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 25150916  10 QKPSKSQAQQRRQMENYEFSQLANELPLARAIsGQHIDKTTMVRLATAYIKLHNIF 65
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLPPAV-GSKLDKLSVLRLAVAYLRLKKFL 55

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 25150916 214 SNSFVIITSIDLHITFADEKAHQLLNnpfYPDSNIKGMSLYSLIDISDSEVISKMHFDIFNLGAYKTPYYRMILNQTSEt 293
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLG---YSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSV- 76

                        90
                ....*....|..
gi 25150916 294 FYVESNIFRHTS 305
Cdd:cd00130  77 IWVLVSLTPIRD 88

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 25150916  10 QKPSKSQAQQRRQMENYEFSQLANELPLARAIsGQHIDKTTMVRLATAYIKLHNIF 65
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLPPAV-GSKLDKLSVLRLAVAYLRLKKFL 55

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        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 25150916     87 NNHLDLLDGFFVILDRRGDVLYISETISIYLGLSQVEMTGNAMVDYIHEQDINCFNSALN 146
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQ 63

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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 25150916    90 LDLLDGFFVILDRRGDVLYISETISIYLGLSQVEMTGNAMVDYIHEQDINCFNSAL 145
Cdd:pfam00989   7 LESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELL 62

helix loop helix domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 25150916     17 AQQRRQMENYEFSQLANELPLARaiSGQHIDKTTMVRLATAYIK 60
Cdd:smart00353   4 ERRRRRKINEAFDELRSLLPTLP--KNKKLSKAEILRLAIEYIK 45

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 25150916  10 QKPSKSQAQQRRQMENYEFSQLANELPLARAIsGQHIDKTTMVRLATAYIKLHNIF 65
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLPPAV-GSKLDKLSVLRLAVAYLRLKKFL 55

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 25150916   9 KQKpSKSQAQQRRQMENYEFSQLANELPLARAISGQhIDKTTMVRLATAYIKLHNIF 65
Cdd:cd19740   2 KEK-SKNAARSRREKENAEFLELAKLLPLPAAITSQ-LDKASIIRLTTSYLKMRQVF 56

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25150916  10 QKPSKSQAQQRRQMENYEFSQLANELPLARAISGQhIDKTTMVRLATAYIKLHNIF--------GQSQRA 71
Cdd:cd19739   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQ-LDKASIIRLTTSYLKMRAVFpeglgdawGQPSRI 70

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 25150916   9 KQKpSKSQAQQRRQMENYEFSQLANELPLARAISGQhIDKTTMVRLATAYIKLHNIF 65
Cdd:cd19738   2 KEK-SKNAARTRREKENSEFYELAKLLPLPSAITSQ-LDKASIIRLTTSYLKMRVVF 56

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 25150916   5 LSEEKQKPSKSQAQQRRQMENYEFSQLANELPLARAISGQhIDKTTMVRLATAYIKLHNIFGQ 67
Cdd:cd19732   2 LQALRKEKSRDAARSRRGKENFEFYELAKLLPLPAAITSQ-LDKASIIRLTISYLKMRDFANQ 63

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 25150916   9 KQKpSKSQAQQRRQMENYEFSQLANELPLARAISGQhIDKTTMVRLATAYIKL 61
Cdd:cd11432   1 KEK-SRNAARSRRGKENYEFYELAKLLPLPAAISSQ-LDKASIVRLTISYLKL 51

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
                ....*....|....*....|....*....|....*....|....*....|...
gi 25150916  93 LDGFFVILDRRGDVLYISETISIYLGLSQVEMTGNAMVDYIHEQDINCFNSAL 145
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL 53

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 25150916 214 SNSFVIITSIDLHITFADEKAHQLLNnpfYPDSNIKGMSLYSLIDISDSEVISKMHFDIFNLGAYKTPYYRMILNQTSEt 293
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLG---YSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSV- 76

                        90
                ....*....|..
gi 25150916 294 FYVESNIFRHTS 305
Cdd:cd00130  77 IWVLVSLTPIRD 88

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        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 25150916    214 SNSFVIITSIDLHITFADEKAHQLLNnpfYPDSNIKGMSLYSLIDISDSEVISKMHFDIFN 274
Cdd:smart00091  10 LPDGIFVLDLDGRILYANPAAEELLG---YSPEELIGKSLLELIHPEDRERVQEALQRLLS 67

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 25150916  18 QQRRQMENYEFSQLANELPLARAISGQhiDKTTMVRLATAYIK 60
Cdd:cd00083   2 RRRRDKINDAFEELKRLLPELPDSKKL--SKASILQKAVEYIR 42