bHLH-MYC and R2R3-MYB transcription factors N-terminal; This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174   52 LQNKLSDLVErpngaNFSWNYAIFWQISRSKSGELVLGWGDGCCREPrEGEGSEITRilnlrleneaqqrmrkrvleklh 131
Cdd:pfam14215   1 LQQRLRSLVE-----SSQWSYAIFWQISRSQSGRLVLGWGDGYYNGG-EEGGKGKTR----------------------- 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174  132 mlfggtdednyafgldkvtdtemfflasmyfsfprgeGGPGKCFGSGKYVWLSDvmKSSVDYCSRSFLMKSAGMQTIVLI 211
Cdd:pfam14215  52 -------------------------------------GLPGKAFASGKHIWLTG--ADELDYCSRSLLAKSAGIQTIVCI 92

                         170       180
                  ....*....|....*....|....*....
gi 697147174  212 PTDVGVVELGSVRAISESLELVQSIKSCF 240
Cdd:pfam14215  93 PVPGGVLELGSTELVPEDLELVQHIKSLF 121

bHLH-MYC and R2R3-MYB transcription factors N-terminal; This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174   52 LQNKLSDLVErpngaNFSWNYAIFWQISRSKSGELVLGWGDGCCREPrEGEGSEITRilnlrleneaqqrmrkrvleklh 131
Cdd:pfam14215   1 LQQRLRSLVE-----SSQWSYAIFWQISRSQSGRLVLGWGDGYYNGG-EEGGKGKTR----------------------- 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174  132 mlfggtdednyafgldkvtdtemfflasmyfsfprgeGGPGKCFGSGKYVWLSDvmKSSVDYCSRSFLMKSAGMQTIVLI 211
Cdd:pfam14215  52 -------------------------------------GLPGKAFASGKHIWLTG--ADELDYCSRSLLAKSAGIQTIVCI 92

                         170       180
                  ....*....|....*....|....*....
gi 697147174  212 PTDVGVVELGSVRAISESLELVQSIKSCF 240
Cdd:pfam14215  93 PVPGGVLELGSTELVPEDLELVQHIKSLF 121

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 697147174   442 EAERQRREKLNQRFYALRAVVP---NISKMDKASLLGDAIAHITELQKKLRD 490
Cdd:smart00353   2 ARERRRRRKINEAFDELRSLLPtlpKNKKLSKAEILRLAIEYIKSLQEELQK 53

bHLH-MYC and R2R3-MYB transcription factors N-terminal; This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174   52 LQNKLSDLVErpngaNFSWNYAIFWQISRSKSGELVLGWGDGCCREPrEGEGSEITRilnlrleneaqqrmrkrvleklh 131
Cdd:pfam14215   1 LQQRLRSLVE-----SSQWSYAIFWQISRSQSGRLVLGWGDGYYNGG-EEGGKGKTR----------------------- 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174  132 mlfggtdednyafgldkvtdtemfflasmyfsfprgeGGPGKCFGSGKYVWLSDvmKSSVDYCSRSFLMKSAGMQTIVLI 211
Cdd:pfam14215  52 -------------------------------------GLPGKAFASGKHIWLTG--ADELDYCSRSLLAKSAGIQTIVCI 92

                         170       180
                  ....*....|....*....|....*....
gi 697147174  212 PTDVGVVELGSVRAISESLELVQSIKSCF 240
Cdd:pfam14215  93 PVPGGVLELGSTELVPEDLELVQHIKSLF 121

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 697147174 442 EAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKKLRDMESESERLGSTSRDANASA 509
Cdd:cd11443    5 MAERRRRKKLNDRLYMLRSVVPKITKMDRASILGDAIDYVKELLQEINELQDELEGLPESESGETLSQ 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174 435 EEPLNHVEAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKKLRDMESESErlgstsrdanasASDSPS 514
Cdd:cd11451    1 DEDGSHAMAERRRREKLNERFITLRSMVPFVTKMDKVSILGDAIEYLKQLQRRVEELESRRK------------SSDTET 68

                 ....*.
gi 697147174 515 SETQNR 520
Cdd:cd11451   69 RPTMER 74

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 697147174 440 HVEAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKKLRDME 492
Cdd:cd11393    1 HSIAERKRREKINERIRALRSLVPNGGKTDKASILDEAIEYIKFLQEQVKVLS 53

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 697147174 439 NHVEAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKK 487
Cdd:cd11455   10 SHSEAERRRRERINSHLATLRTLLPNLSKTDKASLLAEVVQHVKELKRQ 58

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 697147174 440 HVEAERQRREKLNQRFYALRAVVPNISKM-DKASLLGDAIAHITELQKKLRDMESESERLGST 501
Cdd:cd11453    7 HSATEQRRRSKINERLQALRDLIPHSDQKrDKASFLLEVIEYIQALQEKVAKLEEQVQGWGGE 69

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        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 697147174 440 HVEAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKKLRDM 491
Cdd:cd11445    6 HNLSERRRRDRINEKMKALQELIPNCNKTDKASMLDEAIEYLKSLQLQVQMM 57

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 697147174  438 LNHVEAERQRREKLNQRFYALRAVVPNI---SKMDKASLLGDAIAHITELQ 485
Cdd:pfam00010   3 EAHNERERRRRDRINDAFDELRELLPTLppdKKLSKAEILRLAIEYIKHLQ 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein FAMA and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as FAMA, MUTE and SPEECHLESS, which work together to regulate the sequential cell fate specification during stomatal development and differentiation. FAMA, also termed AtbHLH97, or EN 14, is a transcription activator required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. It mediates the formation of stomata. MUTE, also termed AtbHLH45, or EN 20, is required for the differentiation of stomatal guard cells, by promoting successive asymmetric cell divisions and the formation of guard mother cells. It promotes the conversion of the leaf epidermis into stomata. SPEECHLESS, also termed AtbHLH98, or EN 19, is required for the initiation and the formation of stomata, by promoting the first asymmetric cell divisions. FAMA, MUTE and SPEECHLESS form heterodimers with SCREAM/ICE1 and SCRM2 to regulate transcription of genes during stomatal development.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 697147174 438 LNHVEAERQRREKLNQRFYALRAVVPN--ISKMDKASLLGDAIAHITELQKKLRDMESESER 497
Cdd:cd11448    1 MTHIAVERNRRKQMNEHLNVLRSLMPGsyIQRGDQASIVGGAIEFVKELEQLLQSLEAQKRR 62

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 697147174 438 LNHVEAERQRREKLNQRFYALRAVVPN--ISKMDKASLLGDAIAHITELQKKLRDMESESERL 498
Cdd:cd11404    4 LNHVRSEKKRRELIKKGYDELCALVPGldPQKRTKADILQKAADWIQELKEENEKLEEQLDEL 66

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 697147174 438 LNHVEAERQRREKLNQRFYALRAVVPNI-----SKMDKASLLGDAIAHITELQKKLRDMESESERLGS 500
Cdd:cd11405    5 LSHISAEQKRRFNIKSGFDTLQSLIPSLgqnpnQKVSKAAMLQKAAEYIKSLKRERQQMQEEAEQLRQ 72

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 697147174 440 HVEAERQRREKLNQRFYALRAVVPNIS-KMDKASLLGDAIAHITELQKKLRDM 491
Cdd:cd19683    6 HNAKERQRRERIKIACDQLRKLVPGCSrKTDKATVFEFTVAYIKFLREKLGDS 58

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 697147174 438 LNHVEAERQRREKLNQRFYALRAVV--PNISKMDKASLLGDAIAHITELQKKLRDMESESERL 498
Cdd:cd19682    2 LRHKKRERERRSELRELFDKLKQLLglDSDEKASKLAVLTEAIEEIQQLKREEDELQKEKARL 64

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 697147174 439 NHVEAERQRREKLNQRFYALRAVVPNISK-MDKASLLGDAIAHITELQkklRDMESESERLGSTS 502
Cdd:cd18919   15 SHSLAERVRREKISERMKLLQDLVPGCNKvTGKALMLDEIINYVQSLQ---RQVEFLSMKLAAVN 76

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 697147174 426 RGRKPANGREeplnhveaeRQRREKLNQRFYALRAVVPNIS---KMDKASLLGDAIAHITELQKKLRDMESE 494
Cdd:cd19714    7 RRRLAANARE---------RRRMQGLNTAFDRLRKVVPQWGqdkKLSKYETLQMALSYIMALTRILAEAERY 69

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana suppressor of acaulis 51 (SAC51) and similar proteins; SAC51, also termed AtbHLH142, or EN 128, is a bHLH transcription factor that is involved in stem elongation, probably by regulating a subset of genes involved in this process.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 697147174 442 EAERQRREKLNQRFYALRAVVPNISKMDKASLLGDAIAHITELQKKLRDME 492
Cdd:cd18917    3 SNEKSRKEKIKKAVKLLRSIVPGGESMDTALVLDEAIDYLKSLKMELQSLE 53

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174 428 RKPANGREEPLNHVEAERQRREKLNQRFYALRAVVPNISKMD----KASLLGDAIAHITELQKKL---RDMESESERLGS 500
Cdd:cd18927    3 RALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKTNDLDvrwnKGTILKASVDYIKRMQKDLqrsRELENHSRRLEM 82

                 ...
gi 697147174 501 TSR 503
Cdd:cd18927   83 TNK 85

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) family; The ARNT family of bHLH-PAS transcription regulators includes ARNT, ARNT-like proteins (ARNTL and ARNTL2), and Drosophila melanogaster protein cycle. They act as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 697147174 439 NHVEAERQRREKLNQRFYALRAVVPNIS----KMDKASLLGDAIAHITEL 484
Cdd:cd11437    4 NHSEIEKRRRDKMNAYIQELSALVPACNamsrKLDKLTVLRMAVQHLKSL 53

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 697147174 442 EAERQRREKLNQRFYALRAVVP----NISKMDKASLLGDAIAHI 481
Cdd:cd11391    6 EAAKKRRDKENAEISELASLLPlppaVGSKLDKLSVLRLAVAYL 49

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein cycle and similar proteins; Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 697147174 439 NHVEAERQRREKLNQRFYALRAVVPNIS----KMDKASLLGDAIAHITELQ 485
Cdd:cd19726    4 NHSEIEKRRRDKMNTYITELSSMIPMCNamsrKLDKLTVLRMAVQHMKTLR 54

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP) and similar proteins; 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697147174 438 LNHVEAERQRREKLNQRFYALRAVVPNI---SKMDKASLLGDAIAHITELQKKLRDMESESERL 498
Cdd:cd19688    5 MKHISAEQKRRFNIKICFDTLNSLVSTLknsKPISNAITLQKTVEYIAKLQQERTQMQEETKRL 68

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 697147174 440 HVEAERQRREKLNQRFYALRAVVPNI--SKMDKASLLGDAIAHITELQKKLRDMESESERL 498
Cdd:cd11406    5 HNALERKRRDHIKDSFHSLRDSVPSLqgEKASRAQILKKATEYIQYMRRKNHTHQQDIDDL 65

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697147174 428 RKPANGREeplnhveaeRQRREKLNQRFYALRAVVPNIS---KMDKASLLGDAIAHITELQKKL 488
Cdd:cd11430    2 RLAANARE---------RRRMNGLNRAFDQLRSVVPSIGndkKLSKYETLQMAQIYIETLSELL 56

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 697147174 428 RKPANGREeplnhveaeRQRREKLNQRFYALRAVVPNIS---KMDKASLLGDAIAHITELQKKLR 489
Cdd:cd11422    1 RRVANARE---------RERVRNLNSGFSKLRRIVPLIPrdrKPSKVDTLKGATEYIRLLQRILE 56

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) and similar proteins; ARNT, also termed Class E basic helix-loop-helix protein 2 (bHLHe2), or Dioxin receptor, nuclear translocator, or hypoxia-inducible factor 1-beta (HIF1b), or HIF-1-beta, or HIF1-beta, is a member of bHLH-PAS transcription regulators that acts as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 697147174 439 NHVEAERQRREKLNQRFYALRAVVPNIS----KMDKASLLGDAIAHItelqKKLRDMESESE 496
Cdd:cd18947    8 NHSEIERRRRNKMTAYITELSDMVPTCSalarKPDKLTILRMAVSHM----KSLRGTGNTST 65

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster Enhancer of split proteins, E(spl)m5, E(spl)m8 and similar proteins; The family includes two bHLH-O transcriptional repressors, E(spl)m5 and E(spl)m8, which participate in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo. They bind DNA on N-box motifs, 5'-CACNAG-3'.

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                 ....*....|....*....|....*....|....*....|....*....|
gi 697147174 444 ERQRREKLNQRFYALRAVV------PNISKMDKASLLGDAIAHITELQKK 487
Cdd:cd18916    8 ERQRRARINKCLSELKTLVaecsgdDGCLRMDKAEMLETAVAFMRQQQTA 57

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).

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697147174 428 RKPANGREEPLNHVEAERQRREKLNQRFYALRAVVPNISKMD----KASLLGDAIAHITELQK---KLRDMESESERLGS 500
Cdd:cd18926    5 RALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDmrwnKGTILKASVDYIRKLQReqqRAKELENRQKKLEH 84

                 ...
gi 697147174 501 TSR 503
Cdd:cd18926   85 ANR 87

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.

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                 ....*....|....*....|....*....|....*....|....*....|
gi 697147174 442 EAERQRREKLNQRFYALRAVVPNIS---KMDKASLLGDAIAHITELQKKL 488
Cdd:cd11418    7 ERERRRVQAVNDAFDRLRQHVPYLKrrkKLSKVKTLRRAIEYIRHLQKLL 56