nuclear export signal 2 (NES2) and nuclear import signal (NLS) domains found in carbohydrate-responsive element-binding protein (ChREBP), MLX-interacting protein (MLXIP), and similar proteins; This family includes two transcription factors: ChREBP and MLXIP. ChREBP, also called class D basic helix-loop-helix protein 14 (bHLHd14), Max-like protein (MLX) interactor or MIO, MLX-interacting protein-like (MLXIPL), WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), functions at two levels; nuclear localization and DNA binding. ChREBP binds to the canonical and non-canonical E box sequences 5'-CACGTG-3'. It also binds DNA as a heterodimer with TCFL4/MLX. MLXIP, also called class E basic helix-loop-helix protein 36 (bHLHe36), transcriptional activator MondoA, or MIR, is a novel basic helix-loop-helix-leucine zipper transcriptional activator that constitutes a positive branch of a max-like network. MLXIP binds DNA by forming a heterodimer with Max-like protein (MLX), and activates transcription. It binds to the canonical E box sequence 5'-CACGTG-3'. MLXIP plays a role in transcriptional activation of glycolytic target genes and is involved in glucose-responsive gene regulation. Members in this family may contain functional domains, including two nuclear export signals, NES1 and NES2, and a nuclear import signal (NLS) in the N-terminal region. This model corresponds to NES2 and NLS domains.

                          10
                  ....*....|....*....
gi 1317840698   1 MREYHKWRIYYKKRLRKSS 19
Cdd:cd21771    98 MKEYHKWRIYYKKRLRKSS 116

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLsaQPSLKVSKATTLQKTAEYILMLQ 539
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPTL--PPDKKLSKAEILRLAIEYIKHLQ 53

nuclear export signal 2 (NES2) and nuclear import signal (NLS) domains found in carbohydrate-responsive element-binding protein (ChREBP), and similar proteins; ChREBP, also called class D basic helix-loop-helix protein 14 (bHLHd14), Max-like protein (MLX) interactor or MIO, MLX-interacting protein-like (MLXIPL), WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a large transcription factor that functions at two levels, nuclear localization and DNA binding. It binds to the canonical and non-canonical E box sequences 5'-CACGTG-3'. It also binds DNA as a heterodimer with TCFL4/MLX. ChREBP contains functional domains, including two nuclear export signals, NES1 and NES2, and a nuclear import signal (NLS) in the N-terminal region. This model corresponds to NES2 and NLS domains.

                          10
                  ....*....|....*....
gi 1317840698   1 MREYHKWRIYYKKRLRKSS 19
Cdd:cd21771    98 MKEYHKWRIYYKKRLRKSS 116

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 1317840698 159 LAPEMPSPASSSSSSGMTPHSGNTRLQARNSCSGPLDPNPflSSEFLLPEDPKT--KIPPAPGPTPLLPFPTPVKVHGLE 236
Cdd:pfam03154 300 LTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQP--PREQPLPPAPLSmpHIKPPPTTPIPQLPNPQSHKHPPH 377

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698 237 PCTPSPF--PTMAPPPSLLPEESLLSARFPFTSAPPA----PGVSTLPAPTTFVPTPQPGPGPVPFSVDHLPHGYLEPV- 309
Cdd:pfam03154 378 LSGPSPFqmNSNLPPPPALKPLSSLSTHHPPSAHPPPlqlmPQSQQLPPPPAQPPVLTQSQSLPPPAASHPPTSGLHQVp 457

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698 310 ----FGPHFTVPQG----MQPRCKPSSPSPGGQKASPPTLASATASPTATATARDNNPCLTqlLRAAKPEQALEPPTMPG 381
Cdd:pfam03154 458 sqspFPQHPFVPGGpppiTPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQ--IKEEALDEAEEPESPPP 535

                         250
                  ....*....|....*..
gi 1317840698 382 TLLRPpeSPQDTVSEIP 398
Cdd:pfam03154 536 PPRSP--SPEPTVVNTP 550

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins; The family includes MLXIP and MLXIPL. 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. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1317840698 483 ENRRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQPSLKVSKATTLQKTAEYILMLQQERAAMQEEAQQLRDEI 556
Cdd:cd11405     1 EQRRLSHISAEQKRRFNIKSGFDTLQSLIPSLGQNPNQKVSKAAMLQKAAEYIKSLKRERQQMQEEAEQLRQEI 74

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1317840698 484 NRRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQP---SLKVSKATTLQKTAEYILMLQQERAAMQEEAQQLRDEI 556
Cdd:cd19687     1 RRREAHTQAEQKRRDAIKKGYDDLQDIVPTCQQQDdigSQKLSKATILQRSIDYIQFLHQQKKKQEEELSALRKEV 76

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 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQPslKVSKATTLQKTAEYILMLQQERAAMQEEAQQLRDEIEELNA 561
Cdd:cd11400     1 KRRLHNVLERQRRNDLKNSFEKLRDLVPELADNE--KASKVVILKKATEYIKQLQQEEKKLEKEKDKLKARNEQLRK 75

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 1317840698 483 ENRRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQ-------------PSLKVSKATTLQKTAEYILMLQQERAAMQEEA 549
Cdd:cd11395     1 PRKRLPHNAIEKRYRSNLNTKIERLRDAIPSLRSPegksddgglgglaPTTKLSKATILTKAIEYIRHLEQENERLEEEN 80

                  ....*..
gi 1317840698 550 QQLRDEI 556
Cdd:cd11395    81 EELRQQV 87

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and similar proteins; INO2 is a positive regulatory factor required for depression of the co-regulated phospholipid biosynthetic enzymes in Saccharomyces cerevisiae. It is also involved in the expression of ITR1.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQPSLKVSKATTLQKTAEYILMLQQERAAMQEEA 549
Cdd:cd11388     3 KKWKHVEAEKKRRNQIKKGFEDLINLINYPRNNNEKRISKSELLNKAVDDIRGLLKANEQLQEEI 67

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 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQPSLkvSKATTLQKTAEYILMLQQERAAMQEEA 549
Cdd:cd11403     2 KKENHISSEHKRREAIREGFDRLCAIVPALSSSQSR--SEAVVYVKTVEYLKELYERRAKLRSQL 64

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQpslKVSKATTLQKTAEYILMLQQERAAM 545
Cdd:cd11419     4 RREIANSNERRRMQSINAGFQSLRTLLPHCDGE---KLSKAAILQQTAEYIFSLEQEKTRL 61

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. 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 1317840698 486 RITHISAEQKRRFNIKLGFDTLHGLVsTLSAQPslKVSKATTLQKTAEYILMLQQERAAMQEEAQQLR 553
Cdd:cd19682     1 RLRHKKRERERRSELRELFDKLKQLL-GLDSDE--KASKLAVLTEAIEEIQQLKREEDELQKEKARLT 65

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in c-Myc and similar proteins; c-Myc, also termed Myc proto-oncogene protein, or Class E basic helix-loop-helix protein 39 (bHLHe39), or transcription factor p64, a bHLHZip proto-oncogene protein that functions as a transcription factor, which binds DNA in a non-specific manner, yet also specifically recognizes the core sequence 5'-CAC[GA]TG-3'. It activates the transcription of growth-related genes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1317840698 481 KMENRRITHISAEQKRRFNIKLGFDTLHGLVSTLSAQPslKVSKATTLQKTAEYILMLQQERAAMQEEAQQLRDEIEEL 559
Cdd:cd11458     1 EENDKRRTHNVLERQRRNELKLSFFALRDQIPEVANNE--KAPKVVILKKATEYILSMQADEQRLISEKEQLRRRREQL 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1317840698 480 NKMENRRITHISaeqkrrfnikLGFDTLHGLVSTLSaqPSLKVSKATTLQKTAEYILMLQQE 541
Cdd:cd11418     6 NERERRRVQAVN----------DAFDRLRQHVPYLK--RRKKLSKVKTLRRAIEYIRHLQKL 55

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 1317840698 481 KMENRRITHISAEQKRRFNIKLGFDTLHGLVSTlSAQPSLKVSKATTLQKTAEYILMLQQERAAMQEEAQQLRdEIEELN 560
Cdd:cd18928     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIPK-STDPEMRWNKGTILKASVDYIRKLQKEQQRSKEIEMRQR-KLEQAN 84

                  ....*
gi 1317840698 561 AAINL 565
Cdd:cd18928    85 RSLQL 89

transcriptional regulator ICP4; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  232 VHGLEPCTPSPFPTMAPP-------------PSLLPEESLLSARFPFTSAPPAPGVSTLPAPTTFVPTPQPGPGPVPFSV 298
Cdd:PHA03307    56 VAGAAACDRFEPPTGPPPgpgteapanesrsTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLS 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  299 DHLPHGYLEPVFGPHFTVPQGMQPRCKPSSPSPGGQKASPptLASATASPTATATARDNNPCLTQLLRAAKPEQALEPPT 378
Cdd:PHA03307   136 EMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALP--LSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPI 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  379 MPGTLLRPPESPQDTVSEIPRARAFFPPIPAPTPPRPPPGPATLAPPRSLVVPKAERL-----------SPPASSGSERR 447
Cdd:PHA03307   214 SASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEasgwngpssrpGPASSSSSPRE 293

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1317840698  448 LSGDLNSIQPSGALSVhlSPPQTVLSRGRVDN 479
Cdd:PHA03307   294 RSPSPSPSSPGSGPAP--SSPRASSSSSSSRE 323

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 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVSTLSAqpslKVSKATTLQKTAEYILMLQ 539
Cdd:cd19683     2 SRERHNAKERQRRERIKIACDQLRKLVPGCSR----KTDKATVFEFTVAYIKFLR 52

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVstlsAQPSLKVSKATTLQKTAEYILMLQQERAAMQEEAQQLR 553
Cdd:cd11394     6 KRSAHNAIEKRYRSSINDRIIELKDLV----VGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALK 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 1317840698 481 KMENRRITHISAEQKRRFNIKLGFDTLHGLVSTlSAQPSLKVSKATTLQKTAEYILMLQQEraamQEEAQQLRDEIEELN 560
Cdd:cd18926     9 KERQKKDNHNLIERRRRFNINDRIKELGTLIPK-SNDPDMRWNKGTILKASVDYIRKLQRE----QQRAKELENRQKKLE 83

                  ..
gi 1317840698 561 AA 562
Cdd:cd18926    84 HA 85

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  131 PPQTPTSSNYIESPSF-GPMADSLFSSGILAPEMPSPASSSSSSGMTPhSGNTRLQARNSCSGPLDPNPflssefllPED 209
Cdd:PHA03247  2704 PPPTPEPAPHALVSATpLPPGPAAARQASPALPAAPAPPAVPAGPATP-GGPARPARPPTTAGPPAPAP--------PAA 2774

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  210 PKTkiPPAPGPTPLLPFPTPVKVHGL-EPCTPSPFPTMAPPPSllpeesllsARFPFTSAPPAPgvstLPAPTTFVPTPQ 288
Cdd:PHA03247  2775 PAA--GPPRRLTRPAVASLSESRESLpSPWDPADPPAAVLAPA---------AALPPAASPAGP----LPPPTSAQPTAP 2839

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  289 PGPgPVPFSVDHLPHGYLEPvFGPHFTVPQGMQPRCKPSSPS-PGGQKASPPTLASATASPtatatardnnpcltqllra 367
Cdd:PHA03247  2840 PPP-PGPPPPSLPLGGSVAP-GGDVRRRPPSRSPAAKPAAPArPPVRRLARPAVSRSTESF------------------- 2898

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  368 AKPEQALEPPTMPGTLLRPPESPQDTVSEIPR-------------------ARAFFPPIPAPTPPRPPPGPATLAPPRSL 428
Cdd:PHA03247  2899 ALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQppppppprpqpplapttdpAGAGEPSGAVPQPWLGALVPGRVAVPRFR 2978

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1317840698  429 VVPKAERLSPPASSGSERRLSGD--LNSIQPSGALSVHLSPPQTVL 472
Cdd:PHA03247  2979 VPQPAPSREAPASSTPPLTGHSLsrVSSWASSLALHEETDPPPVSL 3024

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 1317840698 488 THISAEQKRRFNIKLGFDTLHGLV-STLSAQPSLKVSKATTLQKTAEYILMLQQE 541
Cdd:cd11387     1 SHNAVERRRRDNINEKIQELGSLVpPSRLETKDLKPNKGSILSKAVEYIRELQNQ 55

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  207 PEDPKTKIPPAPGPTPLLPFPTPVKVHGLEPCTP-SPFPTMAPPPSLLPEESLLSARFPFTSAPPAPGVSTLPAPTTFVP 285
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPLPPGPAAARQASPALPaAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRR 2782

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  286 TPQPGPGPVPFSVDHLPH-----GYLEPVFGPHFTVPQGMQPRCKPSSPSPGGQKASPPTLASATASPTATATARDNNPc 360
Cdd:PHA03247  2783 LTRPAVASLSESRESLPSpwdpaDPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGD- 2861

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317840698  361 ltqlLRAAKPEQAlePPTMPGTLLRPPESPQDTVSEIPRARAFFPPIPAPTPPRPPPGPATLAPPRSLVVPKAERLSPPA 440
Cdd:PHA03247  2862 ----VRRRPPSRS--PAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPP 2935

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1317840698  441 SSGSERRLSGDLNSIQPSGALSVHLSPPQTVLSRGRV 477
Cdd:PHA03247  2936 PPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRV 2972

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 1317840698 485 RRITHISAEQKRRFNIKLGFDTLHGLVstlsAQPSLKVSKATTLQKTAEYILMLqQERAAMQEEAQQLR 553
Cdd:cd11453     3 PRSKHSATEQRRRSKINERLQALRDLI----PHSDQKRDKASFLLEVIEYIQAL-QEKVAKLEEQVQGW 66

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster achaete-scute complex (AS-C) proteins, achaete-scute-like proteins, ASCL1-2, and similar proteins; This subfamily includes Drosophila melanogaster AS-C proteins and two ASCL family of transcription factors, ASCL-1 and ASCL-2. Drosophila melanogaster AS-C proteins includes 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. 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 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 involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1317840698 493 EQKRRFNIKLGFDTLHGLVSTLSAqpSLKVSKATTLQKTAEYILMLQQ 540
Cdd:cd19723     9 ERNRVKLVNLGFATLREHVPNGRA--NKKMSKVETLRSAVEYIRQLQQ 54