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= 0001.0003.p (832 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... 1652 0.0 gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B ... 343 4e-95 >gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspirillum seropedicae SmR1] Length = 832 Score = 1652 bits (4278), Expect = 0.0, Method: Compositional matrix adjust. Identities = 811/832 (97%), Positives = 824/832 (99%) Query: 1 MSSSPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID 60 MS+SPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID Sbjct: 1 MSTSPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSID 60 Query: 61 EALAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD 120 EALAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD Sbjct: 61 EALAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFD 120 Query: 121 QNSYKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVSP 180 QNSYKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVSP Sbjct: 121 QNSYKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVSP 180 Query: 181 IKVVGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLSDQRTGKEE 240 IKV+GESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKL+DQRTGKEE Sbjct: 181 IKVIGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKEE 240 Query: 241 DFAFEGGTRGFVEYINKNKSILNPTIFQATGEKQSDQGTLVSVDVSMQWNDAFNEQVLCF 300 DFAFEGGTRGFVEYINKNKSILNPTIFQATGEKQSDQGT+++VDVSMQWNDAFNEQVLCF Sbjct: 241 DFAFEGGTRGFVEYINKNKSILNPTIFQATGEKQSDQGTMITVDVSMQWNDAFNEQVLCF 300 Query: 301 TNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPE 360 TNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPE Sbjct: 301 TNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTCVLSVKVPE 360 Query: 361 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKAR 420 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKAR Sbjct: 361 PKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARAREAARKAR 420 Query: 421 ELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK 480 ELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK Sbjct: 421 ELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQAILPLRGK 480 Query: 481 VLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTL 540 VLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTL Sbjct: 481 VLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPDKLRYHRIIIMTDADVDGAHIRTL 540 Query: 541 LLTLFYRQMPALVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPA 600 LLTLFYRQMPALVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPA Sbjct: 541 LLTLFYRQMPALVERGHIYIAQPPLYKVKAGKDERYLKDDFEEAQYMMQIALNDAEIKPA 600 Query: 601 EDAAPISGEALVELARQYNTANAIIMRLSRAIDESALNAIMTGGVALKLENLEQATATAE 660 EDA I+GEALVELARQYNTANAIIMRL+RAIDESAL+AIMTGGV LK++NLEQATATAE Sbjct: 601 EDAPAITGEALVELARQYNTANAIIMRLTRAIDESALDAIMTGGVVLKMDNLEQATATAE 660 Query: 661 ELKKAINDINIDVQARVDEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYLQLSNAAET 720 ELKKAINDINIDVQAR+DEHSEKVALHIHRRQHGNIKATVIDADFVSGPDY LS AAET Sbjct: 661 ELKKAINDINIDVQARMDEHSEKVALHIHRRQHGNIKATVIDADFVSGPDYQVLSTAAET 720 Query: 721 FKGLIGKGAVVARGQGEKRKESVITEFRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWE 780 FKGLI KGA VARGQGEKRKESVIT+FRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWE Sbjct: 721 FKGLIRKGATVARGQGEKRKESVITDFRQAMAWLRDEAERGVNKQRYKGLGEMNPEQLWE 780 Query: 781 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV 832 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV Sbjct: 781 TTMDPTVRRLLKVQIEDAIAADQIFMTLMGDDVEPRRAFIESNALQAGNIDV 832 >gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B [Herbaspirillum seropedicae SmR1] Length = 662 Score = 343 bits (879), Expect = 4e-95, Method: Compositional matrix adjust. Identities = 214/580 (36%), Positives = 324/580 (55%), Gaps = 43/580 (7%) Query: 3 SSPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSIDEA 62 +SP+D Y SSI++L+GLE V++RPGMY + H++ EV+DN+ DEA Sbjct: 6 TSPSD--------YSESSIRVLKGLEPVKQRPGMYTRTENP----LHILQEVIDNASDEA 53 Query: 63 LAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFDQN 122 L GY I VT++AD S+S+ D+GRGIP GL E K EIV T LHAGGKFD+ Sbjct: 54 LGGYGKSIIVTMNADGSVSVEDDGRGIPVGLH----PEEKVPTVEIVFTRLHAGGKFDKG 109 Query: 123 S---YKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVS 179 S Y SGGLHGVGVS NAL+ +L++T+ R+G VH + F+ G ++++ ++ Sbjct: 110 SGGAYAFSGGLHGVGVSVTNALATRLEITVWREGGVHTLAFSGG-------DVIEKLKSR 162 Query: 180 PIKVVGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLSDQRTGKE 239 P + K GT V W D + F L + +R + L GV + L++ +TG Sbjct: 163 P--ATRDDKKSGTRVTVWPDAKYFDSPTIPMGELQRLLRSKAVLLPGVKVTLTNGKTGDS 220 Query: 240 EDFAFEGGTRGFV-EYINKNKS--ILNPTIFQATGEKQSDQGTLVSVDVSMQWNDAFNEQ 296 + + ++ G RG++ E + + S L P +F+ D + W A+ E+ Sbjct: 221 QSWQYDQGLRGYLMEQLAQTGSGETLIP-LFEGEQFAGKDADGFAEGE-GASWVVAWTEE 278 Query: 297 VLC----FTNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTC 352 + N IP +GGTH +GLR + + + E + L K V++ +D+ ++ Sbjct: 279 GAVVRESYVNLIPTSNGGTHESGLREGLFSAVKSFAEMHSLLPKG-VKLLAEDVFARVSF 337 Query: 353 VLSVKVPEPKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARA 412 VLS KV +P+F Q K++L S + V L +L + + K + +++ A++ Sbjct: 338 VLSAKVLDPQFQGQIKERLNSRDAVRLVAGFSRPALELWLNQHVDYGKKLAELVIKQAQS 397 Query: 413 REAARKARELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQ 472 R + + E + GV L KL DC+ D + EL++VEGDSAGGSAK GRD++FQ Sbjct: 398 RLRSAQKVEKKKSSGVAV---LPGKLTDCESSDVSRNELFLVEGDSAGGSAKMGRDKEFQ 454 Query: 473 AILPLRGKVLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPD--KLRYHRIIIMTDA 530 AILPLRGKVLN + +++ ++ +I + +G PD LRY +I I++DA Sbjct: 455 AILPLRGKVLNAWETERDRLFANNEIHDIAVAIGVDPHGINDTPDLSGLRYGKICILSDA 514 Query: 531 DVDGAHIRTLLLTLFYRQMPALVERGHIYIAQPPLYKVKA 570 DVDG+HI+ LLLTLF+R P L+E G+I +A+PPLY+V A Sbjct: 515 DVDGSHIQVLLLTLFFRHFPKLIENGNICVARPPLYRVDA 554 Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 32/65 (49%), Positives = 43/65 (66%), Gaps = 3/65 (4%) Query: 766 RYKGLGEMNPEQLWETTMDPTVRRLLKVQI-EDAI-AADQIFMTLMGD-DVEPRRAFIES 822 R+KGLGEMN EQLWETTM+P RRLL + E + +++ F LMG + RRA+IE Sbjct: 594 RFKGLGEMNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEE 653 Query: 823 NALQA 827 + +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 0.133 0.372 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: 2,402,518 Number of extensions: 97309 Number of successful extensions: 274 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 3 Length of query: 832 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 739 Effective length of database: 1,179,515 Effective search space: 871661585 Effective search space used: 871661585 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)