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 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQN-----------------VSAAPSKATTVEAACRYIRHLQQNVST 312
Cdd:cd11392   2 KRTAHKVAERGRRDRLNAALKELASLMPAEFVEGKmgadgsasdsndkekaaASAAGSKAATVEMAIDYIKHLQKEVEE 80

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 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQN-----------------VSAAPSKATTVEAACRYIRHLQQNVST 312
Cdd:cd11392   2 KRTAHKVAERGRRDRLNAALKELASLMPAEFVEGKmgadgsasdsndkekaaASAAGSKAATVEMAIDYIKHLQKEVEE 80

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 14318559    258 AEQARRNRLAVALHELASLIPAEwkqqNVSAAPSKATTVEAACRYIRHLQQNVST 312
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTL----PKNKKLSKAEILRLAIEYIKSLQEELQK 53

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 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQN-----------------VSAAPSKATTVEAACRYIRHLQQNVST 312
Cdd:cd11392   2 KRTAHKVAERGRRDRLNAALKELASLMPAEFVEGKmgadgsasdsndkekaaASAAGSKAATVEMAIDYIKHLQKEVEE 80

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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 14318559 259 EQARRNRLAVALHELASLIPAEWKQQNvsaaPSKATTVEAACRYIRHLQQ 308
Cdd:cd00083   1 ERRRRDKINDAFEELKRLLPELPDSKK----LSKASILQKAVEYIRELQS 46

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14318559 250 DKRESHKHAEQARRNRLAVALHELASLIPAewkqqnVSAAPSKATTVEAACRYIRHLQQNVST 312
Cdd:cd19683   1 KSRERHNAKERQRRERIKIACDQLRKLVPG------CSRKTDKATVFEFTVAYIKFLREKLGD 57

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
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 14318559 249 DDKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNvsaapsKATTVEAACRYIRHLQQN 309
Cdd:cd11398   5 RQRRDNHKEVERRRRENINEGINELAALVPGNAREKN------KGAILARAVEYIQELQET 59

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 14318559 252 RESHKHAEQARRNRLAVALHELASLIPAEwkqQNVSAAPSKATTVEAACRYIR 304
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLP---PAVGSKLDKLSVLRLAVAYLR 50

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 14318559 254 SHKHAEQARRNRLAVALHELASLIPAEWKQQNvSAAPSKATTVEAACRYIRHLQ 307
Cdd:cd11408   1 SHKVIEKRRRDRINRCLNELGKTVPMALAKQT-SGKLEKAEILEMTVQYLRALH 53

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 14318559 248 DDDKRESHKHAEQARRNRLAVALHELASLIPaEWKQQNVSAAPSKATTVEAACRYIRHLQQN 309
Cdd:cd18924   2 DEKRRAQHNEVERRRRDKINNWIVQLSKIIP-DCSMESTKSGQSKGGILSKACDYIQELRQS 62

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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAapskATTVEAACRYIRHLQQNV 310
Cdd:cd18914   1 KKLLHNDVERQRRQEMASLFSSLRSLLPLQYIKGKLSV----SDHVDEAVNYIKELQEKI 56

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
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 14318559 250 DKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEaacrYIRHLQQ 308
Cdd:cd19688   2 NRRMKHISAEQKRRFNIKICFDTLNSLVSTLKNSKPISNAITLQKTVE----YIAKLQQ 56

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPA---------EWKQQNVSAA--PSKATTVEAACRYIRHLQQNVST 312
Cdd:cd11395   3 KRLPHNAIEKRYRSNLNTKIERLRDAIPSlrspegksdDGGLGGLAPTtkLSKATILTKAIEYIRHLEQENER 75

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 14318559 258 AEQARRNRLAVALHELASLIPaeWKQQNvsaapSKATTVEAACRYIRHLQQNV 310
Cdd:cd11393   4 AERKRREKINERIRALRSLVP--NGGKT-----DKASILDEAIEYIKFLQEQV 49

basic helix-loop-helix (bHLH) domain found in 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        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 14318559 251 KRESHKHAEQARRNRLAVALHELASLIPAewkqqnVSAAPSKATTVEAACRYIRHLQQ 308
Cdd:cd18909   2 RRERHNRMERDRRRRIRICCDELNLLVPF------CNAETDKATTLQWTTAFLKYIQE 53

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein-like (MLXIPL) and similar proteins; 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
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 14318559 249 DDKRESHKHAEQARRNRLAVALHELASLIPAEWKQQnvSAAPSKATTVEAACRYIRHLQQ 308
Cdd:cd19689   3 ETRRITHISAEQKRRFNIKLGFDTLHSLVTTLSSQP--SIKISKATTLQKTAEYISKLQQ 60