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.

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                 ....*....|....*....|....*....|....*....|
gi 1904958414  1 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 40
Cdd:cd18924   26 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 65

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).

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                 ....*....|....*....|....*....|....*....|
gi 1904958414  1 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 40
Cdd:cd18924   26 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 65

helix loop helix domain;

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                  ....*....|....*....|....*....|....*....
gi 1904958414   1 QLSKIIPDCSmESTKsgQSKGGILSKACDYIQELRQSNH 39
Cdd:smart00353 17 ELRSLLPTLP-KNKK--LSKAEILRLAIEYIKSLQEELQ 52

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 1904958414  1 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 40
Cdd:cd18924   26 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 65

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins; Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements.

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                 ....*....|....*....|....*....|....*....|
gi 1904958414  1 QLSKIIPDCSMESTKSGQSKGGILSKACDYIQELRQSNHR 40
Cdd:cd11396   19 KLAKIVPDCEKDNSKQGQSKGGILSKACDYIQELRSQNER 58

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.

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gi 1904958414  1 QLSKIIPDCSMESTKSGQ------------SKGGILSKACDYIQELRQSNHRLSEELQGLDQ 50
Cdd:cd11395   24 RLRDAIPSLRSPEGKSDDgglgglapttklSKATILTKAIEYIRHLEQENERLEEENEELRQ 85

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.

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                 ....*....|....*....|....*....|
gi 1904958414 19 SKGGILSKACDYIQELRQSNHRLSEELQGL 48
Cdd:cd11394   40 NKSAVLRKAIDYIRYLQKVNQKLKQENMAL 69

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins; SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis.

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                 ....*....|....*....|....*....|.
gi 1904958414 14 TKSGQSKGGILSKACDYIQELRQSNHRLSEE 44
Cdd:cd18922   35 TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE 65

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.

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gi 1904958414  2 LSKIIPDCSMEstksgQSKGGILSKACDYIQELRQSNHRLSEELQ 46
Cdd:cd11398   29 LAALVPGNARE-----KNKGAILARAVEYIQELQETEAKNIEKWT 68

rod shape-determining protein MreC; Provisional

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                  ....*....|....*....|....*....|.
gi 1904958414  31 IQELRQSNHRLSEELQGLDQLQLDNDVLRQQ 61
Cdd:PRK13922   78 NEELKKELLELESRLQELEQLEAENARLREL 108

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).

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gi 1904958414 19 SKGGILSKACDYIQELRQSNHRLSEElqgLDQLQLDNDVLRQQ 61
Cdd:cd11400   37 SKVVILKKATEYIKQLQQEEKKLEKE---KDKLKARNEQLRKK 76

helix loop helix domain;

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                  ....*....|....*....|....*....|....*....
gi 1904958414   1 QLSKIIPDCSmESTKsgQSKGGILSKACDYIQELRQSNH 39
Cdd:smart00353 17 ELRSLLPTLP-KNKK--LSKAEILRLAIEYIKSLQEELQ 52