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= 0003.0152.p (581 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... 1134 0.0 gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B ... 191 2e-49 >gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspirillum seropedicae SmR1] Length = 832 Score = 1134 bits (2934), Expect = 0.0, Method: Compositional matrix adjust. Identities = 564/581 (97%), Positives = 574/581 (98%) Query: 1 VEYINKNKSILNPTIFQATGEKQSDQGTLVSVDVSMQWNDAFNEQVLCFTNNIPQRDGGT 60 VEYINKNKSILNPTIFQATGEKQSDQGT+++VDVSMQWNDAFNEQVLCFTNNIPQRDGGT Sbjct: 252 VEYINKNKSILNPTIFQATGEKQSDQGTMITVDVSMQWNDAFNEQVLCFTNNIPQRDGGT 311 Query: 61 HLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPEPKFSSQTKDKL 120 HLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPEPKFSSQTKDKL Sbjct: 312 HLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPEPKFSSQTKDKL 371 Query: 121 VSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKARELTRRKGVMDG 180 VSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKARELTRRKGVMDG Sbjct: 372 VSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKARELTRRKGVMDG 431 Query: 181 LGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARFEK 240 LGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARFEK Sbjct: 432 LGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARFEK 491 Query: 241 MLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTLLLTLFYRQMPA 300 MLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTLLLTLFYRQMPA Sbjct: 492 MLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTLLLTLFYRQMPA 551 Query: 301 LVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPSEGAAPISGEAL 360 LVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKP+E A I+GEAL Sbjct: 552 LVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPAEDAPAITGEAL 611 Query: 361 VELARQYNTANAIIMRLSRAIDESALNAIMTGGVALKMDNIEQATATAEELKKAINDINI 420 VELARQYNTANAIIMRL+RAIDESAL+AIMTGGV LKMDN+EQATATAEELKKAINDINI Sbjct: 612 VELARQYNTANAIIMRLTRAIDESALDAIMTGGVVLKMDNLEQATATAEELKKAINDINI 671 Query: 421 DVQARVDEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYQQLSTAAETFKGLIGKGAIV 480 DVQAR+DEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYQ LSTAAETFKGLI KGA V Sbjct: 672 DVQARMDEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYQVLSTAAETFKGLIRKGATV 731 Query: 481 ARGQGEKRKESVITEFRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWETTMDPTVRRLL 540 ARGQGEKRKESVIT+FRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWETTMDPTVRRLL Sbjct: 732 ARGQGEKRKESVITDFRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWETTMDPTVRRLL 791 Query: 541 KVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV 581 KVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV Sbjct: 792 KVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV 832 >gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B [Herbaspirillum seropedicae SmR1] Length = 662 Score = 191 bits (484), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 106/274 (38%), Positives = 162/274 (59%), Gaps = 6/274 (2%) Query: 48 CFTNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKV 107 + N IP +GGTH +GLR + + + E + L K V++ +D+ ++ VLS KV Sbjct: 285 SYVNLIPTSNGGTHESGLREGLFSAVKSFAEMHSLLPKG-VKLLAEDVFARVSFVLSAKV 343 Query: 108 PEPKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARK 167 +P+F Q K++L S + V L +L + + K + +++ A++R + + Sbjct: 344 LDPQFQGQIKERLNSRDAVRLVAGFSRPALELWLNQHVDYGKKLAELVIKQAQSRLRSAQ 403 Query: 168 ARELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLR 227 E + GV L KL DC+ D + EL++VEGDSAGGSAK GRD++FQAILPLR Sbjct: 404 KVEKKKSSGVAV---LPGKLTDCESSDVSRNELFLVEGDSAGGSAKMGRDKEFQAILPLR 460 Query: 228 GKVLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPD--KLRYHRIIIMTDADVDGAH 285 GKVLN + +++ ++ +I + +G PD LRY +I I++DADVDG+H Sbjct: 461 GKVLNAWETERDRLFANNEIHDIAVAIGVDPHGINDTPDLSGLRYGKICILSDADVDGSH 520 Query: 286 IRTLLLTLFYRQMPALVERGHIYIAQPPLYKVKA 319 I+ LLLTLF+R P L+E G+I +A+PPLY+V A Sbjct: 521 IQVLLLTLFFRHFPKLIENGNICVARPPLYRVDA 554 Score = 59.7 bits (143), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 32/65 (49%), Positives = 43/65 (66%), Gaps = 3/65 (4%) Query: 515 RYKGLGEMNPEQLWETTMDPTVRRLLKVQI-EDAI-AADQIFMTLMG-DDVEPRRAFIES 571 R+KGLGEMN EQLWETTM+P RRLL + E + +++ F LMG + RRA+IE Sbjct: 594 RFKGLGEMNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEE 653 Query: 572 NALQA 576 + +A Sbjct: 654 HGNEA 658 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 0.316 0.132 0.367 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: 1,606,622 Number of extensions: 62178 Number of successful extensions: 192 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 189 Number of HSP's successfully gapped: 3 Length of query: 581 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 491 Effective length of database: 1,193,720 Effective search space: 586116520 Effective search space used: 586116520 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: 133 (55.8 bits)