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Conserved domains on  [gi|90421311|ref|NP_690008|]
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hypoxia-inducible factor 3-alpha isoform c [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 12-74 6.76e-40

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins; HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


:

Pssm-ID: 381572  Cd Length: 63  Bit Score: 140.15  E-value: 6.76e-40
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90421311  12 TELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE 74
Cdd:cd19729   1 TEQRKEKSRDAARCRRSQETEVFYELAHTLPFPRGVSSHLDKASIMRLTISYLRMHRLIASGE 63
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 241-348 4.67e-17

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).


The actual alignment was detected with superfamily member pfam14598:

Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 77.33  E-value: 4.67e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311   241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALD-SDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQ 319
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDlRTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....*....
gi 90421311   320 ATVVSGGRGPQSESIVCVHFLISqvEETG 348
Cdd:pfam14598  84 SKLFLNQNSNQQPFIMCTHTILR--EENA 110
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 478-509 6.07e-12

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


:

Pssm-ID: 463274  Cd Length: 32  Bit Score: 60.39  E-value: 6.07e-12
                          10        20        30
                  ....*....|....*....|....*....|..
gi 90421311   478 IAQDADALDLEMLAPYISMDDDFQLNASEQLP 509
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMDDDFQLNPIIPEE 32
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 95-170 1.19e-10

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: 58.80  E-value: 1.19e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  95 GFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRKveaPTERCFSLRMKS 170
Cdd:cd00130   3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL--ENLLSGGE---PVTLEVRLRRKD 73
 
Name Accession Description Interval E-value
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 12-74 6.76e-40

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins; HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


Pssm-ID: 381572  Cd Length: 63  Bit Score: 140.15  E-value: 6.76e-40
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90421311  12 TELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE 74
Cdd:cd19729   1 TEQRKEKSRDAARCRRSQETEVFYELAHTLPFPRGVSSHLDKASIMRLTISYLRMHRLIASGE 63
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 241-348 4.67e-17

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: 77.33  E-value: 4.67e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311   241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALD-SDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQ 319
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDlRTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....*....
gi 90421311   320 ATVVSGGRGPQSESIVCVHFLISqvEETG 348
Cdd:pfam14598  84 SKLFLNQNSNQQPFIMCTHTILR--EENA 110
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 241-338 1.56e-15

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: 72.67  E-value: 1.56e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQA 320
Cdd:cd00130   4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSL 83

                        90
                ....*....|....*...
gi 90421311 321 TVVSGGRGPQSESIVCVH 338
Cdd:cd00130  84 TPIRDEGGEVIGLLGVVR 101
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 478-509 6.07e-12

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


Pssm-ID: 463274  Cd Length: 32  Bit Score: 60.39  E-value: 6.07e-12
                          10        20        30
                  ....*....|....*....|....*....|..
gi 90421311   478 IAQDADALDLEMLAPYISMDDDFQLNASEQLP 509
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMDDDFQLNPIIPEE 32
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 95-170 1.19e-10

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: 58.80  E-value: 1.19e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  95 GFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRKveaPTERCFSLRMKS 170
Cdd:cd00130   3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL--ENLLSGGE---PVTLEVRLRRKD 73
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 90-149 2.92e-10

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: 56.64  E-value: 2.92e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311     90 LKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALTPQQ 149
Cdd:smart00091   7 LESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
PAS COG2202
PAS domain [Signal transduction mechanisms];
247-362 4.21e-07

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 51.95  E-value: 4.21e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 247 LDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQATVVSGG 326
Cdd:COG2202  29 LDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDE 108

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 90421311 327 RGpQSESIVCVHFLIS---QVEETgvvlsLEQTEQHSRR 362
Cdd:COG2202 109 DG-EITGFVGIARDITerkRAEEA-----LRESEERLRL 141
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 241-295 7.58e-07

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: 46.62  E-value: 7.58e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 90421311    241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLS 295
Cdd:smart00091  13 GIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
HLH smart00353
helix loop helix domain;
20-68 2.33e-06

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 44.90  E-value: 2.33e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 90421311     20 RDAARSRRSQETEVLYQLAHTLPFARgVSAHLDKASIMRLTISYLRMHR 68
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLP-KNKKLSKAEILRLAIEYIKSLQ 48
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 96-146 2.16e-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: 2.16e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 90421311    96 FVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALT 146
Cdd:pfam00989  13 GIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
PAS COG2202
PAS domain [Signal transduction mechanisms];
97-330 5.50e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 45.40  E-value: 5.50e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311  97 VMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRKVEAPTERCfslrmkstLTSRG 176
Cdd:COG2202  24 IIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELL--RAALAGGGVWRGELRN--------RRKDG 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 177 RTLNLKAATWKVLNCSGHMRAY-----------------KppaqtspagspDSEpplQCLVLICEAIPHpgslepplgrg 239
Cdd:COG2202  94 SLFWVELSISPVRDEDGEITGFvgiarditerkraeealR-----------ESE---ERLRLLVENAPD----------- 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 240 aFLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKG-QAVTGQYRFLARSGGYLWTQT 318
Cdd:COG2202 149 -GIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGrESYELELRLKDGDGRWVWVEA 227

                       250
                ....*....|..
gi 90421311 319 QATVVSGGRGPQ 330
Cdd:COG2202 228 SAVPLRDGGEVI 239
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 90-145 5.81e-04

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: 42.80  E-value: 5.81e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  90 LKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDAL 145
Cdd:COG5805 163 IENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
 
Name Accession Description Interval E-value
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 12-74 6.76e-40

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins; HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


Pssm-ID: 381572  Cd Length: 63  Bit Score: 140.15  E-value: 6.76e-40
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90421311  12 TELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE 74
Cdd:cd19729   1 TEQRKEKSRDAARCRRSQETEVFYELAHTLPFPRGVSSHLDKASIMRLTISYLRMHRLIASGE 63
bHLH-PAS_HIF cd11433
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) ...
 15-72 3.68e-30

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) family; The HIF family contains bHLH-PAS transcription regulators involved in oxygen homeostasis, including HIF1a, HIF2a, and HIF3a. They have been implicated in development, postnatal physiology as well as disease pathogenesis. HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia. HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes. HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


Pssm-ID: 381439  Cd Length: 58  Bit Score: 112.72  E-value: 3.68e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 90421311  15 RKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAA 72
Cdd:cd11433   1 RKEKSRDAARCRRGKESEIFYELAHQLPLPHSVSSQLDKASIMRLTISYLKLRKLLSA 58
bHLH-PAS_HIF2a_PASD2 cd19728
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 9-73 8.35e-28

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 2-alpha (HIF2a) and similar proteins; HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes.


Pssm-ID: 381571  Cd Length: 66  Bit Score: 106.32  E-value: 8.35e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 90421311   9 RSTTELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAG 73
Cdd:cd19728   1 RSSSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSVSSHLDKASIMRLAISFLRTHKLLSSV 65
bHLH-PAS_HIF1a_PASD8 cd19727
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 11-74 4.24e-27

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 1-alpha (HIF1a) and similar proteins; HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia.


Pssm-ID: 381570  Cd Length: 71  Bit Score: 104.34  E-value: 4.24e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 90421311  11 TTELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE 74
Cdd:cd19727   2 SSERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASIMRLTISYLRMRKLLDAGE 65
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 16-70 9.20e-20

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: 83.01  E-value: 9.20e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLC 70
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLPPAVGSKLDKLSVLRLAVAYLRLKKFL 55
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 13-77 1.29e-19

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins; NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation.


Pssm-ID: 381575  Cd Length: 78  Bit Score: 83.51  E-value: 1.29e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 90421311  13 ELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE--WNQ 77
Cdd:cd19732   4 ALRKEKSRDAARSRRGKENFEFYELAKLLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDppWNL 70
bHLH-PAS_trachealess_like cd19733
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 13-77 8.78e-19

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein trachealess and similar proteins; Protein trachealess is a bHLH-PAS transcription factor that acts as an inducer of tracheal cell fates in Drosophila. It is necessary for the development of the salivary gland duct and the posterior spiracles.


Pssm-ID: 381576  Cd Length: 79  Bit Score: 81.13  E-value: 8.78e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 90421311  13 ELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE--WNQ 77
Cdd:cd19733   3 ELRKEKSRDAARSRRGKENYEFYELAKMLPLPAAITSQLDKASIIRLTISYLKLRDFSGHGDppWNR 69
bHLH-PAS_NPAS1_PASD5 cd19731
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 13-81 1.63e-18

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins; NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development.


Pssm-ID: 381574  Cd Length: 74  Bit Score: 80.35  E-value: 1.63e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 90421311  13 ELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGE--WNQVGAG 81
Cdd:cd19731   2 ALRKEKSRNAARSRRGKENFEFYELAKMLPLPGAITSQLDKASIVRLTISYLKMRDFASHGDppWSLRAEG 72
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 241-348 4.67e-17

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: 77.33  E-value: 4.67e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311   241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALD-SDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQ 319
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDlRTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....*....
gi 90421311   320 ATVVSGGRGPQSESIVCVHFLISqvEETG 348
Cdd:pfam14598  84 SKLFLNQNSNQQPFIMCTHTILR--EENA 110
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 251-338 9.40e-17

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: 75.45  E-value: 9.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311   251 FTYCDDRIAEVAGYSPDDLIG--CSAYEYIHALDSDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQATVVSGGRG 328
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGkgESWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDENG 80

                          90
                  ....*....|
gi 90421311   329 pQSESIVCVH 338
Cdd:pfam08447  81 -KPVRVIGVA 89
bHLH-PAS_NPAS1_3_like cd11432
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 16-68 6.55e-16

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing proteins, NPAS1, NPAS3 and similar proteins; The family includes neuronal PAS domain proteins NPAS1 and NPAS3, both of which are master regulators of neuropsychiatric function. NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development. NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation.


Pssm-ID: 381438  Cd Length: 55  Bit Score: 72.22  E-value: 6.55e-16
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHR 68
Cdd:cd11432   1 KEKSRNAARSRRGKENYEFYELAKLLPLPAAISSQLDKASIVRLTISYLKLRD 53
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 241-338 1.56e-15

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: 72.67  E-value: 1.56e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQA 320
Cdd:cd00130   4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSL 83

                        90
                ....*....|....*...
gi 90421311 321 TVVSGGRGPQSESIVCVH 338
Cdd:cd00130  84 TPIRDEGGEVIGLLGVVR 101
bHLH-PAS_SIM cd11434
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The ...
 16-66 2.39e-14

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The SIM family includes Drosophila melanogaster protein SIM and its homologs from vertebrates, single-minded homolog 1 (SIM1) and single-minded homolog 2 (SIM2). SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila. SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult. SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development.


Pssm-ID: 381440  Cd Length: 61  Bit Score: 68.09  E-value: 2.39e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRM 66
Cdd:cd11434   2 KEKSKNAARTRREKENAEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKM 52
bHLH-PAS_dSIM_like cd19740
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 16-73 2.75e-14

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein single-minded (SIM) and similar proteins; SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila.


Pssm-ID: 381583  Cd Length: 62  Bit Score: 67.79  E-value: 2.75e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAG 73
Cdd:cd19740   2 KEKSKNAARSRREKENAEFLELAKLLPLPAAITSQLDKASIIRLTTSYLKMRQVFPDG 59
bHLH-PAS_SIM1 cd19738
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) ...
 16-78 1.56e-13

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) and similar proteins; SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult.


Pssm-ID: 381581  Cd Length: 71  Bit Score: 65.96  E-value: 1.56e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAG---EWNQV 78
Cdd:cd19738   2 KEKSKNAARTRREKENSEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRVVFPEGlgeAWGHS 67
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
 16-86 2.96e-13

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) and similar proteins; SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development.


Pssm-ID: 381582  Cd Length: 74  Bit Score: 65.14  E-value: 2.96e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 90421311  16 KEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAG---EWNQVGAGGePLD 86
Cdd:cd19739   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGlgdAWGQPSRIG-PLD 74
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 478-509 6.07e-12

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


Pssm-ID: 463274  Cd Length: 32  Bit Score: 60.39  E-value: 6.07e-12
                          10        20        30
                  ....*....|....*....|....*....|..
gi 90421311   478 IAQDADALDLEMLAPYISMDDDFQLNASEQLP 509
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMDDDFQLNPIIPEE 32
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 95-170 1.19e-10

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: 58.80  E-value: 1.19e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  95 GFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRKveaPTERCFSLRMKS 170
Cdd:cd00130   3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL--ENLLSGGE---PVTLEVRLRRKD 73
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 90-149 2.92e-10

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: 56.64  E-value: 2.92e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311     90 LKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALTPQQ 149
Cdd:smart00091   7 LESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
PAS COG2202
PAS domain [Signal transduction mechanisms];
247-362 4.21e-07

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 51.95  E-value: 4.21e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 247 LDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKGQAVTGQYRFLARSGGYLWTQTQATVVSGG 326
Cdd:COG2202  29 LDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDE 108

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 90421311 327 RGpQSESIVCVHFLIS---QVEETgvvlsLEQTEQHSRR 362
Cdd:COG2202 109 DG-EITGFVGIARDITerkRAEEA-----LRESEERLRL 141
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 241-295 7.58e-07

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: 46.62  E-value: 7.58e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 90421311    241 FLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLS 295
Cdd:smart00091  13 GIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
HLH smart00353
helix loop helix domain;
20-68 2.33e-06

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 44.90  E-value: 2.33e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 90421311     20 RDAARSRRSQETEVLYQLAHTLPFARgVSAHLDKASIMRLTISYLRMHR 68
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLP-KNKKLSKAEILRLAIEYIKSLQ 48
bHLH-PAS_AhR_like cd19696
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor ...
 25-65 2.36e-06

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor (AhR) family; The AhR family includes AhR, AhR repressor (AhRR) and Drosophila melanogaster protein spineless. AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR, also termed Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR, playing key roles in development and environmental sensing. AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive. Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic.


Pssm-ID: 381539  Cd Length: 59  Bit Score: 44.98  E-value: 2.36e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 90421311  25 SRRSQE--TEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLR 65
Cdd:cd19696   8 SKRHRDrlNSELDELASLLPFPEDVISKLDKLSVLRLSVSYLR 50
bHLH-PAS_AhR cd11436
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) ...
 18-65 3.40e-06

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) and similar proteins; AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerize with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator).


Pssm-ID: 381442  Cd Length: 61  Bit Score: 44.91  E-value: 3.40e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 90421311  18 KSRDAARSRRSQETEvLYQLAHTLPFARGVSAHLDKASIMRLTISYLR 65
Cdd:cd11436   5 KSNPSKRHRDRLNTE-LDRLASLLPFPQDVISKLDKLSVLRLSVSYLR 51
bHLH-PAS_AhRR cd11435
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 17-66 1.73e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor repressor (AhRR) and similar proteins; AhRR, also termed AhR repressor, or Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR (or Dioxin Receptor), playing key roles in development and environmental sensing. AhR is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes, AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive.


Pssm-ID: 381441  Cd Length: 60  Bit Score: 42.66  E-value: 1.73e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 90421311  17 EKSRDAARSRRSQETEvLYQLAHTLPFARGVSAHLDKASIMRLTISYLRM 66
Cdd:cd11435   3 EKSNPSKRHRDRLNAE-LDHLASLLPFPPDIISKLDKLSVLRLSVSYLRV 51
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 96-146 2.16e-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: 2.16e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 90421311    96 FVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALT 146
Cdd:pfam00989  13 GIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR 63
PAS COG2202
PAS domain [Signal transduction mechanisms];
97-330 5.50e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 45.40  E-value: 5.50e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311  97 VMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRKVEAPTERCfslrmkstLTSRG 176
Cdd:COG2202  24 IIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELL--RAALAGGGVWRGELRN--------RRKDG 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 177 RTLNLKAATWKVLNCSGHMRAY-----------------KppaqtspagspDSEpplQCLVLICEAIPHpgslepplgrg 239
Cdd:COG2202  94 SLFWVELSISPVRDEDGEITGFvgiarditerkraeealR-----------ESE---ERLRLLVENAPD----------- 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311 240 aFLSRHSLDMKFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLLSKG-QAVTGQYRFLARSGGYLWTQT 318
Cdd:COG2202 149 -GIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGrESYELELRLKDGDGRWVWVEA 227

                       250
                ....*....|..
gi 90421311 319 QATVVSGGRGPQ 330
Cdd:COG2202 228 SAVPLRDGGEVI 239
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 250-338 5.87e-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: 42.79  E-value: 5.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311   250 KFTYCDDRIAEVAGYSPDDLIGCSAYEYIHALDSDAVSKSIHTLL-SKGQAVTGQYRFLARSGGYLWTQTQATVVSGGRG 328
Cdd:pfam00989  22 RILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALlQGEESRGFEVSFRVPDGRPRHVEVRASPVRDAGG 101

                          90
                  ....*....|
gi 90421311   329 pQSESIVCVH 338
Cdd:pfam00989 102 -EILGFLGVL 110
bHLH-PAS_spineless_like cd19730
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 18-65 1.31e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein spineless and similar proteins; Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic.


Pssm-ID: 381573  Cd Length: 64  Bit Score: 40.22  E-value: 1.31e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 90421311  18 KSRDAARSRRSQETEvLYQLAHTLPFARGVSAHLDKASIMRLTISYLR 65
Cdd:cd19730   7 KSNPSKRHRERLNAE-LDHLASLLPFEQSVISKLDKLSILRLSVSYLR 53
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 90-145 5.81e-04

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: 42.80  E-value: 5.81e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 90421311  90 LKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDAL 145
Cdd:COG5805 163 IENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERI 218
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 301-343 1.20e-03

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 37.16  E-value: 1.20e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 90421311    301 TGQYRFLARSGGYLWTQTQATVVSGGRGpQSESIVCVHFLISQ 343
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRDEDG-EVEGILGVVRDITE 42
bHLH-O_HELT cd11408
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related ...
 24-65 1.37e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related protein HELT and similar proteins; HELT, also termed HES/HEY-like transcription factor, is a bHLH-O transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. HELT could homodimerize and heterodimerize with other bHLH-O protein such as HES-5 or HEY-2 and bound to E box to repress gene transcription.


Pssm-ID: 381414 [Multi-domain]  Cd Length: 56  Bit Score: 37.28  E-value: 1.37e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 90421311  24 RSRRSQETEVLYQLAHTLP--FARGVSAHLDKASIMRLTISYLR 65
Cdd:cd11408   7 KRRRDRINRCLNELGKTVPmaLAKQTSGKLEKAEILEMTVQYLR 50
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 26-66 3.02e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP)-like family; The HERP-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this family. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.


Pssm-ID: 381395 [Multi-domain]  Cd Length: 55  Bit Score: 36.15  E-value: 3.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 90421311  26 RRSQETEVLYQLAHTLP--FARGVSAHLDKASIMRLTISYLRM 66
Cdd:cd11389   8 RRDRINESLAELRRLVPeaRKSKGSGKLEKAEILEMTLQHLKA 50
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 24-72 5.99e-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: 35.47  E-value: 5.99e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 90421311  24 RSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAA 72
Cdd:cd11437  10 KRRRDKMNAYIQELSALVPACNAMSRKLDKLTVLRMAVQHLKSLRGTGS 58
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 94-188 6.35e-03

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: 36.89  E-value: 6.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90421311    94 EGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALtpQQTLSRRkvEAPTERCFSLRmkstlT 173
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHL--REIIQTR--GRATSPSYRLR-----L 72

                          90
                  ....*....|....*
gi 90421311   174 SRGRTLNLKaATWKV 188
Cdd:pfam14598  73 RDGDFLSVH-TKSKL 86
 
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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