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= 0026.0056.p (668 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B ... 1226 0.0 gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspir... 337 2e-93 >gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B [Herbaspirillum seropedicae SmR1] Length = 662 Score = 1226 bits (3171), Expect = 0.0, Method: Compositional matrix adjust. Identities = 600/668 (89%), Positives = 631/668 (94%), Gaps = 6/668 (0%) Query: 1 MATKKTSPSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGGHARN 60 MATKKTSPSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGG+ ++ Sbjct: 1 MATKKTSPSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGGYGKS 60 Query: 61 IMVTLNPDGSVSVEDDGRGIPVGLHPEEGVPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL 120 I+VT+N DGSVSVEDDGRGIPVGLHPEE VPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL Sbjct: 61 IIVTMNADGSVSVEDDGRGIPVGLHPEEKVPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL 120 Query: 121 HGVGVSVTNALASRLEITVWREAGVHTLAFSDGDLIEKLKSRPITREDKKSGTRVSVWPN 180 HGVGVSVTNALA+RLEITVWRE GVHTLAFS GD+IEKLKSRP TR+DKKSGTRV+VWP+ Sbjct: 121 HGVGVSVTNALATRLEITVWREGGVHTLAFSGGDVIEKLKSRPATRDDKKSGTRVTVWPD 180 Query: 181 PKYFDSPTISQQELQRLLRSKAVLLPGVKVSLINGKTGDVQTWQYDQGLRGYLMESLAQS 240 KYFDSPTI ELQRLLRSKAVLLPGVKV+L NGKTGD Q+WQYDQGLRGYLME LAQ+ Sbjct: 181 AKYFDSPTIPMGELQRLLRSKAVLLPGVKVTLTNGKTGDSQSWQYDQGLRGYLMEQLAQT 240 Query: 241 TSVDPLIPLFEGEQYAGPDAEGFAEGEGAAWVVAWTEEGNVVRESYVNLIPTSAGGTHES 300 S + LIPLFEGEQ+AG DA+GFAEGEGA+WVVAWTEEG VVRESYVNLIPTS GGTHES Sbjct: 241 GSGETLIPLFEGEQFAGKDADGFAEGEGASWVVAWTEEGAVVRESYVNLIPTSNGGTHES 300 Query: 301 GLREGLFSAVKSFVEMHSLLPKGVKLLPEDVFARVSFVLSAKVLDPQFQGQIKERLNSRD 360 GLREGLFSAVKSF EMHSLLPKGVKLL EDVFARVSFVLSAKVLDPQFQGQIKERLNSRD Sbjct: 301 GLREGLFSAVKSFAEMHSLLPKGVKLLAEDVFARVSFVLSAKVLDPQFQGQIKERLNSRD 360 Query: 361 AVRLVSTFSRPALELWLNQHVEYGKKLADLVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL 420 AVRLV+ FSRPALELWLNQHV+YGKKLA+LVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL Sbjct: 361 AVRLVAGFSRPALELWLNQHVDYGKKLAELVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL 420 Query: 421 TDCESSDVTRNEIFLVEGDSAGGSAKMGRDKEFQAILPLRGKVLNSWETERDRLFANNEI 480 TDCESSDV+RNE+FLVEGDSAGGSAKMGRDKEFQAILPLRGKVLN+WETERDRLFANNEI Sbjct: 421 TDCESSDVSRNELFLVEGDSAGGSAKMGRDKEFQAILPLRGKVLNAWETERDRLFANNEI 480 Query: 481 HDIAVAIGVDPHGYNDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFFKHFPKLIDHG 540 HDIAVAIGVDPHG NDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFF+HFPKLI++G Sbjct: 481 HDIAVAIGVDPHGINDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFFRHFPKLIENG 540 Query: 541 HICIARPPLYRVDALLGVDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISR 600 +IC+ARPPLYR VDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISR Sbjct: 541 NICVARPPLYR------VDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISR 594 Query: 601 FKGLGEMNAEQLWETTMNPDTRRLLPVALGELDQIASDARFTMLMGKGEAASRRAWIEEH 660 FKGLGEMNAEQLWETTMNPDTRRLLP++ GE S+ RF MLMGKGEAASRRAWIEEH Sbjct: 595 FKGLGEMNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEEH 654 Query: 661 GNEAEADI 668 GNEAEADI Sbjct: 655 GNEAEADI 662 >gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspirillum seropedicae SmR1] Length = 832 Score = 337 bits (863), Expect = 2e-93, Method: Compositional matrix adjust. Identities = 221/616 (35%), Positives = 333/616 (54%), Gaps = 53/616 (8%) Query: 6 TSPSD--------YSESSIRVLKGLEPVKQRPGMY---TRTENPLH-ILQEVIDNASDEA 53 TSP+D Y SSI++L+GLE V++RPGMY T LH ++ EV+DN+ DEA Sbjct: 3 TSPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSIDEA 62 Query: 54 LGGHARNIMVTLNPDGSVSVEDDGRGIPVGLH----PEEGVPTVEIVFTRLHAGGKFDKG 109 L G+ I VT++ D S+S+ D+GRGIP GL E EIV T LHAGGKFD+ Sbjct: 63 LAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFDQN 122 Query: 110 SGGAYAFSGGLHGVGVSVTNALASRLEITVWREAGVHTLAFSDG-------DLIEKLKSR 162 S Y SGGLHGVGVS NAL+ +L++T+ R+ VH + F+ G ++++ ++ Sbjct: 123 S---YKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVS 179 Query: 163 PITR--EDKKSGTRVSVWPNPKYFDSPTISQQELQRLLRSKAVLLPGVKVSLINGKTGDV 220 PI E K GT V W + + F + L + +R + L GV + L + +TG Sbjct: 180 PIKVIGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKE 239 Query: 221 QTWQYDQGLRGYLMESLAQSTSVDPLIPLFEGEQYAGPDAEGFAEGEGAAWVV----AWT 276 + + ++ G RG++ + ++P I GE+ + +G V W Sbjct: 240 EDFAFEGGTRGFVEYINKNKSILNPTIFQATGEKQSD---------QGTMITVDVSMQWN 290 Query: 277 EEGNVVRESYVNLIPTSAGGTHESGLREGLFSAVKSFVEMHSLLPKG-VKLLPEDVFARV 335 + N + N IP GGTH +GLR + + ++E + L K V++ +D+ + Sbjct: 291 DAFNEQVLCFTNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGL 350 Query: 336 SFVLSAKVLDPQFQGQIKERLNSRDAVRLVSTFSRPALELWLNQHVEYGKKLADLVIKQA 395 + VLS KV +P+F Q K++L S + V L +L + K + +++ A Sbjct: 351 TCVLSVKVPEPKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAA 410 Query: 396 QSRLRSAQKVEKKKSSGVAV---LPGKLTDCESSDVTRNEIFLVEGDSAGGSAKMGRDKE 452 ++R + + E + GV L KL DC+ D E+++VEGDSAGGSAK GRD++ Sbjct: 411 RAREAARKARELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRK 470 Query: 453 FQAILPLRGKVLNSWETERDRLFANNEIHDIAVAIGVDPHGYNDTPDLSGLRYGKICILS 512 FQAILPLRGKVLN + +++ ++ +I + +G PD LRY +I I++ Sbjct: 471 FQAILPLRGKVLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPD--KLRYHRIIIMT 528 Query: 513 DADVDGSHIQVLLLTLFFKHFPKLIDHGHICIARPPLYRVDALLGVDAPARGKKPVQKLY 572 DADVDG+HI+ LLLTLF++ P L++ GHI IA+PPLY+V A G D + Y Sbjct: 529 DADVDGAHIRTLLLTLFYRQMPALVERGHIYIAQPPLYKVKA--GKDERYLKDDFEEAQY 586 Query: 573 ----ALDDGELEAIED 584 AL+D E++ ED Sbjct: 587 MMQIALNDAEIKPAED 602 Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 36/65 (55%), Positives = 44/65 (67%), Gaps = 3/65 (4%) Query: 600 RFKGLGEMNAEQLWETTMNPDTRRLLPVALGELDQIASDARFTMLMGKGEAASRRAWIEE 659 R+KGLGEMN EQLWETTM+P RRLL V + D IA+D F LMG + RRA+IE Sbjct: 766 RYKGLGEMNPEQLWETTMDPTVRRLLKVQIE--DAIAADQIFMTLMGD-DVEPRRAFIES 822 Query: 660 HGNEA 664 + +A Sbjct: 823 NALQA 827 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 0.135 0.393 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: 2,152,137 Number of extensions: 93758 Number of successful extensions: 281 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 272 Number of HSP's successfully gapped: 3 Length of query: 668 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 576 Effective length of database: 1,184,250 Effective search space: 682128000 Effective search space used: 682128000 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: 134 (56.2 bits)