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= 0029.0014.p (835 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspir... 1447 0.0 gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B ... 339 5e-94 >gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspirillum seropedicae SmR1] Length = 832 Score = 1447 bits (3745), Expect = 0.0, Method: Compositional matrix adjust. Identities = 716/832 (86%), Positives = 763/832 (91%), Gaps = 2/832 (0%) Query: 5 SQAPADNTVQPQQNQYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID 64 S +PADNT QQ+ YGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID Sbjct: 2 STSPADNTNSAQQS-YGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID 60 Query: 65 ESLAGHCTEIHVTIHSDNSISVIDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD 124 E+LAG+C+EIHVTIH+DNSIS+ DNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD Sbjct: 61 EALAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD 120 Query: 125 QNSYKVSGGLHGVGVSCVNGLSKLLRLTIRRDGKAYAMEFVRGIPQDRLIEVIDGVQVSP 184 QNSYKVSGGLHGVGVSCVN LSK L+LTIRRDGK +AMEF +GI Q+R +E++DGVQVSP Sbjct: 121 QNSYKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVSP 180 Query: 185 IRVTGDTDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKEE 244 I+V G++DKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKEE Sbjct: 181 IKVIGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKEE 240 Query: 245 NFAFEGGTRGFVEYINKNKSILNPTIFQATGERMSDQNTNISVDVSMQWNDAYNEQVLCF 304 +FAFEGGTRGFVEYINKNKSILNPTIFQATGE+ SDQ T I+VDVSMQWNDA+NEQVLCF Sbjct: 241 DFAFEGGTRGFVEYINKNKSILNPTIFQATGEKQSDQGTMITVDVSMQWNDAFNEQVLCF 300 Query: 305 TNNIPQRDGGTHLTGLRAAMTRVINKYIEEHEFAKKAKVEVSGDDMREGLTCVLSVKVPE 364 TNNIPQRDGGTHLTGLRAAMTRVINKYIEE++ AKKAKVE+SGDDMREGLTCVLSVKVPE Sbjct: 301 TNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPE 360 Query: 365 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLQERPNDAKIICGKIVEAARAREAARKAR 424 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFL E+PNDAKIICGKIVEAARAREAARKAR Sbjct: 361 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKAR 420 Query: 425 ELTRRKGVMDGLGLSAKLADCQEKDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK 484 ELTRRKGVMDGLGLS+KLADCQE+DPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK Sbjct: 421 ELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK 480 Query: 485 VLNVEKARFEKMLSSEQITTLIATLGTSIGPDEFNADKLRYHRIIIMTDADVDGAHIRTL 544 VLNVEKARFEKMLSSEQITTLIATLGTSIG DEFN DKLRYHRIIIMTDADVDGAHIRTL Sbjct: 481 VLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTL 540 Query: 545 LLTLFYRQMPQLVERGHIYIAQPPLYKVKAGKDERYLKDDVEEAQYMMQIALNDAELVPS 604 LLTLFYRQMP LVERGHIYIAQPPLYKVKAGKDERYLKDD EEAQYMMQIALNDAE+ P+ Sbjct: 541 LLTLFYRQMPALVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPA 600 Query: 605 EGAAPISGAPLTELVRQYNTANAIIMRLTRMIDAGALSAIMT-GVTLQLNTAAEAEQSAA 663 E A I+G L EL RQYNTANAIIMRLTR ID AL AIMT GV L+++ +A +A Sbjct: 601 EDAPAITGEALVELARQYNTANAIIMRLTRAIDESALDAIMTGGVVLKMDNLEQATATAE 660 Query: 664 ALKAAINEPGVDVVVRSDELTDKHILRINRLYHGNIKATAIDADFVNGPDYQVLENAAAT 723 LK AIN+ +DV R DE ++K L I+R HGNIKAT IDADFV+GPDYQVL AA T Sbjct: 661 ELKKAINDINIDVQARMDEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYQVLSTAAET 720 Query: 724 FRGLIGRGALIRRGSGEKIKESAINDFHQAVAWLREEAERGVSKQRYKGLGEMNPGQLWE 783 F+GLI +GA + RG GEK KES I DF QA+AWLR+EAERGV+KQRYKGLGEMNP QLWE Sbjct: 721 FKGLIRKGATVARGQGEKRKESVITDFRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWE 780 Query: 784 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIELNALQAGNIDV 835 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIE NALQAGNIDV Sbjct: 781 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV 832 >gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B [Herbaspirillum seropedicae SmR1] Length = 662 Score = 339 bits (870), Expect = 5e-94, Method: Compositional matrix adjust. Identities = 213/578 (36%), Positives = 327/578 (56%), Gaps = 41/578 (7%) Query: 12 TVQPQQNQYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSIDESLAGHC 71 T + + Y SSI++L+GLE V++RPGMY + H++ EV+DN+ DE+L G+ Sbjct: 3 TKKTSPSDYSESSIRVLKGLEPVKQRPGMYTRTENP----LHILQEVIDNASDEALGGYG 58 Query: 72 TEIHVTIHSDNSISVIDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFDQNS---Y 128 I VT+++D S+SV D+GRGIP GL E K EIV T LHAGGKFD+ S Y Sbjct: 59 KSIIVTMNADGSVSVEDDGRGIPVGLH----PEEKVPTVEIVFTRLHAGGKFDKGSGGAY 114 Query: 129 KVSGGLHGVGVSCVNGLSKLLRLTIRRDGKAYAMEFVRGIPQDRLIEVIDGVQVSPIRVT 188 SGGLHGVGVS N L+ L +T+ R+G + + F G +VI+ ++ P T Sbjct: 115 AFSGGLHGVGVSVTNALATRLEITVWREGGVHTLAFSGG-------DVIEKLKSRP--AT 165 Query: 189 GDTDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKEENFAF 248 D K GT V W D + F L + +R + L GV + LT+ +TG +++ + Sbjct: 166 RDDKKSGTRVTVWPDAKYFDSPTIPMGELQRLLRSKAVLLPGVKVTLTNGKTGDSQSWQY 225 Query: 249 EGGTRGFV-EYINKNKS--ILNPTIFQATGERMSDQNTN-ISVDVSMQWNDAYNEQVLC- 303 + G RG++ E + + S L P +F+ GE+ + ++ + + W A+ E+ Sbjct: 226 DQGLRGYLMEQLAQTGSGETLIP-LFE--GEQFAGKDADGFAEGEGASWVVAWTEEGAVV 282 Query: 304 ---FTNNIPQRDGGTHLTGLRAAMTRVINKYIEEHEFAKKAKVEVSGDDMREGLTCVLSV 360 + N IP +GGTH +GLR + + + E H K V++ +D+ ++ VLS Sbjct: 283 RESYVNLIPTSNGGTHESGLREGLFSAVKSFAEMHSLLPKG-VKLLAEDVFARVSFVLSA 341 Query: 361 KVPEPKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLQERPNDAKIICGKIVEAARAREAA 420 KV +P+F Q K++L S + V L +L + + K + +++ A++R + Sbjct: 342 KVLDPQFQGQIKERLNSRDAVRLVAGFSRPALELWLNQHVDYGKKLAELVIKQAQSRLRS 401 Query: 421 RKARELTRRKGVMDGLGLSAKLADCQEKDPALCELYIVEGDSAGGSAKQGRDRKFQAILP 480 + E + GV L KL DC+ D + EL++VEGDSAGGSAK GRD++FQAILP Sbjct: 402 AQKVEKKKSSGVAV---LPGKLTDCESSDVSRNELFLVEGDSAGGSAKMGRDKEFQAILP 458 Query: 481 LRGKVLNVEKARFEKMLSSEQITTLIATLGTSIGP----DEFNADKLRYHRIIIMTDADV 536 LRGKVLN + +++ ++ +I + +G + P D + LRY +I I++DADV Sbjct: 459 LRGKVLNAWETERDRLFANNEIHDIAVAIG--VDPHGINDTPDLSGLRYGKICILSDADV 516 Query: 537 DGAHIRTLLLTLFYRQMPQLVERGHIYIAQPPLYKVKA 574 DG+HI+ LLLTLF+R P+L+E G+I +A+PPLY+V A Sbjct: 517 DGSHIQVLLLTLFFRHFPKLIENGNICVARPPLYRVDA 554 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.317 0.134 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 2,348,300 Number of extensions: 92872 Number of successful extensions: 287 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 278 Number of HSP's successfully gapped: 2 Length of query: 835 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 742 Effective length of database: 1,179,515 Effective search space: 875200130 Effective search space used: 875200130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 135 (56.6 bits)