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 1924575318  319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA---------KAIDYIRFLQHSNQKLKQENLSLRTAVHK 384
Cdd:cd18921      1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAklnksavlrKAIDYIRFLQQSNQKLKQENMALKMAVQK 75

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 1924575318   49 PPYAGSGAGGTdPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIkeeSVP 128
Cdd:pfam05109  476 PTPAGTTSGAS-PVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAV---TTP 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  129 LSILQTPTP---QPLPGALLP---QSFPAPA---PPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPLpglpLASPPGVPPV 199
Cdd:pfam05109  552 TPNATSPTPavtTPTPNATIPtlgKTSPTSAvttPTPNATSPTVGETSPQANTTNHTLGGTSSTPV----VTSPPKNATS 627

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  200 SLHT---QVQSVVPQQLLTVTAAPTAAPVTTTVTSQIQQVPVLLQPHFIKADSLL-LTAMKTDGATVKAAGLSPLVSGTT 275
Cdd:pfam05109  628 AVTTgqhNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPLLTSAHPTGGENITqVTPASTSTHHVSTSSPAPRPGTTS 707

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 1924575318  276 VQTGPlptlvsGGTILATVPLVVDAEKLPINRLAAGSKAPASAQS 320
Cdd:pfam05109  708 QASGP------GNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKT 746

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 1924575318  319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA---------KAIDYIRFLQHSNQKLKQENLSLRTAVHK 384
Cdd:cd18921      1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAklnksavlrKAIDYIRFLQQSNQKLKQENMALKMAVQK 75

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 1924575318   87 LSGPQAAPSPlsPPQPAPTPLKMYPSMPafsPGPGIKeesvPLSILQT---PTPQPLPGALLPQSFPAPAPP-------Q 156
Cdd:pfam03154  366 LPNPQSHKHP--PHLSGPSPFQMNSNLP---PPPALK----PLSSLSThhpPSAHPPPLQLMPQSQQLPPPPaqppvltQ 436

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1924575318  157 FSSTPVLGYPSPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVP 210
Cdd:pfam03154  437 SQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMP 490

EBNA-3B; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   87 LSGPQAAPSPLSPPQPAPTPLKmypsMPAFSPGPGIKEESVPlsiLQTPTPQPLPGALL-PQSFPAPAPPQfSSTPVLGY 165
Cdd:PHA03378   704 MRPPAAPPGRAQRPAAATGRAR----PPAAAPGRARPPAAAP---GRARPPAAAPGRARpPAAAPGRARPP-AAAPGAPT 775

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1924575318  166 PSPPggfsTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVPQQ 212
Cdd:PHA03378   776 PQPP----PQAPPAPQQRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQ 818

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318    95 SPLSPPQPAPTPLKMYPSMPAFSPGPGiKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFST 174
Cdd:smart00818   43 SQQHPPTHTLQPHHHIPVLPAQQPVVP-QQPLMPVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPVH 121

                            90       100
                    ....*....|....*....|....*
gi 1924575318   175 GSPPGNTQQPLPGLPLASPPgvPPV 199
Cdd:smart00818  122 PIPPLPPQPPLPPMFPMQPL--PPL 144

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 1924575318  319 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA---------KAIDYIRFLQHSNQKLKQENLSLRTAVHK 384
Cdd:cd18921      1 PSKGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAklnksavlrKAIDYIRFLQQSNQKLKQENMALKMAVQK 75

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 1924575318  321 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA---------KAIDYIRFLQHSNQKLKQENLSLRTAVHKSK 386
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 1924575318  323 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTE--------------------------AKAIDYIRFLQHSNQKLKQENL 376
Cdd:cd11395      2 RKRLPHNAIEKRYRSNLNTKIERLRDAIPSLRspegksddgglgglapttklskatilTKAIEYIRHLEQENERLEEENE 81

                   ....*.
gi 1924575318  377 SLRTAV 382
Cdd:cd11395     82 ELRQQV 87

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 1924575318  324 KRTAHNAIEKRYRSSINDKIIELKDLV-----------VGTEAKA-IDYIRFLQHSNQKLKQ 373
Cdd:cd11397      5 KKDNHNMIERRRRFNINDRIKELGTLLpksndpdmrwnKGTILKAsVDYIRKLQKEQERLRQ 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 1924575318  325 RTAHNAIEKRYRSSINDKIIELKDLVVGTEAKA---------IDYIRFLQHSNQKL 371
Cdd:cd11453      4 RSKHSATEQRRRSKINERLQALRDLIPHSDQKRdkasfllevIEYIQALQEKVAKL 59

helix loop helix domain;

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1924575318   329 NAIEKRYRSSINDKIIELKDLVVGTEA-----------KAIDYIRFLQHSNQK 370
Cdd:smart00353    1 NARERRRRRKINEAFDELRSLLPTLPKnkklskaeilrLAIEYIKSLQEELQK 53

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 1924575318  323 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTE---------AKAIDYIRFLQHSNQKLKQE 374
Cdd:cd11398      6 QRRDNHKEVERRRRENINEGINELAALVPGNAreknkgailARAVEYIQELQETEAKNIEK 66

EBNA-3B; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   87 LSGPQAAPSPLSPPQPAPTPLKmypsMPAFSPGPGIKEESVPlsiLQTPTPQPLPGALL-PQSFPAPAPPQfSSTPVLGY 165
Cdd:PHA03378   704 MRPPAAPPGRAQRPAAATGRAR----PPAAAPGRARPPAAAP---GRARPPAAAPGRARpPAAAPGRARPP-AAAPGAPT 775

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1924575318  166 PSPPggfsTGSPPGNTQQPLPGLPLASPPGVPPVSLHTQVQSVVPQQ 212
Cdd:PHA03378   776 PQPP----PQAPPAPQQRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQ 818

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 1924575318  324 KRTAHNAIEKRYRSSINDKIIELKDLVVGTE----------AKAIDYIRFLQHSNQKLKQENLSLRTAV 382
Cdd:cd11404      2 RRLNHVRSEKKRRELIKKGYDELCALVPGLDpqkrtkadilQKAADWIQELKEENEKLEEQLDELKEAA 70

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins; MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  312 SKAPASAQSRgEKRTAHNAIEKRYRSSINDKIIELKDLV-----------VGTEAKA-IDYIRFLQHSNQKLKQENLSLR 379
Cdd:cd18926      2 SEARALAKER-QKKDNHNLIERRRRFNINDRIKELGTLIpksndpdmrwnKGTILKAsVDYIRKLQREQQRAKELENRQK 80

                   ....*....
gi 1924575318  380 TAVHKSKSL 388
Cdd:cd18926     81 KLEHANRHL 89

EBNA-3B; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   44 PGLFDPPYAGSGAGGTDPASPDTSSPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKmypsMPAFSPGPGIK 123
Cdd:PHA03378   691 PGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRAR----PPAAAPGRARP 766

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1924575318  124 EESVPLSILQTPTPQPLPGAL-LPQSFPAPA-PPQFSSTPV-LGYPSPPG 170
Cdd:PHA03378   767 PAAAPGAPTPQPPPQAPPAPQqRPRGAPTPQpPPQAGPTSMqLMPRAAPG 816

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   93 APSPLSPPQPAPTPLKMYPSMPAfSPGPGIKEESVPLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPvlGYPSPPGGF 172
Cdd:PHA03247  2699 ADPPPPPPTPEPAPHALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP--PAPAPPAAP 2775

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1924575318  173 STGSPPGNTQQP-------LPGLPLASPPGVPPVSLHTQVQSVVPQQ 212
Cdd:PHA03247  2776 AAGPPRRLTRPAvaslsesRESLPSPWDPADPPAAVLAPAAALPPAA 2822

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  313 KAPASAQSRgEKRTAHNAIEKRYRSSINDKIIEL-------KDLVV----GTEAKA-IDYIRFLQHSNQKLKQ-ENLSLR 379
Cdd:cd18927      1 EARALAKER-QKKDNHNLIERRRRFNINDRIKELgtlipktNDLDVrwnkGTILKAsVDYIKRMQKDLQRSRElENHSRR 79

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 1924575318  320 SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAK----------AIDYIRFLQHSNQKL 371
Cdd:cd18910      1 RREKKRESHNEVERRRKDKINAGINKIGELLPDRDAKkqsknmileqAYKYIVELKKKNDKL 62

basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1924575318  332 EKRYRSSINDKIIELKDLVVGTEA-----------KAIDYIRFLQ 365
Cdd:cd00083      1 ERRRRDKINDAFEELKRLLPELPDskklskasilqKAVEYIRELQ 45

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 1924575318  325 RTAHNAIEKRYRSSINDKIIELKDLVV---GTEA-------KAIDYIRFLQHSNQKLKQENLSLR 379
Cdd:cd19690      1 RVSHKLAERKRRKEMKELFEDLRDALPqerGTKAskweiltKAISYIQQLKRHIRELRSEVNDLR 65

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   94 PSPLSPPQPAPTPLKMYPSMpaFSPGPgikeESVPLSILQTPTPQPLPgaLLPQSFPAPAPPQF---SSTPVLGYP---- 166
Cdd:pfam15279  175 GKPQQHPPPSPLPAFMEPSS--MPPPF----LRPPPSIPQPNSPLSNP--MLPGIGPPPKPPRNlgpPSNPMHRPPfsph 246

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1924575318  167 -SPPGGFSTGSPPGNTQQPLPGLPLASPPGVPPVS 200
Cdd:pfam15279  247 hPPPPPTPPGPPPGLPPPPPRGFTPPFGPPFPPVN 281

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 1924575318  328 HNAIEKRYRSSINDKIIELKDLVVGTE--------------AKAIDYIRFLQHSNQK 370
Cdd:cd11396      2 HNEVERRRRDKINNWIVKLAKIVPDCEkdnskqgqskggilSKACDYIQELRSQNER 58

putative scaffolding protein

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   83 LEAFLSGPQAAPSPLSPPQPAPTPLkMYPSMPAFSPGPGIKEEsvplsiLQTPTPQPLP---GALLPQSFP-APAPPQFS 158
Cdd:PHA01929     8 LPPGLAGLVANVPPAAAPTPQPNPV-IQPQAPVQPGQPGAPQQ------LAIPTQQPQPvptSAMTPHVVQqAPAQPAPA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1924575318  159 STPVLGYPSP----PGGFSTGSPPGNTQQPLPGLPLASPPGVPPVS 200
Cdd:PHA01929    81 APPAAGAALPealeVPPPPAFTPNGEIVGTLAGNLEGDPQLAPSVS 126

ORF080 virion core protein; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   95 SPLSPPQPAPTPlkmYPSMPAFSPgpgikeesvplsilqtptPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFST 174
Cdd:PHA02682    80 SPLAPSPACAAP---APACPACAP------------------AAPAPAVTCPAPAPACPPATAPTCPPPAVCPAPARPAP 138

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1924575318  175 GSPPGNTQ-QPLPGLPLASP-PGVPPVSLHTQV 205
Cdd:PHA02682   139 ACPPSTRQcPPAPPLPTPKPaPAAKPIFLHNQL 171

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318   49 PPYAGSGAGGTDPASPDTS-SPGSLSPPPATLSSSLEAFLSGPQAAPSPLSPPQPAPTPLKMYPSMPAFSPGPGIKEESV 127
Cdd:PHA03247  2760 PPTTAGPPAPAPPAAPAAGpPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  128 PLSILQTPTPQPLPGALLPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQ---QPLPGLPLASPPgVPPVSLHTQ 204
Cdd:PHA03247  2840 PPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRStesFALPPDQPERPP-QPQAPPPPQ 2918

                   ....*...
gi 1924575318  205 VQSVVPQQ 212
Cdd:PHA03247  2919 PQPQPPPP 2926

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect embryo arrest 8 (AtMEE8) and similar proteins; AtMEE8, also termed AtbHLH108, or EN 132, is a bHLH transcription factor required during early embryo development, for the endosperm formation.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1924575318  328 HNAIEKRYRSSINDKIIELKDL---------VVGTEAKAIDYIRFLQHSNQKLKQE 374
Cdd:cd19698      1 HNLLEKKRRERIKDKIEILKGLtpnctpksdIASILSCVIDYIKSLLLQVEKLSMG 56

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 1924575318  331 IEKRYRSSINDKIIELKDLVVGTEAK--------------AIDYIRFLQ 365
Cdd:cd19685      1 SEKRRRQRINDKLNQLKELLPPNLSKqsrsklskaeilemAITELRRLQ 49

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 1924575318  324 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEA-----------KAIDYIRFLQ---HSNQK----LKQENLSLR 379
Cdd:cd11400      1 KRRLHNVLERQRRNDLKNSFEKLRDLVPELADnekaskvvilkKATEYIKQLQqeeKKLEKekdkLKARNEQLR 74

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1924575318  106 PLKMYPSMPaFSPGPGIKEESVPLSILQTPTPqplpgallPQSFPAPAPPQFSSTPVLGYPSPPGGFSTGSPPGNTQQPL 185
Cdd:cd21577      2 PVKTDMETS-FYSPSHSQLEPVDLSLSKRSSP--------PSSSSSSSSSSSSSSSPSSRASPPSPYSKSSPPSPPQQRP 72

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1924575318  186 PGLPLASPPGVPPVSLHT--------QVQSVVPQQL 213
Cdd:cd21577     73 LSPPLSLPPPVAPPPLSPgsvpgglpVISPVMVQPV 108