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 42569863 290 RSIAERVRRTRISERMRKLQELVPNMdKQTNTSDMLDLAVDYIKDLQRQYKIL 342
Cdd:cd11393   1 HSIAERKRREKINERIRALRSLVPNG-GKTDKASILDEAIEYIKFLQEQVKVL 52

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 42569863 290 RSIAERVRRTRISERMRKLQELVPNMdKQTNTSDMLDLAVDYIKDLQRQYKIL 342
Cdd:cd11393   1 HSIAERKRREKINERIRALRSLVPNG-GKTDKASILDEAIEYIKFLQEQVKVL 52

Helix-loop-helix DNA-binding domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 42569863   290 RSIAERVRRTRISERMRKLQELVP--NMDKQTNTSDMLDLAVDYIKDLQ 336
Cdd:pfam00010   5 HNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKHLQ 53

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 42569863 290 RSIAERVRRTRISERMRKLQELVPNMdKQTNTSDMLDLAVDYIKDLQRQYKIL 342
Cdd:cd11393   1 HSIAERKRREKINERIRALRSLVPNG-GKTDKASILDEAIEYIKFLQEQVKVL 52

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42569863 286 ATHPRSIAERVRRTRISERMRKLQELVPNMDKqTNTSDMLDLAVDYIKDLQRQYKILNDNR 346
Cdd:cd11454   1 STDPQSVAARHRRERISERIRILQRLVPGGTK-MDTASMLDEAIHYVKFLQLQVKLLQSDD 60

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 42569863    291 SIAERVRRTRISERMRKLQELVP--NMDKQTNTSDMLDLAVDYIKDLQRQ 338
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPtlPKNKKLSKAEILRLAIEYIKSLQEE 50

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 42569863 294 ERVRRTRISERMRKLQELVPN--MDKQTNTSDMLDLAVDYIKDLQR 337
Cdd:cd00083   1 ERRRRDKINDAFEELKRLLPElpDSKKLSKASILQKAVEYIRELQS 46

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect embryo arrest 8 (AtMEE8) and similar proteins; AtMEE8, also termed AtbHLH108, or EN 132, is a bHLH transcription factor required during early embryo development, for the endosperm formation.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 42569863 290 RSIAERVRRTRISERMRKLQELVPNMDKQTNTSDMLDLAVDYIKDLQRQ 338
Cdd:cd19698   1 HNLLEKKRRERIKDKIEILKGLTPNCTPKSDIASILSCVIDYIKSLLLQ 49

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 42569863 294 ERVRRTRISERMRKLQELVPNMDKQTNTSDMLDLAVDYIKDLQRqykilndnranCKCMNKEK 356
Cdd:cd11398  15 ERRRRENINEGINELAALVPGNAREKNKGAILARAVEYIQELQE-----------TEAKNIEK 66

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 42569863 292 IAERVRRTRISERMRKLQELVPNMDKQTNTSDMLDlAVDYIKDLQRQYKIL 342
Cdd:cd11450   9 VSERNRRQKLNQRLFALRSVVPNITKMDKASIIKD-AISYIQELQYQEKKL 58

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
                ....*....|....*....|....*....|....*....|....*
gi 42569863 294 ERVRRTRISERMRKLQELVPNMDKQTNTSDMLDLAVDYIKDLQRQ 338
Cdd:cd19683  10 ERQRRERIKIACDQLRKLVPGCSRKTDKATVFEFTVAYIKFLREK 54

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 42569863 292 IAERVRRTRISERMRKLQELVPNMdKQTNTSDMLDLAVDYIKDLQRQYKILNDNR 346
Cdd:cd11452   8 LAERKRREKLSQRFIALSALVPGL-KKMDKASVLGDAIKHIKQLQERVKELEEEK 61

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family 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 family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 42569863 292 IAERVRRTRISERMRKLQELVP---NMDKQTNTSDMLDLAVDYIKDLQR 337
Cdd:cd11397  11 MIERRRRFNINDRIKELGTLLPksnDPDMRWNKGTILKASVDYIRKLQK 59

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; 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. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 42569863 286 ATHPRSiaERVRRTRISERMRKLQELVPNMDKQTNT-SDMLDLAVDYIKDLQ 336
Cdd:cd11404   4 LNHVRS--EKKRRELIKKGYDELCALVPGLDPQKRTkADILQKAADWIQELK 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein ABA-INDUCIBLE bHLH-TYPE (AIB) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AIB and MYC proteins (MYC2, MYC3 and MYC4). AIB, also termed AtbHLH17, or EN 35, is a transcription activator that regulates positively abscisic acid (ABA) response. MYC2, also termed protein jasmonate insensitive 1, or R-homologous Arabidopsis protein 1 (RAP-1), or AtbHLH6, or EN 38, or Z-box binding factor 1 protein, is a transcriptional activator involved in abscisic acid (ABA), jasmonic acid (JA), and light signaling pathways. MYC3, also termed protein altered tryptophan regulation 2, or AtbHLH5, or transcription factor ATR2, or EN 36, is a transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. MYC4, also termed AtbHLH4, or EN 37, is a transcription factor involved in jasmonic acid (JA) gene regulation. MYC2, together with MYC3 and MYC4, controls additively subsets of JA-dependent responses.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 42569863 293 AERVRRTRISERMRKLQELVPNMDKQTNTSdMLDLAVDYIKDLQRQYKILNDNR 346
Cdd:cd11449  12 AERQRREKLNQRFYALRAVVPNVSKMDKAS-LLGDAISYINELKSKVQDMETEK 64

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42569863 286 ATHprSIAERVRRTRISERMRKLQELVPNMDKQTNTSDMLDLAVDYIKDLQR-QYKILNDN 345
Cdd:cd18922   8 TTH--NIIEKRYRSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQvNHKLRQEN 66

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family; HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. 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 are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 42569863 290 RSIAERVRRTRISERMRKLQELVPN-MDKQTNT----SDMLDLAVDYIKDLQ 336
Cdd:cd11407   5 RGIIEKRRRDRINNSLAELRRLVPTaFEKQGSAklekAEILQMTVDHLKMLH 56

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 42569863 290 RSIAERVRRTRISERMRKLQELVP--NMDKQTNTSDMLDLAVDYIKDLQRQYKILNDNR 346
Cdd:cd18914   5 HNDVERQRRQEMASLFSSLRSLLPlqYIKGKLSVSDHVDEAVNYIKELQEKIKELSEKR 63

basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family; The HERP/HES-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. The HERP (HES-related repressor protein) subfamily proteins 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. Hairy and enhancer of split (HES)-related repressor protein (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 subfamily. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. The HES subfamily proteins 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. They 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
                ....*....|....*....|....*....|....*....|....*....
gi 42569863 294 ERVRRTRISERMRKLQELVPNMDKQTNTS-----DMLDLAVDYIKDLQR 337
Cdd:cd19685   2 EKRRRQRINDKLNQLKELLPPNLSKQSRSklskaEILEMAITELRRLQQ 50

basic helix-loop-helix (bHLH) domain found in the DNA-binding protein inhibitor (ID) family; The ID family includes a dominant negative group of helix-loop-helix (dnHLH) proteins, ID1-4, that are negative regulators of bHLH transcription factors. They contain the HLH-dimerization domain but lack the basic domain necessary for DNA-binding. ID proteins inhibit binding to DNA and transcriptional transactivation by heterodimerization with bHLH proteins. They also interact with many non-bHLH proteins in complex networks. ID proteins have been implicated in regulating gene expression as well as cell-cycle progression. Whereas ID-1, ID-2 and ID-3, are generally considered as tumor promoters, ID4 on the contrary has emerged as a tumor suppressor.

                        10        20        30
                ....*....|....*....|....*....|....
gi 42569863 305 MRKLQELVPNM--DKQTNTSDMLDLAVDYIKDLQ 336
Cdd:cd19684  12 YSKLKELVPTIpqNKKVSKVEILQHVIDYILDLQ 45

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 42569863 293 AERVRRTRISERMRKLQELVPNMDKQTNTS-------DMLDLAVDYIKDLQRQY 339
Cdd:cd11410   1 MEKKRRARINKSLEQLKTLVLEALNKDNTRysklekaDILEMTVKYLKQLQRSK 54

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
                ....*....|....*....|....*....|....*....|....*...
gi 42569863 294 ERVRRTRISERMRKLQELVP---NMDKQTNTSDMLDLAVDYIKDLQRQ 338
Cdd:cd18927  19 ERRRRFNINDRIKELGTLIPktnDLDVRWNKGTILKASVDYIKRMQKD 66

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
                ....*....|....*....|....*....|....*....|....*...
gi 42569863 294 ERVRRTRISERMRKLQELVPNMD-KQTNTSDMLDLAVDYIKDLQRQYK 340
Cdd:cd11402  10 EKNRRAHLKECFETLKRQIPNLDdKKTSNLNILRSALRYIQILKRKEK 57