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Conserved domains on  [gi|2038223459|ref|XP_041421048|]
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nuclear receptor coactivator 1 isoform X4 [Xenopus laevis]

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), ...
 285-395 1.22e-34

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: 128.57  E-value: 1.22e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  285 ESFITKQDATGKIISIDTsslRASGSLGWED--LVRKCIYAFFQAQGtePSYAKQLFQEVM-TRGTACSPSYKFTLSDGT 361
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDGD 76

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2038223459  362 ELSAHTKCKLCYPQSPDVQPYIMGIHIIERDQSS 395
Cdd:pfam14598   77 FLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 51-99 6.27e-28

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: 107.75  E-value: 6.27e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2038223459   51 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILIKRMD 99
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVD 49
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 670-744 2.83e-18

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: 80.90  E-value: 2.83e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  670 KLVQLLASTAEQQLR-------DVDTSCRDPLTCPVVTNTSCGSSSSGTCPSSHSSLTERHKILHRLLQEG-SPSDINSL 741
Cdd:pfam08832    5 KLLQLLTTPTEQLGPsplrshaDADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDDVAKL 84


                   ...
gi 2038223459  742 SLD 744
Cdd:pfam08832   85 TAE 87
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1284-1340 1.08e-17

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: 78.27  E-value: 1.08e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459 1284 NVGGQFGSGINPQMQQNVFQYSAT-GISQQGDPTFAPSLSPTSPLMSPRITPSQSPML 1340
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
NCOA_u2 super family cl25027
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 495-652 5.64e-17

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.


The actual alignment was detected with superfamily member pfam16665:

Pssm-ID: 465223 [Multi-domain]  Cd Length: 119  Bit Score: 78.24  E-value: 5.64e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  495 PMSSPGISPPQ---FMSPRPRASPglvsrsRASGNPFSPpVPAMHSPVSISNSGCnnnnnrpfsnvplnsmpvvndpntp 571
Cdd:pfam16665    9 PQGSPGMTPPQqnlMMSPRHRGSP------KMPANQFSP-GMGLHSPMGSVSSGG------------------------- 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  572 lgfsslspgmtnnvSTINNGRIFSNTPMNTVQGINEGPNPTVGYSTTSPVLRQLNSQNspgrLNMQPVKMELKDNSNGNS 651
Cdd:pfam16665   57 --------------SGGGGSRTYSSSSLNALQAISEGVGNSLGSSLTSPVPKQDSSPN----INSTQQKKEGSSDSKSPS 118


                   .
gi 2038223459  652 S 652
Cdd:pfam16665  119 S 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 999-1042 4.50e-15

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: 70.51  E-value: 4.50e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2038223459  999 EGRSDEKALFEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLE 1042
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLD 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 140-197 2.88e-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: 60.49  E-value: 2.88e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459   140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNL 197
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
DUF4927 super family cl24752
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 760-846 1.28e-09

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: 56.34  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  760 KMESESDKKKdsKDHQLLRYLLDKDEkevkpSSALTLDDVKVKLEKAE-QGEQCSSTPNKLIKPGQEDIKMETQVQFADD 838
Cdd:pfam16279    1 KQEQLSPKKK--KNNALLRYLLDKDD-----SKDPLSKDIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELS 73


                   ....*...
gi 2038223459  839 FDQLDQLL 846
Cdd:pfam16279   74 LDNLDAIL 81
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 1161-1383 4.66e-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: 45.00  E-value: 4.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1161 GMRPGMQQTISPQPPLNaQMLAQ---RQRELYSQQHRQRQLMQQRSLLMRQQGFGNNLPPSGNLPVTRLPQGPPQQFPYP 1237
Cdd:pfam09606  228 GMNPQQMGGAPNQVAMQ-QQQPQqqgQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNY 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1238 HNYGTNPGNPPPSTSPFSPLTTTPeaalpNRTGANGGVMV-----NRGMMGNVGGQFGSGINPQMQQNVFQYS------- 1305
Cdd:pfam09606  307 QQQQTRQQQQQQGGNHPAAHQQQM-----NQSVGQGGQVValgglNHLETWNPGNFGGLGANPMQRGQPGMMSspspvpg 381

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1306 ATGISQQGDPTFAPSLSPTSP-LMSPRITPSQSPMLQQTPSTPGYQSPDLKTWQQSPLG-NSGVYSQGGQTQPPNGQQGM 1383
Cdd:pfam09606  382 QQVRQVTPNQFMRQSPQPSVPsPQGPGSQPPQSHPGGMIPSPALIPSPSPQMSQQPAQQrTIGQDSPGGSLNTPGQSAVN 461
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 285-395 1.22e-34

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: 128.57  E-value: 1.22e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  285 ESFITKQDATGKIISIDTsslRASGSLGWED--LVRKCIYAFFQAQGtePSYAKQLFQEVM-TRGTACSPSYKFTLSDGT 361
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDGD 76

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2038223459  362 ELSAHTKCKLCYPQSPDVQPYIMGIHIIERDQSS 395
Cdd:pfam14598   77 FLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 51-99 6.27e-28

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: 107.75  E-value: 6.27e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2038223459   51 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILIKRMD 99
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVD 49
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 670-744 2.83e-18

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: 80.90  E-value: 2.83e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  670 KLVQLLASTAEQQLR-------DVDTSCRDPLTCPVVTNTSCGSSSSGTCPSSHSSLTERHKILHRLLQEG-SPSDINSL 741
Cdd:pfam08832    5 KLLQLLTTPTEQLGPsplrshaDADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDDVAKL 84


                   ...
gi 2038223459  742 SLD 744
Cdd:pfam08832   85 TAE 87
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1284-1340 1.08e-17

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: 78.27  E-value: 1.08e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459 1284 NVGGQFGSGINPQMQQNVFQYSAT-GISQQGDPTFAPSLSPTSPLMSPRITPSQSPML 1340
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
NCOA_u2 pfam16665
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 495-652 5.64e-17

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: 78.24  E-value: 5.64e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  495 PMSSPGISPPQ---FMSPRPRASPglvsrsRASGNPFSPpVPAMHSPVSISNSGCnnnnnrpfsnvplnsmpvvndpntp 571
Cdd:pfam16665    9 PQGSPGMTPPQqnlMMSPRHRGSP------KMPANQFSP-GMGLHSPMGSVSSGG------------------------- 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  572 lgfsslspgmtnnvSTINNGRIFSNTPMNTVQGINEGPNPTVGYSTTSPVLRQLNSQNspgrLNMQPVKMELKDNSNGNS 651
Cdd:pfam16665   57 --------------SGGGGSRTYSSSSLNALQAISEGVGNSLGSSLTSPVPKQDSSPN----INSTQQKKEGSSDSKSPS 118


                   .
gi 2038223459  652 S 652
Cdd:pfam16665  119 S 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 999-1042 4.50e-15

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: 70.51  E-value: 4.50e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2038223459  999 EGRSDEKALFEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLE 1042
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLD 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 140-197 2.88e-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: 60.49  E-value: 2.88e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459   140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNL 197
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 145-238 8.22e-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: 60.34  E-value: 8.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  145 LDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFvKNLLPKSLVNGGSWSQEA--NRRNSHTLNC 222
Cdd:cd00130      1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL-RERLENLLSGGEPVTLEVrlRRKDGSVIWV 79

                           90
                   ....*....|....*.
gi 2038223459  223 RMLIRPPDDPGAENQE 238
Cdd:cd00130     80 LVSLTPIRDEGGEVIG 95
DUF4927 pfam16279
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 760-846 1.28e-09

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: 56.34  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  760 KMESESDKKKdsKDHQLLRYLLDKDEkevkpSSALTLDDVKVKLEKAE-QGEQCSSTPNKLIKPGQEDIKMETQVQFADD 838
Cdd:pfam16279    1 KQEQLSPKKK--KNNALLRYLLDKDD-----SKDPLSKDIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELS 73


                   ....*...
gi 2038223459  839 FDQLDQLL 846
Cdd:pfam16279   74 LDNLDAIL 81
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 140-197 2.49e-07

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: 55.12  E-value: 2.49e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNL 197
Cdd:COG5805    161 TLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 141-198 4.94e-05

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: 43.95  E-value: 4.94e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459  141 LLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNLL 198
Cdd:pfam00989    6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 1161-1383 4.66e-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: 45.00  E-value: 4.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1161 GMRPGMQQTISPQPPLNaQMLAQ---RQRELYSQQHRQRQLMQQRSLLMRQQGFGNNLPPSGNLPVTRLPQGPPQQFPYP 1237
Cdd:pfam09606  228 GMNPQQMGGAPNQVAMQ-QQQPQqqgQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNY 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1238 HNYGTNPGNPPPSTSPFSPLTTTPeaalpNRTGANGGVMV-----NRGMMGNVGGQFGSGINPQMQQNVFQYS------- 1305
Cdd:pfam09606  307 QQQQTRQQQQQQGGNHPAAHQQQM-----NQSVGQGGQVValgglNHLETWNPGNFGGLGANPMQRGQPGMMSspspvpg 381

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1306 ATGISQQGDPTFAPSLSPTSP-LMSPRITPSQSPMLQQTPSTPGYQSPDLKTWQQSPLG-NSGVYSQGGQTQPPNGQQGM 1383
Cdd:pfam09606  382 QQVRQVTPNQFMRQSPQPSVPsPQGPGSQPPQSHPGGMIPSPALIPSPSPQMSQQPAQQrTIGQDSPGGSLNTPGQSAVN 461
HLH smart00353
helix loop helix domain;
56-94 8.80e-04

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 38.74  E-value: 8.80e-04
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 2038223459    56 EKRRREQENKYLEELAELLSANigdidSLSVKPDKCKIL 94
Cdd:smart00353    4 ERRRRRKINEAFDELRSLLPTL-----PKNKKLSKAEIL 37
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 140-195 2.29e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 39.58  E-value: 2.29e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIySILHVGDHEEFVK 195
Cdd:TIGR00229    7 AIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNV-LELIPEEDREEVR 61
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 148-391 3.11e-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: 41.88  E-value: 3.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  148 FFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILH---VGDHEEFVKNLLPKSLVNGgsWSQEANRRNSHTLNCRM 224
Cdd:COG5809     27 AILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHpddEKELREILKLLKEGESRDE--LEFELRHKNGKRLEFSS 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  225 LIRPPDDpgaenqearQRYEVMQCFTVSQP----KSFKEEGEDFQSCLiciaRRLprpapITSLESFITKQDATGKIISI 300
Cdd:COG5809    105 KLSPIFD---------QNGDIEGMLAISRDiterKRMEEALRESEEKF----RLI-----FNHSPDGIIVTDLDGRIIYA 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  301 DTSSLRASGsLGWEDLVRKCIYAFFqaqgtePSYAKQ----LFQEVMTRGTACSPSYKFTLSDGT--ELSAHtkcklCYP 374
Cdd:COG5809    167 NPAACKLLG-ISIEELIGKSILELI------HSDDQEnvaaFISQLLKDGGIAQGEVRFWTKDGRwrLLEAS-----GAP 234

                          250       260
                   ....*....|....*....|
gi 2038223459  375 QSPDVQP---YIMGIHIIER 391
Cdd:COG5809    235 IKKNGEVdgiVIIFRDITER 254
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 285-395 1.22e-34

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: 128.57  E-value: 1.22e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  285 ESFITKQDATGKIISIDTsslRASGSLGWED--LVRKCIYAFFQAQGtePSYAKQLFQEVM-TRGTACSPSYKFTLSDGT 361
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDT---RAPFSLGYEKdeLVGRSIYDLVHPQD--LRTAKSHLREIIqTRGRATSPSYRLRLRDGD 76

                           90       100       110
                   ....*....|....*....|....*....|....
gi 2038223459  362 ELSAHTKCKLCYPQSPDVQPYIMGIHIIERDQSS 395
Cdd:pfam14598   77 FLSVHTKSKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_NCoA1_SRC1 cd18948
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 ...
 51-99 6.27e-28

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: 107.75  E-value: 6.27e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2038223459   51 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILIKRMD 99
Cdd:cd18948      1 TAQSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILKKTVD 49
bHLH-PAS_NCoA3_SRC3 cd18949
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 3 ...
 54-125 6.63e-22

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: 90.87  E-value: 6.63e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2038223459   54 STEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKILikRMDQIQQLKKKKQEKASGADDDVQKSDIS 125
Cdd:cd18949      4 SGEKRRREQESKYIEELAELISANLSDIDNFNVKPDKCAIL--KETVRQIRQIKEQGKSSSNDDDVQKADVS 73
bHLH-PAS_SRC cd11439
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator ...
 54-98 2.15e-21

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: 88.64  E-value: 2.15e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2038223459   54 STEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKIL------IKRM 98
Cdd:cd11439      4 LNEKRRREQENKYIEELAELISASISDMDSLSVKPDKCAILqetvkqIRQI 54
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 670-744 2.83e-18

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: 80.90  E-value: 2.83e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  670 KLVQLLASTAEQQLR-------DVDTSCRDPLTCPVVTNTSCGSSSSGTCPSSHSSLTERHKILHRLLQEG-SPSDINSL 741
Cdd:pfam08832    5 KLLQLLTTPTEQLGPsplrshaDADTDCKDSLAGVTSPSSGVSSSSGSSCPSHHSSLQEKHKILHRLLQNGnSPDDVAKL 84


                   ...
gi 2038223459  742 SLD 744
Cdd:pfam08832   85 TAE 87
DUF1518 pfam07469
Nuclear receptor coactivator, DUF1518; This conserved domain of unknown function is usually ...
 1284-1340 1.08e-17

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: 78.27  E-value: 1.08e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459 1284 NVGGQFGSGINPQMQQNVFQYSAT-GISQQGDPTFAPSLSPTSPLMSPRITPSQSPML 1340
Cdd:pfam07469    1 GMGGQFGGPRNPQAQPQQFPYPPNyGMSQQPDPAFTSALSPQSPMMSPRMGPSQSPMM 58
bHLH-PAS_NCoA2_SRC2 cd18950
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 2 ...
 53-94 3.76e-17

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: 77.04  E-value: 3.76e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2038223459   53 QSTEKRRREQENKYLEELAELLSANIGDIDSLSVKPDKCKIL 94
Cdd:cd18950      5 RSTEKRNREQENKYIEELAELIFANFNDIDNFNVKPDKCAIL 46
NCOA_u2 pfam16665
Unstructured region on nuclear receptor coactivator protein; NCOA_u2 is a region of natively ...
 495-652 5.64e-17

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: 78.24  E-value: 5.64e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  495 PMSSPGISPPQ---FMSPRPRASPglvsrsRASGNPFSPpVPAMHSPVSISNSGCnnnnnrpfsnvplnsmpvvndpntp 571
Cdd:pfam16665    9 PQGSPGMTPPQqnlMMSPRHRGSP------KMPANQFSP-GMGLHSPMGSVSSGG------------------------- 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  572 lgfsslspgmtnnvSTINNGRIFSNTPMNTVQGINEGPNPTVGYSTTSPVLRQLNSQNspgrLNMQPVKMELKDNSNGNS 651
Cdd:pfam16665   57 --------------SGGGGSRTYSSSSLNALQAISEGVGNSLGSSLTSPVPKQDSSPN----INSTQQKKEGSSDSKSPS 118


                   .
gi 2038223459  652 S 652
Cdd:pfam16665  119 S 119
Nuc_rec_co-act pfam08815
Nuclear receptor coactivator; This region is found on eukaryotic nuclear receptor coactivators ...
 999-1042 4.50e-15

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: 70.51  E-value: 4.50e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2038223459  999 EGRSDEKALFEQLVSFLSGKDETELAELDRALGIDKLV-QGGGLE 1042
Cdd:pfam08815    1 EGPSDEGALLDQLVSFLSNTDETGLEEIDRALGIPELVgQGQGLD 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 140-197 2.88e-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: 60.49  E-value: 2.88e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459   140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNL 197
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 145-238 8.22e-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: 60.34  E-value: 8.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  145 LDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFvKNLLPKSLVNGGSWSQEA--NRRNSHTLNC 222
Cdd:cd00130      1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL-RERLENLLSGGEPVTLEVrlRRKDGSVIWV 79

                           90
                   ....*....|....*.
gi 2038223459  223 RMLIRPPDDPGAENQE 238
Cdd:cd00130     80 LVSLTPIRDEGGEVIG 95
DUF4927 pfam16279
Domain of unknown function (DUF4927); This family, around 80 residues, consists of ...
 760-846 1.28e-09

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: 56.34  E-value: 1.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  760 KMESESDKKKdsKDHQLLRYLLDKDEkevkpSSALTLDDVKVKLEKAE-QGEQCSSTPNKLIKPGQEDIKMETQVQFADD 838
Cdd:pfam16279    1 KQEQLSPKKK--KNNALLRYLLDKDD-----SKDPLSKDIKPKLEGLDgKTGPCSSSKIPTSKSEKEESKIKTEPPDELS 73


                   ....*...
gi 2038223459  839 FDQLDQLL 846
Cdd:pfam16279   74 LDNLDAIL 81
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 140-197 2.49e-07

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: 55.12  E-value: 2.49e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNL 197
Cdd:COG5805    161 TLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
PAS COG2202
PAS domain [Signal transduction mechanisms];
140-215 2.36e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 47.71  E-value: 2.36e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNLlpKSLVNGGSWSQEANRR 215
Cdd:COG2202    141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL--RRLLEGGRESYELELR 214
PAS COG2202
PAS domain [Signal transduction mechanisms];
140-231 4.25e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 46.94  E-value: 4.25e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIySILHVGDHEEFVKNLLPKSLVNGGSWSQEA--NRRNS 217
Cdd:COG2202     15 ALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTL-RDLLPPEDDDEFLELLRAALAGGGVWRGELrnRRKDG 93

                           90
                   ....*....|....
gi 2038223459  218 HTLNCRMLIRPPDD 231
Cdd:COG2202     94 SLFWVELSISPVRD 107
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 141-198 4.94e-05

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: 43.95  E-value: 4.94e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038223459  141 LLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNLL 198
Cdd:pfam00989    6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 158-211 2.02e-04

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: 41.56  E-value: 2.02e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2038223459  158 IVFVSENVTNYLGYKQEEL--MKDSIYSILHVGDhEEFVKNLLPKSLVNGGSWSQE 211
Cdd:pfam08447    1 IIYWSPRFEEILGYTPEELlgKGESWLDLVHPDD-RERVREALWEALKGGEPYSGE 55
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 1161-1383 4.66e-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: 45.00  E-value: 4.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1161 GMRPGMQQTISPQPPLNaQMLAQ---RQRELYSQQHRQRQLMQQRSLLMRQQGFGNNLPPSGNLPVTRLPQGPPQQFPYP 1237
Cdd:pfam09606  228 GMNPQQMGGAPNQVAMQ-QQQPQqqgQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNY 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1238 HNYGTNPGNPPPSTSPFSPLTTTPeaalpNRTGANGGVMV-----NRGMMGNVGGQFGSGINPQMQQNVFQYS------- 1305
Cdd:pfam09606  307 QQQQTRQQQQQQGGNHPAAHQQQM-----NQSVGQGGQVValgglNHLETWNPGNFGGLGANPMQRGQPGMMSspspvpg 381

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459 1306 ATGISQQGDPTFAPSLSPTSP-LMSPRITPSQSPMLQQTPSTPGYQSPDLKTWQQSPLG-NSGVYSQGGQTQPPNGQQGM 1383
Cdd:pfam09606  382 QQVRQVTPNQFMRQSPQPSVPsPQGPGSQPPQSHPGGMIPSPALIPSPSPQMSQQPAQQrTIGQDSPGGSLNTPGQSAVN 461
HLH smart00353
helix loop helix domain;
56-94 8.80e-04

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 38.74  E-value: 8.80e-04
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 2038223459    56 EKRRREQENKYLEELAELLSANigdidSLSVKPDKCKIL 94
Cdd:smart00353    4 ERRRRRKINEAFDELRSLLPTL-----PKNKKLSKAEIL 37
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 56-94 9.61e-04

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: 38.71  E-value: 9.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2038223459   56 EKRRREQENKYLEELAELL--SANIGdidslsVKPDKCKIL 94
Cdd:cd11391      8 AKKRRDKENAEISELASLLplPPAVG------SKLDKLSVL 42
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 56-94 2.22e-03

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: 37.50  E-value: 2.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2038223459   56 EKRRREQENKYLEELAELLSANigdidSLSVKPDKCKIL 94
Cdd:cd00083      1 ERRRRDKINDAFEELKRLLPEL-----PDSKKLSKASIL 34
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 140-195 2.29e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 39.58  E-value: 2.29e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2038223459  140 LLLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIySILHVGDHEEFVK 195
Cdd:TIGR00229    7 AIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNV-LELIPEEDREEVR 61
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 148-391 3.11e-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: 41.88  E-value: 3.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  148 FFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILH---VGDHEEFVKNLLPKSLVNGgsWSQEANRRNSHTLNCRM 224
Cdd:COG5809     27 AILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHpddEKELREILKLLKEGESRDE--LEFELRHKNGKRLEFSS 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  225 LIRPPDDpgaenqearQRYEVMQCFTVSQP----KSFKEEGEDFQSCLiciaRRLprpapITSLESFITKQDATGKIISI 300
Cdd:COG5809    105 KLSPIFD---------QNGDIEGMLAISRDiterKRMEEALRESEEKF----RLI-----FNHSPDGIIVTDLDGRIIYA 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  301 DTSSLRASGsLGWEDLVRKCIYAFFqaqgtePSYAKQ----LFQEVMTRGTACSPSYKFTLSDGT--ELSAHtkcklCYP 374
Cdd:COG5809    167 NPAACKLLG-ISIEELIGKSILELI------HSDDQEnvaaFISQLLKDGGIAQGEVRFWTKDGRwrLLEAS-----GAP 234

                          250       260
                   ....*....|....*....|
gi 2038223459  375 QSPDVQP---YIMGIHIIER 391
Cdd:COG5809    235 IKKNGEVdgiVIIFRDITER 254
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 141-227 6.58e-03

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 40.91  E-value: 6.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038223459  141 LLEALDGFFFVVNQEGRIVFVSENVTNYLGYKQEELMKDSIYSILHVGDHEEFVKNLLPKSLVNggswsQEANRRNSHTL 220
Cdd:COG3829     16 ILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSPLLEVLKTGKPVTGVI-----QKTGGKGKTVI 90


                   ....*..
gi 2038223459  221 NCRMLIR 227
Cdd:COG3829     91 VTAIPIF 97
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 55-98 7.37e-03

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: 36.24  E-value: 7.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2038223459   55 TEKRRREQENKYLEELAELLSAnigdIDSLSVKPDKCKILikRM 98
Cdd:cd11437      8 IEKRRRDKMNAYIQELSALVPA----CNAMSRKLDKLTVL--RM 45
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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