basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063682291 166 SKNLHSERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDELKGINEMECKEIAAE 237
Cdd:cd11443     1 SKNLMAERRRRKKLNDRLYMLRSVVPKITKMDRASILGDAIDYVKELLQEINELQDELEGLPESESGETLSQ 72

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063682291 166 SKNLHSERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDELKGINEMECKEIAAE 237
Cdd:cd11443     1 SKNLMAERRRRKKLNDRLYMLRSVVPKITKMDRASILGDAIDYVKELLQEINELQDELEGLPESESGETLSQ 72

bHLH-MYC and R2R3-MYB transcription factors N-terminal; This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063682291   6 GIHGEVVMSKSPKWLVNSGS----------KMEMFSTRVLVPVSDGLVELFAFDMRPFDESMVHLIMS 63
Cdd:pfam14215  52 GLPGKAFASGKHIWLTGADEldycsrsllaKSAGIQTIVCIPVPGGVLELGSTELVPEDLELVQHIKS 119

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063682291 166 SKNLHSERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDELKGINEMECKEIAAE 237
Cdd:cd11443     1 SKNLMAERRRRKKLNDRLYMLRSVVPKITKMDRASILGDAIDYVKELLQEINELQDELEGLPESESGETLSQ 72

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 1063682291 172 ERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDELKGI 226
Cdd:cd11449    13 ERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAISYINELKSKVQDMETEKKEM 67

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1063682291  171 SERKRRERINQAMYGLRAVVP---KITKLNKIGIFSDAVDYINELLVEKQK 218
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPtlpKNKKLSKAEILRLAIEYIKSLQEELQK 53

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 1063682291 172 ERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDEL 223
Cdd:cd18918     5 ERERREKLNEKFSDLRNLIPNPTKNDRASILSDAIKYINELQRTVEELKSLV 56

bHLH-MYC and R2R3-MYB transcription factors N-terminal; This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063682291   6 GIHGEVVMSKSPKWLVNSGS----------KMEMFSTRVLVPVSDGLVELFAFDMRPFDESMVHLIMS 63
Cdd:pfam14215  52 GLPGKAFASGKHIWLTGADEldycsrsllaKSAGIQTIVCIPVPGGVLELGSTELVPEDLELVQHIKS 119

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
                  ....*....|....*....|....*....|....*....|..
gi 1063682291 171 SERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINEL 212
Cdd:cd11455    14 AERRRRERINSHLATLRTLLPNLSKTDKASLLAEVVQHVKEL 55

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein NAI1 and similar proteins; NAI1, also termed AtbHLH20, or EN 27, is a bHLH transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1. It is required for and mediates the formation of endoplasmic reticulum bodies (ER bodies). It plays a role in the symbiotic interactions with the endophytes of the Sebacinaceae fungus family, such as Piriformospora indica and Sebacina.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063682291 171 SERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINELLVEKQKLEDELKGINEME 230
Cdd:cd11452     9 AERKRREKLSQRFIALSALVPGLKKMDKASVLGDAIKHIKQLQERVKELEEEKKEKRLMS 68

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 1063682291 171 SERKRRERINQAMYGLRAVVPKITKLNKIGIFSDAVDYINEL 212
Cdd:cd11445     9 SERRRRDRINEKMKALQELIPNCNKTDKASMLDEAIEYLKSL 50

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 1063682291 172 ERKRRERINQAMYGLRAVVPKIT--KLNKIGIFSDAVDYINELLVEKQKL 219
Cdd:cd11419    12 ERRRMQSINAGFQSLRTLLPHCDgeKLSKAAILQQTAEYIFSLEQEKTRL 61

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063682291 164 FKSKNLHSERKRRERINQAMYGLRAVVPK-ITKLNKIGIFSDAVDYInELLVEK-QKLEDELKGIN 227
Cdd:cd11453     3 PRSKHSATEQRRRSKINERLQALRDLIPHsDQKRDKASFLLEVIEYI-QALQEKvAKLEEQVQGWG 67

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 1063682291 172 ERKRRERINQAMYGLRAVVPKI---TKLNKIGIFSDAVDYINEL 212
Cdd:cd11390     8 ERRRMHDLNDAFEALRKVLPTVppdKKLSKIETLRLAINYIAAL 51

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins; USF1, also termed Class B basic helix-loop-helix protein 11 (bHLHb11), or major late transcription factor 1, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters. It is ubiquitously expressed and involved in the transcription activation of various functional genes implicated in lipid and glucose metabolism, stress response, immune response, cell cycle control and tumour suppression. USF-1 recruits chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. Genetic polymorphisms of USF1 are associated with some metabolic and cardiovascular diseases, like diabetes, atherosclerosis, coronary artery calcifications and familial combined hyperlipidaemia (FCHL).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063682291 172 ERKRRERINQAMYGLRAVVPKITKLN------KIGIFSDAVDYINEL 212
Cdd:cd18924    13 ERRRRDKINNWIVQLSKIIPDCSMEStksgqsKGGILSKACDYIQEL 59

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 1063682291 172 ERKRRERINQAMYGLRA-VVPKITKLNKIGIFSDAVDYINELLVEKQKLEDEL 223
Cdd:cd11394    14 EKRYRSSINDRIIELKDlVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQEN 66

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 1063682291 165 KSKNLHS--ERKRRERINQAMYGLRAVVPKIT-KLNKIGIFSDAVDYI 209
Cdd:cd19683     1 KSRERHNakERQRRERIKIACDQLRKLVPGCSrKTDKATVFEFTVAYI 48

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 1063682291 171 SERKRRERINQAMYGLRAVVP--KITKLNKIGIFSDAVDYINELLVEKQKLEDELK 224
Cdd:cd19690     7 AERKRRKEMKELFEDLRDALPqeRGTKASKWEILTKAISYIQQLKRHIRELRSEVN 62

basic helix-loop-helix (bHLH) domain found in heart- and neural crest derivatives-expressed protein (HAND) family; The HAND family includes two bHLH transcription factors, HAND1 and HAND2. HAND1, also termed Class A basic helix-loop-helix protein 27 (bHLHa27), or extraembryonic tissues, heart, autonomic nervous system and neural crest derivatives-expressed protein 1 (eHAND), plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. HAND2, also termed Class A basic helix-loop-helix protein 26 (bHLHa26), or deciduum, heart, autonomic nervous system and neural crest derivatives-expressed protein 2 (dHAND), is essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063682291 172 ERKRRERINQAMYGLRAVVPKI---TKLNKIGIFSDAVDYINELL 213
Cdd:cd11466     9 ERRRTQSINSAFADLRECIPNVpadTKLSKIKTLRLATSYIAYLM 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family 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 family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063682291 172 ERKRRERINQAMYGLRAVVPKIT----KLNKIGIFSDAVDYINELLVEKQKLED 221
Cdd:cd11397    13 ERRRRFNINDRIKELGTLLPKSNdpdmRWNKGTILKASVDYIRKLQKEQERLRQ 66

basic helix-loop-helix (bHLH) domain found in pancreas transcription factor 1 subunit alpha (PTF1A) and similar proteins; PTF1A, also termed Class A basic helix-loop-helix protein 29 (bHLHa29), or pancreas-specific transcription factor 1a, or bHLH transcription factor p48, or p48 DNA-binding subunit of transcription factor PTF1 (PTF1-p48), is a bHLH transcription factor implicated in the cell fate determination in various organs. It binds to the E-box consensus sequence 5'-CANNTG-3' and plays a role in early and late pancreas development and differentiation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063682291 172 ERKRRERINQAMYGLRAVVPKI---TKLNKIGIFSDAVDYINEL 212
Cdd:cd11417     9 ERRRMQSINDAFEGLRSHIPTLpyeKRLSKVDTLRLAIGYINFL 52