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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127 135 GYIHVRARRGQATDSHSLAERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQVEFLSMRIASMSPVLY 214
Cdd:cd18919    1 DYIHVRARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSLQRQVEFLSMKLAAVNPRLD 80

                 ....*..
gi 670358127 215 gFGLDSD 221
Cdd:cd18919   81 -FNSEDL 86

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127 135 GYIHVRARRGQATDSHSLAERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQVEFLSMRIASMSPVLY 214
Cdd:cd18919    1 DYIHVRARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSLQRQVEFLSMKLAAVNPRLD 80

                 ....*..
gi 670358127 215 gFGLDSD 221
Cdd:cd18919   81 -FNSEDL 86

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 670358127  149 SHSLAERVRRERISERMRMLQALVPGCD---KVTgKALILDEIINYVQSLQ 196
Cdd:pfam00010   4 AHNERERRRRDRINDAFDELRELLPTLPpdkKLS-KAEILRLAIEYIKHLQ 53

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127 135 GYIHVRARRGQATDSHSLAERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQVEFLSMRIASMSPVLY 214
Cdd:cd18919    1 DYIHVRARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNKVTGKALMLDEIINYVQSLQRQVEFLSMKLAAVNPRLD 80

                 ....*..
gi 670358127 215 gFGLDSD 221
Cdd:cd18919   81 -FNSEDL 86

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127 146 ATDSHSLAERVRRERISERMRMLQALVPGCDKvTGKALILDEIINYVQSLQNQVEFLSMR 205
Cdd:cd11445    2 AAEVHNLSERRRRDRINEKMKALQELIPNCNK-TDKASMLDEAIEYLKSLQLQVQMMSMG 60

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 670358127   151 SLAERVRRERISERMRMLQALVPGC--DKVTGKALILDEIINYVQSLQNQVE 200
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLpkNKKLSKAEILRLAIEYIKSLQEELQ 52

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127 150 HSLAERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQVEFLSMRIASM 209
Cdd:cd19698    1 HNLLEKKRRERIKDKIEILKGLTPNCTPKSDIASILSCVIDYIKSLLLQVEKLSMGICDD 60

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana ILI1-BINDING BHLH 1 (IBH1) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as IBH1, UPBEAT1, PAR1 and PAR2. IBH1, also termed bHLH zeta, or AtbHLH158, is an atypical and probable non DNA-binding bHLH transcription factor that acts as transcriptional repressor that negatively regulates cell and organ elongation in response to gibberellin (GA) and brassinosteroid (BR) signaling. IBH1 forms heterodimer with BHLH49, thus inhibiting DNA binding of BHLH49, which is a transcriptional activator that regulates the expression of a subset of genes involved in cell expansion by binding to the G-box motif. UPBEAT1, also termed AtbHLH151, or EN 146, is a bHLH transcription factor that modulates the balance between cellular proliferation and differentiation in root growth. It does not act through cytokinin and auxin signaling, but by repressing peroxidase expression in the elongation zone. PAR1 (also termed AtbHLH165, or protein helix-loop-helix 1, or protein phytochrome rapidly regulated 1) and PAR2 (also termed AtbHLH166, or protein helix-loop-helix 2, or protein phytochrome rapidly regulated 2) are two atypical bHLH transcription factors that act as negative regulators of a variety of shade avoidance syndrome (SAS) responses, including seedling elongation and photosynthetic pigment accumulation. They act as direct transcriptional repressor of two auxin-responsive genes, SAUR15 and SAUR68. They may function in integrating shade and hormone transcriptional networks in response to light and auxin changes.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 670358127 153 AERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQVEFLSM 204
Cdd:cd11444    4 RRRRGEEAIERRLRALRRLVPGGRESMEVEELLQETADYIMFLEMQVKVMKS 55

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 670358127 147 TDSHSLAERVRRERISERMRMLQALVPGCDKvTGKALILDEIINYVQSLQNQV 199
Cdd:cd11452    3 AQDHILAERKRREKLSQRFIALSALVPGLKK-MDKASVLGDAIKHIKQLQERV 54

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 670358127 154 ERVRRERISERMRMLQALVPGC---DKVTgKALILDEIINYVQSLQ 196
Cdd:cd00083    1 ERRRRDKINDAFEELKRLLPELpdsKKLS-KASILQKAVEYIRELQ 45

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 670358127 149 SHSLAERVRRERISERMRMLQALVPGCDKVTG-----KALILDEIINYVQSLQNQVE 200
Cdd:cd11387    1 SHNAVERRRRDNINEKIQELGSLVPPSRLETKdlkpnKGSILSKAVEYIRELQNQNQ 57

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 670358127 150 HSLAERVRRERISERMRMLQALVPGCDKVtGKALILDEIINYVQSLQNQVEFLSM 204
Cdd:cd18918    1 LFATERERREKLNEKFSDLRNLIPNPTKN-DRASILSDAIKYINELQRTVEELKS 54

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 670358127  149 SHSLAERVRRERISERMRMLQALVPGCD---KVTgKALILDEIINYVQSLQ 196
Cdd:pfam00010   4 AHNERERRRRDRINDAFDELRELLPTLPpdkKLS-KAEILRLAIEYIKHLQ 53

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 670358127 145 QATDSHSLAERVRRERISERMRMLQALVPGCDKVTGKALILDEIINYVQSLQNQV 199
Cdd:cd19683    1 KSRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDKATVFEFTVAYIKFLREKL 55

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 670358127 142 RRGQAtdsHSLAERVRRERISERMRMLQALVPGCDKV-TGKALILDEIINYVQSLQ 196
Cdd:cd11404    1 QRRLN---HVRSEKKRRELIKKGYDELCALVPGLDPQkRTKADILQKAADWIQELK 53

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
                 ....*....|....*....|....*....|....*....|....*..
gi 670358127 154 ERVRRERISERMRMLQALVPGCDKVTgKALILDEIINYVQSLQNQVE 200
Cdd:cd18917    5 EKSRKEKIKKAVKLLRSIVPGGESMD-TALVLDEAIDYLKSLKMELQ 50

transcription termination factor Rho; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670358127  53 DASLQSSSAVVDTSPQPQGSAAAASPMERKRKPAEDSATLSSAQSKEDCKQQQESKSRRGKRPHNKEANTEEKSATEDEA 132
Cdd:PRK12678  82 RAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAA 161

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 670358127 133 TRGY---IHVRARRGQATDSHSLAERVRRERISERMR 166
Cdd:PRK12678 162 ERTEeeeRDERRRRGDREDRQAEAERGERGRREERGR 198

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins; Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 670358127 149 SHSLAERVRRERISERMRMLQALVPGCDK-----VTGKALILDEIINYVQSLQNQVE 200
Cdd:cd11396    1 THNEVERRRRDKINNWIVKLAKIVPDCEKdnskqGQSKGGILSKACDYIQELRSQNE 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).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 670358127 141 ARRGQATDSHSLAERVRRERISERMRMLQALVPGC---DKVTGKALILDEIINYVQSLQNQ 198
Cdd:cd18926    8 AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSndpDMRWNKGTILKASVDYIRKLQRE 68

basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein (DEC) family; The DEC family includes two bHLH-O transcriptional repressors, DEC1 and DEC2, which 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. They mediate the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes. They are induced by CLOCK:BMAL1 heterodimer via the CACGTG E-box in the promoter.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 670358127 150 HSLAERVRRERISERMRMLQALVPGCDKVTG-----KALILDEIINYVQSLQNQVEFLSMRIASM 209
Cdd:cd11409    8 HRLIEKKRRDRINECIAQLKDLLPEHLKLTTlghleKAVVLELTLKHLKALTALTEQQQQKIIAL 72

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins; USF3, also termed upstream transcription factor 3, is a bHLHzip protein that is involved in the negative regulation of epithelial-mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 670358127 142 RRGQATDSHSLAERVRRERISERMRMLQALVPGCD-KVTGKALILDEIINYVQSLQNQVEFL 202
Cdd:cd18910    1 RREKKRESHNEVERRRKDKINAGINKIGELLPDRDaKKQSKNMILEQAYKYIVELKKKNDKL 62