basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID3 and similar proteins; ID3, also termed Class B basic helix-loop-helix protein 25 (bHLHb25), or helix-loop-helix protein HEIR-1, or ID-like protein inhibitor HLH 1R21, or inhibitor of DNA binding 3, or inhibitor of differentiation 3, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It negatively regulates muscle differentiation by inhibiting the DNA-binding activities of the myogenic regulatory factors.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 410898128  24 SLVIGRNKHSCLEEPVSALHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIA 84
Cdd:cd19693    1 SSRNGSNKGPALEEPVSLLYDMNDCYSRLRELVPGVPQGTKLSQVEILQHVIDYILDLQIV 61

basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID3 and similar proteins; ID3, also termed Class B basic helix-loop-helix protein 25 (bHLHb25), or helix-loop-helix protein HEIR-1, or ID-like protein inhibitor HLH 1R21, or inhibitor of DNA binding 3, or inhibitor of differentiation 3, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It negatively regulates muscle differentiation by inhibiting the DNA-binding activities of the myogenic regulatory factors.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 410898128  24 SLVIGRNKHSCLEEPVSALHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIA 84
Cdd:cd19693    1 SSRNGSNKGPALEEPVSLLYDMNDCYSRLRELVPGVPQGTKLSQVEILQHVIDYILDLQIV 61

helix loop helix domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 410898128    43 HDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIALQ 86
Cdd:smart00353   9 RKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID3 and similar proteins; ID3, also termed Class B basic helix-loop-helix protein 25 (bHLHb25), or helix-loop-helix protein HEIR-1, or ID-like protein inhibitor HLH 1R21, or inhibitor of DNA binding 3, or inhibitor of differentiation 3, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It negatively regulates muscle differentiation by inhibiting the DNA-binding activities of the myogenic regulatory factors.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 410898128  24 SLVIGRNKHSCLEEPVSALHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIA 84
Cdd:cd19693    1 SSRNGSNKGPALEEPVSLLYDMNDCYSRLRELVPGVPQGTKLSQVEILQHVIDYILDLQIV 61

basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID4 and similar proteins; ID4, also termed Class B basic helix-loop-helix protein 27 (bHLHb27), or inhibitor of DNA binding 4, or inhibitor of differentiation 4, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It plays a role in adipose cell differentiation.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 410898128  36 EEPVSALH-DMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIALQAEEA 90
Cdd:cd19694    1 EEEALCLQyDMNDCYSRLKRLVPTIPPNKKVSKVEILQHVIDYILDLQLALETHPA 56

basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID1 and similar proteins; ID1, also termed Class B basic helix-loop-helix protein 24 (bHLHb24), or inhibitor of DNA binding 1, or inhibitor of differentiation 1, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. ID1 interferes with centrosomal function. It has been implicated in the regulation of cell proliferation and differentiation in myogenesis, neurogenesis, and/or hematopoiesis.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 410898128  42 LHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIALQAE 88
Cdd:cd19691    5 LYDMNGCYSRLKELVPTLPQNRKVSKVEILQHVIDYIWDLQVELDSG 51

Helix-loop-helix DNA-binding domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 410898128   43 HDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQ 82
Cdd:pfam00010  14 DRINDAFDELRELLPTLPPDKKLSKAEILRLAIEYIKHLQ 53

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
                 ....*....|....*....|....*....|....*...
gi 410898128  45 MNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQ 82
Cdd:cd00083    8 INDAFEELKRLLPELPDSKKLSKASILQKAVEYIRELQ 45

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
                 ....*....|....*....|....*....|....*....|.
gi 410898128  45 MNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIAL 85
Cdd:cd11442   12 KNDLYSRLRALLPSIATSDKVSKATVLEEACNYIRNLHREV 52

tissue specific basic helix-loop-helix (bHLH-TS) domain family; Tissue specific bHLH domain family includes transcription regulators whose expression are restricted to certain tissues. They are involved in cell-fate determination and process in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis and include proteins from myogenic regulatory factor (MRF) family, twist-related protein (TWIST) family, scleraxis-like family, heart- and neural crest derivatives-expressed protein (HAND) family, helix-loop-helix protein (HEN) family, musculin-like family, germline alpha (FIGLA) family, T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family, ovary, uterus and testis protein (OUT) family, mesoderm posterior protein (Mesp) family, muscle, intestine and stomach expression 1 (MIST-1) family, protein atonal homologs (ATOH) family, neurogenin (NGN) family, neurogenic differentiation factor (NeuroD) family, achaete-scute complex-like (ASCL) family, Fer3-like protein (FERD3L)-like family, and Oligodendrocyte lineage genes (OLIG) family of transcription factors.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 410898128  42 LHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQ 82
Cdd:cd11390   12 MHDLNDAFEALRKVLPTVPPDKKLSKIETLRLAINYIAALS 52

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
                 ....*....|....*....|....*....|....*....|....*
gi 410898128  45 MNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIALQAEE 89
Cdd:cd19714   23 LNTAFDRLRKVVPQWGQDKKLSKYETLQMALSYIMALTRILAEAE 67

basic helix-loop-helix (bHLH) domain found in neurogenin-2 (NGN-2) and similar proteins; NGN-2, also termed Class A basic helix-loop-helix protein 8 (bHLHa8), or protein atonal homolog 4 (ATOH4), is a neural-specific bHLH transcription factor required for sensory neurogenesis. It activates transcription by binding to the E box (5'-CANNTG-3').

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 410898128  42 LHDMNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQIALQ 86
Cdd:cd19717   22 MHNLNAALDSLREVLPTFPEDAKLTKIETLRFAHNYIWALSETLR 66

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 410898128  45 MNDCYSRLKQLVP---SIPQNESVSQVEILQHVIDYIFDLQIAL 85
Cdd:cd19685    9 INDKLNQLKELLPpnlSKQSRSKLSKAEILEMAITELRRLQQEV 52

basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 4 (ASCL-4) and similar proteins; ASCL-4, also termed Class A basic helix-loop-helix protein 44 (bHLHa44), or achaete-scute homolog 4 (ASH-4), or Hash4, is a bHLH transcriptional regulator that may be involved in skin development.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 410898128  45 MNDCYSRLKQLVPSIPQNESVSQVEILQHVIDYIFDLQ 82
Cdd:cd19746   23 VNEGYARLREHLPQELADKRLSKVETLRAAIDYIKHLQ 60