large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630   92 PGELSLSSPGPLSPSGIKSSSQYYPSFPSNPRRRA--ADGGLADTQPKKVRKVPPGLPSSVYPPSSGDSYSR--DAAAYP 167
Cdd:PHA03247  2601 PVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAAnePDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRaaQASSPP 2680

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630  168 SAKTPSSAYPSPFYVADGSLHPSAE--------LWSTPSQVGFGPMLGDGSSP-LPLAPGSSSVGSGTfgglqqqdrmgy 238
Cdd:PHA03247  2681 QRPRRRAARPTVGSLTSLADPPPPPptpepaphALVSATPLPPGPAAARQASPaLPAAPAPPAVPAGP------------ 2748

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630  239 qlhgsevngSLPAVSSFSAAPGTYSGTSGHTPPVSGAAAESLLGTRGTTASSSGDALGKALASIYSPDHSSNNFSPSPST 318
Cdd:PHA03247  2749 ---------ATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                          250       260       270
                   ....*....|....*....|....*....|
gi 1039732630  319 PVGSPQGL--PGTSQWPRAGA-PSALSPNY 345
Cdd:PHA03247  2820 PAASPAGPlpPPTSAQPTAPPpPPGPPPPS 2849

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039732630  518 NARERLRVRDINEAFKELGRMCQLHLSSEKPqTKLLILHQAVAVILSLEQQVRE 571
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLPKNKKL-SKAEILRLAIEYIKSLQEELQK 53

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630   92 PGELSLSSPGPLSPSGIKSSSQYYPSFPSNPRRRA--ADGGLADTQPKKVRKVPPGLPSSVYPPSSGDSYSR--DAAAYP 167
Cdd:PHA03247  2601 PVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAAnePDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRaaQASSPP 2680

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630  168 SAKTPSSAYPSPFYVADGSLHPSAE--------LWSTPSQVGFGPMLGDGSSP-LPLAPGSSSVGSGTfgglqqqdrmgy 238
Cdd:PHA03247  2681 QRPRRRAARPTVGSLTSLADPPPPPptpepaphALVSATPLPPGPAAARQASPaLPAAPAPPAVPAGP------------ 2748

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630  239 qlhgsevngSLPAVSSFSAAPGTYSGTSGHTPPVSGAAAESLLGTRGTTASSSGDALGKALASIYSPDHSSNNFSPSPST 318
Cdd:PHA03247  2749 ---------ATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                          250       260       270
                   ....*....|....*....|....*....|
gi 1039732630  319 PVGSPQGL--PGTSQWPRAGA-PSALSPNY 345
Cdd:PHA03247  2820 PAASPAGPlpPPTSAQPTAPPpPPGPPPPS 2849

basic helix-loop-helix (bHLH) domain found in transcription factor 12 (TCF-12) and similar proteins; TCF-12, also termed HEB, or Class B basic helix-loop-helix protein 20 (bHLHb20), or DNA-binding protein HTF4, or E-box-binding protein, or transcription factor HTF-4, is a bHLH transcription factor that is involved in the initiation of neuronal differentiation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039732630 513 RRVANNARERLRVRDINEAFKELGRMCQLHLSSEKPQTKLLILHQAVAVILSLEQQVRERNLNPKAACLKRREEEKVSGV 592
Cdd:cd18946     1 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLLILHQAVAVILSLEQQVRERNLNPKAACLKRREEEKVSAV 80

                  ...
gi 1039732630 593 VGD 595
Cdd:cd18946    81 SAE 83

basic helix-loop-helix (bHLH) domain found in transcription factor E47 and similar proteins; E47 is a class I bHLH transcriptional regulator that forms heterodimers with class II bHLH proteins to regulate distinct differentiation pathways. Its homodimers regulate B lymphocytes development.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039732630 504 EQKAEREKERRVANNARERLRVRDINEAFKELGRMCQLHLSSEKPQTKLLILHQAVAVILSLEQQVRERNLNPK 577
Cdd:cd18943     1 EEKDLRDRERRMANNARERVRVRDINEAFKELGRMCQMHLKSDKAQTKLIILQQAVQVILGLEQQVRERNLNPK 74

basic helix-loop-helix (bHLH) domain found in E proteins family; The E proteins family corresponds to class I bHLH proteins, which are widely expressed within the immune system and on which the majority of this chapter will be focused. Members in this family include E2A (also referred to as TCF-3), E47, TCF-12 (also referred to as HEB), and TCF-4 (also referred to as E2-2) in vertebrates, as well as the E protein ortholog, Daughterless (Da), from Drosophila melanogaster. E-proteins are expressed broadly and in certain complexes they are restricted to specific cell types. E-proteins homodimerize and heterodimerize with the tissue specific bHLH factors to bind DNA and regulate transcription and differentiation of cells during development. The activity of the E-proteins is regulated by two main mechanisms: first, the relative concentrations of E-proteins, tissue specific bHLH factors, and the Id proteins, and second, covalent modification.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1039732630 521 ERLRVRDINEAFKELGRMCQLHLSSEKPQTKLLILHQAVAVILSLEQ 567
Cdd:cd11420     1 ERIRVRDINEAFKELGRMCQLHLKSDKPQTKLLILHQAVSVITSLEQ 47

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1039732630 513 RRVANNARERLRVRDINEAFKELgRMCQLHLSSEKPQTKLLILHQAVAVILSLE 566
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDEL-RELLPTLPPDKKLSKAEILRLAIEYIKHLQ 53

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1039732630 521 ERLRVRDINEAFKELGRMCQLHLSSEKPqTKLLILHQAVAVILSLEQ 567
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPELPDSKKL-SKASILQKAVEYIRELQS 46

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 1039732630 511 KERRVANNARERLRVRDINEAFKELgRMCQLHLSSEKpQTKLLILHQAVAVILSLEQQVRE 571
Cdd:cd11419     2 RIRREIANSNERRRMQSINAGFQSL-RTLLPHCDGEK-LSKAAILQQTAEYIFSLEQEKTR 60

basic helix-loop-helix (bHLH) domain found in Class A basic helix-loop-helix protein 9 (bHLHa9) and similar proteins; bHLHa9, also termed Class F basic helix-loop-helix factor 42 (bHLHf42), is a bHLH transcription factor that plays an essential role in limb development.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039732630 509 REKERRVANNARERLRVRDINEAFKELgRMCQLHLSSEKPQTKLLILHQAVAVILSL 565
Cdd:cd18912     4 RSKARRVAANVRERKRILDYNQAFNAL-RLALKHDLGGKRLSKIATLRRAINRISAL 59

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 1039732630 511 KERRvanNARERLRVRDINEAFKELgRMCQLHLSSEKPQTKLLILHQAVAVILSLEQQ 568
Cdd:cd11418     2 VARR---NERERRRVQAVNDAFDRL-RQHVPYLKRRKKLSKVKTLRRAIEYIRHLQKL 55

basic helix-loop-helix (bHLH) domain found in muscle, intestine and stomach expression 1 (MIST-1) family; MIST-1, also termed Class A basic helix-loop-helix protein 15 (bHLHa15), or Class B basic helix-loop-helix protein 8 (bHLHb8), is a bHLH transcription factor expressed in pancreatic acinar cells and other serous exocrine cells. It is essential for cytoskeletal organization and secretory activity. It also functions as a potent endoplasmic reticulum (ER) stress-inducible transcriptional regulator. MIST-1 is capable of binding to E-box (CANNTG) motifs as a homodimer or a heterodimer with E-proteins (E12 and E47) to regulate transcription. The family also includes Drosophila melanogaster protein dimmed and similar proteins. Dimmed, also termed DIMM, is a bHLH transcription factor that regulates neurosecretory (NS) cell function and neuroendocrine cell fate in Drosophila.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039732630 513 RRVANNARERLRVRDINEAFKELGRMCQlHLSSEKPQTKLLILHQAVAVILSL 565
Cdd:cd11426     1 RRLESNERERLRMHQLNDAFQALREVIP-HVRSERKLSKIETLTLAKNYIKSL 52

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster myogenic-determination protein (dMYOD) and similar proteins; dMYOD, also termed protein nautilus, or Myd, may play an important role in the early development of muscle in Drosophila.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039732630 512 ERRVANNARERLRVRDINEAFKELGRmcqlHLSSEKPQ--TKLLILHQAVAVILSLEQ 567
Cdd:cd19699     1 DRRKAATMRERRRLRKVNEAFEVLKR----RTCPNPNQrlPKVEILRNAIEYIESLED 54

basic helix-loop-helix (bHLH) domain found in myoblast determination protein 1 (MYOD1) and similar proteins; MYOD1, also termed Class C basic helix-loop-helix protein 1 (bHLHc1), or myogenic factor 3 (Myf-3), is a bHLH transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with Myf-5 and MYOG, MYOD1 co-occupies muscle-specific gene promoter core region during myogenesis.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039732630 512 ERRVANNARERLRVRDINEAFKELGRMCQLHLSSEKPqtKLLILHQAVAVILSLEQQVR 570
Cdd:cd18936     5 DRRKAATMRERRRLSKVNEAFETLKRCTSTNPNQRLP--KVEILRNAIRYIESLQALLR 61

basic helix-loop-helix (bHLH) domain found in Fer3-like protein (FERD3L), pancreas transcription factor 1 subunit alpha (PTF1A) and similar proteins; The family corresponds to a group of bHLH transcription factors, including FERD3L and PTF1A. FERD3L, also termed basic helix-loop-helix protein N-twist, or Class A basic helix-loop-helix protein 31 (bHLHa31), or nephew of atonal 3 (NATO3), or Neuronal twist (NTWIST), is expressed in the developing central nervous system (CNS). It regulates floor plate (FP) cells development. FP is a critical organizing center located at the ventral-most midline of the neural tube. FERD3L binds to the E-box and functions as inhibitor of transcription. PTF1A, also termed Class A basic helix-loop-helix protein 29 (bHLHa29), or pancreas-specific transcription factor 1a, or bHLH transcription factor p48, or p48 DNA-binding subunit of transcription factor PTF1 (PTF1-p48), is implicated in the cell fate determination in various organs. It binds to the E-box consensus sequence 5'-CANNTG-3' and plays a role in early and late pancreas development and differentiation.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1039732630 512 ERRVANNaRERLRVRDINEAFKELgRMCQLHLSSEKPQTKLLILHQAVAVI 562
Cdd:cd19686     1 QRQAANI-RERKRMRSINDAFDGL-RRHIPTFPYEKRLSKVDTLRLAIQYI 49

basic helix-loop-helix (bHLH) domain found in myogenic regulatory factor (MRF) family; MRFs are a family of muscle-specific bHLH transcription proteins (MyoD, Myf5, Mrf4 and MyoG) that plays an essential role in regulating skeletal muscle development and growth. MRFs are capable of binding to E-box motifs as a heterodimer with E-proteins to regulate transcription expression.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1039732630 512 ERRVANNARERLRVRDINEAFKELGRMCQLHLSSEKPqtKLLILHQAVAVILSLE 566
Cdd:cd11411     1 DRRKAATMRERRRLKKVNEAFEALKRCTSANPNQRLP--KVEILRNAIEYIESLQ 53

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 1039732630 513 RRVANNARERLRVRDINEAFKELgRMCQLHLSSEKPQTKLLILHQAVAVILSLEQQvrERNLNPKAACLKRREEE 587
Cdd:cd11400     1 KRRLHNVLERQRRNDLKNSFEKL-RDLVPELADNEKASKVVILKKATEYIKQLQQE--EKKLEKEKDKLKARNEQ 72

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster helix loop helix protein 3B (dHLH3B) and similar proteins; Drosophila HLH3B is an uncharacterized bHLH transcription factor that belongs to the T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039732630 513 RRVANNARERLRVRDINEAFKELGRMCQLHlSSEKPQTKLLILHQAVAVILSLEQQVR 570
Cdd:cd19708     1 RRMFTNSRERWRQQNVNGAFAELRKLVPTH-PPDKKLSKNEILRLAIKYIRLLSNVLE 57

basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family; The TAL/LYL family includes a group of bHLH transcription factors (TAL1, TAL2 and LYL1) implicated in T cell acute leukaemia. They act as mediators of T cell leukaemogenesis. TAL-1, also termed Class A basic helix-loop-helix protein 17 (bHLHa17), or stem cell protein (SCL), or T-cell leukemia/lymphoma protein 5, is a hematopoietic-specific bHLH transcription factor that functions in embryonic and adult hematopoiesis in vertebrates. It is also required for embryonic vascular remodeling. It acts as a regulator of erythroid differentiation and binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. TAL-2, also termed Class A basic helix-loop-helix protein 19 (bHLHa19), is a bHLH transcription factor essential for the normal brain development. Lyl-1, also termed Class A basic helix-loop-helix protein 18 (bHLHa18), or lymphoblastic leukemia-derived sequence 1, is a proto-oncogenic bHLH transcription factor that plays an important role in hematopoietic stem cell function and is required for the late stages of postnatal angiogenesis to limit the formation of new blood vessels, notably by regulating the activity of the small GTPase Rap1. LYL-1 deficiency induces a stress erythropoiesis.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1039732630 513 RRVANNARERLRVRDINEAFKELGRMCQLHlSSEKPQTKLLILHQAVAVILSLE 566
Cdd:cd11413     1 RRIFTNTRERWRQQNVNGAFAELRKLIPTH-PPDKKLSKNEILRLAMKYIKFLE 53

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1039732630 514 RVANNARERLRVRDINEAFKELgrMCQLHLSSEKPQTKLLILHQAVAVILSLEQQ 568
Cdd:cd19682     1 RLRHKKRERERRSELRELFDKL--KQLLGLDSDEKASKLAVLTEAIEEIQQLKRE 53