNVFQYP----GAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLLQQTPPA-------SGYQSPD 1281
Cdd:PHA03247  2889 ----------PAVSRSTESFAlppdQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLApttdpagAGEPSGA 2958

                          330       340       350
                   ....*....|....*....|....*....|....
gi 2462578048 1282 MKAWQQGAIGNNNV------FSQAVQNQPTPAQP 1309
Cdd:PHA03247  2959 VPQPWLGALVPGRVavprfrVPQPAPSREAPASS 2992
PAS COG2202
PAS domain [Signal transduction mechanisms];
115-209 1.09e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 45.79  E-value: 1.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048  115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVySILHVGDHAEFVKNLLPKSLVNGVPWPQEAT--RRNS 192
Cdd:COG2202     15 ALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTL-RDLLPPEDDDEFLELLRAALAGGGVWRGELRnrRKDG 93

                           90
                   ....*....|....*...
gi 2462578048  193 HTFNCRMLIHPP-DEPGT 209
Cdd:COG2202     94 SLFWVELSISPVrDEDGE 111
bHLHzip_Mlx_like cd11404
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, ...
 30-94 3.19e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.


Pssm-ID: 381410 [Multi-domain]  Cd Length: 70  Bit Score: 40.36  E-value: 3.19e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462578048   30 STEKRRREQENKYLEELAELlsanISDIDslSVKPDKCKILKKTVDQIQLMK----RMEQEKSTTDDDV 94
Cdd:cd11404      8 RSEKKRRELIKKGYDELCAL----VPGLD--PQKRTKADILQKAADWIQELKeeneKLEEQLDELKEAA 70
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 130-203 3.26e-04

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 41.29  E-value: 3.26e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462578048  130 EGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNLLpKSLVNGVPWPQEATRRNSHTFNCRMLIHP 203
Cdd:pfam13426    1 DGRIIYVNDAALRLLGYTREELLGKSITDLFAEPEDSERLREAL-REGKAVREFEVVLYRKDGEPFPVLVSLAP 73
PAS COG2202
PAS domain [Signal transduction mechanisms];
115-190 4.77e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 43.47  E-value: 4.77e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462578048  115 LLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHVGDHAEFVKNLlpKSLVNGVPWPQEATRR 190
Cdd:COG2202    141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL--RRLLEGGRESYELELR 214
bHLH_AtAIG1_like cd11455
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar ...
 29-101 7.74e-04

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins; AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo.


Pssm-ID: 381461  Cd Length: 80  Bit Score: 39.58  E-value: 7.74e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462578048   29 SSTEKRRREQENKYLEELAELLSANIsdidslsvKPDKCKILKKTVDQIQLMKRMEQEKSTTDDDVQKSDISS 101
Cdd:cd11455     12 SEAERRRRERINSHLATLRTLLPNLS--------KTDKASLLAEVVQHVKELKRQAAEITTPPDVPTEDEEDT 76
bHLH_O_HES cd11410
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 31-87 1.15e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) family; The HES family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. HES family proteins form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system.


Pssm-ID: 381416 [Multi-domain]  Cd Length: 54  Bit Score: 38.22  E-value: 1.15e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462578048   31 TEKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVdqiQLMKRMEQEK 87
Cdd:cd11410      1 MEKKRRARINKSLEQLKTLVLEALNKDNTRYSKLEKADILEMTV---KYLKQLQRSK 54
bHLH-PAS_CLOCK_like cd11441
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
 32-81 1.16e-03

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.


Pssm-ID: 381447  Cd Length: 54  Bit Score: 38.49  E-value: 1.16e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2462578048   32 EKRRREQENKYLEELAELLSANisdidslSVKPDKCKILKKTVDQIQLMK 81
Cdd:cd11441      8 EKKRRDQFNVLINELASMLPGR-------GRKMDKSTVLKKTIAFLRKHK 50
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 1153-1272 1.21e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 43.26  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048 1153 QMGNPRLPQGAPQQ--FPYPPNYGTNPGtppastspfSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVF 1230
Cdd:TIGR01628  379 QPRMRQLPMGSPMGgaMGQPPYYGQGPQ---------QQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2462578048 1231 QYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLLQQTP 1272
Cdd:TIGR01628  450 AQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNK 491
bHLH-O_HES7 cd11462
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) ...
 32-84 1.36e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) and similar proteins; HES-7, also termed Class B basic helix-loop-helix protein 37 (bHLHb37), or bHLH factor Hes7, is a bHLH-O transcriptional repressor that is expressed in an oscillatory manner and acts as a key regulator of the pace of the segmentation clock. It is regulated by the Notch and Fgf/Mapk pathways. HES-7 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability.


Pssm-ID: 381468 [Multi-domain]  Cd Length: 61  Bit Score: 38.48  E-value: 1.36e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462578048   32 EKRRREQENKYLEELAELLSANISDIDSLSVKPDKCKILKKTVDQIQLMKRME 84
Cdd:cd11462      9 EKRRRDRINRSLEELRVLLLQNTQDEKLKNPKVEKAEILELTVQFLRNSSLSA 61
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 29-81 1.44e-03

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 2 (ARNTL2) and similar proteins; ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. ARNT-2 heterodimerize with other bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM).


Pssm-ID: 381475  Cd Length: 60  Bit Score: 38.47  E-value: 1.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462578048   29 SSTEKRRREQENKYLEElaelLSANISDIDSLSVKPDKCKILKKTVDQIQLMK 81
Cdd:cd11469      6 SQTEKRRRDKMNNLIEE----LSAMIPQCNPMARKLDKLTVLRMAVQHLKSLK 54
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 95-182 1.99e-03

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 42.65  E-value: 1.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462578048   95 QKSDISS---SSQGVIEKESLGPLLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQEELMNTSVYSILHvGDHAEFVKN 171
Cdd:COG5809    122 ISRDITErkrMEEALRESEEKFRLIFNHSPDGIIVTDLDGRIIYANPAACKLLGISIEELIGKSILELIH-SDDQENVAA 200

                           90
                   ....*....|.
gi 2462578048  172 LLPKSLVNGVP 182
Cdd:COG5809    201 FISQLLKDGGI 211
bHLHzip_MITF_like cd11397
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated ...
 32-87 2.02e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.


Pssm-ID: 381403  Cd Length: 69  Bit Score: 38.04  E-value: 2.02e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462578048   32 EKRRREQENKYLEELAELLSANiSDIDslsVKPDKCKILKKTVDQIQLMKRmEQEK 87
Cdd:cd11397     13 ERRRRFNINDRIKELGTLLPKS-NDPD---MRWNKGTILKASVDYIRKLQK-EQER 63
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 133-186 7.81e-03

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 36.93  E-value: 7.81e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462578048  133 IVFVSENVTSYLGYNQEELMNT--SVYSILHVGDhAEFVKNLLPKSLVNGVPWPQE 186
Cdd:pfam08447    1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDD-RERVREALWEALKGGEPYSGE 55
bHLHzip_USF cd11396
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, ...
 32-86 8.44e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins; Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements.


Pssm-ID: 381402  Cd Length: 58  Bit Score: 36.12  E-value: 8.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2462578048   32 EKRRREQENKYLEELAELLSANISDIDSLSVKpdKCKILKKTVDQIQLMKRMEQE 86
Cdd:cd11396      6 ERRRRDKINNWIVKLAKIVPDCEKDNSKQGQS--KGGILSKACDYIQELRSQNER 58
 
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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