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).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24660399    261 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 339
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                           90       100
                   ....*....|....*....|....*
gi 24660399    340 TDYYVSYHQFNSKPDYVVCTHKVVS 364
Cdd:pfam14598   82 TKSKLFLNQNSNQQPFIMCTHTILR 106

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).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24660399    261 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 339
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                           90       100
                   ....*....|....*....|....*
gi 24660399    340 TDYYVSYHQFNSKPDYVVCTHKVVS 364
Cdd:pfam14598   82 TKSKLFLNQNSNQQPFIMCTHTILR 106

Helix-loop-helix DNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 24660399     12 KRKSRNLSEKKRRDQFNSLVNDLSALI--STSSRKMDKSTVLKSTIAFLK 59
Cdd:pfam00010    1 RREAHNERERRRRDRINDAFDELRELLptLPPDKKLSKAEILRLAIEYIK 50

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 24660399      89 HLMLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMN 149
Cdd:smart00091    4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660399   95 LDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMNPTPVIEPRQTDIS 162
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVR 68

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 24660399   13 RKSRNLSEKKRRDQFNSLVNDLSALISTSSRKMDKSTVLKSTIAFLKNHNEATD 66
Cdd:cd11441    1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIAFLRKHKELTA 54

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).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24660399    261 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 339
Cdd:pfam14598    2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                           90       100
                   ....*....|....*....|....*
gi 24660399    340 TDYYVSYHQFNSKPDYVVCTHKVVS 364
Cdd:pfam14598   82 TKSKLFLNQNSNQQPFIMCTHTILR 106

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 24660399    273 FLFLDHRAPPIIGYMPFEVLGT--SGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQtDYYVSYHQFN 350
Cdd:pfam08447    1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVE-ARARPIRDEN 79

                           90
                   ....*....|
gi 24660399    351 SKPDYVVCTH 360
Cdd:pfam08447   80 GKPVRVIGVA 89

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 24660399  260 SNEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 339
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|...
gi 24660399  340 TDYYVSYHQFNSKPDYVVCTHKV 362
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVVRDI 103

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        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24660399   20 EKKRRDQFNSLVNDLSALI---STSSRKMDKSTVLKSTIAFLKNHNEATD 66
Cdd:cd11437    9 EKRRRDKMNAYIQELSALVpacNAMSRKLDKLTVLRMAVQHLKSLRGTGS 58

Helix-loop-helix DNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 24660399     12 KRKSRNLSEKKRRDQFNSLVNDLSALI--STSSRKMDKSTVLKSTIAFLK 59
Cdd:pfam00010    1 RREAHNERERRRRDRINDAFDELRELLptLPPDKKLSKAEILRLAIEYIK 50

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 24660399   20 EKKRRDQFNSLVNDLSALI---STSSRKMDKSTVLKSTIAFLK 59
Cdd:cd19726    9 EKRRRDKMNTYITELSSMIpmcNAMSRKLDKLTVLRMAVQHMK 51

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 24660399   20 EKKRRDQFNSLVNDLSALIST--SSRKMDKSTVLKSTIAFLKN 60
Cdd:cd00083    1 ERRRRDKINDAFEELKRLLPElpDSKKLSKASILQKAVEYIRE 43

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 24660399   20 EKKRRDQFNSLVNDLSALI-----STSSRKMDKSTVLKSTIAFLK 59
Cdd:cd11389    5 EKRRRDRINESLAELRRLVpearkSKGSGKLEKAEILEMTLQHLK 49

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif-like protein (HEYL) and similar proteins; HEYL, also termed Class B basic helix-loop-helix protein 33 (bHLHb33), or hairy-related transcription factor 3 (HRT-3), is a bHLH-O transcriptional repressor that is strongly expressed in the presomitic mesoderm, the somites, the peripheral nervous system and smooth muscle of all arteries and is a downstream effector of the Notch and transforming growth factor-beta pathways. It promotes neuronal differentiation by activating proneural genes and inhibiting other hairy and enhancer of split (HES) and hairy/enhancer-of-split related with YRPW motif protein (HEY) proteins. HEYL also functions as a tumor suppressor involved in the progression of human cancers.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALISTS-----SRKMDKSTVLKSTIAFLK 59
Cdd:cd11447    9 RKKRRGIIEKRRRDRINSSLSELRRLVPTAfekqgSSKLEKAEILQMTVDHLK 61

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 24660399      89 HLMLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMN 149
Cdd:smart00091    4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24660399   15 SRNLSEKKRRDQFNSLVNDLS-----ALISTSSRKMDKSTVLKSTIAFLK 59
Cdd:cd11408    1 SHKVIEKRRRDRINRCLNELGktvpmALAKQTSGKLEKAEILEMTVQYLR 50

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALI-STSSRKMDKSTVLKSTIAFLK 59
Cdd:cd11404    2 RRLNHVRSEKKRRELIKKGYDELCALVpGLDPQKRTKADILQKAADWIQ 50

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 24660399   17 NLSEKKRRDQFNSLVNDLSALISTSSrKMDKSTVLKSTIAFLKN 60
Cdd:cd11445    7 NLSERRRRDRINEKMKALQELIPNCN-KTDKASMLDEAIEYLKS 49

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins; MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALISTSS---RKMDKSTVLKSTIAFLKNHNEATDRSKVFEIQQ 75
Cdd:cd18926   13 KKDNHNLIERRRRFNINDRIKELGTLIPKSNdpdMRWNKGTILKASVDYIRKLQREQQRAKELENRQ 79

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator (SRC) family; The SRC family of coactivators includes SRC-1 (NcoA-1/p160), SRC-2(TIF2/GRIP1/NcoA-2) and SRC-3(NcoA-3/pCIP/RAC3/ACTR/pCIP/AIB1/TRAM1), which are critical mediators of steroid receptor action. They contain bHLH-PAS domain at the N-terminal that is followed by receptor interacting domain and C-terminal transcriptional activation domain. SRC coactivators interact with nuclear receptors in a ligand-dependent manner and enhance transcriptional activation by the receptor via histone acetylation/methylation.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 24660399   15 SRNLSEKKRRDQFNSLVNDLSALISTS-------SRKMDKSTVLKSTI 55
Cdd:cd11439    1 NKCLNEKRRREQENKYIEELAELISASisdmdslSVKPDKCAILQETV 48

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 2 (HEY2) and similar proteins; HEY2, also termed cardiovascular helix-loop-helix factor 1 (CHF-1), or Class B basic helix-loop-helix protein 32 (bHLHb32), or HES-related repressor protein 2, or hairy and enhancer of split-related protein 2 (HESR-2), or hairy-related transcription factor 2 (HRT-2), or protein gridlock homolog, is a bHLH-O transcriptional repressor expressed preferentially in the developing and adult cardiovascular system. As a downstream effector of Notch signaling, HEY2 may be required for cardiovascular development. It also plays an important role in neurologic development, as well as in the progression of human cancers.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALISTS-----SRKMDKSTVLKSTIAFLK 59
Cdd:cd18920   10 RKKRRGIIEKRRRDRINNSLSELRRLVPTAfekqgSAKLEKAEILQMTVDHLK 62

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
                 ....*....|....*....|....*....|....*....|....*...
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALISTSSRKMDKSTVLKSTIAFLK 59
Cdd:cd19683    2 SRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDKATVFEFTVAYIK 49

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 24660399   13 RKSRNLSEKKRRDQFNSLVNDLSALISTSSR-KMDKSTVLKSTIA 56
Cdd:cd19682    1 RLRHKKRERERRSELRELFDKLKQLLGLDSDeKASKLAVLTEAIE 45

basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family; 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24660399   14 KSRNLSEKKRRDQFNSLVNDLSALI-STSSRKMDKSTVLKSTIAFLK 59
Cdd:cd18908    4 SSHSLKERLRRERIKSSCDQLRDLLpYIKGRKLDMASVLEMTVKYIR 50

basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-5 and similar proteins; HES-5, also termed Class B basic helix-loop-helix protein 38 (bHLHb38), or hairy and enhancer of split 5, is a bHLH-O transcription factor that is involved in cell differentiation and proliferation in a variety of tissues. HES-5 is an essential effector for Notch signaling. It acts as a transducer of Notch signals in brain vascular development. It also acts as a key mediator of Wnt-3a-induced neuronal differentiation and plays a crucial role in normal inner ear hair cell development. HES-5 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24660399   20 EKKRRDQFNSLVNDLSALISTS------SRKMDKSTVLKSTIAFLKNHNEAT 65
Cdd:cd11461    8 EKTRRDRINSSIEQLKTLLEKEfqrhqpNSKLEKADILEMTVSFLKQSAKLS 59

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        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24660399   12 KRKSRNLSEKKRRDQFNSLVNDLSALISTSS---RKMDKSTVLKSTIAFLK 59
Cdd:cd18947    5 ARENHSEIERRRRNKMTAYITELSDMVPTCSalaRKPDKLTILRMAVSHMK 55