MITF/TFEB/TFEC/TFE3 N-terminus; This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681   78 RVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVIGVSAgghtlSRPPPAQVPREVLKVQTHLENPTRYHLQ 157
Cdd:pfam15951   1 RILLRQQLMREQAQQEEQREQQQQQQNHQYMQPAPPPSSTPAISVPQ-----SPPSPAQVPVEVLKVQTHLENPTKYHIQ 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564398681  158 QARRQQVKQYLSTTLGPKLASQALTPPPGPSSAQPLPAPETA--HATGPTGSAPNSPMALLTIGSSSEKEIDDVID 231
Cdd:pfam15951  76 QAQRQQVKQYLSTTYGAKQALIPSASPPPPAQSPPPRTSPLMrgNQLPPGNSAPNSPMAMLSIGSSEEKEIDDVID 151

MITF/TFEB/TFEC/TFE3 N-terminus; This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681   78 RVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVIGVSAgghtlSRPPPAQVPREVLKVQTHLENPTRYHLQ 157
Cdd:pfam15951   1 RILLRQQLMREQAQQEEQREQQQQQQNHQYMQPAPPPSSTPAISVPQ-----SPPSPAQVPVEVLKVQTHLENPTKYHIQ 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564398681  158 QARRQQVKQYLSTTLGPKLASQALTPPPGPSSAQPLPAPETA--HATGPTGSAPNSPMALLTIGSSSEKEIDDVID 231
Cdd:pfam15951  76 QAQRQQVKQYLSTTYGAKQALIPSASPPPPAQSPPPRTSPLMrgNQLPPGNSAPNSPMAMLSIGSSEEKEIDDVID 151

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 564398681   317 NLIERRRRFNINDRIKELGTLIPKSNDPEmRWNKGTILKASVDYIRKLQKEQQ 369
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLPKNK-KLSKAEILRLAIEYIKSLQEELQ 52

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 300 ETEAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQR 379
Cdd:cd18926    1 ESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKELENRQK 80

                         90       100
                 ....*....|....*....|....
gi 564398681 380 SLEQANRSLQLRIQELELQAQIHG 403
Cdd:cd18926   81 KLEHANRHLLLRIQELEMQARAHG 104

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins; TFEB, also termed Class E basic helix-loop-helix protein 35 (bHLHe35), is a bHLHzip transcription factor that is required for vascularization of the mouse placenta. 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 TFE3 or MITF.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 302 EAKALLKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSL 381
Cdd:cd18927    1 EARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKTNDLDVRWNKGTILKASVDYIKRMQKDLQRSRELENHSRRL 80

                         90
                 ....*....|.
gi 564398681 382 EQANRSLQLRI 392
Cdd:cd18927   81 EMTNKQLWLRI 91

MITF/TFEB/TFEC/TFE3 N-terminus; This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681   78 RVLLRQQLMRAQAQEQERRERREQAAAAPFPSPAPASPAISVIGVSAgghtlSRPPPAQVPREVLKVQTHLENPTRYHLQ 157
Cdd:pfam15951   1 RILLRQQLMREQAQQEEQREQQQQQQNHQYMQPAPPPSSTPAISVPQ-----SPPSPAQVPVEVLKVQTHLENPTKYHIQ 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564398681  158 QARRQQVKQYLSTTLGPKLASQALTPPPGPSSAQPLPAPETA--HATGPTGSAPNSPMALLTIGSSSEKEIDDVID 231
Cdd:pfam15951  76 QAQRQQVKQYLSTTYGAKQALIPSASPPPPAQSPPPRTSPLMrgNQLPPGNSAPNSPMAMLSIGSSEEKEIDDVID 151

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPkSNDPEMrwNKGTILKASVDYIRKLQKEQqrskdlesrQRSLEQANRS 387
Cdd:cd11398    3 WHRQRRDNHKEVERRRRENINEGINELAALVP-GNAREK--NKGAILARAVEYIQELQETE---------AKNIEKWTLE 70

                         90
                 ....*....|....
gi 564398681 388 LQLRIQ-ELELQAQ 400
Cdd:cd11398   71 KLLTDQaIAELAAL 84

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKsndPEMRWNKGTILKASVDYIRKLQKEQQRskdlesrqrsLEQANRS 387
Cdd:cd11394    2 PKVEKRSAHNAIEKRYRSSINDRIIELKDLVVG---PDAKMNKSAVLRKAIDYIRYLQKVNQK----------LKQENMA 68

                 ....
gi 564398681 388 LQLR 391
Cdd:cd11394   69 LKKA 72

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins; SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 311 QKKDNHNLIERRRRFNINDRIKELGTLIPksnDPEMRWNKGTILKASVDYIRKLQKEQQRskdlesrqrsLEQANRSLQL 390
Cdd:cd18921    5 EKRTAHNAIEKRYRSSINDKIIELKDLVV---GTEAKLNKSAVLRKAIDYIRFLQQSNQK----------LKQENMALKM 71

                 ....
gi 564398681 391 RIQE 394
Cdd:cd18921   72 AVQK 75

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription factor HMS1 and similar proteins; HMS1, also termed high-copy MEP suppressor protein 1, is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 310 RQKKDNHNLIERRRRFNINDRIKELGTLIP-------------------KSNDPEMRWNKGTILKASVDYIRKLQKEQQR 370
Cdd:cd11399    1 PSKKTAHNMIEKRYRSNINDRIAELRDSVPalreayksargededeedlGGLTPATKLNKATILSKATEYIRHLEKKNKR 80

                         90       100
                 ....*....|....*....|....*.
gi 564398681 371 skdlesrqrsLEQANRSLQLRIQELE 396
Cdd:cd11399   81 ----------LSRENASLRERLAAHE 96

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family and similar proteins; 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. The family also includes Saccharomyces cerevisiae transcription factor HMS1 (also termed high-copy MEP suppressor protein 1) and serine-rich protein TYE7. HMS1 is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. TYE7, also termed basic-helix-loop-helix protein SGC1, is a putative bHLHzip transcription activator required for Ty1-mediated glycolytic gene expression. TYE7 N-terminal is extremely rich in serine residues. It binds DNA on E-box motifs, 5'-CANNTG-3'. TYE7 is not essential for growth.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 310 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRW--------------NKGTILKASVDYIRKLQKEQQRskdLE 375
Cdd:cd11395    1 PRKRLPHNAIEKRYRSNLNTKIERLRDAIPSLRSPEGKSddgglgglapttklSKATILTKAIEYIRHLEQENER---LE 77

                 ....*...
gi 564398681 376 SRQRSLEQ 383
Cdd:cd11395   78 EENEELRQ 85

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins; USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSN--DPEMRWNKGTILKASVDYIRKLQKEQQRSKD 373
Cdd:cd18923    4 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCNtdNSKTGASKGGILSKACDYIRELRQTNQRMQE 71

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins; The family includes MLXIP and MLXIPL. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564398681 310 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSN-DPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRS 380
Cdd:cd11405    1 EQRRLSHISAEQKRRFNIKSGFDTLQSLIPSLGqNPNQKVSKAAMLQKAAEYIKSLKRERQQMQEEAEQLRQ 72

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWN--KGTILKASVDYIRKLQKEQQR 370
Cdd:cd18924    1 RDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDCSMESTKSGqsKGGILSKACDYIQELRQSNHR 65

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPkSNDPEMrwNKGTILKASVDYIRK 363
Cdd:cd19734    3 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLP-GNARKM--DKSTVLQKSIDFLRK 55

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564398681 308 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQKEQQRS 371
Cdd:cd18947    1 KERFARENHSEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVSHMKSLRGTGNTS 64

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 564398681 316 HNLIERRRRFNINDRIKELGTLIPKSNdpemRWNKGTILKASVDYIRKLQK 366
Cdd:cd11393    1 HSIAERKRREKINERIRALRSLVPNGG----KTDKASILDEAIEYIKFLQE 47

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 564398681 312 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKL 364
Cdd:cd11437    1 SRSNHSEIEKRRRDKMNAYIQELSALVPACNAMSRKLDKLTVLRMAVQHLKSL 53

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 564398681 316 HNLIERRRRFNINDRIKELGTLIPKSNdpEMRwNKGTILKASVDYIRKLQKeqqRSKDLES 376
Cdd:cd11453    7 HSATEQRRRSKINERLQALRDLIPHSD--QKR-DKASFLLEVIEYIQALQE---KVAKLEE 61

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        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564398681 316 HNLIERRRRFNINDRIKELGTLIPKSNdpemRWNKGTILKASVDYIRKLQKEQQ 369
Cdd:cd11445    6 HNLSERRRRDRINEKMKALQELIPNCN----KTDKASMLDEAIEYLKSLQLQVQ 55

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP) and similar proteins; MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564398681 315 NHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTiLKASVDYIRKLQKEQQRSKDLESRQR 379
Cdd:cd19688    6 KHISAEQKRRFNIKICFDTLNSLVSTLKNSKPISNAIT-LQKTVEYIAKLQQERTQMQEETKRLR 69

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        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564398681 312 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQ 365
Cdd:cd19726    1 RRQNHSEIEKRRRDKMNTYITELSSMIPMCNAMSRKLDKLTVLRMAVQHMKTLR 54

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 564398681 318 LIERRRRFNINDRIKELGTLIPKS--NDPEMRWNKGTILKASVDYIRKLQKEQQ 369
Cdd:cd18916    6 MLERQRRARINKCLSELKTLVAECsgDDGCLRMDKAEMLETAVAFMRQQQTAKN 59

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 564398681 315 NHNLIERRRRFNINDRIKELGTLIPK--SNDPEMRWNKGTILKASVDYIRKLQ 365
Cdd:cd11408    1 SHKVIEKRRRDRINRCLNELGKTVPMalAKQTSGKLEKAEILEMTVQYLRALH 53

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 564398681 320 ERRRRFNINDRIKELGTLIPKSNDPEMrwNKGTILKASVDYIRKLQKEQQR 370
Cdd:cd11419   12 ERRRMQSINAGFQSLRTLLPHCDGEKL--SKAAILQQTAEYIFSLEQEKTR 60

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae phosphate system positive regulatory protein PHO4 and similar proteins; PHO4 is a transcriptional activator that regulates the expression of repressible phosphatase under phosphate starvation conditions in Saccharomyces cerevisiae. The PHO4 protein has four functional domains with the bHLH domain at its carboxyl-terminal region. It regulates transcription by binding to promoter of the genes as a homodimer.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564398681 311 QKKDNHNLIERRRRFNINDRIKELGTLIPK---------------SND-----PEMRWNKGTILKASVDYIRKLQKE 367
Cdd:cd11392    1 SKRTAHKVAERGRRDRLNAALKELASLMPAefvegkmgadgsasdSNDkekaaASAAGSKAATVEMAIDYIKHLQKE 77

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 564398681 317 NLI-ERRRRFNINDRIKELGTLIPksNDPEMrwNKGTILKASVDYIRKLQKEQqrsKDLESRQRSLEQANRSL 388
Cdd:cd11450    7 NLVsERNRRQKLNQRLFALRSVVP--NITKM--DKASIIKDAISYIQELQYQE---KKLEAEIRELESRPPST 72

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 564398681 313 KDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQ 365
Cdd:cd11469    2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNPMARKLDKLTVLRMAVQHLKSLK 54

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-binding protein Mnt and similar proteins; Mnt, also termed Class D basic helix-loop-helix protein 3 (bHLHd3), or Myc antagonist MNT, or protein ROX, is a bHLHZip transcriptional repressor that binds DNA as a heterodimer with MAX. It binds to the canonical E box sequence 5'-CACGTG-3' and, with higher affinity, to 5'-CACGCG-3'. Mnt has an important role as an antagonist and regulator of Myc activities and it is a potential tumor suppressor. Mnt is ubiquitously expressed. Mnt-deficient mice shown to exhibit early postnatal lethality.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564398681 316 HNLIERRRRFNINDRIKELGTLIPKSNDPemRWNKGTILKASVDYIRKLQKEQqrsKDLESRQRSLEQANRSLQLRI 392
Cdd:cd11402    6 HNKLEKNRRAHLKECFETLKRQIPNLDDK--KTSNLNILRSALRYIQILKRKE---KEYEHEMERLAREKIALQQRL 77

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BIG PETAL (BPE) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as BPE, HBI1 and BEE proteins (BEE1-3). BPE, also termed AtbHLH31, or EN 88, is involved in the control of Arabidopsis petal size, by interfering with postmitotic cell expansion to limit final petal cell size. HBI1, also termed AtbHLH64, or homolog of bee2 interacting with IBH1, or EN 79, is an atypical bHLH transcription factor that acts as positive regulator of cell elongation downstream of multiple external and endogenous signals by direct binding to the promoters and activation of the two expansin genes EXPA1 and EXPA8, encoding cell wall loosening enzymes. BEEs, also termed protein Brassinosteroid enhanced expression, are positive regulators of brassinosteroid signaling.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564398681 311 QKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPEmrwNKGTILKASVDYIRKLQKE 367
Cdd:cd18919   11 QATDSHSLAERVRREKISERMKLLQDLVPGCNKVT---GKALMLDEIINYVQSLQRQ 64

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins; N-Myc, also termed Class E basic helix-loop-helix protein 37 (bHLHe37), is a bHLHZip proto-oncogene protein that positively regulates the transcription of MYCNOS in neuroblastoma cells. It is also essential during embryonic development. N-Myc has a critical role in regulating the switch between proliferation and differentiation of progenitor cells. It binds DNA as a heterodimer with MAX. The family also includes S-Myc, encoded by rat or mouse intronless myc gene, which has apoptosis-inducing activity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564398681 311 QKKDNHNLIERRRRFNINDRIKELGTLIPK--SNDpemRWNKGTILKASVDYIRKLQKEQQR----SKDLESRQRSL 381
Cdd:cd11456    4 ERRRNHNILERQRRNDLRSSFLTLRDHVPElvKNE---KAAKVVILKKATEYVHSLQAEEQKllleKEKLQARQQQL 77

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 564398681 320 ERRRRFNINDRIKELGTLIPKSNdpemRWNKGTILKASVDYIRKLqkeQQRSKDLESRQRSLEQANRSLQL 390
Cdd:cd11443    7 ERRRRKKLNDRLYMLRSVVPKIT----KMDRASILGDAIDYVKEL---LQEINELQDELEGLPESESGETL 70

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 564398681 312 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPE--MRWNKGTILKASVDYIRKLQ 365
Cdd:cd18920   10 RKKRRGIIEKRRRDRINNSLSELRRLVPTAFEKQgsAKLEKAEILQMTVDHLKMLQ 65

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split HES-1, HES-4 and similar proteins; The family includes two bHLH-O transcriptional repressors, HES-1 and HES-4. HES-1, also termed Class B basic helix-loop-helix protein 39 (bHLHb39), or hairy homolog, or hairy-like protein (HL), plays an essential role in development of both compartment and boundary cells of the central nervous system. It regulates the maintenance of neural stem/progenitor cells by inhibiting proneural gene expression via Notch signaling. HES-4, also termed Class B basic helix-loop-helix protein 42 (bHLHb42), or bHLH factor Hes4, antagonizes the function of Twist-1 to regulate lineage commitment of bone marrow stromal/stem cells (BMSC). Epigenetic dysregulation of HES-4 is associated with striatal degeneration in postmortem Huntington brains. Both HES-1 and HES-4 are mammalian counterparts 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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564398681 311 QKKDNHNLIERRRRFNINDRIKELGTLI----PKSNDPEMRWNKGTILKASVDYIRKLQKEQ 368
Cdd:cd11459    2 HRKSSKPIMEKRRRARINESLSQLKTLIldalKKDSSRHSKLEKADILEMTVKHLRNLQRQQ 63

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        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564398681 320 ERRRRFNINDRIKELGTLIPKS-NDPE---MRWNKGTILKASVDYIRKLQKEQ 368
Cdd:cd11439    6 EKRRREQENKYIEELAELISASiSDMDslsVKPDKCAILQETVKQIRQIKEQE 58

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-interacting protein 1 (MXI1) and similar proteins; MXI1, also termed Max interactor 1, or Class C basic helix-loop-helix protein 11 (bHLHc11), is a bHLHZip transcriptional repressor that binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. It thus antagonizes MYC transcriptional activity by competing for MAX. It plays an important role in the regulation of cell proliferation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 313 KDNHNLIERRRRFNINDRIKELGTLIPKSNDPEMRWNKGTILKASVdYIRKLQKEQQRSK-DLEsrqrSLEQANRSLQLR 391
Cdd:cd18930    2 RSTHNELEKNRRAHLRLCLERLKVLIPLGPDCTRHTTLGLLNKAKA-HIKKLEEADRKSQhQLE----NLEREQRFLKRR 76

                 ....
gi 564398681 392 IQEL 395
Cdd:cd18930   77 LEQL 80

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 4 (Mad4) and similar proteins; Mad4, also termed Max dimerization protein 4, or Max dimerizer 4 (MXD4), or Class C basic helix-loop-helix protein 12 (bHLHc12), or Max-interacting transcriptional repressor MAD4, is a bHLHZip Max-interacting transcriptional repressor that suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation. It is regulated by a transcriptional repressor complex that contains Miz-1 and c-Myc.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564398681 313 KDNHNLIERRRRFNINDRIKELGTLIPKSNDpEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRqrsLEQANRSLQLRI 392
Cdd:cd18929    3 RSSHNELEKHRRAKLRLYLEQLKQLVPLGPD-STRHTTLSLLKRAKMHIKKLEEQDRKALNIKEQ---LQREHRYLKRRL 78

                 ....*..
gi 564398681 393 QELELQA 399
Cdd:cd18929   79 EQLSVQG 85

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 564398681 318 LIERRRRFNINDRIKELGTLIPK---SNDPEMRWNKGTILKASVDYIRKLQKEQ 368
Cdd:cd11461    6 VVEKTRRDRINSSIEQLKTLLEKefqRHQPNSKLEKADILEMTVSFLKQSAKLS 59