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= 0028.0185.p (662 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 ... 1321 0.0 gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspir... 341 1e-94 >gi|300311161|ref|YP_003775253.1| DNA topoisomerase IV subunit B [Herbaspirillum seropedicae SmR1] Length = 662 Score = 1321 bits (3420), Expect = 0.0, Method: Compositional matrix adjust. Identities = 645/662 (97%), Positives = 658/662 (99%) Query: 1 MATKKTTPSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGGYGKS 60 MATKKT+PSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGGYGKS Sbjct: 1 MATKKTSPSDYSESSIRVLKGLEPVKQRPGMYTRTENPLHILQEVIDNASDEALGGYGKS 60 Query: 61 IIVTINADGSVSVEDDGRGIPVGLHPEEKVPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL 120 IIVT+NADGSVSVEDDGRGIPVGLHPEEKVPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL Sbjct: 61 IIVTMNADGSVSVEDDGRGIPVGLHPEEKVPTVEIVFTRLHAGGKFDKGSGGAYAFSGGL 120 Query: 121 HGVGVSVTNALATRLEITVWREGGVHTLAFSGGDVIEKLQSRPATREDKKSGTRVTVWPD 180 HGVGVSVTNALATRLEITVWREGGVHTLAFSGGDVIEKL+SRPATR+DKKSGTRVTVWPD Sbjct: 121 HGVGVSVTNALATRLEITVWREGGVHTLAFSGGDVIEKLKSRPATRDDKKSGTRVTVWPD 180 Query: 181 AKYFDSATIPLGELQRLLRSKAVLLPGVKVTLINAKTGDTQNWQYDQGLRGYLMEQLAQT 240 AKYFDS TIP+GELQRLLRSKAVLLPGVKVTL N KTGD+Q+WQYDQGLRGYLMEQLAQT Sbjct: 181 AKYFDSPTIPMGELQRLLRSKAVLLPGVKVTLTNGKTGDSQSWQYDQGLRGYLMEQLAQT 240 Query: 241 GSGETLIPLFEGEQFAGKDAEGFAEGEGASWVVAWTEEGAVVRESYVNLIPTSNGGTHES 300 GSGETLIPLFEGEQFAGKDA+GFAEGEGASWVVAWTEEGAVVRESYVNLIPTSNGGTHES Sbjct: 241 GSGETLIPLFEGEQFAGKDADGFAEGEGASWVVAWTEEGAVVRESYVNLIPTSNGGTHES 300 Query: 301 GLREGLFSAVKSFAEMHSLLPKGVKLLAEDVFARVSFVLSAKVLDPQFQGQIKERLNSRD 360 GLREGLFSAVKSFAEMHSLLPKGVKLLAEDVFARVSFVLSAKVLDPQFQGQIKERLNSRD Sbjct: 301 GLREGLFSAVKSFAEMHSLLPKGVKLLAEDVFARVSFVLSAKVLDPQFQGQIKERLNSRD 360 Query: 361 AVRLVAGYSRPALELWLNQHVEYGKKLAELVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL 420 AVRLVAG+SRPALELWLNQHV+YGKKLAELVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL Sbjct: 361 AVRLVAGFSRPALELWLNQHVDYGKKLAELVIKQAQSRLRSAQKVEKKKSSGVAVLPGKL 420 Query: 421 TDCESSDVTRNEIFLVEGDSAGGSAKMGRDKEFQAILPLRGKVLNAWETERDRLFANNEI 480 TDCESSDV+RNE+FLVEGDSAGGSAKMGRDKEFQAILPLRGKVLNAWETERDRLFANNEI Sbjct: 421 TDCESSDVSRNELFLVEGDSAGGSAKMGRDKEFQAILPLRGKVLNAWETERDRLFANNEI 480 Query: 481 HDIAVAIGVDPHGINDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFFRHFPKLIEKG 540 HDIAVAIGVDPHGINDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFFRHFPKLIE G Sbjct: 481 HDIAVAIGVDPHGINDTPDLSGLRYGKICILSDADVDGSHIQVLLLTLFFRHFPKLIENG 540 Query: 541 HICVARPPLYRVDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISRFKGLGE 600 +ICVARPPLYRVDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISRFKGLGE Sbjct: 541 NICVARPPLYRVDAPARGKKPVQKLYALDDGELEAIEDKLRKDGLKEGAWSISRFKGLGE 600 Query: 601 MNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEEHGNEAEA 660 MNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEEHGNEAEA Sbjct: 601 MNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEEHGNEAEA 660 Query: 661 DI 662 DI Sbjct: 661 DI 662 >gi|300309349|ref|YP_003773441.1| DNA gyrase subunit B [Herbaspirillum seropedicae SmR1] Length = 832 Score = 341 bits (874), Expect = 1e-94, Method: Compositional matrix adjust. Identities = 223/613 (36%), Positives = 338/613 (55%), Gaps = 53/613 (8%) Query: 6 TTPSD--------YSESSIRVLKGLEPVKQRPGMYTRTENP----LHILQEVIDNASDEA 53 T+P+D Y SSI++L+GLE V++RPGMY + H++ EV+DN+ DEA Sbjct: 3 TSPADNTNSAQQSYGASSIQILEGLEAVRKRPGMYIGDTSDGTGLHHLVFEVLDNSIDEA 62 Query: 54 LGGYGKSIIVTINADGSVSVEDDGRGIPVGLH----PEEKVPTVEIVFTRLHAGGKFDKG 109 L GY I VTI+AD S+S+ D+GRGIP GL E K EIV T LHAGGKFD+ Sbjct: 63 LAGYCSEIHVTIHADNSISITDNGRGIPTGLKMDDKHEPKRSAAEIVMTELHAGGKFDQN 122 Query: 110 SGGAYAFSGGLHGVGVSVTNALATRLEITVWREGGVHTLAFSGG-------DVIEKLQSR 162 S Y SGGLHGVGVS NAL+ +L++T+ R+G VH + F+ G ++++ +Q Sbjct: 123 S---YKVSGGLHGVGVSCVNALSKKLKLTIRRDGKVHAMEFAKGIVQNRELEMVDGVQVS 179 Query: 163 P--ATREDKKSGTRVTVWPDAKYFDSATIPLGELQRLLRSKAVLLPGVKVTLINAKTGDT 220 P E K GT V W D + F L + +R + L GV + L + +TG Sbjct: 180 PIKVIGESDKRGTEVHFWADEEIFTHVEFHYEILAKRIRELSFLNNGVHIKLTDQRTGKE 239 Query: 221 QNWQYDQGLRGYLMEQLAQTGSGETLIP-LFEGEQFAGKDAEGFAEGE-GASWVVAWTEE 278 +++ ++ G RG++ E + + S L P +F+ D + W A+ E+ Sbjct: 240 EDFAFEGGTRGFV-EYINKNKS--ILNPTIFQATGEKQSDQGTMITVDVSMQWNDAFNEQ 296 Query: 279 GAVVRESYVNLIPTSNGGTHESGLREGLFSAVKSFAEMHSLLPKG-VKLLAEDVFARVSF 337 + N IP +GGTH +GLR + + + E + L K V++ +D+ ++ Sbjct: 297 VLC----FTNNIPQRDGGTHLTGLRAAMTRVINKYIEENDLAKKAKVEISGDDMREGLTC 352 Query: 338 VLSAKVLDPQFQGQIKERLNSRDAVRLVAGYSRPALELWLNQHVEYGKKLAELVIKQAQS 397 VLS KV +P+F Q K++L S + V L +L + K + +++ A++ Sbjct: 353 VLSVKVPEPKFSSQTKDKLVSSEVRGPVEEIVAKTLTDFLAEKPNDAKIICGKIVEAARA 412 Query: 398 RLRSAQKVEKKKSSGVAV---LPGKLTDCESSDVTRNEIFLVEGDSAGGSAKMGRDKEFQ 454 R + + E + GV L KL DC+ D E+++VEGDSAGGSAK GRD++FQ Sbjct: 413 REAARKARELTRRKGVMDGLGLSSKLADCQERDPALCELYIVEGDSAGGSAKQGRDRKFQ 472 Query: 455 AILPLRGKVLNAWETERDRLFANNEIHDIAVAIGVDPHGINDTPDLSGLRYGKICILSDA 514 AILPLRGKVLN + +++ ++ +I + +G PD LRY +I I++DA Sbjct: 473 AILPLRGKVLNVEKARFEKMLSSEQITTLIATLGTSIGADEFNPD--KLRYHRIIIMTDA 530 Query: 515 DVDGSHIQVLLLTLFFRHFPKLIEKGHICVARPPLYRVDAPARGKKPVQKLY-------- 566 DVDG+HI+ LLLTLF+R P L+E+GHI +A+PPLY+V A + ++ ++ + Sbjct: 531 DVDGAHIRTLLLTLFYRQMPALVERGHIYIAQPPLYKVKA-GKDERYLKDDFEEAQYMMQ 589 Query: 567 -ALDDGELEAIED 578 AL+D E++ ED Sbjct: 590 IALNDAEIKPAED 602 Score = 59.7 bits (143), Expect = 7e-10, Method: Compositional matrix adjust. Identities = 32/65 (49%), Positives = 43/65 (66%), Gaps = 3/65 (4%) Query: 594 RFKGLGEMNAEQLWETTMNPDTRRLLPISFGEPGVQTSEERFNMLMGKGEAASRRAWIEE 653 R+KGLGEMN EQLWETTM+P RRLL + E + +++ F LMG + RRA+IE Sbjct: 766 RYKGLGEMNPEQLWETTMDPTVRRLLKVQI-EDAI-AADQIFMTLMGD-DVEPRRAFIES 822 Query: 654 HGNEA 658 + +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 0.315 0.135 0.391 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: 2,224,104 Number of extensions: 100611 Number of successful extensions: 232 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 225 Number of HSP's successfully gapped: 4 Length of query: 662 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 571 Effective length of database: 1,188,985 Effective search space: 678910435 Effective search space used: 678910435 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: 42 (22.0 bits) S2: 134 (56.2 bits)