RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780222|ref|YP_003064635.1| DNA topoisomerase IV subunit B [Candidatus Liberibacter asiaticus str. psy62] (686 letters) >1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP; 2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 Length = 391 Score = 420 bits (1082), Expect = e-118 Identities = 145/402 (36%), Positives = 232/402 (57%), Gaps = 16/402 (3%) Query: 41 SDNYDASSIRILEGLEPVRMRPGMYIGGTDE-KALHHLFSEVIDNAMDEVIAGYANLIEV 99 S++ D+SSI++L+GL+ VR RPGMYIG TD+ LHH+ EV+DNA+DE +AG+ I V Sbjct: 1 SNSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV 60 Query: 100 SLDGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGI 159 ++ + ++V D+GRGIP HP+ S E+I+T LHAGGKFD+++Y++SGGLHGVG+ Sbjct: 61 TIHADNSVSVQDDGRGIPTGIHPE-EGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGV 119 Query: 160 SVVNALSDELHVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGDK 219 SVVNALS +L + + R+ I Q + G+P +PL + K GT + F P + F + Sbjct: 120 SVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETE-KTGTMVRFWPSLETFTNV 178 Query: 220 AGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLEN 279 F+ L K + ++L V ++ +++ F++ GG+K +++ +N Sbjct: 179 TEFEYEILAKRLRELSFLDSGVSIRLRDKRD-------GKEDHFHYEGGIKAFVEYLNKN 231 Query: 280 RSLISSEIFTGKTEKKGTHRGTVEWAIAWCEE-NPEITSYCNTILTDEGGTHESGLRVAL 338 ++ I IF TEK G VE A+ W + I + N I +GGTH +G R A+ Sbjct: 232 KTPIHPNIFYFSTEKDGI---GVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAM 288 Query: 339 TRGIKKYAELTQN--KRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTV 396 TR + Y + K +S DD + ++SV + +P+F+ QTK KLVS + + V Sbjct: 289 TRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAV 348 Query: 397 ENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREV 438 E + + YL++NP +A ++ +I+ + R R+ RE+ Sbjct: 349 EQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREM 390 >1kij_A DNA gyrase subunit B; topoisomerase, gyrase B-coumarin complex; HET: DNA NOV; 2.30A {Thermus thermophilus} SCOP: d.14.1.3 d.122.1.2 Length = 390 Score = 362 bits (929), Expect = e-100 Identities = 150/399 (37%), Positives = 217/399 (54%), Gaps = 16/399 (4%) Query: 44 YDASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDG 103 YDAS+IR+L+GLE VR RP MYIGGT + HHLF E++DNA+DE +AGYA I V L+ Sbjct: 3 YDASAIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNE 62 Query: 104 NGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVN 163 +G LTV DNGRGIPV+ P+ K +E+I TLH+GGKF+ Y++SGGLHGVG SVVN Sbjct: 63 DGSLTVEDNGRGIPVDLMPE-EGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVN 121 Query: 164 ALSDELHVTVARQNTIFSQKFSRGIPLSPLEKKEKV-RNKRGTRITFRPDPKIFGDKAGF 222 ALS+ V V R+ FSRG PL + R K GTR+TF+PDP+IF F Sbjct: 122 ALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIF-GNLRF 180 Query: 223 DAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLENRSL 282 D +++ + AYL +K + + ++E F GG+ ++ + E L Sbjct: 181 DPSKIRARLREVAYLVAGLKLVFQDRQH-------GKEEVFLDKGGVASFAKALAEGEDL 233 Query: 283 ISSEIFTGKTEKKGTHRGTVEWAIAWCEENPE-ITSYCNTILTDEGGTHESGLRVALTRG 341 + + F + VE + I +Y N I T +GGTH + + A +R Sbjct: 234 LYEKPFLIRGTH---GEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRA 290 Query: 342 IKKYAEL--TQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENA 399 + +YA+ ++ DDL+ ++SV + P+F GQTK KL++ +A V Sbjct: 291 LNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQV 350 Query: 400 LRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREV 438 + + L +NP A + E + ++ R RK RE+ Sbjct: 351 VYERLLEILEENPRIAKAVYEKALRAAQAREAARKAREL 389 >1s16_A Topoisomerase IV subunit B; two-domain protein complexed with ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 Length = 390 Score = 310 bits (794), Expect = 8e-85 Identities = 137/403 (33%), Positives = 204/403 (50%), Gaps = 17/403 (4%) Query: 41 SDNYDASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVS 100 + Y+A +I +L GLEPVR RPGMY T +HL EVIDN++DE +AG+A ++V Sbjct: 2 TQTYNADAIEVLTGLEPVRRRPGMYTDTT---RPNHLGQEVIDNSVDEALAGHAKRVDVI 58 Query: 101 LDGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGIS 160 L + L V+D+GRG+PV+ HP+ +E+IL LHAGGKF N Y+ SGGLHGVGIS Sbjct: 59 LHADQSLEVIDDGRGMPVDIHPE-EGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGIS 117 Query: 161 VVNALSDELHVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKR-GTRITFRPDPKIFGDK 219 VVNALS + V V R +++ F G + L+ + GT + F PD F D Sbjct: 118 VVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDE-TFFDS 176 Query: 220 AGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLEN 279 F +RL + ++KA L V+ + + ++ + + GL YL + Sbjct: 177 PRFSVSRLTHVLKAKAVLCPGVEITFKDEI-------NNTEQRWCYQDGLNDYLAEAVNG 229 Query: 280 RSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPEITSYCNTILTDEGGTHESGLRVALT 339 + + F G SY N I T +GGTH +GLR L Sbjct: 230 LPTLPEKPFIGNFAGDTEAV-DWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLL 288 Query: 340 RGIKKYAELT-QNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVEN 398 ++++ E R + + ++D+ +LSV +++P+FAGQTK +L S V Sbjct: 289 DAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSG 348 Query: 399 ALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVNRK 441 ++D F +L QN A L E I ++ R+ R ++V RK Sbjct: 349 VVKDAFILWLNQNVQAAELLAEMAISSAQRRM--RAAKKVVRK 389 >1pvg_A DNA topoisomerase II; GHKL ATPase domain; HET: DNA ANP; 1.80A {Saccharomyces cerevisiae} SCOP: d.14.1.3 d.122.1.2 PDB: 1qzr_A* Length = 418 Score = 277 bits (709), Expect = 7e-75 Identities = 87/425 (20%), Positives = 160/425 (37%), Gaps = 37/425 (8%) Query: 35 FANQSASDNYDASSIRILEGLEPVRMRPGMYIGGTDEK---------------------- 72 S + + + LE + RP YIG + + Sbjct: 3 MVTMSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIV 62 Query: 73 -ALHHLFSEVIDNAMDEVIAGYA-NLIEVSLDG-NGFLTVVDNGRGIPVENHPKFPNKST 129 L +F E++ NA D + + I+V++ + V ++G+GIP+E H K N Sbjct: 63 PGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNK-ENIYI 121 Query: 130 LEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTVARQNT--IFSQKFSRG 187 E+I L +D+ +++GG +G G + N S E + A N + QK+ Sbjct: 122 PEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181 Query: 188 IPLSPLEKKEK-VRNKRGTRITFRPDPKIFGDKAGFDAARLLKMTQSKAYLSGRVKTCWS 246 + + K + T++TF+PD FG K D L M + ++G V+ Sbjct: 182 MSICHPPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDINV 240 Query: 247 CDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLENRSLISSEIFTGKTEKKGTHRGTVEWAI 306 + K + + L+ Q S+I T E+ E A Sbjct: 241 YLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNR---WEVAF 297 Query: 307 AWCEENPEITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQNKRAISIISDDLMISA 366 A + + + S+ N+I T GGTH + + + + I + S+ S + + Sbjct: 298 AVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEIL---XXXXXXSVKSFQIKNNM 354 Query: 367 VGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERS 426 ++ I P F QTK +L + + + + +++ + AT++ E Sbjct: 355 FIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDL-ATRMFEIADANE 413 Query: 427 EERLR 431 E L+ Sbjct: 414 ENALK 418 >2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter baumannii} PDB: 2xkk_A* Length = 767 Score = 276 bits (706), Expect = 2e-74 Identities = 109/265 (41%), Positives = 162/265 (61%), Gaps = 10/265 (3%) Query: 419 LEWVIERSEERLRRRKQREVNRKTAIRKLRLPGKLADCSQNIAHGTELFIVEGDSAGGSA 478 +E I ++ RL+ K +V RK + LPGKLADC +ELFIVEGDSAGGSA Sbjct: 1 MEMAISKAGRRLKAAK--KVERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSA 58 Query: 479 KQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQYREEDLRYEKV 538 KQAR+++ QA++P+RGKILN S+++ +Q++ D+ A+G S +LRY K+ Sbjct: 59 KQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDL-SELRYGKI 117 Query: 539 IIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISPPLFRITQGTKSVYAHDEEHKQ 598 I+ DAD DG HIA+LL F + L+E+ HL++ PPLFRI G YA D+E + Sbjct: 118 CILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELE 177 Query: 599 KILEEFKKHGKGKIEISRFKGLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDS 658 IL+ K G +I+RFKGLGEM A QL+ET MD N R L++++++ T Sbjct: 178 TILKNVK--GNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDA----HLTAGL 231 Query: 659 INKL-MGTKADERFKFIQERASFID 682 ++KL +A +R ++++++ + D Sbjct: 232 LDKLLAKKRAADRKQWLEQKGNLAD 256 >3m4i_A DNA gyrase subunit B; GYRB, toprim, type II topoisomerase, tuberculosi quinolone binding site, DNA binding site, ATP-binding; HET: DNA; 1.95A {Mycobacterium tuberculosis} PDB: 3ig0_A* 2zjt_A* Length = 242 Score = 244 bits (623), Expect = 6e-65 Identities = 90/235 (38%), Positives = 134/235 (57%), Gaps = 8/235 (3%) Query: 453 LADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQ 512 + D + +EL++VEGDSAGGSAK R+ QA+LPLRGKI+NV A +++ N + Sbjct: 9 VDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 68 Query: 513 IMDLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHL 572 + ++ ALG ++ LRY K+++M DADVDG HI++LLLT ++ M LIE H+ Sbjct: 69 VQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHV 128 Query: 573 FLISPPLFRIT-QGTKSVYAHDEEHKQKILEEFKKHGK---GKIEISRFKGLGEMLASQL 628 FL PPL+++ Q + +A+ + + +LE K GK + I R+KGLGEM A +L Sbjct: 129 FLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKEL 188 Query: 629 KETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERASFIDD 683 ET MD + R L +V ++ + + LMG D R FI A + Sbjct: 189 WETTMDPSVRVLRQVTLDDA----AAADELFSILMGEDVDARRSFITRNAKDVRF 239 >3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown function, ATP-binding, isomerase, nucleotide-binding, topoisomerase; HET: DNA; 1.95A {Myxococcus xanthus dk 1622} Length = 369 Score = 233 bits (596), Expect = 7e-62 Identities = 68/376 (18%), Positives = 119/376 (31%), Gaps = 27/376 (7%) Query: 52 LEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVD 111 +E VR RPGMY G E LHHL ++D A +E G + + + G+G + + Sbjct: 9 GGIVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFC 68 Query: 112 NGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHV 171 R + EN + + G F G + V ALS V Sbjct: 69 TSRTVTAENLVR-------------VATGAGFLGRPPG-DGWGWDSMLVVSLALSSRYQV 114 Query: 172 TVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGDKAGFDAARLLKMT 231 + + G P + D F+ + Sbjct: 115 DIWADGRQWRVMGEHGHPQGEGAAVTPMEP-MPVSAERGVRVHFVPDATIFEVLAFDRAR 173 Query: 232 QSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLENRSLISSEIFTGK 291 S+ + G ++ PGG+ + E R + E Sbjct: 174 LSRRCNELAALAPGLRVSFADLQRGER--TLWHLPGGVAQWAHVLTEARPQLHPEPVVFD 231 Query: 292 TEKKGTHRGTVEWAIAWCEE-NPEITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQ 350 V+ A+ WCE+ + + S+ N + T G H G+ + ++ Sbjct: 232 FTW---DGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVT----QALRGALAKLS 284 Query: 351 NKRAISIISDDLM--ISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPFDHYL 408 + + + ++A+ +S R+ FAG TK L + + L+ F L Sbjct: 285 GETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELL 344 Query: 409 VQNPIEATKLLEWVIE 424 ++P+ L Sbjct: 345 REHPVTPALLARRTSG 360 >3k9f_C DNA topoisomerase 4 subunit B; quinolone, topoisomerase, protein-DNA cleavage complex; HET: DNA LFX; 2.90A {Streptococcus pneumoniae} PDB: 3fof_C* 3foe_C* Length = 268 Score = 230 bits (587), Expect = 9e-61 Identities = 100/245 (40%), Positives = 139/245 (56%), Gaps = 4/245 (1%) Query: 439 NRKTAIRKLRLPGKLADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILN 498 + K K L GKL EL++VEGDSAGGSAKQ R+R QA+LPLRGK++N Sbjct: 23 HMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVIN 82 Query: 499 VASAGSEKIRNNQQIMDLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTF 558 A A I N++I ++ +G + + ED Y+K+IIMTDAD DGAHI +LLLTF Sbjct: 83 TAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTF 142 Query: 559 FYQEMYDLIEQKHLFLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFK 618 FY+ M L+E H+++ PPL+++++G LEE +K + R+K Sbjct: 143 FYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYK 202 Query: 619 GLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERA 678 GLGEM A QL ET M+ RTL+RV I + +N LMG K + R K+I++ Sbjct: 203 GLGEMNADQLWETTMNPETRTLIRVTIEDL----ARAERRVNVLMGDKVEPRRKWIEDNV 258 Query: 679 SFIDD 683 F + Sbjct: 259 KFTLE 263 >3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently linked comple supercoiling; HET: DNA PTR TSP; 2.48A {Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A 2rgr_A* Length = 757 Score = 216 bits (551), Expect = 1e-56 Identities = 51/211 (24%), Positives = 96/211 (45%), Gaps = 13/211 (6%) Query: 452 KLADCSQNI---AHGTELFIVEGDSA-----GGSAKQARNRSNQAVLPLRGKILNVASAG 503 KL D ++ + L + EGDSA G A R+ PLRGK+LNV A Sbjct: 8 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDY--YGCYPLRGKMLNVREAS 65 Query: 504 SEKIRNNQQIMDLVQALGCRTRSQYRE-EDLRYEKVIIMTDADVDGAHIASLLLTFFYQE 562 +++I N +I + + +G + R +Y + + LRY ++IMTD D DG+HI L++ F Sbjct: 66 ADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESS 125 Query: 563 MYDLIEQK-HLFLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGKG-KIEISRFKGL 620 L++ + L P+ +++ + + + ++ + +KGL Sbjct: 126 FPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGL 185 Query: 621 GEMLASQLKETAMDANKRTLLRVEINKDLNS 651 G LA +++E + ++ + + + Sbjct: 186 GTSLAQEVREYFSNLDRHLKIFHSLQGNDKD 216 >3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization, isomera; HET: DNA; 3.10A {Escherichia coli} Length = 420 Score = 216 bits (551), Expect = 1e-56 Identities = 85/179 (47%), Positives = 120/179 (67%), Gaps = 2/179 (1%) Query: 433 RKQRE-VNRKTAIRKLRLPGKLADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLP 491 RE RK A+ LPGKLADC + +EL++VEGDSAGGSAKQ RNR NQA+LP Sbjct: 2 NAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILP 61 Query: 492 LRGKILNVASAGSEKIRNNQQIMDLVQALGCRT-RSQYREEDLRYEKVIIMTDADVDGAH 550 L+GKILNV A +K+ ++Q++ L+ ALGC R +Y + LRY +IIMTDADVDG+H Sbjct: 62 LKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSH 121 Query: 551 IASLLLTFFYQEMYDLIEQKHLFLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGK 609 I +LLLTFFY++M +++E+ H+++ PPL+++ +G + Y D+E + G Sbjct: 122 IRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180 Score = 93.2 bits (231), Expect = 2e-19 Identities = 38/160 (23%), Positives = 63/160 (39%), Gaps = 11/160 (6%) Query: 527 QYREEDLRYEKVIIMTDADVDGAHI--ASLLLTFFYQEMYDLIEQKHLFLISPPLFRITQ 584 E +E ++ + VD + + Y+ + L E+ L+ F Sbjct: 268 HTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLR-GLLEEDAFIERG 326 Query: 585 GTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKETAMDANKRTLLRVE 644 + A E+ +++E ++ + I R+KGLGEM QL ET MD R +LRV Sbjct: 327 ERRQPVASFEQALDWLVKESRR----GLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVT 382 Query: 645 INKDLNSLKDTQDSINKLMGTKADERFKFIQERASFIDDV 684 + LMG + R FI+E A ++ Sbjct: 383 VKDA----IAADQLFTTLMGDAVEPRRAFIEENALKAANI 418 >3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex, antibiotic resistance, ATP-binding, nucleotide-binding; HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A* Length = 201 Score = 215 bits (549), Expect = 3e-56 Identities = 83/213 (38%), Positives = 118/213 (55%), Gaps = 13/213 (6%) Query: 54 GLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNG 113 GLEPVR RPGMY T +HL EVIDN++DE +AG+A ++V L + L V+D+G Sbjct: 1 GLEPVRRRPGMYTDTTR---PNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDG 57 Query: 114 RGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTV 173 RG+PV+ HP+ +E+IL LHAGGKF N Y+ SGGLHGVGISVVNALS + V V Sbjct: 58 RGMPVDIHPE-EGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNV 116 Query: 174 ARQNTIFSQKFSRGIPLSPLEKKEKVRNKR-GTRITFRPDPKIFGDKAGFDAARLLKMTQ 232 R +++ F G + L+ + GT + F PD F F +RL + + Sbjct: 117 RRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTHVLK 175 Query: 233 SKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYF 265 +KA L V+ + + ++ + + Sbjct: 176 AKAVLCPGVEITFKDEIN-------NTEQRWCY 201 >3g7e_A DNA gyrase subunit B; isomerase; HET: DNA B46; 2.20A {Escherichia coli} PDB: 1kzn_A* 1aj6_A* Length = 203 Score = 211 bits (539), Expect = 4e-55 Identities = 84/212 (39%), Positives = 128/212 (60%), Gaps = 10/212 (4%) Query: 54 GLEPVRMRPGMYIGGTDE-KALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDN 112 GL+ VR RPGMYIG TD+ LHH+ EV+DNA+DE +AG+ I V++ + ++V D+ Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60 Query: 113 GRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVT 172 GRGIP HP+ S E+I+T LHAGGKFD+++Y++SGGLHGVG+SVVNALS +L + Sbjct: 61 GRGIPTGIHPE-EGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELV 119 Query: 173 VARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGDKAGFDAARLLKMTQ 232 + R+ I Q + G+P +PL + K GT + F P + F + F+ L K + Sbjct: 120 IQREGKIHRQIYEHGVPQAPLAVTGETE-KTGTMVRFWPSLETFTNVTEFEYEILAKRLR 178 Query: 233 SKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFY 264 ++L+ V ++ +++ F+ Sbjct: 179 ELSFLNSGVSIRLRDKRD-------GKEDHFH 203 >2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus aureus} PDB: 2xcr_B* 2xcq_A* 2xco_A* Length = 692 Score = 210 bits (536), Expect = 8e-55 Identities = 92/232 (39%), Positives = 122/232 (52%), Gaps = 40/232 (17%) Query: 449 LPGKLADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIR 508 LPGKLADCS E+F+VEGDSAGGS K R+ QA+LPLRGKILNV A ++I Sbjct: 6 LPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRIL 65 Query: 509 NNQQIMDLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIE 568 NN +I ++ A G + RY K++IMTDADVDGAHI +LLLTFFY+ M LIE Sbjct: 66 NNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIE 125 Query: 569 QKHLFLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQL 628 ++++ PP +KGLGEM A QL Sbjct: 126 AGYVYIAQPPT------------------------------------GYKGLGEMNADQL 149 Query: 629 KETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERASF 680 ET M+ R LL+V++ + + LMG + R +FI++ A + Sbjct: 150 WETTMNPEHRALLQVKLEDAIE----ADQTFEMLMGDVVENRRQFIEDNAVY 197 >2zjt_A DNA gyrase subunit B; GYRB-CTD, toprim, tail, DNA topoisomerase II, G- segment, T-segment, ATP-binding, nucleotide-binding; HET: DNA; 2.80A {Mycobacterium tuberculosis} Length = 247 Score = 210 bits (535), Expect = 9e-55 Identities = 84/236 (35%), Positives = 126/236 (53%), Gaps = 8/236 (3%) Query: 453 LADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQ 512 + + +EL++VEGDSAGGSAK R+ QA+LPLRGKI+NV A +++ N + Sbjct: 1 MTPYAFTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 60 Query: 513 IMDLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHL 572 + ++ ALG ++ LRY K+++M DADVDG HI++LLLT ++ M LIE H+ Sbjct: 61 VQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHV 120 Query: 573 FLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGK----GKIEISRFKGLGEMLASQL 628 FL PPL+++ + ++ L E + I R+KGLGEM A +L Sbjct: 121 FLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKEL 180 Query: 629 KETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERASFIDDV 684 ET MD + R L +V ++ + + LMG D R FI A + + Sbjct: 181 WETTMDPSVRVLRQVTLDDA----AAADELFSILMGEDVDARRSFITRNAKDVRFL 232 >1bjt_A Topoisomerase II; quaternary change, DNA-binding, DNA topology; 2.50A {Saccharomyces cerevisiae} SCOP: e.11.1.1 PDB: 1bgw_A 2rgr_A* Length = 793 Score = 210 bits (534), Expect = 1e-54 Identities = 58/239 (24%), Positives = 106/239 (44%), Gaps = 15/239 (6%) Query: 435 QREVNRKTAIRKLRLPG--KLADCSQNI---AHGTELFIVEGDSA-----GGSAKQARNR 484 + + + RK R+ KL D ++ + L + EGDSA G A R+ Sbjct: 1 ENALKKSDGTRKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDY 60 Query: 485 SNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQYRE-EDLRYEKVIIMTD 543 PLRGK+LNV A +++I N +I + + +G + R +Y + + LRY ++IMTD Sbjct: 61 --YGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTD 118 Query: 544 ADVDGAHIASLLLTFFYQEMYDLIE-QKHLFLISPPLFRITQGTKSVYAHDEEHKQKILE 602 D DG+HI L++ F L++ Q L P+ +++ + + + Sbjct: 119 QDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEK 178 Query: 603 EFKKHG-KGKIEISRFKGLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDSIN 660 ++ K + +KGLG LA +++E + ++ + + + D S Sbjct: 179 WREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKK 237 >2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei} Length = 621 Score = 200 bits (509), Expect = 8e-52 Identities = 75/633 (11%), Positives = 154/633 (24%), Gaps = 87/633 (13%) Query: 46 ASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVI-AGYANLIEVSL--- 101 A + + E + + ++L E +DNA+D AG I V + Sbjct: 10 AKKQKSISVAEFFEKNRQILGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVERT 69 Query: 102 -DGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGIS 160 + + DNG GI E PK + L G +F + S G G+GIS Sbjct: 70 GPDYVTVIIEDNGPGIVREQIPK---------VFAKLLYGSRFHA--LKQSRGQQGIGIS 118 Query: 161 VVNALS-----DELHVTVARQNTIFSQKFSRGIPLS---PLEKKEKVRNKRGTRITFRPD 212 + + T + + I S P ++VR+ T Sbjct: 119 AAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGTQIEL 178 Query: 213 PKIFGDKAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTY 272 + + ++ A ++ + E+ + Sbjct: 179 EMRA-AYVKGRRQSIYEYLKATAIVNPHAR-------ITLIDPDGNEEVFERATDKMPEP 230 Query: 273 LQTKLENRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPEITSYCNTILTDEGGTHES 332 + L + I + + + G Sbjct: 231 AEEILPHPEGIELGTLMKMLHYTERQK---------------LAPFLRYSFCKIGLLTA- 274 Query: 333 GLRVALTRGIKKYAELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDA 392 I K A L ++ + V I P + + Sbjct: 275 -------EEICKAAGLDPEIDPHALGRHEARKLIEAFEKVKIMAPP--TDCLSPIGEDLI 325 Query: 393 QRTVENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVN-RKTAIRKLRLPG 451 R +E F + P + V K+ +++ + A R L Sbjct: 326 YRGLEKETTVDFIATSTRKPAVYSGNPFVVEVGMAYGGNLPKEEKISIMRFANRVPLLYQ 385 Query: 452 KLADCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQ 511 + + + + + GG V + + + I + Sbjct: 386 QGGCVTTHAVEDIKWKQYGLNQPGGGIPVGPVILLIHVASINVPFTSE---SKDAIADIP 442 Query: 512 QIMDLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKH 571 I + + + + Y + I + +L ++ ++E+ Sbjct: 443 VIKEEIDLAIK----EVARKLKHYLSKQSNLKKRREKEIIITKVLPKLAAKVAHVLEKDV 498 Query: 572 LFLISPPLFRITQG-----------------TKSVYAHDEEHKQKILEEFKKHGKGKIEI 614 I+P + +I V + E Sbjct: 499 PD-INPVVAKIMGNLLVHRVIKNNGDGTVDVAIKVKNFGTSAYSFRVHEMLP--CKVSGA 555 Query: 615 SRFKGLGEMLASQLK--ETAMDANKRTLLRVEI 645 + M + + A +L +I Sbjct: 556 KPEPKVVTMGNDYDYVWDISASAGSSKVLSYKI 588 >1zxm_A TOPO IIA ATPase, DNA topoisomerase II, alpha isozyme; GHKL nucleotide-binding fold; HET: DNA ANP; 1.87A {Homo sapiens} PDB: 1zxn_A* Length = 400 Score = 187 bits (474), Expect = 8e-48 Identities = 71/408 (17%), Positives = 138/408 (33%), Gaps = 44/408 (10%) Query: 52 LEGLEPVRMRPGMYIGGTDE----------------------KALHHLFSEVIDNAMDEV 89 LE + +RP YIG + L+ +F E++ NA D Sbjct: 9 KTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNK 68 Query: 90 IAG-YANLIEVSLDG-NGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNST 147 + I V++D N +++ +NG+GIPV H +I L +D+ Sbjct: 69 QRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHK-VEKMYVPALIFGQLLTSSNYDDDE 127 Query: 148 YEISGGLHGVGISVVNALSD--ELHVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGT 205 +++GG +G G + N S + +F Q + + + + + + T Sbjct: 128 KKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNGEDYT 187 Query: 206 RITFRPDPKIFGDKAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYF 265 ITF+PD F ++ L + ++ + G + Y Sbjct: 188 CITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYL 247 Query: 266 PGGLKTYLQTKLENRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPEITSYCNTILTD 325 L E E + E+ + S+ N+I T Sbjct: 248 KDKLD---------------ETGNSLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATS 292 Query: 326 EGGTHESGLRVALTRGIKKYAELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKT 385 +GG H + + + + +NK +++ + + ++ I P F QTK Sbjct: 293 KGGRHVDYVADQIVTKLVDVVKK-KNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKE 351 Query: 386 KLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRR 433 + L + F + I +L WV +++ +L ++ Sbjct: 352 NMTLQPKSFGSTCQLSEKFIKAAIGCGI-VESILNWVKFKAQVQLNKK 398 >3g75_A DNA gyrase subunit B; antibiotic resistance, isomerase; HET: DNA B48; 2.30A {Staphylococcus aureus} PDB: 3g7b_A* Length = 184 Score = 175 bits (446), Expect = 2e-44 Identities = 73/212 (34%), Positives = 116/212 (54%), Gaps = 29/212 (13%) Query: 54 GLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNG 113 GLE VR RPGMYIG T E+ LHHL E++DN++DE +AGYAN IEV ++ + ++ V DNG Sbjct: 1 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNG 60 Query: 114 RGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTV 173 RGIPV+ K + +E+ILT+ SVVNALS +L V V Sbjct: 61 RGIPVDIQEK-MGRPAVEVILTS-----------------------SVVNALSQDLEVYV 96 Query: 174 ARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGDKAGFDAARLLKMTQS 233 R TI+ Q + +G+P L++ +K GT I F+ D +IF + ++ L + + Sbjct: 97 HRNETIYHQAYKKGVPQFDLKEVGTT-DKTGTVIRFKADGEIFTETTVYNYETLQQRIRE 155 Query: 234 KAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYF 265 A+L+ ++ +++ ++ +++ Sbjct: 156 LAFLNKGIQITLRDERDEEN----VREDSYHY 183 >2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Length = 530 Score = 108 bits (269), Expect = 5e-24 Identities = 71/578 (12%), Positives = 166/578 (28%), Gaps = 72/578 (12%) Query: 48 SIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVI-AGYANLIEVSLD---- 102 L E + P + +AL+ E+I+N++D G I++++D Sbjct: 6 KFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDD 65 Query: 103 --GNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDN-STYEISG-GLHGVG 158 + VVDNG GIP + + + K+ N T + G G+ Sbjct: 66 ARQIYKVNVVDNGIGIPPQE---------VPNAFGRVLYSSKYVNRQTRGMYGLGVKAAV 116 Query: 159 ISVVNALSDELHVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGD 218 + + + + N S++ + K E + +RG+ R Sbjct: 117 LYSQMHQDKPIEIETSPVN---SKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVA 173 Query: 219 KAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLE 278 + ++K+ + +K + + PE Y+P + E Sbjct: 174 I-----SIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQE 228 Query: 279 NRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPEITSYCNTILTDEGGTHESGLRVAL 338 K G R ++ I + + I + G T Sbjct: 229 V-----------KPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTT-------- 269 Query: 339 TRGIKKYAELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVEN 398 I + A L NK+ ++ +++ ++ F ++ +F + L Sbjct: 270 ADKILELAGLKPNKKVKNLTEEEITR----LVETFKKDEDFRSPSADSLS---------- 315 Query: 399 ALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVNRKTAIRKLRLPGKLADCSQ 458 L++ ++ ++ + + + + +P Sbjct: 316 ----VIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVL 371 Query: 459 NIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQ 518 A+ L E + + + + +++ + S KI + + Sbjct: 372 RYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIA 431 Query: 519 ALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISPP 578 + E + K +M A +++ ++ + + Sbjct: 432 EV---------ENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLAYLKYIPEVSRSL 482 Query: 579 LFRITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISR 616 + G K + + + + L + I I Sbjct: 483 ATFLASGNKELVSKYQNEISEGLFKLISKKLDLINIEE 520 >1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A* Length = 471 Score = 68.4 bits (167), Expect = 5e-12 Identities = 29/164 (17%), Positives = 53/164 (32%), Gaps = 25/164 (15%) Query: 69 TDEKALHHLFSEVIDNAMDEVI-AGYANLIEVSLD------GNGFLTVVDNGRGIPVENH 121 +AL+ E+I+N++D G I++++D + VVDNG GIP + Sbjct: 28 NPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEV 87 Query: 122 PKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTV----ARQN 177 P + K+ N GL + + + + + + Sbjct: 88 PN---------AFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSK 138 Query: 178 TIFSQKFSRGIPLSPL-----EKKEKVRNKRGTRITFRPDPKIF 216 I++ K I + E R GT + Sbjct: 139 RIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWP 182 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 59.2 bits (143), Expect = 3e-09 Identities = 94/595 (15%), Positives = 161/595 (27%), Gaps = 235/595 (39%) Query: 155 HGVGISVVNALSDELHVTVARQNTIFSQKF---SRGI-----PLSPLEKKEKVRNKRGTR 206 HG + V + ++ F++ + G P +P E Sbjct: 13 HG-SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL----------- 60 Query: 207 ITFRPDPKIFGDKAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFP 266 + L Y+S V ++ + F Sbjct: 61 -----------------VGKFL------GYVSSLV-----EPSKVGQ-----------FD 81 Query: 267 GGLKTYLQTKLENRSLISSEI------FTGKTEKKGTHRGTVEWAIAWCEENPEITSY-- 318 L L EN L ++I + + + I +Y Sbjct: 82 QVLNLCLTE-FENCYLEGNDIHALAAKLLQENDTTLVKTKEL------------IKNYIT 128 Query: 319 -CNTILTDEGGTHESGLRVALTRG-IKKYA-------------ELTQNKRAI-----SII 358 S L A+ G + A EL R + ++ Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL----RDLYQTYHVLV 184 Query: 359 SDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPFDHYLVQNP-----I 413 DL+ + LS IR A + T+ L+ +EN P YL+ P I Sbjct: 185 -GDLIKFSAETLSELIRTTLDAEKVFTQ--GLNILEWLENPSNTPDKDYLLSIPISCPLI 241 Query: 414 EATKLLEWVIERSEERLRRRKQREVNRKTAIRKLRL-PGKLADC-------SQNIAHGTE 465 +L +V+ + L PG+L SQ + T Sbjct: 242 GVIQLAHYVV-------------------TAKLLGFTPGELRSYLKGATGHSQGLV--TA 280 Query: 466 LFIVEGDS---AGGSAKQARN-------RSNQA----VLPLRGKILNVASAGSEKIRNNQ 511 + I E DS S ++A R +A LP S + + NN+ Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLP--------PSILEDSLENNE 332 Query: 512 QI---MDLVQALGCRTRSQYREEDLRYEKVIIMTDADVD--GAHIASLLLTFFYQEMYDL 566 + M L +L E+V V+ +H L Sbjct: 333 GVPSPM-----LSIS--------NLTQEQV----QDYVNKTNSH---------------L 360 Query: 567 IEQKHLF--LI-SPPLFRITQGTKSVYAHDEEHKQKILEEFKK----------HGKGKIE 613 K + L+ ++ +S+Y L + K + K++ Sbjct: 361 PAGKQVEISLVNGAKNLVVSGPPQSLY-----GLNLTLRKAKAPSGLDQSRIPFSERKLK 415 Query: 614 IS-RFKGLGEMLA------SQLKETAMDANKRTLLRVEINKDLNSLK----DTQD 657 S RF L S L A D + L++ ++ + ++ DT D Sbjct: 416 FSNRF------LPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD 464 Score = 56.1 bits (135), Expect = 3e-08 Identities = 90/566 (15%), Positives = 154/566 (27%), Gaps = 233/566 (41%) Query: 7 DLF-STLPPQSQGSSEKLKKSGEIPDSPA--------FANQSASDNYDASSIRILE-GLE 56 + F LP ++G + + P +PA + + + ++L L Sbjct: 35 EQFNKILPEPTEGFAAD-----DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT 89 Query: 57 PVRMRPGMYIGGTDEKAL-HHLF--SEVIDNAMDEVIAGYAN----------------LI 97 Y+ G D AL L ++ E+I Y L Sbjct: 90 EFENC---YLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146 Query: 98 EVSLDGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGV 157 +GN L + G+G +++ F E L L+ TY L V Sbjct: 147 RAVGEGNAQLVAIFGGQGN-TDDY--FE-----E--LRDLY-------QTYH---VL--V 184 Query: 158 G--ISVVNALSDELHVTVARQNTIFSQKFSRGIP-LSPLEKKEKVRNKRGTRITFRPD-- 212 G I EL R + F++G+ L LE PD Sbjct: 185 GDLIKFSAETLSEL----IRTTLDAEKVFTQGLNILEWLENPSN-----------TPDKD 229 Query: 213 ---------PKIFGDKAGFD-------AARLLKMT--QSKAYLSG--------------R 240 P I G A+LL T + ++YL G Sbjct: 230 YLLSIPISCPLI-----GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIA 284 Query: 241 VKTCWSCDKEIAEKYGIPEKEEFY----------FPGGLK---TYLQTKLENRSLISSEI 287 W E F+ F G++ Y T L S++ + Sbjct: 285 ETDSW---------------ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP-SILEDSL 328 Query: 288 FTGKTEK------KGTHRGTVEWAIAWCEEN---PE--------ITSYCNTILTDEGGTH 330 + + V+ + N P + N +++ G Sbjct: 329 ENNEGVPSPMLSISNLTQEQVQDYVNKT--NSHLPAGKQVEISLVNGAKNLVVS---GPP 383 Query: 331 ES--GLRVALTRGIKKYAELTQN-----KRAISIISDDLMISAVGILSVFIREPEFAGQT 383 +S GL + L R K + L Q+ +R + + L +++ Sbjct: 384 QSLYGLNLTL-RKAKAPSGLDQSRIPFSERKLKFSNRFLPVAS----------------- 425 Query: 384 KTKLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVNRKTA 443 PF H + LL + + L + N Sbjct: 426 -------------------PF-H---------SHLLVPASDLINKDLVKN-----NVSFN 451 Query: 444 IRKLRLP------GK-LADCSQNIAH 462 + +++P G L S +I+ Sbjct: 452 AKDIQIPVYDTFDGSDLRVLSGSISE 477 Score = 46.1 bits (109), Expect = 3e-05 Identities = 65/373 (17%), Positives = 106/373 (28%), Gaps = 162/373 (43%) Query: 50 RILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAG-------YANL---IEV 99 ++L G P +R Y+ G H S+ + A+ IA + ++ I V Sbjct: 254 KLL-GFTPGELRS--YLKGA---TGH---SQGLVTAV--AIAETDSWESFFVSVRKAITV 302 Query: 100 ---------------SLDGNGFLTVVDNGRGIP-----VENHPKFPNKSTLEIILTTLHA 139 SL + ++N G+P + N + ++ + Sbjct: 303 LFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT----QEQVQDYVNKT-- 356 Query: 140 GGKFDNSTYEISGGL----HGVGISVVNALSDELHVTVARQNTIFSQKFSRGIPLS---- 191 NS L V IS+VN +N + S G P S Sbjct: 357 -----NSH------LPAGKQ-VEISLVN----------GAKNLVVS-----GPPQSLYGL 389 Query: 192 --PLEKKEKVRNKRGTRITF--RPDPKIFGDKAGFDAARLLKMT---QSKAYLSG---RV 241 L K + +RI F R K R L + S L + Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERK-LKFS--------NRFLPVASPFHSH-LLVPASDLI 439 Query: 242 KTCWSCDKEIAEKYGIPEKEEFYFPGG-LK-----TY----LQTKLEN--RSLISSEIFT 289 K++ + F ++ T+ L+ + ++ I Sbjct: 440 N------KDLVK-------NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC-IIR 485 Query: 290 GKTEKKGTHRGTVEWAIAWCEENPEITSYCNT-ILT-DEGGTHESGLRVALTRGIKKYAE 347 V+W T + T IL GG SGL V LT Sbjct: 486 ----------LPVKW--------ETTTQFKATHILDFGPGGA--SGLGV-LTH------- 517 Query: 348 LTQNK--RAISII 358 +NK + +I Sbjct: 518 --RNKDGTGVRVI 528 Score = 28.4 bits (63), Expect = 4.9 Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 5/52 (9%) Query: 17 QGSSEKLKKSGEIPDSPAFANQSASDNYDA----SSIRILEGLEPVRMRPGM 64 + + E LK G IP FA S + Y A + + +E L V GM Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGE-YAALASLADVMSIESLVEVVFYRGM 1791 >3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA damage, nucleus, phosphop DNA binding protein, protein binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae} Length = 367 Score = 54.7 bits (131), Expect = 7e-08 Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 13/99 (13%) Query: 80 EVIDNAMDEVIAGYANLIEVSLDGNG--FLTVVDNGRGIPVENHPKFPNKSTLEIILTTL 137 E++DN++D A AN IE+ G + DNG GI N+ K Sbjct: 32 ELVDNSID---AN-ANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALK-------HYT 80 Query: 138 HAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTVARQ 176 KF + + G G +S + ++ +T Sbjct: 81 SKIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSP 119 >3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag repair, structural genomics consortium, SGC, protein bindin; HET: DNA ATP; 2.50A {Homo sapiens} Length = 348 Score = 48.1 bits (114), Expect = 6e-06 Identities = 25/134 (18%), Positives = 51/134 (38%), Gaps = 17/134 (12%) Query: 80 EVIDNAMDEVIAGYANLIEVSLDGNG--FLTVVDNGRGIPVENHPKFPNKSTLEIILTTL 137 E+I+N +D A + I+V + G + + DNG GI E+ + T Sbjct: 35 EMIENCLD---AK-STSIQVIVKEGGLKLIQIQDNGTGIRKEDLD-------IVCERFTT 83 Query: 138 HAGGKFDNSTYEISGGLHGVGISVVNALSD-ELHVTVARQNTIFSQKFSRGIPLSPLEKK 196 F++ + G G ++ ++ ++ + A + +S G + Sbjct: 84 SKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKA---PP 140 Query: 197 EKVRNKRGTRITFR 210 + +GT+IT Sbjct: 141 KPCAGNQGTQITVE 154 >1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair, HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2 PDB: 1h7u_A* 1ea6_A* Length = 365 Score = 47.8 bits (113), Expect = 8e-06 Identities = 31/134 (23%), Positives = 52/134 (38%), Gaps = 17/134 (12%) Query: 80 EVIDNAMDEVIAGYANLIEVSLDGNG--FLTVVDNGRGIPVENHPKFPNKSTLEIILTTL 137 E+++N++D AG A I++ L G + V DNG G+ EN TL+ + + Sbjct: 41 ELVENSLD---AG-ATNIDLKLKDYGVDLIEVSDNGCGVEEENFE----GLTLKHHTSKI 92 Query: 138 HAGGKFDNSTYEISGGLHGVGISVVNALSD-ELHVTVARQNTIFSQKFSRGIPLSPLEKK 196 + G G +S + ALSD + A F + +K Sbjct: 93 QEFADLTQVE---TFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHN---GKIIQK 146 Query: 197 EKVRNKRGTRITFR 210 RGT ++ + Sbjct: 147 TPYPRPRGTTVSVQ 160 >1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A* 1bkn_A 1nhj_A* 1b62_A* Length = 333 Score = 40.2 bits (93), Expect = 0.001 Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 13/90 (14%) Query: 80 EVIDNAMDEVIAGYANLIEVSLDGNG--FLTVVDNGRGIPVENHPKFPNKSTLEIILTTL 137 E+++N++D AG A I++ ++ G + + DNG GI + + I + Sbjct: 31 ELVENSLD---AG-ATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIAS-- 84 Query: 138 HAGGKFDNSTYEISGGLHGVGISVVNALSD 167 D+ IS G G ++ ++++S Sbjct: 85 -----LDDLEAIISLGFRGEALASISSVSR 109 >2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding, structural genomics, NPPSFA; HET: ANP; 1.86A {Homo sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A* Length = 394 Score = 37.0 bits (85), Expect = 0.014 Identities = 22/109 (20%), Positives = 36/109 (33%), Gaps = 16/109 (14%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANL-----IEVSLDGNG---FLTVVDNGRGIPVENH 121 LHH+ E+ NAM + N IEV + + + D G G+P+ Sbjct: 227 VPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRII 286 Query: 122 PKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELH 170 + L + DNS G G G+ + + + Sbjct: 287 DR------LFSYTYSTAPTPVMDNSRNAPLAGF-GYGLPISRLYA-KYF 327 >2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1; GHKL ATPase/kinase family, pyruvate dehydrogenase complex, mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens} PDB: 2q8f_A* 2q8h_A Length = 407 Score = 35.5 bits (81), Expect = 0.041 Identities = 26/150 (17%), Positives = 49/150 (32%), Gaps = 16/150 (10%) Query: 29 IPDSPAFANQSASDNYDASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDE 88 I D A + Y S LE L + + L+H+ E+ NAM Sbjct: 200 IKDGYENARRLCDLYYINSPELELEELNAKSPGQPIQVVY-VPSHLYHMVFELFKNAMRA 258 Query: 89 VIAGYANL-----IEVSLDGNGF---LTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAG 140 + +AN I+V + + + D G G+P+ + L + + Sbjct: 259 TMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDR------LFNYMYSTAPR 312 Query: 141 GKFDNSTYEISGGLHGVGISVVNALSDELH 170 + + S + G G+ + + Sbjct: 313 PRVETSR-AVPLAGFGYGLPISRLYAQYFQ 341 >2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation, transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A* 2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A* Length = 394 Score = 35.4 bits (81), Expect = 0.042 Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 9/103 (8%) Query: 29 IPDSPAFANQSASDNYDASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDE 88 + D+ A Y AS ++ + + +++ L+H+ E+ NAM Sbjct: 188 VKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVY-VPSHLYHMLFELFKNAMRA 246 Query: 89 VIAGYAN-----LIEVSLDGNG---FLTVVDNGRGIPVENHPK 123 + + + I+V + + + D G G+P+ + Sbjct: 247 TVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIER 289 >1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural genomics, mycobacterium tuberculosis structural proteomics project; 1.78A {Mycobacterium tuberculosis} SCOP: d.122.1.3 PDB: 1ys3_A Length = 150 Score = 35.2 bits (81), Expect = 0.044 Identities = 13/54 (24%), Positives = 17/54 (31%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNGRGIPVENHPK 123 L I NA+ A L VS + + DNG G+P Sbjct: 43 LPAGLRLAVDNAIANAVKHGGATLVQLSAVSSRAGVEIAIDDNGSGVPEGERQV 96 >3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transferase, two-component regulatory system; 3.80A {Thermotoga maritima} Length = 349 Score = 35.0 bits (80), Expect = 0.060 Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 1/55 (1%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGF-LTVVDNGRGIPVENHPK 123 D + + ++ NA++ I ++V ++G IP E K Sbjct: 241 DRTRIKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGPPIPEELKEK 295 >3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I two-component histidine kinase, phosphoprotein; HET: ADP; 2.03A {Geobacillus stearothermophilus} Length = 244 Score = 34.8 bits (80), Expect = 0.069 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 1/55 (1%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNG-FLTVVDNGRGIPVENHPK 123 + + V+ NA++ + G + VS+D + + D G G+ E + Sbjct: 120 EREKFRQCLLNVMKNAIEAMPNGGTLQVYVSIDNGRVLIRIADTGVGMTKEQLER 174 >1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; pyruvate dehydrogenase kinase 3, lipoyl-bearing domain; HET: LPA ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB: 1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A* Length = 419 Score = 34.7 bits (79), Expect = 0.070 Identities = 18/151 (11%), Positives = 44/151 (29%), Gaps = 17/151 (11%) Query: 29 IPDSPAFANQSASDNYDASSIRILEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDE 88 + D+ A Y + +E + + L H+ E+ N+M Sbjct: 210 VKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVY-VPSHLFHMLFELFKNSMRA 268 Query: 89 VIAGYANL------IEVSLDGNG---FLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHA 139 + Y + ++ + + + D G G+P+ + N + + Sbjct: 269 TVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLRKIDRLFNY------MYSTAP 322 Query: 140 GGKFDNSTYEISGGLHGVGISVVNALSDELH 170 + + G G G+ + + Sbjct: 323 RPSLEPTRAAPLAG-FGYGLPISRLYARYFQ 352 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 34.1 bits (77), Expect = 0.095 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 18/78 (23%) Query: 581 RITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKETAM----DAN 636 R+TQ +S+ EE +++ L+E K ++ + +E A + N Sbjct: 79 RLTQEPESIRKWREEQRKR-LQELDAASK-------------VMEQEWREKAKKDLEEWN 124 Query: 637 KRTLLRVEINKDLNSLKD 654 +R +VE NK N + D Sbjct: 125 QRQSEQVEKNKINNRIAD 142 >3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding, cell inner MEM cell membrane, kinase, membrane, nucleotide-binding; 2.50A {Escherichia coli} Length = 222 Score = 33.5 bits (77), Expect = 0.15 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNGRGIPVENHPK 123 L L ++DNA+ G ++++V+L+ + F V DNG G+ E + Sbjct: 114 QPLLLSLLVRNLLDNAVRYSPQG--SVVDVTLNADNF-IVRDNGPGVTPEALAR 164 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 33.4 bits (75), Expect = 0.16 Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 17/42 (40%) Query: 441 KTAIRKLRLPGKL-ADCSQNIAHGTELFIVEGDSAGGSAKQA 481 K A++KL+ KL AD DSA A +A Sbjct: 19 KQALKKLQASLKLYAD----------------DSAPALAIKA 44 >1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase; transferase, mitochondrial protein kinase, potassium; HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1 d.122.1.4 PDB: 1gjv_A 1gkx_A* Length = 388 Score = 31.7 bits (71), Expect = 0.55 Identities = 16/118 (13%), Positives = 32/118 (27%), Gaps = 19/118 (16%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSL---------DGNGFLTVVDNGRGIPVEN 120 L ++ E++ NAM + + + D + + + D G GI ++ Sbjct: 235 IPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKD 294 Query: 121 HPKF--------PNKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELH 170 + + I G G G+ A + E Sbjct: 295 LDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGF-GFGLPTSRAYA-EYL 350 >1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase; HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB: 3cgz_A 3cgy_A Length = 152 Score = 31.2 bits (71), Expect = 0.72 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 7/57 (12%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYANLIEVSL---DGNGFLTVVDNGRGIPVENHPK 123 ++ + V+DNA + +E+S D + ++ V D+G GIP+ Sbjct: 41 EQNDFVEVMGNVLDNACKYCLEF----VEISARQTDEHLYIVVEDDGPGIPLSKREV 93 >1viz_A PCRB protein homolog; structural genomics, unknown function; 1.85A {Bacillus subtilis} SCOP: c.1.4.1 Length = 240 Score = 30.5 bits (68), Expect = 1.4 Identities = 20/124 (16%), Positives = 41/124 (33%), Gaps = 15/124 (12%) Query: 563 MYDLIEQKHLFLISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGE 622 +YD+ E KH+F + P +++ + LE + G + I G+ E Sbjct: 3 LYDVTEWKHVFKLDP---------------NKDLPDEQLEILCESGTDAVIIGGSDGVTE 47 Query: 623 MLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERASFID 682 ++ +L V + + D + L AD Q+ Sbjct: 48 DNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYG 107 Query: 683 DVGT 686 ++ + Sbjct: 108 ELMS 111 >2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair, hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A 2zxp_A 1ir6_A Length = 666 Score = 30.1 bits (67), Expect = 1.9 Identities = 5/24 (20%), Positives = 12/24 (50%) Query: 536 EKVIIMTDADVDGAHIASLLLTFF 559 +++ + D D DG ++L+ Sbjct: 73 KRIRVHGDYDADGLTGTAILVRGL 96 >1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ)); histidine kinase, osmosensor, His-Asp phosphorelay system, signal transduction; HET: ANP; NMR {Escherichia coli} SCOP: d.122.1.3 Length = 161 Score = 29.5 bits (66), Expect = 2.9 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 9/58 (15%) Query: 70 DEKALHHLFSEVIDNAMDEVIAGYAN-LIEVSLD---GNGFLTVVDNGRGIPVENHPK 123 ++ + ++ NA Y N I+VS + V D+G GI E Sbjct: 44 HPLSIKRAVANMVVNAAR-----YGNGWIKVSSGTEPNRAWFQVEDDGPGIAPEQRKH 96 >2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl MAD, two-component systems, transferase; HET: ADP; 1.9A {Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB: 3dge_A* Length = 258 Score = 29.1 bits (65), Expect = 3.6 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%) Query: 70 DEKALHHLFSEVIDNAMD----EVIAGYANLIEVSLDGNGFLTVVDNGRGIPVENHPK 123 D + + +++N + + Y +I DG + V DNG GIP + Sbjct: 135 DPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDEKDGGVLIIVEDNGIGIPDHAKDR 192 >3p01_A Two-component response regulator; PSI-2, midwest center for structural genomics, protein struc initiative, MCSG, signali protein; 2.65A {Nostoc SP} Length = 184 Score = 29.0 bits (64), Expect = 3.6 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 3/45 (6%) Query: 422 VIERSEERLRRRKQREVNRKTAIRKLRLPGKLADCSQNIAHGTEL 466 V++R+ E KQR + A ++ L L Q L Sbjct: 4 VVQRAAETYDLLKQRTEELRRANAQMSL---LTVLVQVTQASNSL 45 >2qr4_A Peptidase M3B, oligoendopeptidase F; structural genomics, PSI-2, protein structure initiative; 2.50A {Enterococcus faecium DO} Length = 587 Score = 28.4 bits (62), Expect = 5.6 Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 5/92 (5%) Query: 593 DEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKET--AMDANKRTLLRVEINKDLN 650 ++ + E + K + + KG + ASQ + R + + L Sbjct: 4 SDQEFDEKYLELSEELK---QSEKHKGTLDQGASQFLNAIEFVLRVYRQTEVIYVYAHLK 60 Query: 651 SLKDTQDSINKLMGTKADERFKFIQERASFID 682 + +DT ++ + + +A F + E S+ + Sbjct: 61 NDQDTGNTDYQALYARASSLFSKVSEAVSWFE 92 >3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; YP_546034.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE CMP; 1.79A {Methylobacillus flagellatus KT} Length = 187 Score = 28.3 bits (62), Expect = 5.9 Identities = 9/40 (22%), Positives = 15/40 (37%) Query: 401 RDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVNR 440 RD L P K+L +++ R R R + + Sbjct: 142 RDALYQLLANMPKLGNKVLIRLLQLLTARFRESYDRILPK 181 >1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269 Score = 28.1 bits (62), Expect = 6.2 Identities = 38/172 (22%), Positives = 58/172 (33%), Gaps = 28/172 (16%) Query: 75 HHLFS-------EVIDNAMD-------------EVIAGYANL-IEVSLDGNGF-LTVVDN 112 + L+ E+I NA D +AG L +++ D L V D Sbjct: 23 NSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDT 82 Query: 113 GRGIPVENHPKFPN---KSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDEL 169 G G+ E K KS L + + ST E+ G GVG ++D++ Sbjct: 83 GVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQ-FGVGFYSAFLVADKV 141 Query: 170 HVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITF--RPDPKIFGDK 219 VT N S S + RGT IT + + + + Sbjct: 142 IVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLEL 193 >1ibj_A CBL, cystathionine beta-lyase; PLP-dependent enzyme, methionine biosynthesis, transsulfuration; HET: PLP; 2.30A {Arabidopsis thaliana} SCOP: c.67.1.3 Length = 464 Score = 27.7 bits (61), Expect = 9.0 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 5/49 (10%) Query: 96 LIEVSLDGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFD 144 ++E S+DG TV + + N + + STL + + KFD Sbjct: 56 VMEKSVDGQTHSTVNNTTDSLNTMNIKEEASVSTLLV-----NLDNKFD 99 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.316 0.134 0.377 Gapped Lambda K H 0.267 0.0508 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 5,748,497 Number of extensions: 276096 Number of successful extensions: 1050 Number of sequences better than 10.0: 1 Number of HSP's gapped: 973 Number of HSP's successfully gapped: 60 Length of query: 686 Length of database: 5,693,230 Length adjustment: 99 Effective length of query: 587 Effective length of database: 3,293,074 Effective search space: 1933034438 Effective search space used: 1933034438 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: 60 (27.4 bits)