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Conserved domains on  [gi|392923313|ref|NP_001023894|]
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Hypoxia-inducible factor 1 [Caenorhabditis elegans]

Protein Classification

helix-loop-helix domain-containing protein( domain architecture ID 15361122)

helix-loop-helix (HLH) domain-containing protein with PAS domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 228-330 6.02e-12

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: 62.70  E-value: 6.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313  228 FTTRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFAK-GHIRTPYYRLIAANDTLAWIQTE 306
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....
gi 392923313  307 ATTITHTTKGQkGQYVICVHYVLG 330
Cdd:pfam14598  84 SKLFLNQNSNQ-QPFIMCTHTILR 106
bHLH_SF super family cl00081
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 4-58 3.29e-11

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.


The actual alignment was detected with superfamily member cd11433:

Pssm-ID: 469605  Cd Length: 58  Bit Score: 58.79  E-value: 3.29e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392923313   4 RRETSRHAARDRRSKESDIFDDLKMCVPiVEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd11433    1 RKEKSRDAARCRRGKESEIFYELAHQLP-LPHSVSSQLDKASIMRLTISYLKLRK 54
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 81-134 6.02e-08

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: 50.09  E-value: 6.02e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 392923313    81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEF 134
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERV 58
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 228-330 6.02e-12

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: 62.70  E-value: 6.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313  228 FTTRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFAK-GHIRTPYYRLIAANDTLAWIQTE 306
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....
gi 392923313  307 ATTITHTTKGQkGQYVICVHYVLG 330
Cdd:pfam14598  84 SKLFLNQNSNQ-QPFIMCTHTILR 106
bHLH-PAS_HIF cd11433
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) ...
 4-58 3.29e-11

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: 58.79  E-value: 3.29e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392923313   4 RRETSRHAARDRRSKESDIFDDLKMCVPiVEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd11433    1 RKEKSRDAARCRRGKESEIFYELAHQLP-LPHSVSSQLDKASIMRLTISYLKLRK 54
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 81-134 6.02e-08

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: 50.09  E-value: 6.02e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 392923313    81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEF 134
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERV 58
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 86-137 8.13e-08

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: 50.71  E-value: 8.13e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392923313  86 LDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQ 137
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRER 52
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 225-304 5.17e-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. 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: 48.40  E-value: 5.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313 225 MGAFTTRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFAKGHIRTPYYRLIAANDTLAWIQ 304
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 80-169 1.25e-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: 44.72  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313   80 DTIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQSKML----HKPRGEDT-----D 150
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQAllqgEESRGFEVsfrvpD 83

                          90
                  ....*....|....*....
gi 392923313  151 TTGINMVLRMKTVISPRGR 169
Cdd:pfam00989  84 GRPRHVEVRASPVRDAGGE 102
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 81-136 4.65e-04

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: 40.74  E-value: 4.65e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 392923313   81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDK 136
Cdd:TIGR00229   7 AIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRE 62
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 223-282 1.81e-03

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: 37.38  E-value: 1.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313   223 SPMGAFttRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFA 282
Cdd:smart00091  10 LPDGIF--VLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PAS COG2202
PAS domain [Signal transduction mechanisms];
81-137 4.31e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 39.62  E-value: 4.31e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392923313  81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQ 137
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLEL 197
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 228-330 6.02e-12

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: 62.70  E-value: 6.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313  228 FTTRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFAK-GHIRTPYYRLIAANDTLAWIQTE 306
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....
gi 392923313  307 ATTITHTTKGQkGQYVICVHYVLG 330
Cdd:pfam14598  84 SKLFLNQNSNQ-QPFIMCTHTILR 106
bHLH-PAS_HIF cd11433
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) ...
 4-58 3.29e-11

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: 58.79  E-value: 3.29e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392923313   4 RRETSRHAARDRRSKESDIFDDLKMCVPiVEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd11433    1 RKEKSRDAARCRRGKESEIFYELAHQLP-LPHSVSSQLDKASIMRLTISYLKLRK 54
bHLH-PAS_HIF2a_PASD2 cd19728
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 2-58 5.58e-10

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: 55.86  E-value: 5.58e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392923313   2 ERRRETSRHAARDRRSKESDIFDDLKMCVPIvEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd19728    5 ERRKEKSRDAARCRRSKETEVFYELAHQLPL-PHSVSSHLDKASIMRLAISFLRTHK 60
bHLH-PAS_HIF1a_PASD8 cd19727
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 2-58 6.40e-10

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: 55.81  E-value: 6.40e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392923313   2 ERRRETSRHAARDRRSKESDIFDDLKMCVPIVEEGTvTHLDRIALLRVAATICRLRK 58
Cdd:cd19727    4 ERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVS-SHLDKASIMRLTISYLRMRK 59
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 1-58 3.40e-09

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: 53.48  E-value: 3.40e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 392923313   1 MERRRETSRHAARDRRSKESDIFDDLKMCVPIvEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd19729    1 TEQRKEKSRDAARCRRSQETEVFYELAHTLPF-PRGVSSHLDKASIMRLTISYLRMHR 57
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 81-134 6.02e-08

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: 50.09  E-value: 6.02e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 392923313    81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEF 134
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERV 58
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 86-137 8.13e-08

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: 50.71  E-value: 8.13e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392923313  86 LDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQ 137
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRER 52
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 5-58 1.24e-07

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: 48.73  E-value: 1.24e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392923313   5 RETSRHAARDRRSKESDIFDDLKMCVPIVEEgTVTHLDRIALLRVAATICRLRK 58
Cdd:cd11391    1 REKSREAAKKRRDKENAEISELASLLPLPPA-VGSKLDKLSVLRLAVAYLRLKK 53
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 225-304 5.17e-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. 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: 48.40  E-value: 5.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313 225 MGAFTTRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFAKGHIRTPYYRLIAANDTLAWIQ 304
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 80-169 1.25e-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: 44.72  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313   80 DTIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQSKML----HKPRGEDT-----D 150
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQAllqgEESRGFEVsfrvpD 83

                          90
                  ....*....|....*....
gi 392923313  151 TTGINMVLRMKTVISPRGR 169
Cdd:pfam00989  84 GRPRHVEVRASPVRDAGGE 102
bHLH-PAS_NPAS1_3_like cd11432
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 5-58 5.42e-05

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: 41.40  E-value: 5.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392923313   5 RETSRHAARDRRSKESDIFDDLKMCVPIVEEgTVTHLDRIALLRVAATICRLRK 58
Cdd:cd11432    1 KEKSRNAARSRRGKENYEFYELAKLLPLPAA-ISSQLDKASIVRLTISYLKLRD 53
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 238-304 7.36e-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.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 41.94  E-value: 7.36e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313  238 ITFVSDKFNYIL---KSELKTlMGTSFYELVHPADMMIVSKSMKELFAKGHIRTPYYRLIAANDTLAWIQ 304
Cdd:pfam08447   1 IIYWSPRFEEILgytPEELLG-KGESWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVE 69
bHLH-PAS_trachealess_like cd19733
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 1-62 1.12e-04

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: 41.07  E-value: 1.12e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392923313   1 MERRRETSRHAARDRRSKESDIFDDLKMCVPIVEEGTvTHLDRIALLRVAATICRLRKTAGN 62
Cdd:cd19733    2 LELRKEKSRDAARSRRGKENYEFYELAKMLPLPAAIT-SQLDKASIIRLTISYLKLRDFSGH 62
bHLH-PAS_NPAS1_PASD5 cd19731
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 4-60 1.47e-04

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: 40.67  E-value: 1.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 392923313   4 RRETSRHAARDRRSKESDIFDDLKMCVPIveEGTVT-HLDRIALLRVAATICRLRKTA 60
Cdd:cd19731    4 RKEKSRNAARSRRGKENFEFYELAKMLPL--PGAITsQLDKASIVRLTISYLKMRDFA 59
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-60 1.56e-04

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: 40.75  E-value: 1.56e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313   1 MERRRETSRHAARDRRSKESDIFDDLKMCVPIVEEGTvTHLDRIALLRVAATICRLRKTA 60
Cdd:cd19732    3 QALRKEKSRDAARSRRGKENFEFYELAKLLPLPAAIT-SQLDKASIIRLTISYLKMRDFA 61
bHLH-PAS_dSIM_like cd19740
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 5-58 4.26e-04

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: 38.90  E-value: 4.26e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392923313   5 RETSRHAARDRRSKESDIFDDLKMCVPIvEEGTVTHLDRIALLRVAATICRLRK 58
Cdd:cd19740    2 KEKSKNAARSRREKENAEFLELAKLLPL-PAAITSQLDKASIIRLTTSYLKMRQ 54
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 81-136 4.65e-04

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: 40.74  E-value: 4.65e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 392923313   81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDK 136
Cdd:TIGR00229   7 AIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRE 62
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 223-282 1.81e-03

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: 37.38  E-value: 1.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392923313   223 SPMGAFttRHTCDMRITFVSDKFNYILKSELKTLMGTSFYELVHPADMMIVSKSMKELFA 282
Cdd:smart00091  10 LPDGIF--VLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PAS COG2202
PAS domain [Signal transduction mechanisms];
81-137 4.31e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 39.62  E-value: 4.31e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392923313  81 TIAECLDGFVMIVDSDSSILYVTESVAMYLGLTQTDLTGRALRDFLHPSDYDEFDKQ 137
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLEL 197
 
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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