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= 0476.0064.p (503 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_350150.1| Topoisomerase B [Clostridium acetobutylicum] >g... 273 6e-72 ref|NP_841983.1| topB; DNA topoisomerase III protein [Nitrosomon... 257 4e-67 ref|NP_518187.1| PROBABLE DNA TOPOISOMERASE III PROTEIN [Ralston... 250 6e-65 ref|ZP_00100244.1| COG0551: Zn-finger domain associated with top... 233 7e-60 ref|NP_831605.1| DNA topoisomerase I [Bacillus cereus ATCC 14579... 207 6e-52 >ref|NP_350150.1| Topoisomerase B [Clostridium acetobutylicum] pir||G97337 topoisomerase B [imported] - Clostridium acetobutylicum gb|AAK81490.1| Topoisomerase B [Clostridium acetobutylicum] Length = 709 Score = 273 bits (698), Expect = 6e-72, Method: Compositional matrix adjust. Identities = 166/457 (36%), Positives = 239/457 (52%), Gaps = 68/457 (14%) Query: 2 KETKEYPNKLYDLTLLQREANGKYAFSAKKTLDLAQALYEKHKVISYPRTNSNYVTEQNI 61 K+ K+ P LYDLT LQR+ N K+ FSA+KTLD+ Q+LYEK K+++YPRT+S Y++ + Sbjct: 264 KKKKQVPPLLYDLTELQRDCNKKFGFSAQKTLDIVQSLYEKRKMVTYPRTDSRYLSHDMV 323 Query: 62 PEMHKTLSALQGTTYDEWVKGANRNLVHKGNKFVCNPSKVEDHHAILPTNRKA--SGLST 119 ++ KT+ L YD++V + K + + SKV DHHAI+PT+ K S L+ Sbjct: 324 NKIKKTIGRLNINPYDKYVGEILKLSKLPMGKRIIDDSKVTDHHAIIPTDVKPNLSTLTK 383 Query: 120 DEAKLYDLIVRRFLSQFYPAAEYKVHTVITEVEGENFKTTVKELLSLGWKVIYXXXXXXX 179 DE K+YD IVRRFL FYP EY + ++TEV ENF T K +L LGW Y Sbjct: 384 DELKVYDAIVRRFLCVFYPNYEYTITKIVTEVVEENFLTQGKTILKLGWMEFYKHDKKEK 443 Query: 180 XXXXXXXXXXXXXXXXXVNEPFSIDPHAGVLCSDAVVKEKDTQPPKHYTEGTLLKAMESA 239 +E + + V D+ +K K T+ P YTE +LL AME+A Sbjct: 444 DDENSEP-----------DELPKLKKNESVQVKDSEIKAKKTKAPSSYTEASLLSAMENA 492 Query: 240 GKQIEDEELRDAMKDSGLGTPATRAATIERLKNVGYVEMQGKKIAITQKGRTAIELIRGA 299 G+ +EDE+L++ +KD GLGTPATRA+ IERL VGY++ +GK + T KG IE++ Sbjct: 493 GRFVEDEQLKEQLKDGGLGTPATRASIIERLIQVGYIQRKGKSLHPTDKGMKLIEIVPYE 552 Query: 300 GVELLTSPEMTGQWERRLNEIARGTAADSQFMANVKRFASMIV-DKVRVQSRADRTSFEG 358 L SPE TG+WE+ L+ I++G A +FM ++KR+ I+ + V+V Sbjct: 553 ----LRSPETTGKWEKGLSSISKGKMASERFMQSIKRYVQYIIQESVKV----------- 597 Query: 359 ETPSLRGGAKGRSTAGSSKPAGKAAPGKRSGEGGKTAAVKPXXXXXXXXXXXXXXXPKII 418 RS + + K+ P+ I Sbjct: 598 ----------NRSVVFQNNDSKFPQKNKQ--------------------------LPEAI 621 Query: 419 GACPRPGCG-GMIFMGRKGYGCSHYKEGCKFVIWKET 454 G C P C G ++ K + CS +K GCKF WK++ Sbjct: 622 GEC--PFCKRGKVYENSKAFYCSEWKGGCKFTTWKDS 656 >ref|NP_841983.1| topB; DNA topoisomerase III protein [Nitrosomonas europaea ATCC 19718] emb|CAD85877.1| topB; DNA topoisomerase III protein [Nitrosomonas europaea ATCC 19718] Length = 832 Score = 257 bits (657), Expect = 4e-67, Method: Compositional matrix adjust. Identities = 146/345 (42%), Positives = 193/345 (55%), Gaps = 13/345 (3%) Query: 2 KETKEYPNKLYDLTLLQREANGKYAFSAKKTLDLAQALYEKHKVISYPRTNSNYVTEQNI 61 K ++E LYDLT LQR+AN ++ FSAK TL LAQALYEKHKV++YPRT+S + E Sbjct: 281 KPSRENCPLLYDLTSLQRDANSRFGFSAKVTLGLAQALYEKHKVLTYPRTDSRALPEDYP 340 Query: 62 PEMHKTLSALQGTTYDEWVKGANRNLVHKGNKFVCNPSKVEDHHAILPTNRKASGLSTDE 121 + TL L+G+ YD + + K NK + N +KV DH AI+PT L+ E Sbjct: 341 AIVKDTLQVLKGSRYDRFASQILESDWVKPNKRIFNNAKVSDHFAIIPTALVPKKLNEAE 400 Query: 122 AKLYDLIVRRFLSQFYPAAEYKVHTVITEVEGENFKTTVKELLSLGWKVIYXXXXXXXXX 181 KLYDL+ +RFL+ FYPAAE+ + T IT VE E FKT K L+ GW+ +Y Sbjct: 401 EKLYDLVTKRFLAIFYPAAEFLITTRITRVENEPFKTEGKVLVHAGWQTVYGKVESAQGQ 460 Query: 182 XXXXXXXXXXXXXXXVNEPFSIDPHAGVLCSDAVVKEKDTQPPKHYTEGTLLKAMESAGK 241 ++ P VL + V T+PP Y E TLL AME AGK Sbjct: 461 EEESVL-------------VAVTPGETVLAQEVAVVAGKTRPPARYNESTLLSAMEGAGK 507 Query: 242 QIEDEELRDAMKDSGLGTPATRAATIERLKNVGYVEMQGKKIAITQKGRTAIELIRGAGV 301 +EDEELR AM GLGTPATRAA IE L + YVE G+++ T K + + L+RG + Sbjct: 508 LVEDEELRAAMSAKGLGTPATRAAIIEGLIHENYVERSGRELQPTAKAFSLVTLLRGLKI 567 Query: 302 ELLTSPEMTGQWERRLNEIARGTAADSQFMANVKRFASMIVDKVR 346 L SPE+TG WE +L +I +G FM + IV++ + Sbjct: 568 PELISPELTGDWEFKLRQIEQGQLKRDVFMEKIAAMTRHIVEQAK 612 >ref|NP_518187.1| PROBABLE DNA TOPOISOMERASE III PROTEIN [Ralstonia solanacearum] emb|CAD13594.1| PROBABLE DNA TOPOISOMERASE III PROTEIN [Ralstonia solanacearum] Length = 877 Score = 250 bits (638), Expect = 6e-65, Method: Compositional matrix adjust. Identities = 144/342 (42%), Positives = 196/342 (57%), Gaps = 23/342 (6%) Query: 11 LYDLTLLQREANGKYAFSAKKTLDLAQALYEKHKVISYPRTNSNYVTEQNIPEMHKTLSA 70 L+DLT LQREAN ++ FSAK TL LAQALYEKHKV++YPRT+S + E + + +TL Sbjct: 290 LFDLTSLQREANSRFGFSAKNTLGLAQALYEKHKVLTYPRTDSRALPEDYLGTVRQTLDM 349 Query: 71 LQGTTYDEWVKGANRNLVH---KGNKFVCNPSKVEDHHAILPTNRKASGLSTDEAKLYDL 127 L ++++ ++ A + L K NK + + SK+ DH AI+PT + LS E KLYDL Sbjct: 350 LADSSHN-YLPHAKKILASQWVKPNKRIFDNSKISDHFAIIPTLQAPKNLSEPEQKLYDL 408 Query: 128 IVRRFLSQFYPAAEYKVHTVITEVEGENFKTTVKELLSLGWKVIYXXXXXXXXXXXXXXX 187 +VRRFL+ F+PAAEY V T +TEV G +FKT K L++ GW V+Y Sbjct: 409 VVRRFLAVFFPAAEYLVTTRVTEVAGHHFKTEGKVLVNPGWLVVYGRESQSKDDKENGNL 468 Query: 188 XXXXXXXXXVN---EPFSIDPHAGVLCSDAVVKEKDTQPPKHYTEGTLLKAMESAGKQIE 244 EP S+ T+PP Y E TLL AME AGK ++ Sbjct: 469 VPVAKAEKVKTDKVEPVSL----------------TTKPPARYNEATLLSAMEGAGKLVD 512 Query: 245 DEELRDAMKDSGLGTPATRAATIERLKNVGYVEMQGKKIAITQKGRTAIELIRGAGVELL 304 D+ LR+AM GLGTPATRAA IE L Y+ +G+++ T K + L+RG GVE L Sbjct: 513 DDALREAMAGKGLGTPATRAAIIEGLLTEKYLLREGRELIPTAKAFQLMTLLRGLGVEEL 572 Query: 305 TSPEMTGQWERRLNEIARGTAADSQFMANVKRFASMIVDKVR 346 T E+TG+WE +L +I RG A +FM + + IV + + Sbjct: 573 TQAELTGEWEHKLAQIERGRLARDEFMREIAQMTQQIVKRAK 614 >ref|ZP_00100244.1| COG0551: Zn-finger domain associated with topoisomerase type I [Desulfitobacterium hafniense] Length = 729 Score = 233 bits (595), Expect = 7e-60, Method: Compositional matrix adjust. Identities = 141/352 (40%), Positives = 201/352 (57%), Gaps = 17/352 (4%) Query: 5 KEYPNKLYDLTLLQREANGKYAFSAKKTLDLAQALYEKHKVISYPRTNSNYVTEQNIPEM 64 +E P + YDLT LQR+AN KY FSAK+T + Q LYE+HK+++YPRT+S Y++E +P + Sbjct: 267 REQPPQAYDLTELQRDANRKYGFSAKQTSSIMQQLYEQHKLVTYPRTDSRYLSEDIVPTL 326 Query: 65 HKTLSALQGTTYDEWVKGANRNLVHKGNKFVCNPSKVEDHHAILPTNRKA--SGLSTDEA 122 + L + Y E + R + + V N SKV DHHAI+PT + + LS +EA Sbjct: 327 PERLKTIAVGPYSELARRVLRTKITPTKRLVDN-SKVTDHHAIIPTEQTVFLNKLSPEEA 385 Query: 123 KLYDLIVRRFLSQFYPAAEYKVHTVITEVEGENFKTTVKELLSLGWKVIYXXXXXXXXXX 182 K+YDLIVRRF++ PA EY+ TV E++GE F K + GW+ +Y Sbjct: 386 KIYDLIVRRFIAVLSPAFEYEQTTVKVEIQGELFTAKGKIVKQKGWRSVYEGREAADEEA 445 Query: 183 XXXXXXXXXXXXXXVNEPFSIDPHAGVLCSDAVVKEKDTQPPKHYTEGTLLKAMESAGKQ 242 N P + P + D + T+PPK YTE TLL AME G++ Sbjct: 446 DHEEQEQ--------NLP-DLQPKQTLEVLDLKLLPGKTKPPKRYTEATLLSAMEHPGQR 496 Query: 243 IEDEELRDAM-KDSGLGTPATRAATIERLKNVGYVEMQGKKIAITQKGRTAIELIRGAGV 301 + DE LR+ + K SGLGTPATRA IE+L + Y+E GK+I T KG I+LI G Sbjct: 497 VNDEALRETLEKTSGLGTPATRADIIEKLFSSFYMERNGKEIVPTSKG---IQLI-GLVP 552 Query: 302 ELLTSPEMTGQWERRLNEIARGTAADSQFMANVKRFASMIVDKVRVQSRADR 353 L SPE+T +WE++L+EI++G +F+ +K +A+ +V +V R R Sbjct: 553 SELKSPELTAKWEQQLSEISKGREDRQRFIQGIKSYATQLVSEVSGSGRTYR 604 >ref|NP_831605.1| DNA topoisomerase I [Bacillus cereus ATCC 14579] gb|AAP08806.1| DNA topoisomerase I [Bacillus cereus ATCC 14579] Length = 714 Score = 207 bits (526), Expect = 6e-52, Method: Compositional matrix adjust. Identities = 163/488 (33%), Positives = 237/488 (48%), Gaps = 87/488 (17%) Query: 3 ETKEY-PNKLYDLTLLQREANGKYAFSAKKTLDLAQALYEKHKVISYPRTNSNYVTE--- 58 E KE+ P L++L+ LQ AN + FS KKTLD+ QALY+K ++SYPR+NSNYVT+ Sbjct: 275 ERKEFQPPLLFNLSSLQATANKAFKFSPKKTLDITQALYQKG-IVSYPRSNSNYVTQGEA 333 Query: 59 QNIPEMHKTLSALQGTTYDEWVKGANRNLVHK--GNKFVCNPSKVEDHHAILPTNR--KA 114 P++ + LS +DE+ KG V NK N KV DH+AI+PT + Sbjct: 334 ATFPDILQKLSQ-----FDEY-KGLLPAPVESIMNNKRYVNEKKVTDHYAIIPTEQVTNP 387 Query: 115 SGLSTDEAKLYDLIVRRFLSQFYPAAEYKVHTVITEV-EGENFKTTVKELLSLGW-KVIY 172 S LS DE K+YD+IVRR ++ Y A + T++T V E F + K+ + GW KVI+ Sbjct: 388 SRLSGDEKKIYDMIVRRLIAAHYEVAIFDYTTIVTLVDERAEFISKGKQQIQEGWRKVIF 447 Query: 173 XXXXXXXXXXXXXXXXXXXXXXXXVNEPFSIDPHAGVLCSDAVVKEKDTQPPKHYTEGTL 232 + VKE TQPPK YTEG L Sbjct: 448 QDDKDDETILPI------------------VAEGEEGKVVKVKVKEGKTQPPKRYTEGQL 489 Query: 233 LKAMESAGKQIEDEELRDAMKDS-GLGTPATRAATIERLKNVGYVEMQGKKIAITQKGRT 291 + M++AGK +E+EEL +K + GLGT ATRA I LK+ Y++++ ++ T KG+ Sbjct: 490 ITLMKTAGKYLENEELEKVLKKTEGLGTEATRAGIITMLKDRKYIDVKKNQVYATDKGKV 549 Query: 292 AIELIRGAGVELLTSPEMTGQWERRLNEIARGTAADSQFMANVKRFASMIV-DKVRVQSR 350 LI G ++L SPEMT +WE+RL EI GTA+ + FM K+ ++ I+ D V + + Sbjct: 550 ---LITAIGDKILASPEMTAKWEQRLAEIGEGTASPATFMEQTKKLSAKIIEDAVEMSEK 606 Query: 351 ADRTSFEGETPSLRGGAKGRSTAGSSKPAGKAAPGKRSGEGGKTAAVKPXXXXXXXXXXX 410 D T E+ +G K GK+ Sbjct: 607 WDFTGLHVESIERKG--------------SKFTTGKK----------------------- 629 Query: 411 XXXXPKIIGACPRPGCGGMIFMGRKGYGCSHYKEG-CKFVIWKETYGRTLTDAQVKALIE 469 +G+C + C G + YGCS+Y C F I K+ +T++ +K L++ Sbjct: 630 -------VGSCKK--CDGDVIDKSTFYGCSNYNTTQCDFTISKKILSKTISQKNMKKLLK 680 Query: 470 KGKTGKLK 477 KT +K Sbjct: 681 GEKTDLIK 688 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.313 0.131 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 692,043,198 Number of extensions: 27188543 Number of successful extensions: 69640 Number of sequences better than 1.0e-05: 368 Number of HSP's gapped: 69625 Number of HSP's successfully gapped: 500 Length of query: 503 Length of database: 757,237,578 Length adjustment: 130 Effective length of query: 373 Effective length of database: 404,274,708 Effective search space: 150794466084 Effective search space used: 150794466084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 128 (53.9 bits)