basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins; NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4 (PASD4), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802416   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77

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 1958802416  84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGhlpgteeesmkglhrsrtlrlclrsevhpverasfslyfLLQSDV 163
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLG---------------------------------------LSREEV 41

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802416 164 MDQNLLNFLPEQEHSEVYKILSSHMLVTDSPSPE---FLKSDNDlEFYCHLLRgslNPKEFPTYEYIKFVGNFR 234
Cdd:pfam00989  42 IGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFevsFRVPDGR-PRHVEVRA---SPVRDAGGEILGFLGVLR 111

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins; NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4 (PASD4), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802416   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77

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 1958802416 289 EFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQFGKGKSCCYRFLTKGQQWIWLQTH 368
Cdd:cd00130     3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVS 82

                          90       100
                  ....*....|....*....|.
gi 1958802416 369 YYITYHQWNSKPEFIVCTHSV 389
Cdd:cd00130    83 LTPIRDEGGEVIGLLGVVRDI 103

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958802416   15 NKSEKKRRDQFNVLIKELSSMLPG--NTRKLDKTTVLEKVIGFLQKHNEVSAQ 65
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQEELQK 53

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 1958802416  84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGhlpgteeesmkglhrsrtlrlclrsevhpverasfslyfLLQSDV 163
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLG---------------------------------------LSREEV 41

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802416 164 MDQNLLNFLPEQEHSEVYKILSSHMLVTDSPSPE---FLKSDNDlEFYCHLLRgslNPKEFPTYEYIKFVGNFR 234
Cdd:pfam00989  42 IGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFevsFRVPDGR-PRHVEVRA---SPVRDAGGEILGFLGVLR 111

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802416  601 AQRPAAQQPLQqRPSAPSQPPlVVNTPLPGQITSTqvtnqhllrESNVMSAQGPKPIRSSQLLPASSRSLSSLPsQFSST 680
Cdd:PHA03247  2863 RRRPPSRSPAA-KPAAPARPP-VRRLARPAVSRST---------ESFALPPDQPERPPQPQAPPPPQPQPQPPP-PPQPQ 2930

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958802416  681 ASVLPPGLSLTTVAPTPQDTSQCQPS-----PDFGHDRQLRYAQSQVTFPSP-DSHPTSSSAPTP 739
Cdd:PHA03247  2931 PPPPPPPRPQPPLAPTTDPAGAGEPSgavpqPWLGALVPGRVAVPRFRVPQPaPSREAPASSTPP 2995

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins; NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4 (PASD4), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802416   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock. It forms heterodimers with another bHLH-PAS protein, Brain-Muscle-Arnt-Like (also known as BMAL or ARNT3 or mop3), which regulates circadian rhythm. BMAL1-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802416   4 DEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSA 64
Cdd:cd19734     1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITA 61

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958802416  11 RASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSA 64
Cdd:cd11441     1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIAFLRKHKELTA 54

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 1958802416 300 FLFLDHRAPPIIGYLPFEVLGT--SGYDYYHIDDLELLARCHQHLMQFGKGKSCCYRFLTKGQQWIWLQTHYYItYHQWN 377
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1958802416 378 SKPEFIVCTH 387
Cdd:pfam08447  80 GKPVRVIGVA 89

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 1958802416  11 RASRNKSEKKRRDQFNVLIKELSSMLPGN---TRKLDKTTVLEKVIGFLQKHN 60
Cdd:cd11391     1 REKSREAAKKRRDKENAEISELASLLPLPpavGSKLDKLSVLRLAVAYLRLKK 53

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958802416  10 KRASRNKSEKKRRDQFNVLIKELSSMLP--GNTRKLDKTTVLEKVIGFLQK 58
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKH 51

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein cycle and similar proteins; 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958802416  10 KRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd19726     1 RRQNHSEIEKRRRDKMNTYITELSSMIPmcnAMSRKLDKLTVL 43

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958802416  10 KRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd11437     1 SRSNHSEIEKRRRDKMNAYIQELSALVPacnAMSRKLDKLTVL 43

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 2 (ARNTL2) and similar proteins; 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. ARNT-2 heterodimerize with other bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958802416  11 RASRNKSEKKRRDQFNVLIKELSSMLPGNT---RKLDKTTVLEKVIGFLQ 57
Cdd:cd11469     2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNpmaRKLDKLTVLRMAVQHLK 51

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958802416  350 SCCYRFLTKGQQWIWLQTHYYITYHqWNSKPEFIVCTHSVVS 391
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41

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
                  ....*....|....*....|....*....|....*...
gi 1958802416  18 EKKRRDQFNVLIKELSSMLPG--NTRKLDKTTVLEKVI 53
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPElpDSKKLSKASILQKAV 38

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins; AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802416   7 DRAKRASRNKS--EKKRRDQFNVLIKELSSMLPGNTrKLDKTTVLEKVIGFLQK-HNEVSAQTEICDIQQD 74
Cdd:cd11455     2 DKALAASKSHSeaERRRRERINSHLATLRTLLPNLS-KTDKASLLAEVVQHVKElKRQAAEITTPPDVPTE 71

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) and similar proteins; ARNT, also termed Class E basic helix-loop-helix protein 2 (bHLHe2), or Dioxin receptor, nuclear translocator, or hypoxia-inducible factor 1-beta (HIF1b), or HIF-1-beta, or HIF1-beta, is a member of bHLH-PAS transcription regulators that acts 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958802416   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd18947     1 KERFARENHSEIERRRRNKMTAYITELSDMVPtcsALARKPDKLTIL 47

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as PIFs, ALC, PIL1, SPATULA, and UNE10. PIFs (PIF1, PIF3, PIF4, PIF5, PIF6 and PIF7) have been shown to control light-regulated gene expression. They directly bind to the photoactivated phytochromes and are degraded in response to light signals. ALC, also termed AtbHLH73, or protein ALCATRAZ, or EN 98, is required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. It promotes the differentiation of a strip of labile non-lignified cells sandwiched between layers of lignified cells. PIL1, also termed AtbHLH124, or protein phytochrome interacting factor 3-like 1, or EN 110, is involved in responses to transient and long-term shade. It is required for the light-mediated inhibition of hypocotyl elongation and necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. PIL1 seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. SPATULA, also termed AtbHLH24, or EN 99, plays a role in floral organogenesis. It promotes the growth of carpel margins and of pollen tract tissues derived from them. UNE10, also termed AtbHLH16, or protein UNFERTILIZED EMBRYO SAC 10, or EN 99, is required during the fertilization of ovules by pollen.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958802416  15 NKSEKKRRDQFNVLIKELSSMLPgNTRKLDKTTVLEKVIGFL 56
Cdd:cd11445     7 NLSERRRRDRINEKMKALQELIP-NCNKTDKASMLDEAIEYL 47

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins; USF3, also termed upstream transcription factor 3, is a bHLHzip protein that is involved in the negative regulation of epithelial-mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802416   5 EKDRaKRASRNKSEKKRRDQFNVLIKELSSMLPG-NTRKLDKTTVLEKV---IGFLQKHNE 61
Cdd:cd18910     1 RREK-KRESHNEVERRRKDKINAGINKIGELLPDrDAKKQSKNMILEQAykyIVELKKKND 60

basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family and similar proteins; The SOHLH family includes two bHLH transcription factors, SOHLH1 and SOHLH2. They are specifically in spermatogonia and oocytes and essential for early spermatogonial and oocyte differentiation. The family also includes transcription factor-like 5 protein (TCFL5) and similar proteins. TCFL5, also termed Cha transcription factor, or HPV-16 E2-binding protein 1 (E2BP-1), is a bHLH transcription factor that plays a crucial role in spermatogenesis. It regulates cell proliferation or differentiation of cells through binding to a specific DNA sequence like other bHLH molecules.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958802416  10 KRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLE---KVIGFLQK 58
Cdd:cd19683     2 SRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDKATVFEftvAYIKFLRE 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins; TFE3, also termed Class E basic helix-loop-helix protein 33 (bHLHe33), is a bHLHzip transcription factor that is involved in B cell function. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958802416   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNT---RKLDKTTVLEKVIGF---LQKHNEVSAQTEI 68
Cdd:cd18928     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSTdpeMRWNKGTILKASVDYirkLQKEQQRSKEIEM 75

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription factors and similar proteins; bHLH proteins are the second largest class of plant transcription factors that regulate transcription of genes that are involve in many essential physiological and developmental process. bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. The Arabidopsis bHLH proteins that have been characterized so far have roles in regulation of fruit dehiscence, cell development (carpel, anther and epidermal), phytochrome signaling, flavonoid biosynthesis, hormone signaling and stress responses.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958802416  17 SEKKRRDQFNVLIKELSSMLPgNTRKLDKTTVLEKVIG---FLQK 58
Cdd:cd11393     4 AERKRREKINERIRALRSLVP-NGGKTDKASILDEAIEyikFLQE 47

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
                   ....*....|....*....|....*....|....*...
gi 1958802416   84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGHLP 121
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSP 38

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802416  601 AQRPAAQQPLQqRPSAPSQPPlVVNTPLPGQITSTqvtnqhllrESNVMSAQGPKPIRSSQLLPASSRSLSSLPsQFSST 680
Cdd:PHA03247  2863 RRRPPSRSPAA-KPAAPARPP-VRRLARPAVSRST---------ESFALPPDQPERPPQPQAPPPPQPQPQPPP-PPQPQ 2930

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958802416  681 ASVLPPGLSLTTVAPTPQDTSQCQPS-----PDFGHDRQLRYAQSQVTFPSP-DSHPTSSSAPTP 739
Cdd:PHA03247  2931 PPPPPPPRPQPPLAPTTDPAGAGEPSgavpqPWLGALVPGRVAVPRFRVPQPaPSREAPASSTPP 2995

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) family; The HES family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. HES family proteins form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system.

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gi 1958802416  18 EKKRRDQFNVLIKELSSMLPGNTR-------KLDKTTVLEKVIGFLQKHN 60
Cdd:cd11410     2 EKKRRARINKSLEQLKTLVLEALNkdntrysKLEKADILEMTVKYLKQLQ 51

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements. The MITF (also known as microphthalmia-TFE, or MiT) subfamily comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

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gi 1958802416  13 SRNKSEKKRRDQFNVLIKELSSMLP-----GNTRKLDKTTVLEKVIGF---LQKHNE 61
Cdd:cd11387     1 SHNAVERRRRDNINEKIQELGSLVPpsrleTKDLKPNKGSILSKAVEYireLQNQNQ 57