Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 75311390    75 KRAKHKELERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQ 127
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPTLPPDKKLSKAEILRLAIEYIKHLQ 53

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 75311390    75 KRAKHKELERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQ 127
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPTLPPDKKLSKAEILRLAIEYIKHLQ 53

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75311390  67 KGDDEPKNkrakHKELERQRRQENTSLFKILRYLLPSQyikGKRSSADHVLEAVNYIKDLQKKIKEVSEKRDRIKRSITH 146
Cdd:cd11449   1 NGREEPLN----HVEAERQRREKLNQRFYALRAVVPNV---SKMDKASLLGDAISYINELKSKVQDMETEKKEMKRQESE 73

                ....*
gi 75311390 147 PSSRG 151
Cdd:cd11449  74 KKTEA 78

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        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 75311390  79 HKELERQRRQENTSLFKILRYLLPSQyikGKRSSADHVLEAVNYIKDLQKKIKEVS 134
Cdd:cd11393   1 HSIAERKRREKINERIRALRSLVPNG---GKTDKASILDEAIEYIKFLQEQVKVLS 53

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        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 75311390  74 NKRAKHKELERQRRQENTSLFKILRYLLPsqYIKGKRSSADHVLEA-VNYIKDLQKKI 130
Cdd:cd18908   1 SDASSHSLKERLRRERIKSSCDQLRDLLP--YIKGRKLDMASVLEMtVKYIRYIQERI 56

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
                ....*....|....*....|....*....|....*....|....*....|....*
gi 75311390  76 RAKHKELERQRRQENTSLFKILRYLLPSQyiKGKRSSADHVLEAVNYIKDLQKKI 130
Cdd:cd11453   4 RSKHSATEQRRRSKINERLQALRDLIPHS--DQKRDKASFLLEVIEYIQALQEKV 56

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins; 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
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 75311390  76 RAKHKELERQRRQENTSLFKILRYLLPSQyiKGKRSSADHVL-EAVNYIKDLQKKIKE 132
Cdd:cd19690   1 RVSHKLAERKRRKEMKELFEDLRDALPQE--RGTKASKWEILtKAISYIQQLKRHIRE 56

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        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 75311390  79 HKELERQRRQENTSLFKILRYLLPSQYIKgKRSSADHVLEAVNYIKDLQKKIKEV-SEKRDRIKRSITHPSS 149
Cdd:cd11448   3 HIAVERNRRKQMNEHLNVLRSLMPGSYIQ-RGDQASIVGGAIEFVKELEQLLQSLeAQKRRRTLNESSVPSS 73

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana paclobutrazol resistance (PRE) family; The PRE family includes several bHLH transcription factors from Arabidopsis thaliana, such as PRE1-6. PRE1 (also termed AtbHLH136, or protein banquo 1), PRE2 (also termed AtbHLH134, or protein banquo 2, or EN 52), PRE4 (also termed AtbHLH161, or protein banquo 3), and PRE5 (also termed AtbHLH164) are atypical and probable non DNA-binding bHLH transcription factors that integrate multiple signaling pathways to regulate cell elongation and plant development. PRE3 (also termed AtbHLH135, or protein activation-tagged BRI1 suppressor 1, or ATBS1, or protein target of MOOPTEROS 7, or EN 67) is an atypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. It promotes the correct definition of the hypophysis cell division plane. PRE5 (also termed AtbHLH163, or protein KIDARI) is an atypical and probable non DNA-binding bHLH transcription factor that regulates light-mediated responses in day light conditions by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 75311390  97 LRYLLPSQYIKGKRSSADHVLEAVNYIKDLQKKIKEVSEKRDRIKRS 143
Cdd:cd11442  19 LRALLPSIATSDKVSKATVLEEACNYIRNLHREVDDLSERLSRLLTS 65

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 75311390  83 ERQRRQENTSLFKILRYLLPSQYIKGKRSSADHVLEAVNYIKDLQK 128
Cdd:cd00083   1 ERRRRDKINDAFEELKRLLPELPDSKKLSKASILQKAVEYIRELQS 46