basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana paclobutrazol resistance (PRE) family; The PRE family includes several bHLH transcription factors from Arabidopsis thaliana, such as PRE1-6. PRE1 (also termed AtbHLH136, or protein banquo 1), PRE2 (also termed AtbHLH134, or protein banquo 2, or EN 52), PRE4 (also termed AtbHLH161, or protein banquo 3), and PRE5 (also termed AtbHLH164) are atypical and probable non DNA-binding bHLH transcription factors that integrate multiple signaling pathways to regulate cell elongation and plant development. PRE3 (also termed AtbHLH135, or protein activation-tagged BRI1 suppressor 1, or ATBS1, or protein target of MOOPTEROS 7, or EN 67) is an atypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. It promotes the correct definition of the hypophysis cell division plane. PRE5 (also termed AtbHLH163, or protein KIDARI) is an atypical and probable non DNA-binding bHLH transcription factor that regulates light-mediated responses in day light conditions by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance.

                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15221264 17 ISEDQINDLIIKLQQLLPELRDSrrsDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN 78
Cdd:cd11442  7 ISDDQKNDLYSRLRALLPSIATS---DKVSKATVLEEACNYIRNLHREVDDLSERLSRLLTS 65

Helix-loop-helix DNA-binding domain;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 15221264   20 DQINDLIIKLQQLLPELRDSRRSDKVSaarVLQDTCNYIRNLH 62
Cdd:pfam00010 14 DRINDAFDELRELLPTLPPDKKLSKAE---ILRLAIEYIKHLQ 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana paclobutrazol resistance (PRE) family; The PRE family includes several bHLH transcription factors from Arabidopsis thaliana, such as PRE1-6. PRE1 (also termed AtbHLH136, or protein banquo 1), PRE2 (also termed AtbHLH134, or protein banquo 2, or EN 52), PRE4 (also termed AtbHLH161, or protein banquo 3), and PRE5 (also termed AtbHLH164) are atypical and probable non DNA-binding bHLH transcription factors that integrate multiple signaling pathways to regulate cell elongation and plant development. PRE3 (also termed AtbHLH135, or protein activation-tagged BRI1 suppressor 1, or ATBS1, or protein target of MOOPTEROS 7, or EN 67) is an atypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. It promotes the correct definition of the hypophysis cell division plane. PRE5 (also termed AtbHLH163, or protein KIDARI) is an atypical and probable non DNA-binding bHLH transcription factor that regulates light-mediated responses in day light conditions by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance.

                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15221264 17 ISEDQINDLIIKLQQLLPELRDSrrsDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN 78
Cdd:cd11442  7 ISDDQKNDLYSRLRALLPSIATS---DKVSKATVLEEACNYIRNLHREVDDLSERLSRLLTS 65

helix loop helix domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15221264    20 DQINDLIIKLQQLLPELRDSRRSDKVSaarVLQDTCNYIRNLHREVDD 67
Cdd:smart00353  9 RKINEAFDELRSLLPTLPKNKKLSKAE---ILRLAIEYIKSLQEELQK 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 15221264 20 DQINDLIIKLQQLLPelrdsrRSDKVSAARVLQDTCNYIRNLHREVDDLS 69
Cdd:cd11393 10 EKINERIRALRSLVP------NGGKTDKASILDEAIEYIKFLQEQVKVLS 53

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
               ....*....|....*....|....*....|....*....|....*..
gi 15221264 20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVD 66
Cdd:cd11387 11 DNINEKIQELGSLVPPSRLETKDLKPNKGSILSKAVEYIRELQNQNQ 57

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

                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15221264 17 ISEDQINDLIIK----LQQLLPELR--DSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL 75
Cdd:cd19687  8 QAEQKRRDAIKKgyddLQDIVPTCQqqDDIGSQKLSKATILQRSIDYIQFLHQQKKKQEEELSAL 72