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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 162 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTNQRMQETFKEAERLQ 241
Cdd:cd18923     1 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCNTDNSKTGASKGGILSKACDYIRELRQTNQRMQETYKEAERLQ 80

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins; USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 162 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTNQRMQETFKEAERLQ 241
Cdd:cd18923     1 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCNTDNSKTGASKGGILSKACDYIRELRQTNQRMQETYKEAERLQ 80

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650056  174 NEVERRRRDKINNWIVQLSKIIPDCHaDNSKTgaSKGGILSKACDYIRELRQTNQ 228
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLP-KNKKL--SKAEILRLAIEYIKSLQEELQ 52

leucine zipper domain found in c-Myc-binding protein and similar proteins; MycBP, also called associate of Myc 1 (AMY-1), is a novel c-Myc binding protein that may control the transcriptional activity of Myc. It stimulates the activation of E box-dependent transcription by Myc. This model corresponds to the conserved region that shows high sequence similarity with the leucine zipper (ZIP) domain located at the C-terminus of TGF-beta-stimulated clone-22 domain (TSC22D) family transcription factors. The first helix of ZIP is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958650056 236 EAERLQMDNELLRQQIEELKNENALLRAQLQQHN 269
Cdd:cd21937    20 DVEALRLENEELKQKNEELEEENKELKAKLQQYE 53

Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958650056 220 IRELRQTNQRMQEtfkEAERLQMDNELLRQQIEELKNENA 259
Cdd:COG3074    27 VEELKEKNEELEQ---ENEELQSENEELQSENEQLKTENA 63

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins; USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 162 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTNQRMQETFKEAERLQ 241
Cdd:cd18923     1 RTPRDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCNTDNSKTGASKGGILSKACDYIRELRQTNQRMQETYKEAERLQ 80

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 1958650056 172 QHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTNQR 229
Cdd:cd11396     1 THNEVERRRRDKINNWIVKLAKIVPDCEKDNSKQGQSKGGILSKACDYIQELRSQNER 58

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 1958650056 165 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPDChadnSKTGASKGGILSKACDYIRELRQTNQRM 230
Cdd:cd18910     1 RREKKRESHNEVERRRKDKINAGINKIGELLPDR----DAKKQSKNMILEQAYKYIVELKKKNDKL 62

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPDChADNSKtgASKGGILSKACDYIRELRQTNQRMQetfKEAERLQMDNELLR 248
Cdd:cd11400     1 KRRLHNVLERQRRNDLKNSFEKLRDLVPEL-ADNEK--ASKVVILKKATEYIKQLQQEEKKLE---KEKDKLKARNEQLR 74

                  ....*.
gi 1958650056 249 QQIEEL 254
Cdd:cd11400    75 KKLERL 80

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650056  174 NEVERRRRDKINNWIVQLSKIIPDCHaDNSKTgaSKGGILSKACDYIRELRQTNQ 228
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLP-KNKKL--SKAEILRLAIEYIKSLQEELQ 52

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 168 RRRAQHNEVERRRRDKINNWIVQLSKIIPDChaDNSKTgaSKGGILSKACDYIRELRQtnqrmqetfkeaerlqmDNELL 247
Cdd:cd11404     1 QRRLNHVRSEKKRRELIKKGYDELCALVPGL--DPQKR--TKADILQKAADWIQELKE-----------------ENEKL 59

                  ....*....
gi 1958650056 248 RQQIEELKN 256
Cdd:cd11404    60 EEQLDELKE 68

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKII--PDchadnskTGASKGGILSKACDYIRELRQTNQRMQEtfkEAERLQM 242
Cdd:cd11394     6 KRSAHNAIEKRYRSSINDRIIELKDLVvgPD-------AKMNKSAVLRKAIDYIRYLQKVNQKLKQ---ENMALKK 71

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family 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 family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958650056 165 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTgaSKGGILSKACDYIRELRQTNQRMQET 233
Cdd:cd11397     1 KDRQKKDNHNMIERRRRFNINDRIKELGTLLPKSNDPDMRW--NKGTILKASVDYIRKLQKEQERLRQL 67

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins; SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958650056 164 PRDERRRAqHNEVERRRRDKINNWIVQLSKIIPDCHADnsktgASKGGILSKACDYIRELRQTNQRMQE 232
Cdd:cd18921     2 SKGEKRTA-HNAIEKRYRSSINDKIIELKDLVVGTEAK-----LNKSAVLRKAIDYIRFLQQSNQKLKQ 64

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNsktgASKGGILSKACDYIRELRQTNQRMQetfkeaerlqmdnellr 248
Cdd:cd11406     1 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEK----ASRAQILKKATEYIQYMRRKNHTHQ----------------- 59

                          90
                  ....*....|
gi 1958650056 249 QQIEELKNEN 258
Cdd:cd11406    60 QDIDDLKRQN 69

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins; SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 164 PRDERRRAQHNEVERRRRDKINNWIVQLSKIIPdchadNSKTGASKGGILSKACDYIRELRQTNQRMQEtfkEAERLQMD 243
Cdd:cd18922     1 PKEGERRTTHNIIEKRYRSSINDKIIELKDLVM-----GTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQ---ENMALKLA 72

                  ..
gi 1958650056 244 NE 245
Cdd:cd18922    73 NQ 74

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 165 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPdcHADNSKTGASKGGILSKACDYIRELRQTNQRMQETFKEAERLQMDN 244
Cdd:cd18928     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIP--KSTDPEMRWNKGTILKASVDYIRKLQKEQQRSKEIEMRQRKLEQAN 84

                  ....*..
gi 1958650056 245 ELLRQQI 251
Cdd:cd18928    85 RSLQLRI 91

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        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958650056 176 VERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTN 227
Cdd:cd19685     1 SEKRRRQRINDKLNQLKELLPPNLSKQSRSKLSKAEILEMAITELRRLQQEV 52

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins; N-Myc, also termed Class E basic helix-loop-helix protein 37 (bHLHe37), is a bHLHZip proto-oncogene protein that positively regulates the transcription of MYCNOS in neuroblastoma cells. It is also essential during embryonic development. N-Myc has a critical role in regulating the switch between proliferation and differentiation of progenitor cells. It binds DNA as a heterodimer with MAX. The family also includes S-Myc, encoded by rat or mouse intronless myc gene, which has apoptosis-inducing activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 166 DERRRAQHNEVERRRRDKINNWIVQLSKIIPDChADNSKtgASKGGILSKACDYIRELRQTNQRMQEtfkEAERLQMDNE 245
Cdd:cd11456     2 DSERRRNHNILERQRRNDLRSSFLTLRDHVPEL-VKNEK--AAKVVILKKATEYVHSLQAEEQKLLL---EKEKLQARQQ 75

                          90
                  ....*....|
gi 1958650056 246 LLRQQIEELK 255
Cdd:cd11456    76 QLLKKIEQAR 85

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958650056 170 RAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKtgASKGGILSKACDYIRELRQTNQ 228
Cdd:cd18947     6 RENHSEIERRRRNKMTAYITELSDMVPTCSALARK--PDKLTILRMAVSHMKSLRGTGN 62

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in L-Myc and similar proteins; L-Myc, also termed Class E basic helix-loop-helix protein 38 (bHLHe38), or protein L-Myc-1, or V-myc myelocytomatosis viral oncogene homolog, is a bHLHZip oncoprotein belonging to the Myc oncogene protein family. It binds DNA as a heterodimer with MAX. L-Myc is co-expressed with another Myc family member and has weaker transformation/transactivation activities. L-Myc knockout mouse did not exhibit any phenotypic abnormalities.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 166 DERRRAQHNEVERRRRDKINNWIVQLSKIIPDChADNSKTgaSKGGILSKACDYIRELRQTNQRM-QETFKEAERLQmdn 244
Cdd:cd11457     4 DVAKRKNHNFLERKRRNDLRSRFLALRDEVPGL-ASCSKT--PKVVILSKATEYLRGLVSAERRMaAEKRQLKSRQQ--- 77

                          90
                  ....*....|..
gi 1958650056 245 ELLRqQIEELKN 256
Cdd:cd11457    78 QLLR-RIAQLKG 88

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 1958650056 173 HNEVERRRRDKINNWIVQLSKIIPDChadnskTGASKGGILSKACDYIRELRQTNQRMQ 231
Cdd:cd11393     1 HSIAERKRREKINERIRALRSLVPNG------GKTDKASILDEAIEYIKFLQEQVKVLS 53

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL) and similar proteins; 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 165 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTgaSKGGILSKACDYIRELR 224
Cdd:cd11438     3 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKL--DKLTVLRMAVQHMKTLR 60

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 1958650056 173 HNEVERRRRDKINNWIVQLSKIIPDCHADNsktgasKGGILSKACDYIRELRQTNQRM 230
Cdd:cd11445     6 HNLSERRRRDRINEKMKALQELIPNCNKTD------KASMLDEAIEYLKSLQLQVQMM 57

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein clockwork orange (Cwo) and similar proteins; Cwo is a bHLH-O transcriptional regulator involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958650056 173 HNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASKGGILSKACDYIRELRQTN 227
Cdd:cd11440     6 HRIIEKRRRDRMNNCLADLSRLIPPTYLKKGRGRIEKTEIIEMAIKHIKHLQQHA 60

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 1958650056 168 RRRAQHNEVERRRRDKINNWIVQLSKIIPDCH--ADNSKTGASKGGILSKACDYIRELRQTNQRMQE 232
Cdd:cd19687     1 RRREAHTQAEQKRRDAIKKGYDDLQDIVPTCQqqDDIGSQKLSKATILQRSIDYIQFLHQQKKKQEE 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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958650056 173 HNEVERRRRDKINNWIVQLSKIIPdchaDNSKTgaSKGGILSKACDYIRELRQT 226
Cdd:cd11455    11 HSEAERRRRERINSHLATLRTLLP----NLSKT--DKASLLAEVVQHVKELKRQ 58

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 1958650056 177 ERRRRDKINNWIVQLSKIIPDChadnskTGASKGGILSKACDYIRELRQTNQRMQETFKE 236
Cdd:cd11443     7 ERRRRKKLNDRLYMLRSVVPKI------TKMDRASILGDAIDYVKELLQEINELQDELEG 60

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 4 (Mad4) and similar proteins; Mad4, also termed Max dimerization protein 4, or Max dimerizer 4 (MXD4), or Class C basic helix-loop-helix protein 12 (bHLHc12), or Max-interacting transcriptional repressor MAD4, is a bHLHZip Max-interacting transcriptional repressor that suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation. It is regulated by a transcriptional repressor complex that contains Miz-1 and c-Myc.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 170 RAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASkggILSKACDYIRELRQTNQRmqeTFKEAERLQMDNELLRQ 249
Cdd:cd18929     3 RSSHNELEKHRRAKLRLYLEQLKQLVPLGPDSTRHTTLS---LLKRAKMHIKKLEEQDRK---ALNIKEQLQREHRYLKR 76

                  ....*
gi 1958650056 250 QIEEL 254
Cdd:cd18929    77 RLEQL 81

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 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKtgASkggILSKACDYIRELR 224
Cdd:cd19683     2 SRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDK--AT---VFEFTVAYIKFLR 52

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 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPdchadNSKTGASKGGILSKACDYIRELRQTNQRMQET 233
Cdd:cd11453     3 PRSKHSATEQRRRSKINERLQALRDLIP-----HSDQKRDKASFLLEVIEYIQALQEKVAKLEEQ 62

basic Helix-Loop-Helix (bHLH) domain found in Saccharomyces cerevisiae INO4 and similar proteins; INO4 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. INO4 dimerizes with INO2 and binds to an UAS DNA element to control expression of the genes whose expression is inositol-responsive.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKtgaSKGGILSKACDYIRELRQTNQRMQE 232
Cdd:cd11403     2 KKENHISSEHKRREAIREGFDRLCAIVPALSSSQSR---SEAVVYVKTVEYLKELYERRAKLRS 62

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae phosphate system positive regulatory protein PHO4 and similar proteins; PHO4 is a transcriptional activator that regulates the expression of repressible phosphatase under phosphate starvation conditions in Saccharomyces cerevisiae. The PHO4 protein has four functional domains with the bHLH domain at its carboxyl-terminal region. It regulates transcription by binding to promoter of the genes as a homodimer.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIP------------DCHADNSKTGA------SKGGILSKACDYIRELRQT 226
Cdd:cd11392     2 KRTAHKVAERGRRDRLNAALKELASLMPaefvegkmgadgSASDSNDKEKAaasaagSKAATVEMAIDYIKHLQKE 77

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-binding protein Mnt and similar proteins; Mnt, also termed Class D basic helix-loop-helix protein 3 (bHLHd3), or Myc antagonist MNT, or protein ROX, is a bHLHZip transcriptional repressor that binds DNA as a heterodimer with MAX. It binds to the canonical E box sequence 5'-CACGTG-3' and, with higher affinity, to 5'-CACGCG-3'. Mnt has an important role as an antagonist and regulator of Myc activities and it is a potential tumor suppressor. Mnt is ubiquitously expressed. Mnt-deficient mice shown to exhibit early postnatal lethality.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 170 RAQHNEVERRRRDKINNWIVQLSKIIPdcHADNSKTgaSKGGILSKACDYIRELRQTNQRMQEtfkEAERLQMDNELLRQ 249
Cdd:cd11402     3 REVHNKLEKNRRAHLKECFETLKRQIP--NLDDKKT--SNLNILRSALRYIQILKRKEKEYEH---EMERLAREKIALQQ 75

                  ..
gi 1958650056 250 QI 251
Cdd:cd11402    76 RL 77

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPdchADNSKTGASKGGILSKACDYIRELRQ 225
Cdd:cd11418     1 RVARRNERERRRVQAVNDAFDRLRQHVP---YLKRRKKLSKVKTLRRAIEYIRHLQK 54

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock. It forms heterodimers with another bHLH-PAS protein, Brain-Muscle-Arnt-Like (also known as BMAL or ARNT3 or mop3), which regulates circadian rhythm. BMAL1-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958650056 165 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPdchaDNSKTgASKGGILSKACDYIRELRQT 226
Cdd:cd19734     3 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLP----GNARK-MDKSTVLQKSIDFLRKHKEI 59

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPdchADNSKTGASKGGILSKACDYIRELRQTNQRMQEtfkEAERLQ 241
Cdd:cd19688     3 RRMKHISAEQKRRFNIKICFDTLNSLVS---TLKNSKPISNAITLQKTVEYIAKLQQERTQMQE---ETKRLR 69

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana OBP3-responsive gene 2 (ORG2), 3 (ORG3) and similar proteins; The family includes ORG2 (also termed AtbHLH38, or EN 8) and ORG3 (also termed AtbHLH39, or EN 9), both of which act as bHLH transcription factors.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958650056 169 RRAQHNEVERRRRDKINNWIVQLSKIIPdchADNSKTGASKGGILSKACDYIRELRqtnQRMQETFKEAERL 240
Cdd:cd18914     1 KKLLHNDVERQRRQEMASLFSSLRSLLP---LQYIKGKLSVSDHVDEAVNYIKELQ---EKIKELSEKRDEL 66

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max-associated protein 1 (Mad1) and similar proteins; Mad1, also termed Max dimerization protein 1 (MXD1), or Max dimerizer 1, or protein MAD, is a bHLHZip transcriptional repressor that binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. It thus antagonizes MYC transcriptional activity by competing for MAX.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958650056 170 RAQHNEVERRRRDKINNWIVQLSKIIPDCHADNSKTGASkggILSKACDYIRELRQTNQRMQETFkeaERLQMDNELLRQ 249
Cdd:cd18931     2 RSTHNEMEKNRRAHLRLCLEKLKMLVPLGPESNRHTTLS---LLMKAKLHIKKLEDSDRKAVHQI---DQLQREQRHLKR 75

                  ....*
gi 1958650056 250 QIEEL 254
Cdd:cd18931    76 QLEKL 80

Cell division protein ZapB; ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958650056 223 LRQTNQRMQETFKEAERLQMDNELLRQQIEELKNENALLRAQLQQ 267
Cdd:pfam06005   6 LEQLETKIQAAVDTIALLQMENEELKEENEELKEEANELEEENQQ 50

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein ABA-INDUCIBLE bHLH-TYPE (AIB) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AIB and MYC proteins (MYC2, MYC3 and MYC4). AIB, also termed AtbHLH17, or EN 35, is a transcription activator that regulates positively abscisic acid (ABA) response. MYC2, also termed protein jasmonate insensitive 1, or R-homologous Arabidopsis protein 1 (RAP-1), or AtbHLH6, or EN 38, or Z-box binding factor 1 protein, is a transcriptional activator involved in abscisic acid (ABA), jasmonic acid (JA), and light signaling pathways. MYC3, also termed protein altered tryptophan regulation 2, or AtbHLH5, or transcription factor ATR2, or EN 36, is a transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. MYC4, also termed AtbHLH4, or EN 37, is a transcription factor involved in jasmonic acid (JA) gene regulation. MYC2, together with MYC3 and MYC4, controls additively subsets of JA-dependent responses.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958650056 173 HNEVERRRRDKINNWIVQLSKIIPDChadnSKTgaSKGGILSKACDYIRELRQTNQRMqetfkEAERLQMDNELLRQ 249
Cdd:cd11449     9 HVEAERQRREKLNQRFYALRAVVPNV----SKM--DKASLLGDAISYINELKSKVQDM-----ETEKKEMKRQESEK 74

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins; NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958650056 180 RRDKINNWIVQLSKIIPDCHADNSKTgaSKGGILSKACDYIR 221
Cdd:cd19697    11 RRDLINAEIRELRDLLPLPESTRQRL--SQLQIMSLACVYIR 50