large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  128 PGELSLSSPGPLSPSGIKSSSQYYPSFPSNPRRRA--ADGGLADTQPKKVRKVPPGLPSSVYPPSSGDSYSR--DAAAYP 203
Cdd:PHA03247 2601 PVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAAnePDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRaaQASSPP 2680

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  204 SAKTPSSAYPSPFYVADGSLHPSAE--------LWSTPSQVGFGPMLGDGSSP-LPLAPGSSSVGSGTfgglqqqdrmgy 274
Cdd:PHA03247 2681 QRPRRRAARPTVGSLTSLADPPPPPptpepaphALVSATPLPPGPAAARQASPaLPAAPAPPAVPAGP------------ 2748

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  275 qlhgsevngSLPAVSSFSAAPGTYSGTSGHTPPVSGAAAESLLGTRGTTASSSGDALGKALASIYSPDHSSNNFSPSPST 354
Cdd:PHA03247 2749 ---------ATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         250       260       270
                  ....*....|....*....|....*....|
gi 255918164  355 PVGSPQGL--PGTSQWPRAGA-PSALSPNY 381
Cdd:PHA03247 2820 PAASPAGPlpPPTSAQPTAPPpPPGPPPPS 2849

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 255918164   550 NARERVRVRDINEAFRELGRMCQLHLKSDKaQTKLLILQQAVQVILGLEQQVRE 603
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTLPKNKK-LSKAEILRLAIEYIKSLQEELQK 53

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  128 PGELSLSSPGPLSPSGIKSSSQYYPSFPSNPRRRA--ADGGLADTQPKKVRKVPPGLPSSVYPPSSGDSYSR--DAAAYP 203
Cdd:PHA03247 2601 PVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAAnePDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRaaQASSPP 2680

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  204 SAKTPSSAYPSPFYVADGSLHPSAE--------LWSTPSQVGFGPMLGDGSSP-LPLAPGSSSVGSGTfgglqqqdrmgy 274
Cdd:PHA03247 2681 QRPRRRAARPTVGSLTSLADPPPPPptpepaphALVSATPLPPGPAAARQASPaLPAAPAPPAVPAGP------------ 2748

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164  275 qlhgsevngSLPAVSSFSAAPGTYSGTSGHTPPVSGAAAESLLGTRGTTASSSGDALGKALASIYSPDHSSNNFSPSPST 354
Cdd:PHA03247 2749 ---------ATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819

                         250       260       270
                  ....*....|....*....|....*....|
gi 255918164  355 PVGSPQGL--PGTSQWPRAGA-PSALSPNY 381
Cdd:PHA03247 2820 PAASPAGPlpPPTSAQPTAPPpPPGPPPPS 2849

basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins; TCF-4, also termed E2-2, or Class B basic helix-loop-helix protein 19 (bHLHb19), or immunoglobulin transcription factor 2 (ITF-2), or SL3-3 enhancer factor 2 (SEF-2), is a bHLH transcription factor that binds to the immunoglobulin enhancer Mu-E5/KE5-motif. It is involved in the initiation of neuronal differentiation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164 541 RDRERRMANNARERVRVRDINEAFRELGRMCQLHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPKAACLKRREEEK 620
Cdd:cd18945    4 REKERRMANNARERLRVRDINEAFKELGRMVQLHLKSDKPQTKLLILHQAVAVILSLEQQVRERNLNPKAACLKRREEEK 83

                 ..
gi 255918164 621 VS 622
Cdd:cd18945   84 VS 85

basic helix-loop-helix (bHLH) domain found in transcription factor E2-alpha (E2A) and similar proteins; E2A, also termed Class B basic helix-loop-helix protein 21 (bHLHb21), or immunoglobulin enhancer-binding factor E12/E47, or immunoglobulin transcription factor 1, or Kappa-E2-binding factor, or transcription factor 3 (TCF-3), or transcription factor ITF-1, is a bHLH transcriptional regulator involved in the initiation of neuronal differentiation.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 255918164 544 ERRMANNARERVRVRDINEAFRELGRMCQLHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPKAACLKRRE 617
Cdd:cd18944    1 ERRVANNARERLRVRDINEAFKELGRMCQLHLNSEKPQTKLLILHQAVSVILNLEQQVRERNLNPKAACLKRRE 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 255918164 553 ERVRVRDINEAFRELGRMCQLHLKSDKAQTKLLILQQAVQVILGLEQ 599
Cdd:cd11420    1 ERIRVRDINEAFKELGRMCQLHLKSDKPQTKLLILHQAVSVITSLEQ 47

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 255918164  545 RRMANNARERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVILGLE 598
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 255918164 553 ERVRVRDINEAFRELGRMCQLHLKSDKaQTKLLILQQAVQVILGLEQ 599
Cdd:cd00083    1 ERRRRDKINDAFEELKRLLPELPDSKK-LSKASILQKAVEYIRELQS 46

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 255918164 540 LRDRERRMANNARERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVILGL 597
Cdd:cd18912    3 VRSKARRVAANVRERKRILDYNQAFNAL-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 255918164 542 DRERRmanNARERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVILGLEQQ 600
Cdd:cd11418    1 RVARR---NERERRRVQAVNDAFDRL-RQHVPYLKRRKKLSKVKTLRRAIEYIRHLQKL 55

basic helix-loop-helix (bHLH) domain found in protein atonal homolog 7 (ATOH7) and similar proteins; ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 255918164 543 RERRMANNARERVRVRDINEAFRELGRMCQlHLKSDKAQTKLLILQQAVQVILGL 597
Cdd:cd19714    6 ARRRLAANARERRRMQGLNTAFDRLRKVVP-QWGQDKKLSKYETLQMALSYIMAL 59

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 255918164 545 RRMANNARERVRVRDINEAFRELGRMCQlHLKSDKAQTKLLILQQAVQVILGL 597
Cdd:cd11426    1 RRLESNERERLRMHQLNDAFQALREVIP-HVRSERKLSKIETLTLAKNYIKSL 52

basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor 2 (NeuroD2) and similar proteins; NeuroD2, also termed Class A basic helix-loop-helix protein 1 (bHLHa1), or NeuroD-related factor (NDRF), is a neuronal calcium-dependent bHLH transcription factor that induces neuronal differentiation and promotes neuronal survival. It plays a central role in thalamocortical synaptic maturation. NeuroD2 mediates calcium-dependent transcription activation by binding to E box-containing promoter.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255918164 502 EDEEIASVADAEEDKKDLKVPRTRTSSTDEvlsleekdlRDRERRMANNARERVRVRDINEAFRELGRMCQLHLKSDKAq 581
Cdd:cd19720    1 EEEEGLEEADGERPKKRGPKKRKMTKARLE---------RSKLRRQKANARERNRMHDLNSALDNLRKVVPCYSKTQKL- 70

                         90       100
                 ....*....|....*....|.
gi 255918164 582 TKLLILQQAVQVILGLEQQVR 602
Cdd:cd19720   71 SKIETLRLAKNYIWALSEILR 91

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 255918164 544 ERRMANNaRERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVI 594
Cdd:cd19686    1 QRQAANI-RERKRMRSINDAFDGL-RRHIPTFPYEKRLSKVDTLRLAIQYI 49

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 255918164 545 RRMANNARERVRVRDINEAFRELGRMCQLHlKSDKAQTKLLILQQAVQVILGLEQQVR 602
Cdd:cd19708    1 RRMFTNSRERWRQQNVNGAFAELRKLVPTH-PPDKKLSKNEILRLAIKYIRLLSNVLE 57

basic helix-loop-helix (bHLH) domain found in helix-loop-helix protein 1 (HEN-1) and similar proteins; HEN-1, also termed nescient helix-loop-helix 1 (Nhlh1), or Class A basic helix-loop-helix protein 35 (bHLHa35), or nescient helix loop helix 1 (NSCL-1), is a neuron-specific bHLH transcription factor that may serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 255918164 533 LSLEEKDLRDR---ERRMANNARERVRVRDINEAFRELGRMCQLhLKSDKAQTKLLILQQAVQVI 594
Cdd:cd19701    1 LSREERRRRRRataKYRTAHATRERIRVEAFNVAFAELRKLLPT-LPPDKKLSKIEILRLAICYI 64

basic helix-loop-helix (bHLH) domain found in myogenic factor 5 (Myf-5) and similar proteins; Myf-5, also termed Class C basic helix-loop-helix protein 2 (bHLHc2), is a nuclear bHLH transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle specification and differentiation. It also acts as an RNA-binding protein which enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 255918164 544 ERRMANNARERVRVRDINEAFRELGRMCQLHlkSDKAQTKLLILQQAVQVILGLEQQVRER 604
Cdd:cd18937    1 DRRKAATMRERRRLKKVNQAFETLKRCTTSN--PNQRLPKVEILRNAIRYIESLQDLLREQ 59

basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein Amos and similar proteins; Amos, also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein, is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 255918164 543 RERRMANNARERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVILGL 597
Cdd:cd19715    6 KKRRLAANARERRRMNSLNVAFDKL-RDVVPSLGDDRKLSKYETLQMAQSYITAL 59

basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein 2 (TAL-2) and similar proteins; TAL-2, also termed Class A basic helix-loop-helix protein 19 (bHLHa19), is a bHLH transcription factor essential for the normal brain development. It has been implicated in T-cell acute lymphoblastic leukemia.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 255918164 545 RRMANNARERVRVRDINEAFRELGRMCQLHlKSDKAQTKLLILQQAVQVI 594
Cdd:cd19707    2 RKIFTNTRERWRQQNVNSAFAELRKLIPTH-PPDKKLSKNEILRLAMKYI 50

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 255918164 544 ERRMANNARERVRVRDINEAFRELGRMCQLHlkSDKAQTKLLILQQAVQVILGLE 598
Cdd:cd11411    1 DRRKAATMRERRRLKKVNEAFEALKRCTSAN--PNQRLPKVEILRNAIEYIESLQ 53

basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein 1 (TAL-1) and similar proteins; 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-1 has been implicated in T-cell acute lymphoblastic leukemia. In common with other tissue-specific bHLH proteins, Tal heterodimerizes with ubiquitously-expressed members of the E2A family and form a DNA-binding complex with an E-box (CANNTG) to regulate transcription at its recognition site.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 255918164 545 RRMANNARERVRVRDINEAFRELGRMCQLHlKSDKAQTKLLILQQAVQVI 594
Cdd:cd19706    4 RRIFTNSRERWRQQNVNGAFAELRKLIPTH-PPDKKLSKNEILRLAMKYI 52

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        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 255918164 550 NARERVRVRDINEAFRELgRMCQLHLKSDKAQTKLLILQQAVQVILGLEQ 599
Cdd:cd19723    6 NERERNRVKLVNLGFATL-REHVPNGRANKKMSKVETLRSAVEYIRQLQQ 54