basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42573704  50 SSPASKNIVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELESTPKSSLSFS 125
Cdd:cd11450   1 SSPASKNLVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPSTLSFQ 76

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42573704  50 SSPASKNIVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELESTPKSSLSFS 125
Cdd:cd11450   1 SSPASKNLVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPSTLSFQ 76

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 42573704    53 ASKNIVsERNRRQKLNQRLFALRSVVPNI---TKMDKASIIKDAISYIEGLQ 101
Cdd:pfam00010   3 EAHNER-ERRRRDRINDAFDELRELLPTLppdKKLSKAEILRLAIEYIKHLQ 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42573704  50 SSPASKNIVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELESTPKSSLSFS 125
Cdd:cd11450   1 SSPASKNLVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPSTLSFQ 76

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein ABA-INDUCIBLE bHLH-TYPE (AIB) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AIB and MYC proteins (MYC2, MYC3 and MYC4). AIB, also termed AtbHLH17, or EN 35, is a transcription activator that regulates positively abscisic acid (ABA) response. MYC2, also termed protein jasmonate insensitive 1, or R-homologous Arabidopsis protein 1 (RAP-1), or AtbHLH6, or EN 38, or Z-box binding factor 1 protein, is a transcriptional activator involved in abscisic acid (ABA), jasmonic acid (JA), and light signaling pathways. MYC3, also termed protein altered tryptophan regulation 2, or AtbHLH5, or transcription factor ATR2, or EN 36, is a transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. MYC4, also termed AtbHLH4, or EN 37, is a transcription factor involved in jasmonic acid (JA) gene regulation. MYC2, together with MYC3 and MYC4, controls additively subsets of JA-dependent responses.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELE 115
Cdd:cd11449  13 ERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAISYINELKSKVQDMETEKKEMK 68

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573704  57 IVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIeglqyeeKKLEAEIRELESTPKSSLSFSK 126
Cdd:cd11451   7 AMAERRRREKLNERFITLRSMVPFVTKMDKVSILGDAIEYL-------KQLQRRVEELESRRKSSDTETR 69

basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 42573704  58 VSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIeglqyeeKKLEAEIRELES 116
Cdd:cd18918   3 ATERERREKLNEKFSDLRNLIPNPTKNDRASILSDAIKYI-------NELQRTVEELKS 54

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like proteins (BIMs) and similar proteins; The family includes Arabidopsis thaliana BIM1 and its homologs (BIM2 and BIM3), which are bHLH transcription factors that interact with BES1 to regulate transcription of Brassinosteroid (BR)-induced gene. BR regulates many growth and developmental processes such as cell elongation, vascular development, senescence stress responses, and photomorphogenesis. BIM1 heterodimerize with BES1 and bind to E-box sequences present in many BR-induced promoters to regulated BR-induced genes.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573704  50 SSPASKNIVSERNRRQKLNQRLFALRSVVPNITKM-DKASIIKDAISYIEGLQYEEKKLEAEIRELESTP 118
Cdd:cd11453   1 STPRSKHSATEQRRRSKINERLQALRDLIPHSDQKrDKASFLLEVIEYIQALQEKVAKLEEQVQGWGGEP 70

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 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGLQ 101
Cdd:cd00083   1 ERRRRDKINDAFEELKRLLPELPdskKLSKASILQKAVEYIRELQ 45

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the Myc family; The Myc family is a member of the bHLHzip family of transcription factors that play important roles in the control of normal cell proliferation, growth, survival and differentiation. All Myc isoforms contain two independently functioning polypeptide chain regions: N-terminal transactivating residues and a C-terminal bHLHzip segment. The bHLHzip family of bHLH transcription factors are characterized by a highly conserved N-terminal basic region that may bind DNA at a consensus hexanucleotide sequence known as the E-box (CANNTG) followed by HLH and leucine zipper motifs that may interact with other proteins to form homo- and heterodimers. Myc heterodimerizes with Max enabling specific binding to E-box DNA sequences in the promoters of target genes. The Myc proto-oncoprotein family includes at least five different functional members: c-, N-, L-, S- and B-Myc (which is lacking the bHLH domain).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNITKMDKAS---IIKDAISYIEGLQYEEKKLEAEIREL 114
Cdd:cd11400   9 ERQRRNDLKNSFEKLRDLVPELADNEKASkvvILKKATEYIKQLQQEEKKLEKEKDKL 66

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein FAMA and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as FAMA, MUTE and SPEECHLESS, which work together to regulate the sequential cell fate specification during stomatal development and differentiation. FAMA, also termed AtbHLH97, or EN 14, is a transcription activator required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. It mediates the formation of stomata. MUTE, also termed AtbHLH45, or EN 20, is required for the differentiation of stomatal guard cells, by promoting successive asymmetric cell divisions and the formation of guard mother cells. It promotes the conversion of the leaf epidermis into stomata. SPEECHLESS, also termed AtbHLH98, or EN 19, is required for the initiation and the formation of stomata, by promoting the first asymmetric cell divisions. FAMA, MUTE and SPEECHLESS form heterodimers with SCREAM/ICE1 and SCRM2 to regulate transcription of genes during stomatal development.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 42573704  57 IVSERNRRQKLNQRLFALRSVVPN--ITKMDKASIIKDAISYIEGLQYEEKKLEAEIR 112
Cdd:cd11448   4 IAVERNRRKQMNEHLNVLRSLMPGsyIQRGDQASIVGGAIEFVKELEQLLQSLEAQKR 61

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42573704  57 IVSERNRRQKLNQRLFALRSVV--PNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELE 115
Cdd:cd19682   5 KKRERERRSELRELFDKLKQLLglDSDEKASKLAVLTEAIEEIQQLKREEDELQKEKARLT 65

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 42573704  60 ERNRRQKLNQRLFALRS-VVPNITKMDKASIIKDAISYIEGLQYEEKKLEAEIRELEST 117
Cdd:cd11394  14 EKRYRSSINDRIIELKDlVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKKA 72

tissue specific basic helix-loop-helix (bHLH-TS) domain family; Tissue specific bHLH domain family includes transcription regulators whose expression are restricted to certain tissues. They are involved in cell-fate determination and process in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis and include proteins from myogenic regulatory factor (MRF) family, twist-related protein (TWIST) family, scleraxis-like family, heart- and neural crest derivatives-expressed protein (HAND) family, helix-loop-helix protein (HEN) family, musculin-like family, germline alpha (FIGLA) family, T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family, ovary, uterus and testis protein (OUT) family, mesoderm posterior protein (Mesp) family, muscle, intestine and stomach expression 1 (MIST-1) family, protein atonal homologs (ATOH) family, neurogenin (NGN) family, neurogenic differentiation factor (NeuroD) family, achaete-scute complex-like (ASCL) family, Fer3-like protein (FERD3L)-like family, and Oligodendrocyte lineage genes (OLIG) family of transcription factors.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNI---TKMDKASIIKDAISYIEGLQ 101
Cdd:cd11390   8 ERRRMHDLNDAFEALRKVLPTVppdKKLSKIETLRLAINYIAALS 52

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42573704  57 IVSERNRRQKLNQRLFALRSVVPNIT--KMDKASIIKDAISYIEGLQYEEKKLEAEIRELE 115
Cdd:cd11404   7 VRSEKKRRELIKKGYDELCALVPGLDpqKRTKADILQKAADWIQELKEENEKLEEQLDELK 67

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNI-TKMDKASIIKDAISYIEGLQYEEKKLEAEIRELEST 117
Cdd:cd11398  15 ERRRRENINEGINELAALVPGNaREKNKGAILARAVEYIQELQETEAKNIEKWTLEKLL 73

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in L-Myc and similar proteins; L-Myc, also termed Class E basic helix-loop-helix protein 38 (bHLHe38), or protein L-Myc-1, or V-myc myelocytomatosis viral oncogene homolog, is a bHLHZip oncoprotein belonging to the Myc oncogene protein family. It binds DNA as a heterodimer with MAX. L-Myc is co-expressed with another Myc family member and has weaker transformation/transactivation activities. L-Myc knockout mouse did not exhibit any phenotypic abnormalities.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNI---TKMDKASIIKDAISYIEGLQYEEKKLEAEIRELES 116
Cdd:cd11457  15 ERKRRNDLRSRFLALRDEVPGLascSKTPKVVILSKATEYLRGLVSAERRMAAEKRQLKS 74

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster achaete-scute complex (AS-C) proteins, achaete-scute-like proteins, ASCL1-2, and similar proteins; This subfamily includes Drosophila melanogaster AS-C proteins and two ASCL family of transcription factors, ASCL-1 and ASCL-2. Drosophila melanogaster AS-C proteins includes lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete scute homolog 1 (Mash1), is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete scute homolog 2 (Mash2), is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGLQ 101
Cdd:cd19723   9 ERNRVKLVNLGFATLREHVPNGRankKMSKVETLRSAVEYIRQLQ 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect embryo arrest 8 (AtMEE8) and similar proteins; AtMEE8, also termed AtbHLH108, or EN 132, is a bHLH transcription factor required during early embryo development, for the endosperm formation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 42573704  59 SERNRRQKLNQRLFALRSVVPNIT-KMDKASIIKDAISYIEGLQYEEKKLEAEI 111
Cdd:cd19698   4 LEKKRRERIKDKIEILKGLTPNCTpKSDIASILSCVIDYIKSLLLQVEKLSMGI 57

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor AP-4 (TFAP4) and similar proteins; TFAP4, also termed activating enhancer-binding protein 4, or Class C basic helix-loop-helix protein 41 (bHLHc41), is a bHLHzip transcription factor that activates both viral and cellular genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition by binding to the symmetrical DNA sequence 5'-CAGCTG-3'.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT--KMDKASIIKDAISYIEGLQYEEKKL 107
Cdd:cd11419  12 ERRRMQSINAGFQSLRTLLPHCDgeKLSKAAILQQTAEYIFSLEQEKTRL 61

basic helix-loop-helix (bHLH) domain found in factor in the germline alpha (FIGLA) and similar proteins; FIGLA, also termed FIGalpha, or Class C basic helix-loop-helix protein 8 (bHLHc8), or folliculogenesis-specific basic helix-loop-helix protein, or transcription factor FIGa, is a germ-cell-specific bHLH transcription factor expressed abundantly in female and less so in male germ cells. It is essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. FIGLA knockout mice cannot form primordial follicles and lose oocytes rapidly after birth, whereas male gonads are unaffected.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGLQY 102
Cdd:cd11422   8 ERERVRNLNSGFSKLRRIVPLIPrdrKPSKVDTLKGATEYIRLLQR 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 42573704  60 ERNRRQKLNQRLFALRSVVPNIT----KMDKASIIKDAISYIEGLQYEE---KKLEAEIRELESTPKS 120
Cdd:cd18928  19 ERRRRFNINDRIKELGTLIPKSTdpemRWNKGTILKASVDYIRKLQKEQqrsKEIEMRQRKLEQANRS 86

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster Enhancer of split proteins, E(spl)m5, E(spl)m8 and similar proteins; The family includes two bHLH-O transcriptional repressors, E(spl)m5 and E(spl)m8, which participate in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo. They bind DNA on N-box motifs, 5'-CACNAG-3'.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 42573704  54 SKNIVSERNRRQKLNQRLFALRSVV------PNITKMDKASIIKDAISYI 97
Cdd:cd18916   2 SKKPMLERQRRARINKCLSELKTLVaecsgdDGCLRMDKAEMLETAVAFM 51

basic helix-loop-helix (bHLH) domain found in achaete-scute complex-like (ASCL) family; The achaete-scute complex-like (ASCL, also known as achaete-scute complex homolog or ASH) family of bHLH transcription factors, ASCL1-5, have been implicated in cell fate specification and differentiation. They are critical for proper development of the nervous system. The deregulation of ASCL plays a key role in psychiatric and neurological disorders. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete-scute homolog 1 (Mash1), is a neural-specific bHLH transcription factor that is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete-scute homolog 2 (Mash2), is a bHLH transcription factor that is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is a bHLH transcription factor specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. The family also includes Drosophila melanogaster achaete-scute complex (AS-C) proteins, which consists of lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGLQ 101
Cdd:cd11418   9 ERRRVQAVNDAFDRLRQHVPYLKrrkKLSKVKTLRRAIEYIRHLQ 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins; 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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42573704  58 VSERNRRQKLNQRLFALRSVVPNIT--------KMDKASIIKDAISYIEGLQYEEKKLEAEIRELE 115
Cdd:cd19687   8 QAEQKRRDAIKKGYDDLQDIVPTCQqqddigsqKLSKATILQRSIDYIQFLHQQKKKQEEELSALR 73

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNITKMD----KASIIKDAISYIEGLQYEE---KKLEAEIRELESTPKSSL 122
Cdd:cd18926  21 ERRRRFNINDRIKELGTLIPKSNDPDmrwnKGTILKASVDYIRKLQREQqraKELENRQKKLEHANRHLL 90

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana OBP3-responsive gene 2 (ORG2), 3 (ORG3) and similar proteins; The family includes ORG2 (also termed AtbHLH38, or EN 8) and ORG3 (also termed AtbHLH39, or EN 9), both of which act as bHLH transcription factors.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 42573704  59 SERNRRQKLNQRLFALRSVVPNITKMDKASI---IKDAISYIEGLQYEEKKLEAEIREL 114
Cdd:cd18914   8 VERQRRQEMASLFSSLRSLLPLQYIKGKLSVsdhVDEAVNYIKELQEKIKELSEKRDEL 66

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42573704  61 RNRRQKLNQRLFALRSVVP---NIT-KMDKASIIKDAISYIEGLQYEEKKLEAEIRELESTPKSS 121
Cdd:cd19733  14 RSRRGKENYEFYELAKMLPlpaAITsQLDKASIIRLTISYLKLRDFSGHGDPPWNRESLSSPPST 78

basic helix-loop-helix (bHLH) domain found in neurogenin (NGN) family; The NGN family includes three neural-specific bHLH transcription factors, NGN1-3, which may function at neuroblast selection genes during the development of several neuronal lineages. NGN-1, also termed Class A basic helix-loop-helix protein 6 (bHLHa6), or neurogenic basic-helix-loop-helix protein, or neurogenic differentiation factor 3 (NeuroD3), is a neural-specific bHLH transcription factor involved in the initiation of neuronal differentiation. NGN-2, also termed Class A basic helix-loop-helix protein 8 (bHLHa8), or protein atonal homolog 4 (ATOH4), is a neural-specific bHLH transcription factor required for sensory neurogenesis. NGN-3, also termed Class A basic helix-loop-helix protein 7 (bHLHa7), or protein atonal homolog 5 (ATOH5), is a neural-specific bHLH transcription factor expressed in the developing central nervous system and the embryonic pancreas. It is involved in neurogenesis and plays an important role in spermatogenesis.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNI---TKMDKASIIKDAISYIEGL 100
Cdd:cd11428   9 ERNRMHNLNDALDALREVLPSFpdeTKLTKIETLRFAHNYIWAL 52

basic helix-loop-helix (bHLH) domain found in protein atonal homolog 7 (ATOH7) and similar proteins; ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGL 100
Cdd:cd19714  16 ERRRMQGLNTAFDRLRKVVPQWGqdkKLSKYETLQMALSYIMAL 59

basic helix-loop-helix (bHLH) domain found in protein atonal homologs ATOH1, ATOH7 and similar proteins; The family includes ATOH1 and ATOH7. ATOH1, also termed Class A basic helix-loop-helix protein 14 (bHLHa14), or helix-loop-helix protein hATH-1 (hATH1), or Math1, or Cath1, is a proneural bHLH transcription factor that is essential for inner ear hair cell differentiation. It dimerizes with E47 and activates E-box (CANNTG) dependent transcription. ATOH1 is a mammalian homolog of the Drosophila melanogaster gene atonal and mouse atonal homolog 1 (Math1). ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells. The family also includes protein Amos (also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein). It is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT---KMDKASIIKDAISYIEGLQ 101
Cdd:cd11430   9 ERRRMNGLNRAFDQLRSVVPSIGndkKLSKYETLQMAQIYIETLS 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins; Max, also termed Class D basic helix-loop-helix protein 4 (bHLHd4), or Myc-associated factor X, is a bHLHZip transcription regulator that forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5'-CAC[GA]TG-3'. The MYC:MAX complex is a transcriptional activator, whereas the MAD:MAX complex is a transcriptional repressor. Max homodimer bind DNA but is transcriptionally inactive. Targeted deletion of max results in early embryonic lethality in mice.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNIT--KMDKASIIKDAISYIEGLQYEEKKLEAEIREL 114
Cdd:cd11406   9 ERKRRDHIKDSFHSLRDSVPSLQgeKASRAQILKKATEYIQYMRRKNHTHQQDIDDL 65

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and similar proteins; TFEC, also termed Class E basic helix-loop-helix protein 34 (bHLHe34), or transcription factor EC-like (TFEC-L), is a bHLHzip transcriptional regulator that acts as a repressor or an activator and regulates gene expression in macrophages. It plays an important role in the niche to expand hematopoietic progenitors through the modulation of several cytokines.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42573704  60 ERNRRQKLNQRLFALRSVVPNITKMD----KASIIKDAISYIEGLQYEEKKleaeIRELESTPK 119
Cdd:cd18925  13 ERRRRYNINYRIKELGTLIPKSNDPDmrwnKGTILKASVEYIKWLQKEQQR----ARELEHRQK 72