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= 0099.0002.p (517 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_832294.1| Class 1 lysyl-tRNA synthetase [Bacillus cereus ... 615 e-175 ref|NP_973151.1| lysyl-tRNA synthetase [Treponema denticola ATCC... 310 5e-83 ref|NP_219081.1| lysyl-tRNA synthetase (lysS-1) [Treponema palli... 308 2e-82 sp|Q937W6|SYK_BORAF Lysyl-tRNA synthetase (Lysine--tRNA ligase) ... 301 2e-80 ref|ZP_00062266.1| COG1384: Lysyl-tRNA synthetase (class I) [Clo... 301 2e-80 >ref|NP_832294.1| Class 1 lysyl-tRNA synthetase [Bacillus cereus ATCC 14579] gb|AAP09495.1| Class 1 lysyl-tRNA synthetase [Bacillus cereus ATCC 14579] Length = 517 Score = 615 bits (1586), Expect = e-175, Method: Compositional matrix adjust. Identities = 289/518 (55%), Positives = 376/518 (72%), Gaps = 2/518 (0%) Query: 1 MHWSEKIANRLIESHPEQQTFVCASGISPSGHIHIGNFREIVTTYFVSRALEKAGKQVRF 60 MHW+ ++A+ LI HP ++ FVCASGISPSG +HIGNFREIVTTYFV RAL+ GK+ RF Sbjct: 1 MHWAYEVAHELIRKHPNKEMFVCASGISPSGSVHIGNFREIVTTYFVVRALQDLGKKTRF 60 Query: 61 IFSWDDFDRFRKVPLQVDPSFEQYIGRPYTQVPCPYGCHTSYAEHFEQEFEEALQSFGIR 120 IFSWDD+DRFRKVP +DPSF +YIG PY +P PYGCH SYAEHFE+EFE++LQ+FGI Sbjct: 61 IFSWDDYDRFRKVPKNIDPSFAKYIGMPYCDIPDPYGCHNSYAEHFEKEFEKSLQAFGIE 120 Query: 121 PEFIYQSKEYQSRRYAPGILHALRSRGEIYDILMSFKTGEASEADRAAFYPVSIYCGDCG 180 EFIYQ EY+S RY IL AL R EIYDILM FKT E SE +R +FYP ++YC CG Sbjct: 121 VEFIYQHDEYRSGRYNKNILEALYKRKEIYDILMGFKTRECSEEERESFYPATLYCERCG 180 Query: 181 KDSTTVHSFDEDKELLTYSCTCGHHSSLSIPEADNIKLQWKIDWPMRWNLEQVLFEPGGR 240 KD+TT+ FDE + + Y C CG+ LS+ + +KL WKIDWPMRW +E V+FEPGGR Sbjct: 181 KDTTTITHFDEVLKTVRYECECGNEKELSVLNTNKMKLNWKIDWPMRWMIEDVIFEPGGR 240 Query: 241 DHSSETGSYNVASVISERIFGSAPPMYEPYEFIRIKGSFAKMSSSSGNNYTPDDLLKVYA 300 DHSSETGSYNV+ I+ +IF P Y Y+FI IKG+ KMSSSSGN+ TP +LLKVY Sbjct: 241 DHSSETGSYNVSKEIARKIFNREVPHYVAYDFIGIKGNHEKMSSSSGNSITPSNLLKVYI 300 Query: 301 PENILFLFAKYQPGAAFHIGMDEDVLRNYTEFERYRKAYGSLTL-TDDIRAALELSLIHP 359 PE ILF+FAKY+PGAAFHIG+DEDV+RNYTE+ER + +Y + TL +D+ A+++S + Sbjct: 301 PEVILFMFAKYKPGAAFHIGLDEDVIRNYTEYERLKDSYENKTLKNEDLFDAIKISRVDS 360 Query: 360 LDEKAPGFGPIAGLLPLIHFDRKLLLEIMTRNGEEVDVQGLEQTAERAEYWIRHWMPQKL 419 ++ P F +AG LPL++FD +L I+ + + + + RAEYWIR++ +KL Sbjct: 361 EIKEYPKFNQVAGTLPLLNFDSTILQGILKKIDRSYALDEMRAISNRAEYWIRNFQSEKL 420 Query: 420 VTVNTRRNNSLYETLEAHEQEWLAAFCRLLRTGGMEDEPLMKAIYAICYDEDKKSMKNNQ 479 + VN +N Y TL+ ++EWL C++LR+ + LM+ +Y IC+ E+KK MK NQ Sbjct: 421 IAVNEEKNAEFYYTLDERQKEWLVEVCKILRSNK-DYSNLMEQLYGICHHENKKIMKENQ 479 Query: 480 KRLFTLIYQLVLGQETGPRIPVLIQAVGIEKLLALLDF 517 K+LFT+IY+L++ Q GPRIP+LI VGIE + LLDF Sbjct: 480 KQLFTIIYKLIMNQSNGPRIPLLIHVVGIENFITLLDF 517 >ref|NP_973151.1| lysyl-tRNA synthetase [Treponema denticola ATCC 35405] gb|AAS13070.1| lysyl-tRNA synthetase [Treponema denticola ATCC 35405] Length = 528 Score = 310 bits (794), Expect = 5e-83, Method: Compositional matrix adjust. Identities = 179/523 (34%), Positives = 281/523 (53%), Gaps = 21/523 (4%) Query: 1 MHWSEKIANRLIESHPEQQTFVCASGISPSGHIHIGNFREIVTTYFVSRALEKAGKQVRF 60 +HW+++ A ++I + + CASGI+PSG +H+GNFREI++ V RAL GK VRF Sbjct: 8 LHWADQTAEKIIRERGDLDVYTCASGITPSGTVHVGNFREIISVDLVVRALRSRGKNVRF 67 Query: 61 IFSWDDFDRFRKVPLQVDPS--FEQYIGRPYTQVPCPYGCHTSYAEHFEQEFEEALQSFG 118 I+SWDD+D FRKVP + E+Y+ P T VP + +YA H E + E L G Sbjct: 68 IYSWDDYDVFRKVPANMPKPEVLEKYLRYPITMVPDTFERDENYARHHEHDVEAVLPRVG 127 Query: 119 IRPEFIYQSKEYQSRRYAPGILHALRSRGEIYDILMSFKTGEASEADRAAFYPVSIYCGD 178 I PE++YQ++ YQ YA G+ AL +R E+ DIL +++ + S ++PVS++C Sbjct: 128 IHPEYLYQAERYQKGMYAEGMKKALDNREELKDILNTYR--DESHKITEEYWPVSVFCTA 185 Query: 179 CGKDSTTVHSFDEDKELLTYSCTCGHHSSLSIPEADNIKLQWKIDWPMRWNLEQVLFEPG 238 C KD+T + S+D D L YSC CGH +L + +A ++KL W++DWPMRW E+ +FEP Sbjct: 186 CNKDTTKIESWDGD-WTLKYSCECGHCEALDLRKAKSVKLGWRVDWPMRWAFEKTVFEPA 244 Query: 239 GRDHSSETGSYNVASVISERIFGSAPPMYEPYEFIRIKGSFAKMSSSSGNNYTPDDLLKV 298 G+DH S+ GS++ AS++S+RI+ P+ Y+FI +KG KM+SS G + ++L+V Sbjct: 245 GKDHHSQGGSFDTASLVSDRIYNWPAPVSFRYDFIGLKGVPGKMASSKGKVVSLAEVLEV 304 Query: 299 YAPENILFLFAKYQPGAAFHIGMDEDVLRNYTEFERY-------RKAYGSLTLTDDIRAA 351 Y PE +LFA +P F I D DV++ Y ++++ KA T + R Sbjct: 305 YQPEVARYLFAGTRPNTEFVISFDLDVIKIYEDYDKTERIAWKAEKAKNDETFEKEYR-I 363 Query: 352 LELSLIHPLDEKAPGFGPIAGLLPLIHFDRKLLLEIMTR--NGEEVDVQGLEQTAERAEY 409 ELS I + E P L L+ + + ++ + + V L AE A Sbjct: 364 YELSQIDGMPECISYQIPFRHLCNLLQINSGDIEAVIKGLPDVKPAQVDRLRTRAECAWN 423 Query: 410 WIRHWMPQKLVTVNTRRNNSLYETLEAHEQEWLAAFCRLL-RTGGMEDEPLMKAIYAICY 468 WI + R + S E E + LL + M+++ A+Y Sbjct: 424 WITDGGAPEEFKFALRADGSKAELSEPETKAIKTIRDSLLPKMDEMDEKTFSTALY---- 479 Query: 469 DEDKKSMKNNQKRLFTLIYQLVLGQETGPRIPVLIQAVGIEKL 511 + K K++F +YQ ++ ++ GPR+ ++ +G E+L Sbjct: 480 -DAAKECGLEPKQMFVAVYQALVSKDQGPRLAGFMKTIGKERL 521 >ref|NP_219081.1| lysyl-tRNA synthetase (lysS-1) [Treponema pallidum subsp. pallidum str. Nichols] sp|O83650|SYK_TREPA Lysyl-tRNA synthetase (Lysine--tRNA ligase) (LysRS) pir||C71299 lysine-tRNA ligase (EC 6.1.1.6) (lysS-1) - syphilis spirochete gb|AAC65618.1| lysyl-tRNA synthetase (lysS-1) [Treponema pallidum subsp. pallidum str. Nichols] Length = 528 Score = 308 bits (790), Expect = 2e-82, Method: Compositional matrix adjust. Identities = 183/529 (34%), Positives = 285/529 (53%), Gaps = 25/529 (4%) Query: 1 MHWSEKIANRLIESHPEQQTFVCASGISPSGHIHIGNFREIVTTYFVSRALEKAGKQVRF 60 +HW++K+A+++I+ + + CASGI+PSG +HIGNFREI++ V RAL GK VRF Sbjct: 8 LHWADKVAHKIIKERADCDQYTCASGITPSGTVHIGNFREIISVDLVVRALRDQGKSVRF 67 Query: 61 IFSWDDFDRFRKVPLQV--DPSFEQYIGRPYTQVPCPYGCHTSYAEHFEQEFEEALQSFG 118 + SWDD+D FR++P V +QYI P T VP P+ SYA H E+E E AL G Sbjct: 68 VHSWDDYDVFRRIPDNVPAQDELKQYIRMPITSVPDPFQQEDSYARHHEREIESALPEVG 127 Query: 119 IRPEFIYQSKEYQSRRYAPGILHALRSRGEIYDILMSFKTGEASEADRAAFYPVSIYCGD 178 I PE++YQSK+YQ+ YA I AL +R I IL ++ + + ++PVS++C Sbjct: 128 IYPEYVYQSKQYQAGVYAQEIKIALDNRHRIQAILNEYRDEQHKIS--GTYWPVSVFCTA 185 Query: 179 CGKDSTTVHSFDEDKELLTYSCTCGHHSSLSIPEADNIKLQWKIDWPMRWNLEQVLFEPG 238 C KD TTV ++D L Y C CGH + + + +KL W++DW MRW+ E V+FEP Sbjct: 186 CHKDCTTVDAWDS-HWCLQYHCECGHGEQVDLRQTSAVKLSWRVDWAMRWSKEHVVFEPA 244 Query: 239 GRDHSSETGSYNVASVISERIFGSAPPMYEPYEFIRIKGSFAKMSSSSGNNYTPDDLLKV 298 G+DH S+ GS++ A +IS+ I+ P+ Y+FI +KG KMSSS+G D+L+V Sbjct: 245 GKDHHSQGGSFDTARLISDHIYHWPAPVSFRYDFIGLKGLPGKMSSSAGKVVGLRDVLEV 304 Query: 299 YAPENILFLFAKYQPGAAFHIGMDEDVLRNYTEFERY-RKAYGSLTLTDD-----IRAAL 352 Y PE + +LF +P F I D DVL+ Y ++++ R A+G + + Sbjct: 305 YQPEVLRYLFVSTRPNTEFSISFDLDVLKIYEDYDKSERVAWGIHAAKSEHEFMRHKRIY 364 Query: 353 ELSLIH---PLDEKAPGFGPIAGLLPLIHFDRKLLLEIMTRNGEEVDVQGLEQTAERAEY 409 ELS + P F + +L + D +L + ++ ++ + + A Sbjct: 365 ELSQVRGMPPCISYQVPFRHVCNILQINSGDISAVLAFFSDIHKD-QIERFVRRCQCAWN 423 Query: 410 WIRH-WMPQKLVTVNTRRNNSLYETLEAHEQEWLAAFCRLL--RTGGMEDEPLMKAIYAI 466 WIR P T + + + L A E L L RT + ++ L +YA+ Sbjct: 424 WIRDAGAPDDFKF--TLKEDGVRVPLSAEITEALRLIRDTLVPRTDVLSEKELSAELYAV 481 Query: 467 CYDEDKKSMKNNQKRLFTLIYQLVLGQETGPRIPVLIQAVGIEKLLALL 515 + + K LFT +YQ+++G+ GPR+ ++ +G ++L +L Sbjct: 482 A-----RQIPVGSKELFTALYQVLIGKNQGPRLAGFMKVIGTQRLHRML 525 >sp|Q937W6|SYK_BORAF Lysyl-tRNA synthetase (Lysine--tRNA ligase) (LysRS) emb|CAC95160.1| class 1 lysyl-tRNA synthetase [Borrelia afzelii] Length = 521 Score = 301 bits (772), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 182/528 (34%), Positives = 290/528 (54%), Gaps = 29/528 (5%) Query: 2 HWSEKIANRLIESHPEQQTFVCASGISPSGHIHIGNFREIVTTYFVSRALEKAGKQVRFI 61 HW++ A ++ + + + ASGI+PSG +HIGNFRE+++ V+RAL+ +G +VRFI Sbjct: 5 HWADFYAEKIKKDKGPKNLYTVASGITPSGTVHIGNFREVISVDLVARALKDSGSKVRFI 64 Query: 62 FSWDDFDRFRKVPLQVDPS--FEQYIGRPYTQVPCPYGCHTSYAEHFEQEFEEALQSFGI 119 +SWD++D FRKVP + Y+ + T+VP TSYA E EFE+ L GI Sbjct: 65 YSWDNYDVFRKVPKNMPEQELLTTYLRQAITRVPDTRSHKTSYARANEIEFEKYLPIVGI 124 Query: 120 RPEFIYQSKEYQSRRYAPGILHALRSRGEIYDILMSFKTGEASEADRAAFYPVSIYCGDC 179 PEFI QSK+Y + YA I AL + E+ + L ++T + E +YP+SI+C C Sbjct: 125 NPEFIDQSKQYTNGVYASQIKFALNHKKELSNALNEYRTSKLEE----NWYPISIFCTKC 180 Query: 180 GKDSTTVHSFDEDKELLTYSCTCGHHSSLSIPEADNIKLQWKIDWPMRWNLEQVLFEPGG 239 +D+TTV+++D + + YSC CG+ SL I IKL W+IDWPMRW E+V FEP G Sbjct: 181 NRDTTTVNNYD-NHYSVEYSCECGNQESLDIRTTWAIKLPWRIDWPMRWKYEEVDFEPAG 239 Query: 240 RDHSSETGSYNVASVISERIFGSAPPMYEPYEFIRIKGSFAKMSSSSGNNYTPDDLLKVY 299 +DH S GS++ + I +IF +PP+ Y+FI IKG K+SSSSG+ + D+L+VY Sbjct: 240 KDHHSSGGSFDTSKNIV-KIFQGSPPVTFQYDFISIKGRGGKISSSSGDVISLKDVLEVY 298 Query: 300 APENILFLFAKYQPGAAFHIGMDEDVLRNYTEFERY-RKAYGSLTLTDDIRAAL----EL 354 PE FLFA +P F I D DV++ Y +++R+ R YG + ++ + A EL Sbjct: 299 TPEVTRFLFASTRPNTEFSISFDLDVIKIYEDYDRFERIYYGVEDIKEEKKRAFKRIYEL 358 Query: 355 SLIHPLDEKAP---GFGPIAGLLPLIHFDRKLLLEIMTRNGEEVDVQGLEQTAERAEYWI 411 S + ++ P GF ++ + + + +L + +N +E L + A WI Sbjct: 359 SQPYMPSKRIPYQIGFRHLSVICQIFENNINKILNYL-KNVQEDQKDKLINKIKCAINWI 417 Query: 412 RHWMPQKLVTVNTRRNNSLYETLEAHEQEWLAAFCRLLRTG--GMEDEPLMKAIYAICYD 469 R + P+ + R E L+ + ++ + L+ ++ + IY I Sbjct: 418 RDFAPEDF-KFSLRSKFDSIEILKENSKKAINELLNFLKKNFEVATEQDIQNEIYKI--- 473 Query: 470 EDKKSMKNNQK--RLFTLIYQLVLGQETGPRIPVLIQAVGIEKLLALL 515 S +NN + F IY++++ +E GP++ I+ +GIE+ ++ Sbjct: 474 ----SRENNIEPALFFKQIYKILIDKEKGPKLAGFIKIIGIERFEKIV 517 >ref|ZP_00062266.1| COG1384: Lysyl-tRNA synthetase (class I) [Clostridium thermocellum ATCC 27405] Length = 250 Score = 301 bits (771), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 135/249 (54%), Positives = 182/249 (73%), Gaps = 5/249 (2%) Query: 1 MHWSEKIANRLIESHPEQQTFVCASGISPSGHIHIGNFREIVTTYFVSRALEKAGKQVRF 60 MHWS++IAN+LI HP++ FV A+G SPSG +HIGNFR+ VT YFV++AL K GK+ Sbjct: 1 MHWSDEIANKLISMHPDKDEFVLAAGTSPSGTVHIGNFRDAVTVYFVAKALRKKGKKTVL 60 Query: 61 IFSWDDFDRFRKVPLQVD----PSFEQYIGRPYTQVPCPYGCHTSYAEHFEQEFEEALQS 116 + SWDD+DRFRKVP + +E+YIG PY+ VP P+GCH SYAEH+E+E+EE+L+ Sbjct: 61 LLSWDDYDRFRKVPKNLPQEKIEEYEKYIGMPYSAVPDPFGCHASYAEHYEKEYEESLEK 120 Query: 117 FGIRPEFI-YQSKEYQSRRYAPGILHALRSRGEIYDILMSFKTGEASEADRAAFYPVSIY 175 G++ + I YQ++EY S RY GI+ AL++R EIYDI+ FKT E S +R FYP+S+Y Sbjct: 121 IGLKFDIIRYQTREYMSGRYKDGIITALKNRKEIYDIMQEFKTQEYSAEERENFYPLSVY 180 Query: 176 CGDCGKDSTTVHSFDEDKELLTYSCTCGHHSSLSIPEADNIKLQWKIDWPMRWNLEQVLF 235 C CGKD+T + ED +++YSC CG+ S+++I E N KL WK+DWPMRW E V F Sbjct: 181 CDKCGKDTTKITDVSEDCNVVSYSCKCGNVSTVNISEQGNCKLPWKVDWPMRWMYEGVDF 240 Query: 236 EPGGRDHSS 244 EPGG+DH+S Sbjct: 241 EPGGKDHAS 249 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.321 0.137 0.420 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 811,147,103 Number of extensions: 34842521 Number of successful extensions: 76595 Number of sequences better than 1.0e-05: 240 Number of HSP's gapped: 76104 Number of HSP's successfully gapped: 242 Length of query: 517 Length of database: 757,237,578 Length adjustment: 130 Effective length of query: 387 Effective length of database: 404,274,708 Effective search space: 156454311996 Effective search space used: 156454311996 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 128 (53.9 bits)