BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= lcl|Aclame:protein:vir:79096|NCBI_annot:gp2|genbank:acc:YP_0011 11202;genbank:gi:134288795;genbank:GeneID:4960770 (500 letters) Database: capsid_neck_tail 514 sequences; 206,069 total letters Searching...................................................done Score E Sequences producing significant alignments: (bits) Value gi|11818|lcl|protein:vir:79096 Length: 500 # NCBI annotation: gp... 1027 0.0 gi|5606|lcl|protein:vir:107886 Length: 500 # NCBI annotation: gp... 1014 0.0 gi|108|lcl|protein:vir:1985 Length: 551 # NCBI annotation: putat... 412 e-117 gi|1931|lcl|protein:vir:99847 Length: 486 # NCBI annotation: lar... 166 7e-43 gi|16897|lcl|protein:vir:5867 Length: 508 # NCBI annotation: sim... 44 6e-06 gi|22578|lcl|protein:vir:95547 Length: 605 # NCBI annotation: OR... 28 0.26 gi|9399|lcl|protein:vir:99333 Length: 605 # NCBI annotation: hyp... 28 0.26 gi|23415|lcl|protein:vir:103176 Length: 202 # NCBI annotation: g... 23 6.4 >gi|11818|lcl|protein:vir:79096 Length: 500 # NCBI annotation: gp2 # Family: family:all:460 # MgeID: mge:1862 # MgeName: phiE255 # Cross-refs: genbank:acc:YP_001111202;genbank:gi:134288795;genbank:Ge neID:4960770 Length = 500 Score = 1027 bits (2655), Expect = 0.0, Method: Compositional matrix adjust. Identities = 500/500 (100%), Positives = 500/500 (100%) Query: 1 MTIVETRADRAPAVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV 60 MTIVETRADRAPAVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV Sbjct: 1 MTIVETRADRAPAVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV 60 Query: 61 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRV 120 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRV Sbjct: 61 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRV 120 Query: 121 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE 180 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE Sbjct: 121 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE 180 Query: 181 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE 240 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE Sbjct: 181 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE 240 Query: 241 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLDATLG 300 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLDATLG Sbjct: 241 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLDATLG 300 Query: 301 PLLAALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFY 360 PLLAALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFY Sbjct: 301 PLLAALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFY 360 Query: 361 LLDRLPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT 420 LLDRLPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT Sbjct: 361 LLDRLPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT 420 Query: 421 IDGLPKDADVLADLRAVQVIKGVPRIPDVRTTGQDDGKRHGDAAVAVALAYYASRELNKG 480 IDGLPKDADVLADLRAVQVIKGVPRIPDVRTTGQDDGKRHGDAAVAVALAYYASRELNKG Sbjct: 421 IDGLPKDADVLADLRAVQVIKGVPRIPDVRTTGQDDGKRHGDAAVAVALAYYASRELNKG 480 Query: 481 PVTAKSRRRRSSVRMTEGYA 500 PVTAKSRRRRSSVRMTEGYA Sbjct: 481 PVTAKSRRRRSSVRMTEGYA 500 >gi|5606|lcl|protein:vir:107886 Length: 500 # NCBI annotation: gp28 # Family: family:all:460 # MgeID: mge:1565 # MgeName: BcepMu # Cross-refs: genbank:acc:YP_024701;genbank:gi:48696938;genbank:GeneID :2845974 Length = 500 Score = 1014 bits (2622), Expect = 0.0, Method: Compositional matrix adjust. Identities = 491/500 (98%), Positives = 495/500 (99%) Query: 1 MTIVETRADRAPAVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV 60 MT VETRADRAPAVLLPYQQKW ADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV Sbjct: 1 MTTVETRADRAPAVLLPYQQKWCADTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDV 60 Query: 61 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRV 120 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILA+VIRFASGFRV Sbjct: 61 WYVGYNKDMAQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAFVIRFASGFRV 120 Query: 121 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE 180 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE Sbjct: 121 TALSSRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNE 180 Query: 181 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE 240 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE Sbjct: 181 LVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAE 240 Query: 241 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLDATLG 300 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWL+ATLG Sbjct: 241 EELDCVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLEATLG 300 Query: 301 PLLAALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFY 360 PLL ALP DARSYNGEDFGRTGDLTVHVPLIEQQNL+RRVPFIVELRNVPFRQQEQIAFY Sbjct: 301 PLLTALPVDARSYNGEDFGRTGDLTVHVPLIEQQNLVRRVPFIVELRNVPFRQQEQIAFY 360 Query: 361 LLDRLPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT 420 LLDRLPRFTGGAFDARGNGQYLAE+AMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT Sbjct: 361 LLDRLPRFTGGAFDARGNGQYLAEVAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT 420 Query: 421 IDGLPKDADVLADLRAVQVIKGVPRIPDVRTTGQDDGKRHGDAAVAVALAYYASRELNKG 480 IDGLPKDADVLADLRAVQVIKGVPRIPDVR TGQDDGKRHGDAAVAVALAYYASRELNKG Sbjct: 421 IDGLPKDADVLADLRAVQVIKGVPRIPDVRATGQDDGKRHGDAAVAVALAYYASRELNKG 480 Query: 481 PVTAKSRRRRSSVRMTEGYA 500 PVTAKSRRRRSSVRMTEGYA Sbjct: 481 PVTAKSRRRRSSVRMTEGYA 500 >gi|108|lcl|protein:vir:1985 Length: 551 # NCBI annotation: putative portal protein # Family: family:all:460 # MgeID: mge:320 # MgeName: Mu # Cross-refs: genbank:acc:NP_050632;genbank:gi:9633519;genbank:GeneID: 2636303 Length = 551 Score = 412 bits (1059), Expect = e-117, Method: Compositional matrix adjust. Identities = 232/475 (48%), Positives = 295/475 (62%), Gaps = 13/475 (2%) Query: 10 RAPAVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEAADSALLAASQR---GMDVWYVGYN 66 R V L YQ++W D S + + EKSRR GL+W EA + + AA + G +V+YVG Sbjct: 40 RNEPVFLGYQRRWFEDESQICIAEKSRRTGLTWAEAGRNVMTAAKPKRRGGRNVFYVGSR 99 Query: 67 KDMAQEFIRDCADWAK-FYSLAADEIEETEEVFQDKDGDKSILAYVIRFA-SGFRVTALS 124 ++MA E+I CA +A+ F LA ++ E+ F D D + IL Y+IRF SGF++ ALS Sbjct: 100 QEMALEYIAACALFARAFNQLAKADV--WEQTFWDSDKKEEILTYMIRFPNSGFKIQALS 157 Query: 125 SRPSNLRGKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNELVTD 184 SRPSNLRG QG V+IDEAAFHE L ELLKAA AL MWG V IISTH+GVDN FN+ + D Sbjct: 158 SRPSNLRGLQGDVVIDEAAFHEALDELLKAAFALNMWGASVRIISTHNGVDNLFNQYIQD 217 Query: 185 VRSGKKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDI--RASYGADAEEE 242 R G+K YS+HRIT DA+ DGLY+RIC + W+ E E W + A A+EE Sbjct: 218 AREGRKDYSVHRITLDDAIADGLYRRICYVTNQPWSPEAEKAWRDGLYRNAPNKESADEE 277 Query: 243 LDCVPKNSGGAWLSRALIESRMSA--DTPVLRWACKQGFEVLPDHIRAAECRDWLDATLG 300 C+PK SGGA+LSR LIE+ M+ D PVLR+ FE L +R +DW + L Sbjct: 278 YGCIPKKSGGAYLSRVLIEAAMTPARDIPVLRFEAPDDFESLTPQMRHGIVQDWCEQELL 337 Query: 301 PLLAALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFY 360 PLL AL + GEDF R GDLTV VPL +L +R F VELRNV + QQ QI + Sbjct: 338 PLLDALSPLNKHVLGEDFARRGDLTVFVPLAITPDLRKRECFRVELRNVTYDQQRQILLF 397 Query: 361 LLDRLPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGT 420 +L RLPRFTG AFDA GNG YLAE A YG I + L+ +WY+E MP +K FE Sbjct: 398 ILSRLPRFTGAAFDATGNGGYLAEAARLIYGPEMIDCISLTPAWYQEWMPKLKGEFEAQN 457 Query: 421 IDGLPKDADVLADLRAVQVIKGVPRIPDVRTTGQ-DDGKRHGDAAVAVALAYYAS 474 I + + L DL ++V KG+P+I RT + G+RHGD AVA+ +A AS Sbjct: 458 IT-IARHQTTLDDLLHIKVDKGIPQIDKGRTKDEGGKGRRHGDFAVALCMAVRAS 511 >gi|1931|lcl|protein:vir:99847 Length: 486 # NCBI annotation: large terminase subunit # Family: family:all:460 # MgeID: mge:1480 # MgeName: B3 # Cross-refs: genbank:acc:YP_164067;genbank:gi:56692599;genbank:GeneID :3192575 Length = 486 Score = 166 bits (419), Expect = 7e-43, Method: Compositional matrix adjust. Identities = 146/489 (29%), Positives = 219/489 (44%), Gaps = 54/489 (11%) Query: 13 AVLLPYQQKWAADTSPVKVCEKSRRVGLSWGEA-ADSALLAASQRGMDVWYVGYNKDMAQ 71 A+ LPYQ +W D S +K+ +KSR++GLSW A A AA +D W + A+ Sbjct: 16 AIFLPYQSRWITDPSRLKLMQKSRQIGLSWSTAYAAGERTAAESARVDQWVSSRDDLQAR 75 Query: 72 EFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRVTALSSRPSNLR 131 F+ DC WA + AA ++ E ++K I AYV+ FA+G R+ ++SS P Sbjct: 76 LFLEDCKMWAGIMNQAAKDLGEIVIDVKNK-----ISAYVLEFANGRRIHSMSSNPDAQA 130 Query: 132 GKQGRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNELVTDVRSGKKP 191 GK+G I+DE A H +L A + WGG + IISTH G N FN+LV ++ G P Sbjct: 131 GKRGGRILDEFALHPDPRKLWSIAYPGITWGGAMEIISTHRGSQNFFNQLVREIVEGGNP 190 Query: 192 --YSLHRITFADAVQDGLYQRI--CLRKGEAWTAEGEAKWVKDIRASYGADAE---EELD 244 SLH +T DA+ G ++ L + EA++ IRA AD E +E Sbjct: 191 KNISLHTVTLQDALNQGFLFKLQQMLPADDEIQGMDEAQYFDFIRAGC-ADEESFQQEYM 249 Query: 245 CVPKNSGGAWLSRALIESRMSADTPVLRWACKQGFEVLPDHIRAAECRDWLDATLGPLLA 304 C P + A+L LI SA+ P + +W Sbjct: 250 CNPADDDVAFLEYDLI---ASAEYP--------------------QTANWQQ-------- 278 Query: 305 ALPADARSYNGEDFGRTGDLTVHVPLIEQQNLIRRVPFIVELRNVPFRQQEQIAFYLLDR 364 P R + G D GR DLTV + ++E + + L+N+ QE I + R Sbjct: 279 --PEGGRLFAGVDIGRKKDLTV-LWILELLGDVLYTRHVERLQNMRKSAQEAILWPWFQR 335 Query: 365 LPRFTGGAFDARGNGQYLAEIAMQRYGASRIQQVMLSESWYREHMPPVKAAFEDGTIDGL 424 R DA G G A+ A ++G R++ V + P++ A ED + + Sbjct: 336 CERI---CIDATGLGIGWADDAQDQFGEHRVEAVTFTPRVKEALAYPIRGAMEDHKVR-I 391 Query: 425 PKDADVLADLRAVQVIKGVPRIPDVRTTGQDDGKRHGDAAVAVALAYYASRELNKGPVTA 484 P D + A LR +V K ++R T + H D A+ LA +A+ L P+ Sbjct: 392 PYDPKIRAALR--EVTKQTTAAGNIRFTAERTADGHADEFWALGLAIHAASGLVDMPIDY 449 Query: 485 KSRRRRSSV 493 +S R+ + Sbjct: 450 QSAGTRTQL 458 >gi|16897|lcl|protein:vir:5867 Length: 508 # NCBI annotation: similar to terminase DNA packaging enzyme, large subunit # Family: family:all:147 # MgeID: mge:123 # MgeName: RM 378 # Cross-refs: genbank:acc:NP_835653;genbank:gi:30044056 Length = 508 Score = 43.5 bits (101), Expect = 6e-06, Method: Compositional matrix adjust. Identities = 57/266 (21%), Positives = 111/266 (41%), Gaps = 32/266 (12%) Query: 12 PAVLLPYQQKWAA--DTSPVKVCEKSRRVGLSWGEAADSALLAASQRGMDVWYVGYNKDM 69 P L P Q+K T + EK R++G++W A + V + NK+ Sbjct: 37 PFDLYPIQEKLINFYHTHRYVITEKPRQMGVTWCAVAYALHQMIFNSNYKV-LIAANKEA 95 Query: 70 AQEFIRDCADWAKFYSLAADEIEETEEVFQDKDGDKSILAYVIRFASGFRVTALSSRPSN 129 ++ + KF A +++ ++ + + +K+ I F++ A+SS+ + Sbjct: 96 TA---KNVLERIKF---AYEQLPRFLQI-KKRTWNKT----YIEFSNYSSARAVSSKSDS 144 Query: 130 LRGKQ-GRVIIDEAAFHEQLGELLKAAMALLMWGGQVHIISTHDGVDNAFNELVTDVRSG 188 R + +I++EAAF + EL + L GG+ + ST++GV N + + + G Sbjct: 145 GRSESITLLIVEEAAFISNMEELWASVQQTLATGGKCIVNSTYNGVGNWYERTIRAAKEG 204 Query: 189 KKPYSLHRITFADAVQDGLYQRICLRKGEAWTAEGEAKWVKDIRASYGADAEEELDCVPK 248 K + I ++D + + E W E + + A +E+ C+P+ Sbjct: 205 KSEFKYFGIKWSDHPE----------RDEKWFEEQKRLLPPRVFA-------QEILCIPQ 247 Query: 249 NSGGAWLSRALIESRMSADTPVLRWA 274 SG + LI D V+++ Sbjct: 248 GSGENVIPFHLIREEEFIDPFVVKYG 273 >gi|22578|lcl|protein:vir:95547 Length: 605 # NCBI annotation: ORF010 # Family: family:all:1430 # MgeID: mge:1577 # MgeName: G1 # Cross-refs: genbank:acc:YP_240892;genbank:gi:66394959;genbank:GeneID :5132488 Length = 605 Score = 28.1 bits (61), Expect = 0.26, Method: Compositional matrix adjust. Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 15/81 (18%) Query: 17 PYQQKWAADTSPVKVCEKSRRVGLS---------------WGEAADSALLAASQRGMDVW 61 P+Q + DT P K KSR++GLS + A +++ Sbjct: 65 PWQTRIVNDTHPNKAVIKSRQLGLSEMGVMEMVHFADMHSYANAKCLYTFPTNEQMKKFV 124 Query: 62 YVGYNKDMAQEFIRDCADWAK 82 N + +E+ RD DW K Sbjct: 125 QSRLNPVLEKEYFRDIVDWDK 145 >gi|9399|lcl|protein:vir:99333 Length: 605 # NCBI annotation: hypothetical protein # Family: family:all:1430 # MgeID: mge:1655 # MgeName: K # Cross-refs: genbank:acc:YP_024465;genbank:gi:48696425;genbank:GeneID :2948061 Length = 605 Score = 28.1 bits (61), Expect = 0.26, Method: Compositional matrix adjust. Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 15/81 (18%) Query: 17 PYQQKWAADTSPVKVCEKSRRVGLS---------------WGEAADSALLAASQRGMDVW 61 P+Q + DT P K KSR++GLS + A +++ Sbjct: 65 PWQTRIVNDTHPNKAVIKSRQLGLSEMGVMEMVHFADMHSYANAKCLYTFPTNEQMKKFV 124 Query: 62 YVGYNKDMAQEFIRDCADWAK 82 N + +E+ RD DW K Sbjct: 125 QSRLNPVLEKEYFRDIVDWDK 145 >gi|23415|lcl|protein:vir:103176 Length: 202 # NCBI annotation: gp130 # Family: family:all:1107 # MgeID: mge:1583 # MgeName: Syn9 # Cross-refs: genbank:acc:YP_717797;genbank:gi:113200634;genbank:GeneI D:4239185 Length = 202 Score = 23.5 bits (49), Expect = 6.4, Method: Compositional matrix adjust. Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%) Query: 175 DNAFNELVTDVRSGKKPYSLHRITFADAVQDGLYQRICLRKG-----EAWTAEGEAKWVK 229 D ++L D+R G+KP L F D + I L G E +T E + ++ K Sbjct: 130 DMYVHQLSRDIRDGRKPQPLRSYKFIDVFPSNI-SSIDLDFGSNDAIEEFTVELQVQYWK 188 Query: 230 DIR 232 ++ Sbjct: 189 PVK 191 Database: capsid_neck_tail Posted date: Nov 7, 2013 12:16 PM Number of letters in database: 206,069 Number of sequences in database: 514 Lambda K H 0.320 0.135 0.406 Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 225,258 Number of Sequences: 514 Number of extensions: 10299 Number of successful extensions: 78 Number of sequences better than 100.0: 9 Number of HSP's better than 100.0 without gapping: 9 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 53 Number of HSP's gapped (non-prelim): 13 length of query: 500 length of database: 206,069 effective HSP length: 75 effective length of query: 425 effective length of database: 167,519 effective search space: 71195575 effective search space used: 71195575 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 39 (19.6 bits)