helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1373943967  183 VSERKRRKKLNDGLYSLRSLVP---KISKMDKASIIGDSIVYVQELQQQIQT 231
Cdd:smart00353   2 ARERRRRRKINEAFDELRSLLPtlpKNKKLSKAEILRLAIEYIKSLQEELQK 53

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
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1373943967 178 ASKNLVSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQT 231
Cdd:cd11450     4 ASKNLVSERNRRQKLNQRLFALRSVVPNITKMDKASIIKDAISYIQELQYQEKK 57

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 183 VSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd11451     8 MAERRRREKLNERFITLRSMVPFVTKMDKVSILGDAIEYLKQLQRRVE 55

basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 183 VSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd18918     3 ATERERREKLNEKFSDLRNLIPNPTKNDRASILSDAIKYINELQRTVE 50

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1373943967 176 GLASKNLVSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQT 231
Cdd:cd11452     1 SLAQDHILAERKRREKLSQRFIALSALVPGLKKMDKASVLGDAIKHIKQLQERVKE 56

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins; AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1373943967 173 KSVGLASKNLVSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd11455     3 KALAASKSHSEAERRRRERINSHLATLRTLLPNLSKTDKASLLAEVVQHVKELKRQAA 60

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
                  ....*....|....*....|....*....|....*....|....*.
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVP---KISKMDKASIIGDSIVYVQELQQ 227
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPelpDSKKLSKASILQKAVEYIRELQS 46

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein INDEHISCENT (IND) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as IND, HEC proteins (HEC1, HEC2 and HEC3) and UNE12. IND, also termed AtbHLH40, or EN 120, is a bHLH transcription regulator required for seed dispersal. It is involved in the differentiation of all three cell types required for fruit dehiscence. HEC1 (also termed AtbHLH88, or protein HECATE 1, or EN 118), HEC2 (also termed AtbHLH37, or protein HECATE 2, or EN 117) and HEC3 (also termed AtbHLH43, or protein HECATE 3, or EN 119) are required for the female reproductive tract development and fertility. Both IND and HEC proteins have been implicated in regulation of auxin signaling. They heterodimerize with SPATULA (SPT) bHLH transcription factor to regulate reproductive tract development in plant. UNE12, also termed AtbHLH59, or protein UNFERTILIZED EMBRYO SAC 12, or EN 93, is required for ovule fertilization.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 183 VSERKRRKKLNDGLYSLRSLVPKISKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd11454     7 VAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLQLQVK 54

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. 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. The MITF (also known as microphthalmia-TFE, or MiT) subfamily comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1373943967 179 SKNLVsERKRRKKLNDGLYSLRSLVPKI------SKMDKASIIGDSIVYVQELQQQIQT 231
Cdd:cd11387     1 SHNAV-ERRRRDNINEKIQELGSLVPPSrletkdLKPNKGSILSKAVEYIRELQNQNQE 58

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVPKI--SKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd11419    12 ERRRMQSINAGFQSLRTLLPHCdgEKLSKAAILQQTAEYIFSLEQEKT 59

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVP--KISKMDKASIIGDSIVYVQELQQQIQ 230
Cdd:cd11446     5 EKLRRDKLNERFMELSNVLEpgRPPKTDKATILGDAIRMLKQLRGEVQ 52

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 1373943967 185 ERKRRKKLNDGLYSLRSLVPKI------SKMDKASIIGDSIVYVQELQQQ 228
Cdd:cd11389     5 EKRRRDRINESLAELRRLVPEArkskgsGKLEKAEILEMTLQHLKALQSS 54

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVPKIS---KMDKASIIGDSIVYVQELQQQI 229
Cdd:cd11418     9 ERRRVQAVNDAFDRLRQHVPYLKrrkKLSKVKTLRRAIEYIRHLQKLL 56

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
                  ....*....|....*....|....*....|....*....|....*..
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVPKISKMDKAS---IIGDSIVYVQELQQQ 228
Cdd:cd11400     9 ERQRRNDLKNSFEKLRDLVPELADNEKASkvvILKKATEYIKQLQQE 55

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1373943967 178 ASKNLvSERKRRKKLNDGLYSLRSLVPKIS-KMDKASIIGDSIVYVQELQQ 227
Cdd:cd11441     2 KSRNL-SEKKRRDQFNVLINELASMLPGRGrKMDKSTVLKKTIAFLRKHKE 51

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) family; The HES family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. HES family proteins form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVP--------KISKMDKASIIGDSIVYVQELQQQ 228
Cdd:cd11410     2 EKKRRARINKSLEQLKTLVLealnkdntRYSKLEKADILEMTVKYLKQLQRS 53

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1373943967 184 SERKRRKKLNDGLYSLRSLVPKISKMDKASI---IGDSIVYVQELQQQIQ 230
Cdd:cd18914     8 VERQRRQEMASLFSSLRSLLPLQYIKGKLSVsdhVDEAVNYIKELQEKIK 57

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster achaete-scute complex (AS-C) proteins, achaete-scute-like proteins, ASCL1-2, and similar proteins; This subfamily includes Drosophila melanogaster AS-C proteins and two ASCL family of transcription factors, ASCL-1 and ASCL-2. Drosophila melanogaster AS-C proteins includes 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. 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 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 involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVP---KISKMDKASIIGDSIVYVQELQQ 227
Cdd:cd19723     9 ERNRVKLVNLGFATLREHVPngrANKKMSKVETLRSAVEYIRQLQQ 54

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
                  ....*....|....*....|....*....|....*....|....*....
gi 1373943967 185 ERKRRKKLNDGLYSLRSLVPKI--SKMDKASIIGDSIVYVQELQQQIQT 231
Cdd:cd11406     9 ERKRRDHIKDSFHSLRDSVPSLqgEKASRAQILKKATEYIQYMRRKNHT 57