helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 42571357    221 ERERRVHFKDRFGDLKNLIPNPTKN---DRASIVGEAIDYIKELLRTIDE 267
Cdd:smart00353   4 ERRRRRKINEAFDELRSLLPTLPKNkklSKAEILRLAIEYIKSLQEELQK 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
                ....*....|....*....|....*....|....*....|....*....
gi 42571357 219 PTERERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKELLRTIDE 267
Cdd:cd11393   3 IAERKRREKINERIRALRSLVPNGGKTDKASILDEAIEYIKFLQEQVKV 51

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKNDRAS---IVGEAIDYIKELlrTIDEFKLLVEKKRVKQRNRE 283
Cdd:cd11400   9 ERQRRNDLKNSFEKLRDLVPELADNEKASkvvILKKATEYIKQL--QQEEKKLEKEKDKLKARNEQ 72

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 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKELLRTIDE 267
Cdd:cd11451  10 ERRRREKLNERFITLRSMVPFVTKMDKVSILGDAIEYLKQLQRRVEE 56

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42571357 221 ERERRVHFKDRFGDLKNLI-PN-PTKNDRASIVGEAIDYIKELLRTIDefKLLVEKKRVKQRNRE 283
Cdd:cd11446   5 EKLRRDKLNERFMELSNVLePGrPPKTDKATILGDAIRMLKQLRGEVQ--KLKEENSSLQEESKE 67

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
                ....*....|....*....|....*....|....*....|....*..
gi 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKELLRTIDE 267
Cdd:cd11455  15 ERRRRERINSHLATLRTLLPNLSKTDKASLLAEVVQHVKELKRQAAE 61

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 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKELLRTIDEFKLLVEKKRV 277
Cdd:cd11452  10 ERKRREKLSQRFIALSALVPGLKKMDKASVLGDAIKHIKQLQERVKELEEEKKEKRL 66

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as PIFs, ALC, PIL1, SPATULA, and UNE10. PIFs (PIF1, PIF3, PIF4, PIF5, PIF6 and PIF7) have been shown to control light-regulated gene expression. They directly bind to the photoactivated phytochromes and are degraded in response to light signals. ALC, also termed AtbHLH73, or protein ALCATRAZ, or EN 98, is required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. It promotes the differentiation of a strip of labile non-lignified cells sandwiched between layers of lignified cells. PIL1, also termed AtbHLH124, or protein phytochrome interacting factor 3-like 1, or EN 110, is involved in responses to transient and long-term shade. It is required for the light-mediated inhibition of hypocotyl elongation and necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. PIL1 seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. SPATULA, also termed AtbHLH24, or EN 99, plays a role in floral organogenesis. It promotes the growth of carpel margins and of pollen tract tissues derived from them. UNE10, also termed AtbHLH16, or protein UNFERTILIZED EMBRYO SAC 10, or EN 99, is required during the fertilization of ovules by pollen.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKEL 261
Cdd:cd11445  10 ERRRRDRINEKMKALQELIPNCNKTDKASMLDEAIEYLKSL 50

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42571357 213 KKRKIFpTERERRVHFKDRFGDLKNL--IPNPTKNDRASIVGEAIDYIKELLRTIDEfkLLVEKKR 276
Cdd:cd19682   1 RLRHKK-RERERRSELRELFDKLKQLlgLDSDEKASKLAVLTEAIEEIQQLKREEDE--LQKEKAR 63

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 42571357 222 RERRVHFKDRFGDLKNLIPNPTKNDRASIVGEAIDYIKELLRTI 265
Cdd:cd11454  10 RHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLQLQV 53

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 42571357 221 ERERRVHFKDRFGDLKNLIPN--PTKNDRASIVGEAIDYIKELLRTIDEFK 269
Cdd:cd11404  10 EKKRRELIKKGYDELCALVPGldPQKRTKADILQKAADWIQELKEENEKLE 60

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like proteins (BIMs) and similar proteins; The family includes Arabidopsis thaliana BIM1 and its homologs (BIM2 and BIM3), which are bHLH transcription factors that interact with BES1 to regulate transcription of Brassinosteroid (BR)-induced gene. BR regulates many growth and developmental processes such as cell elongation, vascular development, senescence stress responses, and photomorphogenesis. BIM1 heterodimerize with BES1 and bind to E-box sequences present in many BR-induced promoters to regulated BR-induced genes.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 42571357 220 TERERRVHFKDRFGDLKNLIPN-PTKNDRASIVGEAIDYIKEL 261
Cdd:cd11453  10 TEQRRRSKINERLQALRDLIPHsDQKRDKASFLLEVIEYIQAL 52

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
                ....*....|....*....|....*....|....*....|....*....
gi 42571357 220 TERERRVHFKDRFGDLKNLIPNPT-----KNDRASIVGEAIDYIKELLR 263
Cdd:cd11405  10 AEQKRRFNIKSGFDTLQSLIPSLGqnpnqKVSKAAMLQKAAEYIKSLKR 58

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins; TFE3, also termed Class E basic helix-loop-helix protein 33 (bHLHe33), is a bHLHzip transcription factor that is involved in B cell function. 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 TFEB or MITF.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42571357 221 ERERRVHFKDRFGDLKNLIPNPT----KNDRASIVGEAIDYIKELLRTIDEFK-LLVEKKRVKQRNR 282
Cdd:cd18928  19 ERRRRFNINDRIKELGTLIPKSTdpemRWNKGTILKASVDYIRKLQKEQQRSKeIEMRQRKLEQANR 85

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
                ....*....|....*....|....*....|....*....|....*..
gi 42571357 221 ERERRVHFKDRFGDLKNLIPN--PTKNDRASIVGEAIDYIKELLRTI 265
Cdd:cd18908  10 ERLRRERIKSSCDQLRDLLPYikGRKLDMASVLEMTVKYIRYIQERI 56

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins; MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR).

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42571357 221 ERERRVHFKDRFGDLKNLIPNPTKND----RASIVGEAIDYIKELLRTIDEFKLLVEK-KRVKQRNR 282
Cdd:cd18926  21 ERRRRFNINDRIKELGTLIPKSNDPDmrwnKGTILKASVDYIRKLQREQQRAKELENRqKKLEHANR 87