basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins; NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 193207275  78 QRSTRGASKQRRDQINVEIQKLRDLLPLSDLIKDRLFQLQVMSLGCIFIRKHRYQQT 134
Cdd:cd19697    1 GRSTKGASKQRRDLINAEIRELRDLLPLPESTRQRLSQLQIMSLACVYIRKSNFFSQ 57

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 193207275 161 LRGFMLMVTRSGKILHVSDNASEYLGHSVEEIMcqGDSIYDLVDGRDHGAVQAELASGPPGAATFPEERVFICR 234
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELI--GKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRK 72

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins; NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 193207275  78 QRSTRGASKQRRDQINVEIQKLRDLLPLSDLIKDRLFQLQVMSLGCIFIRKHRYQQT 134
Cdd:cd19697    1 GRSTKGASKQRRDLINAEIRELRDLLPLPESTRQRLSQLQIMSLACVYIRKSNFFSQ 57

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207275 302 THVFSTQHYLDMKFKEADTMASQHLGFSKEQLKGMSWYGMIHPNHVPEIAHKHRLLcQEKEGSVLALIRLQAANGEWIWL 381
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENL-LSGGEPVTLEVRLRRKDGSVIWV 79

                         90
                 ....*....|....*.
gi 193207275 382 HTVFSIRPNNELNSDG 397
Cdd:cd00130   80 LVSLTPIRDEGGEVIG 95

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 193207275   160 ALRGFMLMVTRSGKILHVSDNASEYLGHSVEEIMcqGDSIYDLVDGRDHGAVQAELASG 218
Cdd:smart00091   9 SLPDGIFVLDLDGRILYANPAAEELLGYSPEELI--GKSLLELIHPEDRERVQEALQRL 65

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207275  160 ALRGFMLMVTRSGKILHVSDNASEYLGHSVEEIMcqGDSIYDLVDGRDHGAVQAELasgppgaatfpeervficRLNLAR 239
Cdd:pfam00989   9 SLPDGIFVVDEDGRILYVNAAAEELLGLSREEVI--GKSLLDLIPEEDDAEVAELL------------------RQALLQ 68

                          90       100
                  ....*....|....*....|
gi 193207275  240 TAKRQLQYHKFVLFQGRYIQ 259
Cdd:pfam00989  69 GEESRGFEVSFRVPDGRPRH 88

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins; NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 193207275  78 QRSTRGASKQRRDQINVEIQKLRDLLPLSDLIKDRLFQLQVMSLGCIFIRKHRYQQT 134
Cdd:cd19697    1 GRSTKGASKQRRDLINAEIRELRDLLPLPESTRQRLSQLQIMSLACVYIRKSNFFSQ 57

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 193207275  78 QRSTRGASKQRRDQINVEIQKLRDLLPLSDLIKDRLFQLQVMSLGCIFIRKHRY 131
Cdd:cd11391    1 REKSREAAKKRRDKENAEISELASLLPLPPAVGSKLDKLSVLRLAVAYLRLKKF 54

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 193207275 161 LRGFMLMVTRSGKILHVSDNASEYLGHSVEEIMcqGDSIYDLVDGRDHGAVQAELASGPPGAATFPEERVFICR 234
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELI--GKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRK 72

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207275  323 SQHLGFSKEQLKGM--SWYGMIHPNHVPEIAHKH-RLLcqeKEGSVLAL-IRLQAANGEWIWLHTVFSIRPnnelNSDGK 398
Cdd:pfam08447   9 EEILGYTPEELLGKgeSWLDLVHPDDRERVREALwEAL---KGGEPYSGeYRIRRKDGEYRWVEARARPIR----DENGK 81

                  ...
gi 193207275  399 RLR 401
Cdd:pfam08447  82 PVR 84

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207275  160 ALRGFMLMVTRSGKILHVSDNASEYLGHSVEEIMcqGDSIYDLVDGRDHGAVQAELasgppgaatfpeervficRLNLAR 239
Cdd:pfam00989   9 SLPDGIFVVDEDGRILYVNAAAEELLGLSREEVI--GKSLLDLIPEEDDAEVAELL------------------RQALLQ 68

                          90       100
                  ....*....|....*....|
gi 193207275  240 TAKRQLQYHKFVLFQGRYIQ 259
Cdd:pfam00989  69 GEESRGFEVSFRVPDGRPRH 88

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 193207275  85 SKQRRDQINVEIQKLRDLLPLSDLIKDRLFQLQVMSLGCIFIRKHRYQQTV 135
Cdd:cd11435    8 SKRHRDRLNAELDHLASLLPFPPDIISKLDKLSVLRLSVSYLRVKSFFQAI 58

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 193207275  86 KQRRDQINVEIQKLRDLLPLSDLIKdRLFQLQVMSLGCIFIR 127
Cdd:cd00083    2 RRRRDKINDAFEELKRLLPELPDSK-KLSKASILQKAVEYIR 42