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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453040303  313 QSRGEKRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSA 384
Cdd:cd18921     1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQQSNQKLKQENMALKMA 72

Predicted ATPase [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  562 RPHSGPAVHFWRHRKQADLDLARGDFAQAAQQLWLALQALGRP----LPTSNLDLACSLLWNLVRHLLQRLWVGRWLAGQ 637
Cdd:COG3899   736 PPDPEEEYRLALLLELAEALYLAGRFEEAEALLERALAARALAalaaLRHGNPPASARAYANLGLLLLGDYEEAYEFGEL 815

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  638 AGGLQRDYRLRKDARASARDAAVVYHKLHQLHAmgkyTGGHLVASNLALSALNLAECAGDAISMATLAEIYVAAALRVKT 717
Cdd:COG3899   816 ALALAERLGDRRLEARALFNLGFILHWLGPLRE----ALELLREALEAGLETGDAALALLALAAAAAAAAAAAALAAAAA 891

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  718 SLPRALHFLTRFFLSSARQACLAQSGAVPLAMQWLCHpVGHRFFVDGDWAVHGAPQESLYSVAGNPVDPLAQVTRLFCEH 797
Cdd:COG3899   892 AAARLLAAAAAALAAAAAAAALAAAELARLAAAAAAA-AALALAAAAAAAAAAALAAAAAAAALAAALALAAAAAAAAAA 970

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  798 LLERALNCIAQPSPGAADGDREFSDALGYLQLLNSCSDAVGAPACSFSVSSSMATTTGTDPVAKWWASLTAVVIHWLRRD 877
Cdd:COG3899   971 ALAAAAAAAAAAAAAAAAAALEAAAAALLALLAAAAAAAAAAAALAAALLAAALAALAAAAAAAALLAAAAALALLAALA 1050

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  878 EEAAERLYPLVEHIPQVLQETERPLPRAALYSFKAARALLDHRKVESSPASLAICEKASGYLRDSLASTSTASSIDKAMQ 957
Cdd:COG3899  1051 AAAAAAAAAAALAAAAALLAAAAAAAAAAAAAAAAAALAAALAAAALAAAAAAALALAAALAALALAAALAALALAAAAR 1130

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  958 LLLCDLLLVARTSLWRRQQSAASAQGAHGTSNGPQASALELRGFQHDLSSLRRLAQSFRPAMRRVFLHEATARLMAGASP 1037
Cdd:COG3899  1131 AAAALLLLAAALALALAALLLLAALLLALALLLLALAALALAAALAALAAALLAAAAAAAAAAALLAALLALAARLAALL 1210

                         490       500       510
                  ....*....|....*....|....*....|....
gi 453040303 1038 ARTHQLLDRSLRRRAGSSGKGGAAAELEPRPTWR 1071
Cdd:COG3899  1211 ALALLALEAAALLLLLLLAALALAAALLALRLLA 1244

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453040303  313 QSRGEKRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSA 384
Cdd:cd18921     1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQQSNQKLKQENMALKMA 72

helix loop helix domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 453040303    323 NAIEKRYRSSINDKIVELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQK 373
Cdd:smart00353    1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQEELQK 53

Predicted ATPase [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  562 RPHSGPAVHFWRHRKQADLDLARGDFAQAAQQLWLALQALGRP----LPTSNLDLACSLLWNLVRHLLQRLWVGRWLAGQ 637
Cdd:COG3899   736 PPDPEEEYRLALLLELAEALYLAGRFEEAEALLERALAARALAalaaLRHGNPPASARAYANLGLLLLGDYEEAYEFGEL 815

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  638 AGGLQRDYRLRKDARASARDAAVVYHKLHQLHAmgkyTGGHLVASNLALSALNLAECAGDAISMATLAEIYVAAALRVKT 717
Cdd:COG3899   816 ALALAERLGDRRLEARALFNLGFILHWLGPLRE----ALELLREALEAGLETGDAALALLALAAAAAAAAAAAALAAAAA 891

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  718 SLPRALHFLTRFFLSSARQACLAQSGAVPLAMQWLCHpVGHRFFVDGDWAVHGAPQESLYSVAGNPVDPLAQVTRLFCEH 797
Cdd:COG3899   892 AAARLLAAAAAALAAAAAAAALAAAELARLAAAAAAA-AALALAAAAAAAAAAALAAAAAAAALAAALALAAAAAAAAAA 970

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  798 LLERALNCIAQPSPGAADGDREFSDALGYLQLLNSCSDAVGAPACSFSVSSSMATTTGTDPVAKWWASLTAVVIHWLRRD 877
Cdd:COG3899   971 ALAAAAAAAAAAAAAAAAAALEAAAAALLALLAAAAAAAAAAAALAAALLAAALAALAAAAAAAALLAAAAALALLAALA 1050

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  878 EEAAERLYPLVEHIPQVLQETERPLPRAALYSFKAARALLDHRKVESSPASLAICEKASGYLRDSLASTSTASSIDKAMQ 957
Cdd:COG3899  1051 AAAAAAAAAAALAAAAALLAAAAAAAAAAAAAAAAAALAAALAAAALAAAAAAALALAAALAALALAAALAALALAAAAR 1130

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  958 LLLCDLLLVARTSLWRRQQSAASAQGAHGTSNGPQASALELRGFQHDLSSLRRLAQSFRPAMRRVFLHEATARLMAGASP 1037
Cdd:COG3899  1131 AAAALLLLAAALALALAALLLLAALLLALALLLLALAALALAAALAALAAALLAAAAAAAAAAALLAALLALAARLAALL 1210

                         490       500       510
                  ....*....|....*....|....*....|....
gi 453040303 1038 ARTHQLLDRSLRRRAGSSGKGGAAAELEPRPTWR 1071
Cdd:COG3899  1211 ALALLALEAAALLLLLLLAALALAAALLALRLLA 1244

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453040303  313 QSRGEKRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSA 384
Cdd:cd18921     1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQQSNQKLKQENMALKMA 72

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 453040303  315 RGEKRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSA-HKSK 388
Cdd:cd18922     3 EGERRTTHNIIEKRYRSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMALKLAnQKNK 77

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family and similar proteins; 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. The family also includes Saccharomyces cerevisiae transcription factor HMS1 (also termed high-copy MEP suppressor protein 1) and serine-rich protein TYE7. HMS1 is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. TYE7, also termed basic-helix-loop-helix protein SGC1, is a putative bHLHzip transcription activator required for Ty1-mediated glycolytic gene expression. TYE7 N-terminal is extremely rich in serine residues. It binds DNA on E-box motifs, 5'-CANNTG-3'. TYE7 is not essential for growth.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303  317 EKRTAHNAIEKRYRSSINDKIVELKDLV-----------------VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENL 379
Cdd:cd11395     2 RKRLPHNAIEKRYRSNLNTKIERLRDAIpslrspegksddgglggLAPTTKLSKATILTKAIEYIRHLEQENERLEEENE 81

                  ....*.
gi 453040303  380 TLRSAH 385
Cdd:cd11395    82 ELRQQV 87

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 453040303  322 HNAIEKRYRSSINDKIVELKDLV-----VGTEAKLNKSAVLRKAIDYIRFLQHSNQ 372
Cdd:cd11387     2 HNAVERRRRDNINEKIQELGSLVppsrlETKDLKPNKGSILSKAVEYIRELQNQNQ 57

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453040303  317 EKRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE 377
Cdd:cd11398     6 QRRDNHKEVERRRRENINEGINELAALVPGNAREKNKGAILARAVEYIQELQETEAKNIEK 66

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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 453040303  319 RTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 374
Cdd:cd11453     4 RSKHSATEQRRRSKINERLQALRDLIPHSDQKRDKASFLLEVIEYIQALQEKVAKL 59

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 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLVVG-TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLR 382
Cdd:cd11404     2 RRLNHVRSEKKRRELIKKGYDELCALVPGlDPQKRTKADILQKAADWIQELKEENEKLEEQLDELK 67

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLVVGTEA-KLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLR 382
Cdd:cd11406     1 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGeKASRAQILKKATEYIQYMRRKNHTHQQDIDDLK 66

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 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLV--------VGTEaKLNKSAVLRKAIDYIRFLQHsnQKLKQE 377
Cdd:cd19687     2 RREAHTQAEQKRRDAIKKGYDDLQDIVptcqqqddIGSQ-KLSKATILQRSIDYIQFLHQ--QKKKQE 66

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 453040303  317 EKRTAHNAIEKRYRSSINDKIVELKDLVVGT---EAKLNKSAVLRKAIDYIRFLQHSNQKLKQ-ENLTLRSAHKSKSL 390
Cdd:cd18927    10 QKKDNHNLIERRRRFNINDRIKELGTLIPKTndlDVRWNKGTILKASVDYIKRMQKDLQRSRElENHSRRLEMTNKQL 87

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins; USF1, also termed Class B basic helix-loop-helix protein 11 (bHLHb11), or major late transcription factor 1, 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. It is ubiquitously expressed and involved in the transcription activation of various functional genes implicated in lipid and glucose metabolism, stress response, immune response, cell cycle control and tumour suppression. USF-1 recruits chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. Genetic polymorphisms of USF1 are associated with some metabolic and cardiovascular diseases, like diabetes, atherosclerosis, coronary artery calcifications and familial combined hyperlipidaemia (FCHL).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 453040303  315 RGEKRTA-HNAIEKRYRSSINDKIVELKDLVV-----GTEAKLNKSAVLRKAIDYIRFLQHSNQK 373
Cdd:cd18924     1 RDEKRRAqHNEVERRRRDKINNWIVQLSKIIPdcsmeSTKSGQSKGGILSKACDYIQELRQSNHR 65

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 453040303  322 HNAIEKRYRSSINDKIVELKDLVVGTEAKLN-----KSAVLRKAIDYIRFLQHSNQK 373
Cdd:cd11396     2 HNEVERRRRDKINNWIVKLAKIVPDCEKDNSkqgqsKGGILSKACDYIQELRSQNER 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 453040303  314 SRGEKRTAHNAIEKRYRSSINDKIVELKDLVVGTEA-KLNKSAVLRKAIDYIRFLQHSNQKL 374
Cdd:cd18910     1 RREKKRESHNEVERRRKDKINAGINKIGELLPDRDAkKQSKNMILEQAYKYIVELKKKNDKL 62

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor AP-4 (TFAP4) and similar proteins; TFAP4, also termed activating enhancer-binding protein 4, or Class C basic helix-loop-helix protein 41 (bHLHc41), is a bHLHzip transcription factor that activates both viral and cellular genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition by binding to the symmetrical DNA sequence 5'-CAGCTG-3'.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 374
Cdd:cd11419     4 RREIANSNERRRMQSINAGFQSLRTLLpHCDGEKLSKAAILQQTAEYIFSLEQEKTRL 61

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLN--KSAVLRKAIDYIRFLQ---HSNQK----LKQENLTLRS 383
Cdd:cd11400     1 KRRLHNVLERQRRNDLKNSFEKLRDLVPELADNEKasKVVILKKATEYIKQLQqeeKKLEKekdkLKARNEQLRK 75

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and similar proteins; TFEC, also termed Class E basic helix-loop-helix protein 34 (bHLHe34), or transcription factor EC-like (TFEC-L), is a bHLHzip transcriptional regulator that acts as a repressor or an activator and regulates gene expression in macrophages. It plays an important role in the niche to expand hematopoietic progenitors through the modulation of several cytokines.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 453040303  317 EKRTAHNAIEKRYRSSINDKIVELKDLVVGT---EAKLNKSAVLRKAIDYIRFLQHSNQKLKQ 376
Cdd:cd18925     4 QKKDNHNLIERRRRYNINYRIKELGTLIPKSndpDMRWNKGTILKASVEYIKWLQKEQQRARE 66

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins; 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 453040303  319 RTAHNAIEKRYRSSINDKIVELKDLVV---GTEAklNKSAVLRKAIDYIRFLQHSNQKLKQENLTLR 382
Cdd:cd19690     1 RVSHKLAERKRRKEMKELFEDLRDALPqerGTKA--SKWEILTKAISYIQQLKRHIRELRSEVNDLR 65

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
                  ....*....|....*....|....*....|....*....|....
gi 453040303  326 EKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDYIRFLQH 369
Cdd:cd11444     5 RRRGEEAIERRLRALRRLVPGGRESMEVEELLQETADYIMFLEM 48

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family; HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. They 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. HERP proteins are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLV------VGTeAKLNKSAVLRKAIDYIRFLQ 368
Cdd:cd11407     1 RKKRRGIIEKRRRDRINNSLAELRRLVptafekQGS-AKLEKAEILQMTVDHLKMLH 56

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 453040303  326 EKRYRSSINDKIVELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSahKSKSLKD 392
Cdd:cd11446     5 EKLRRDKLNERFMELSNVLePGRPPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQE--ESKELKA 70

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 453040303  319 RTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAIDyirFLQHSNQ 372
Cdd:cd11441     1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIA---FLRKHKE 51

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins; dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 453040303  318 KRTAHNAIEKRYRSSINDKIVELKDLVVGTEAKLNKSAVLRKAidyIRFLQHSNQKLKQ 376
Cdd:cd19735    10 KRKSRNLSEKKRRDQFNVLINELCSMVSTSNRKMDKSTVLKST---IAFLKNHNEVTMQ 65

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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 453040303  319 RTAHNAIEKRYRSSINDKIVELKDLVVGTEA---KLNKSAVLRKAIDYIRFLQ 368
Cdd:cd11438     8 REAHSQIEKRRRDKMNSFIDELASLVPTCNAmsrKLDKLTVLRMAVQHMKTLR 60

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 453040303  317 EKRtahNAIEKRYRSSINDKIVELKDLV--VGTEAKLNKSAVLRKAIDYIRFLQ 368
Cdd:cd11418     3 ARR---NERERRRVQAVNDAFDRLRQHVpyLKRRKKLSKVKTLRRAIEYIRHLQ 53

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303    58 DTGPSSPGASSPESFSSPASLGSSLEAFLGGPKVTPAPLSPPPSAPTAVKMYPSVPPFSPGPG---IKEEPVPLTILQPP 134
Cdd:pfam03154  140 DNRSTSPSIPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSapsVPPQGSPATSQPPN 219

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303   135 APQP--SPGTLLPPSFPPPPVQL-SPAPVLGYSSLPSGFSGTLPGNTQQT-------PSSLPLGSTPGISPTPLHTQ--- 201
Cdd:pfam03154  220 QTQStaAPHTLIQQTPTLHPQRLpSPHPPLQPMTQPPPPSQVSPQPLPQPslhgqmpPMPHSLQTGPSHMQHPVPPQpfp 299

                          170       180       190
                   ....*....|....*....|....*....|.
gi 453040303   202 --VQSSAAQQPPPASaaPRMSTVASQIQQVP 230
Cdd:pfam03154  300 ltPQSSQSQVPPGPS--PAAPGQSQQRIHTP 328

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303    44 PGLFDAPYAGGETGDTGPSSpgASSPESFSSPASLGssleaflggPKVTPAPLSPPPSAPTAVKMYPSVPPFSPGPGIKE 123
Cdd:pfam05109  432 PTLNTTGFAAPNTTTGLPSS--THVPTNLTAPASTG---------PTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTE 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303   124 EPVP-LTILQPPAPQPSPGTLLPPSFPPPPVQLSPAPVLGYSSLPSGFSGTLPGNTQQTPS-SLPlgsTPGISPTPLHTQ 201
Cdd:pfam05109  501 SKAPdMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAvTTP---TPNATIPTLGKT 577

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453040303   202 VQSSAAQQPPPASAAPRMSTVASQ----------IQQVPVVLQPHfIKADSLLLTAVKTDTGATMKTAGI------NTLA 265
Cdd:pfam05109  578 SPTSAVTTPTPNATSPTVGETSPQanttnhtlggTSSTPVVTSPP-KNATSAVTTGQHNITSSSTSSMSLrpssisETLS 656

                   ....
gi 453040303   266 PGTA 269
Cdd:pfam05109  657 PSTS 660

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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 453040303  320 TAHNAIEKRYRSSINDKIVELKDLVVGTeAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN 378
Cdd:cd11451     4 GSHAMAERRRREKLNERFITLRSMVPFV-TKMDKVSILGDAIEYLKQLQRRVEELESRR 61

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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 453040303  319 RTAHNAIEKRYRSSINDKIVELKDLV--VGTEAKLNKSAVLRKAIDYIRFLQHS 370
Cdd:cd11390     1 RNAANARERRRMHDLNDAFEALRKVLptVPPDKKLSKIETLRLAINYIAALSDL 54

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
                  ....*....|....*....|....*....|....*....|....*....
gi 453040303  320 TAHNAIEKRYRSSINDKIVELKDLvVGTEAKLNKSAVLRKAIDYIRFLQ 368
Cdd:cd11445     4 EVHNLSERRRRDRINEKMKALQEL-IPNCNKTDKASMLDEAIEYLKSLQ 51

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453040303  326 EKRYRSSINDKIVELKDLVVGTeAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLTLRSAHKS 387
Cdd:cd11450    11 ERNRRQKLNQRLFALRSVVPNI-TKMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPS 71

Predicted ATPase [General function prediction only];