basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38201612  75 RRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDFsIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDV 151
Cdd:cd19687   1 RRREAHTQAEQKRRDAIKKGYDDLQDIVPTCQQQDD-IGSQKLSKATILQRSIDYIQFLHQQKKKQEEELSALRKEV 76

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38201612  75 RRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDFsIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDV 151
Cdd:cd19687   1 RRREAHTQAEQKRRDAIKKGYDDLQDIVPTCQQQDD-IGSQKLSKATILQRSIDYIQFLHQQKKKQEEELSALRKEV 76

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 38201612     83 AEQKRRDAIKRGYDDLQTIVPTCQQqdfsigSQKLSKAIVLQKTIDYIQFL 133
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLPK------NKKLSKAEILRLAIEYIKSL 47

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 38201612  75 RRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDFsIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDV 151
Cdd:cd19687   1 RRREAHTQAEQKRRDAIKKGYDDLQDIVPTCQQQDD-IGSQKLSKATILQRSIDYIQFLHQQKKKQEEELSALRKEV 76

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
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38201612  74 DRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsigSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd11405   1 EQRRLSHISAEQKRRFNIKSGFDTLQSLIPSLGQNP----NQKVSKAAMLQKAAEYIKSLK 57

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 38201612  84 EQKRRDAIKRGYDDLQTIVPTCQQqdfsigSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd00083   1 ERRRRDKINDAFEELKRLLPELPD------SKKLSKASILQKAVEYIRELQ 45

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins; Max, also termed Class D basic helix-loop-helix protein 4 (bHLHd4), or Myc-associated factor X, is a bHLHZip transcription regulator that forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5'-CAC[GA]TG-3'. The MYC:MAX complex is a transcriptional activator, whereas the MAD:MAX complex is a transcriptional repressor. Max homodimer bind DNA but is transcriptionally inactive. Targeted deletion of max results in early embryonic lethality in mice.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 38201612  77 RRAHTQA-EQKRRDAIKRGYDDLQTIVPTCQqqdfsigSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRK 149
Cdd:cd11406   1 KRAHHNAlERKRRDHIKDSFHSLRDSVPSLQ-------GEKASRAQILKKATEYIQYMRRKNHTHQQDIDDLKR 67

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP)-like family; The HERP-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a 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. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this family. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 38201612  80 HTQAEQKRRDAIKRGYDDLQTIVPTCQQqdfSIGSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd11389   1 HKVIEKRRRDRINESLAELRRLVPEARK---SKGSGKLEKAEILEMTLQHLKALQ 52

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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 38201612  74 DRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsigSQKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDV 151
Cdd:cd19689   3 ETRRITHISAEQKRRFNIKLGFDTLHSLVTTLSSQP----SIKISKATTLQKTAEYISKLQQERAQLQEEAQRLRDQI 76

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and similar proteins; INO2 is a positive regulatory factor required for depression of the co-regulated phospholipid biosynthetic enzymes in Saccharomyces cerevisiae. It is also involved in the expression of ITR1.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 38201612  75 RRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQdfsiGSQKLSKAIVLQKTIDYI 130
Cdd:cd11388   2 VKKWKHVEAEKKRRNQIKKGFEDLINLINYPRNN----NEKRISKSELLNKAVDDI 53

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).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsigsqKLSKAIVLQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALK 155
Cdd:cd11400   1 KRRLHNVLERQRRNDLKNSFEKLRDLVPELADNE------KASKVVILKKATEYIKQLQQEEKKLEKEKDKLKARNEQLR 74

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif-like protein (HEYL) and similar proteins; HEYL, also termed Class B basic helix-loop-helix protein 33 (bHLHb33), or hairy-related transcription factor 3 (HRT-3), is a bHLH-O transcriptional repressor that is strongly expressed in the presomitic mesoderm, the somites, the peripheral nervous system and smooth muscle of all arteries and is a downstream effector of the Notch and transforming growth factor-beta pathways. It promotes neuronal differentiation by activating proneural genes and inhibiting other hairy and enhancer of split (HES) and hairy/enhancer-of-split related with YRPW motif protein (HEY) proteins. HEYL also functions as a tumor suppressor involved in the progression of human cancers.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsiGSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd11447   9 RKKRRGIIEKRRRDRINSSLSELRRLVPTAFEKQ---GSSKLEKAEILQMTVDHLKMLH 64

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 38201612  70 ESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTcqqqdfsiGSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd11398   1 EEWHRQRRDNHKEVERRRRENINEGINELAALVPG--------NAREKNKGAILARAVEYIQEL 56

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 1 (HEY1) and similar proteins; HEY1, also termed cardiovascular helix-loop-helix factor 2 (CHF-2), or Class B basic helix-loop-helix protein 31 (bHLHb31), or HES-related repressor protein 1, or hairy and enhancer of split-related protein 1 (HESR-1), or hairy-related transcription factor 1 (HRT-1), is a bHLH-O transcriptional repressor that acts as an essential downstream effector of the Notch signaling pathway and may play a fundamental role in vascular development. HEY1 also participates several cancer-related pathways. It acts as a positive regulator of the tumor suppressor p53.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsiGSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd19748   9 RKRRRGIIEKRRRDRINNSLSELRRLVPSAFEKQ---GSAKLEKAEILQMTVDHLKMLH 64

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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38201612  73 KDRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQqqdfsigSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd11419   1 RRIRREIANSNERRRMQSINAGFQSLRTLLPHCD-------GEKLSKAAILQQTAEYIFSL 54

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
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCqqqdfsigSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd19683   2 SRERHNAKERQRRERIKIACDQLRKLVPGC--------SRKTDKATVFEFTVAYIKFL 51

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 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPT--CQQQDFSIGSQKL-------------SKAIVLQKTIDYIQFLH 134
Cdd:cd11392   2 KRTAHKVAERGRRDRLNAALKELASLMPAefVEGKMGADGSASDsndkekaaasaagSKAATVEMAIDYIKHLQ 75

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 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsiGSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd18920  10 RKKRRGIIEKRRRDRINNSLSELRRLVPTAFEKQ---GSAKLEKAEILQMTVDHLKMLQ 65

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 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVptcqqqdfsIGSQ-KLSKAIVLQKTIDYIQFLHKEKKkqeeevsTLRKDVTAL 154
Cdd:cd11394   6 KRSAHNAIEKRYRSSINDRIIELKDLV---------VGPDaKMNKSAVLRKAIDYIRYLQKVNQ-------KLKQENMAL 69

                .
gi 38201612 155 K 155
Cdd:cd11394  70 K 70

basic helix-loop-helix (bHLH) domain found in achaete-scute complex-like (ASCL) family; The achaete-scute complex-like (ASCL, also known as achaete-scute complex homolog or ASH) family of bHLH transcription factors, ASCL1-5, have been implicated in cell fate specification and differentiation. They are critical for proper development of the nervous system. The deregulation of ASCL plays a key role in psychiatric and neurological disorders. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete-scute homolog 1 (Mash1), is a neural-specific bHLH transcription factor that is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete-scute homolog 2 (Mash2), is a bHLH transcription factor that is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is a bHLH transcription factor specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. The family also includes Drosophila melanogaster achaete-scute complex (AS-C) proteins, which consists of lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 38201612  76 RRRAHtqaEQKRRDAIKRGYDDLQTIVPTCQqqdfsiGSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd11418   4 RRNER---ERRRVQAVNDAFDRLRQHVPYLK------RRKKLSKVKTLRRAIEYIRHL 52

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 38201612  80 HTQAEQKRRDAIKRGYDDLQTIVPTcqqqdfsIGSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd18908   6 HSLKERLRRERIKSSCDQLRDLLPY-------IKGRKLDMASVLEMTVKYIRYI 52

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 38201612  79 AHTQAEQKRRDAIKRGYDDL-QTIVPTCQQQDfsigSQKLSKAIVLQKTIDYIQFLH 134
Cdd:cd11408   1 SHKVIEKRRRDRINRCLNELgKTVPMALAKQT----SGKLEKAEILEMTVQYLRALH 53

basic helix-loop-helix (bHLH) domain found in factor in the germline alpha (FIGLA) and similar proteins; FIGLA, also termed FIGalpha, or Class C basic helix-loop-helix protein 8 (bHLHc8), or folliculogenesis-specific basic helix-loop-helix protein, or transcription factor FIGa, is a germ-cell-specific bHLH transcription factor expressed abundantly in female and less so in male germ cells. It is essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. FIGLA knockout mice cannot form primordial follicles and lose oocytes rapidly after birth, whereas male gonads are unaffected.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 38201612  76 RRRAHTQaEQKRRDAIKRGYDDLQTIVPTcQQQDFsigsqKLSKAIVLQKTIDYIQFLH 134
Cdd:cd11422   1 RRVANAR-ERERVRNLNSGFSKLRRIVPL-IPRDR-----KPSKVDTLKGATEYIRLLQ 52

basic helix-loop-helix (bHLH) domain found in protein atonal homologs ATOH1, ATOH7 and similar proteins; The family includes ATOH1 and ATOH7. ATOH1, also termed Class A basic helix-loop-helix protein 14 (bHLHa14), or helix-loop-helix protein hATH-1 (hATH1), or Math1, or Cath1, is a proneural bHLH transcription factor that is essential for inner ear hair cell differentiation. It dimerizes with E47 and activates E-box (CANNTG) dependent transcription. ATOH1 is a mammalian homolog of the Drosophila melanogaster gene atonal and mouse atonal homolog 1 (Math1). ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells. The family also includes protein Amos (also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein). It is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQdfsigsQKLSKAIVLQKTIDYIQFL 133
Cdd:cd11430   1 RRLAANARERRRMNGLNRAFDQLRSVVPSIGND------KKLSKYETLQMAQIYIETL 52

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.

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                ....*....|....*....|....*....|....*....|....*....|....*..
gi 38201612  77 RRAHTQAEQKRRDAIKRGYDDLQTIVPTCQqqdfsigSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd19682   1 RLRHKKRERERRSELRELFDKLKQLLGLDS-------DEKASKLAVLTEAIEEIQQL 50

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.

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gi 38201612  77 RRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDfsigsQKLSKAIVLQKTIDYIQF 132
Cdd:cd11391   1 REKSREAAKKRRDKENAEISELASLLPLPPAVG-----SKLDKLSVLRLAVAYLRL 51

basic helix-loop-helix (bHLH) domain found in protein atonal homolog 7 (ATOH7) and similar proteins; ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells.

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gi 38201612  75 RRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQdfsigsQKLSKAIVLQKTIDYIQFL 133
Cdd:cd19714   7 RRRLAANARERRRMQGLNTAFDRLRKVVPQWGQD------KKLSKYETLQMALSYIMAL 59

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.

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gi 38201612  76 RRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQdfsigsQKLSKAIVLQKTIDYIQFL 133
Cdd:cd11417   1 QRQAANLRERRRMQSINDAFEGLRSHIPTLPYE------KRLSKVDTLRLAIGYINFL 52

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.

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gi 38201612  73 KDRRRRA-HTQAEQKRRDAIKRGYDDLQTIVPTcqqqdfsiGSQKLSKAIVLQKTIDYIQ 131
Cdd:cd19734   3 KDKAKRVsRNKSEKKRRDQFNVLIKELGSMLPG--------NARKMDKSTVLQKSIDFLR 54

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.

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gi 38201612  75 RRRR-----AHTQAEQKRRDAIKRGYDDLQTIVPTCqqqdfsigSQKLSKAIVLQKTIDYIQFL 133
Cdd:cd18919   6 RARRgqatdSHSLAERVRREKISERMKLLQDLVPGC--------NKVTGKALMLDEIINYVQSL 61