RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780353|ref|YP_003064766.1| DNA topoisomerase IV subunit A [Candidatus Liberibacter asiaticus str. psy62] (753 letters) >1zvu_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling, decatenation, DNA binding, DNA topology; 3.00A {Escherichia coli} Length = 716 Score = 583 bits (1503), Expect = e-167 Identities = 262/724 (36%), Positives = 431/724 (59%), Gaps = 25/724 (3%) Query: 40 ERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV 99 +RA+P + DG KPV RRI++AMSE+GL+ A FKKSAR VG+V+GK HPHGD + Y+++V Sbjct: 2 DRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMV 61 Query: 100 RLAQPFVQRYPLISGQGNFGNIDG-DSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTY 158 +AQPF RYPL+ GQGN+G D S AA RYTE+R+++ +EL+L + + D+ + Sbjct: 62 LMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNF 121 Query: 159 NEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLL 218 + EP + P++ PN+L NGT+GIAVGMAT IP HN++E+ +AA+ALID P+ ++++LL Sbjct: 122 DGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLL 181 Query: 219 EYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQ 278 + + GPD+PT I+ SR I + Y GRG R+RA W E+ +V++ +P+QV Sbjct: 182 DIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKED-----GAVVISALPHQVS 236 Query: 279 KSRLIEKIAELIIAKRIPLLEDIRDESAED--VRIVLFPKNRSLDPDLLMESIFMLSDME 336 +R++E+IA + K++P+++D+RDES + R+V+ P++ +D D +M +F +D+E Sbjct: 237 GARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLE 296 Query: 337 TRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIA 396 + +N+N++ + P V L IL EWL RR+ + RR ++R++ + +R+ IL+GLL+A Sbjct: 297 KSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLVA 356 Query: 397 YLNIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLA 456 +LNIDE+I IIRNED+PKP ++SRF LTE Q +AIL L+LR L KLEE +I+ E L Sbjct: 357 FLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEK 416 Query: 457 EKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIE 516 E++++ +L S ++ N + E++ + + G R + + KA + M+ Sbjct: 417 ERDQLQGILASERKMNNLLKKELQADAQAY------GDDRRSPLQEREEAKAMSEHDMLP 470 Query: 517 KEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLP 576 EP+T+V+S GW+RS K H +D L++K GDS K A+ + ++ + + G++Y + Sbjct: 471 SEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAID 530 Query: 577 AGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTR 636 L S RG GE + + L + + KLL+ S G F+ ++++A R Sbjct: 531 PITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNR 590 Query: 637 KGKTFLKVSSEEKMKLVVKVTG--DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKD 694 GK + + + V + D + + + ++L+F + +P++S+GKG ++ + Sbjct: 591 AGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPS 650 Query: 695 G-------GISDVICFKICEGLTWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKGFPRS 747 G++ + LT R +L G+RG G+L +G R Sbjct: 651 AEAARGEDGLAQLYVLPPQSTLTIH-VGKRKIKLRPEELQKVTGERGRRGTL-MRGLQRI 708 Query: 748 GKFL 751 + Sbjct: 709 DRVE 712 >2wl2_A GYRA, DNA gyrase subunit A; isomerase, aminocoumarin antibiotic, drug target, protein-ligand complex; HET: DNA SM8; 2.62A {Escherichia coli} PDB: 1ab4_A 1x75_A* Length = 522 Score = 509 bits (1313), Expect = e-145 Identities = 218/523 (41%), Positives = 311/523 (59%), Gaps = 45/523 (8%) Query: 13 VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAF 72 + + V++ L+ YL YA+S I RA+PD+RDG KPVHRR+++AM+ +G D+ A+ Sbjct: 3 LAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAY 62 Query: 73 KKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYT 132 KKSAR+VG+VIGK HPHGD +VYD++VR+AQPF RY L+ GQGNFG+IDGDSAAA RYT Sbjct: 63 KKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYT 122 Query: 133 EARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIP 192 E R+ ++A ++ ++++ VDF D Y+ + P V P+K PNLL NG+SGIAVGMAT+IP Sbjct: 123 EIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIP 182 Query: 193 SHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRV 252 HN+ E+ LA ID+ +ISIE L+E+I GPDFPT II R I E+YR GRG + Sbjct: 183 PHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIIN-GRRGIEEAYRTGRGKVYI 241 Query: 253 RARWCVEEVGR-GSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRI 311 RAR VE + G I+V EIPYQV K+RLIEKIAEL+ KR+ + +RDES +D Sbjct: 242 RARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMR 301 Query: 312 VLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREV 371 ++ R ++++ +++ + ++ F +NM L G+ P++M L I+ ++ HRREV Sbjct: 302 IVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQ-PKIMNLKDIIAAFVRHRREV 360 Query: 372 LFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMV------------- 418 + RR+ F ++ R IL+ L +A NID II +IR+ P Sbjct: 361 VTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVA 420 Query: 419 ------------------------SRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNL 454 + LTE Q AIL+LRL+ L LE ++ E L Sbjct: 421 AMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKEL 480 Query: 455 LAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRT 497 L + ++ +L S + I E+ V+E F +RRT Sbjct: 481 LDQIAELLRILGSADRLMEVIREELELVREQFGD-----KRRT 518 >2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA; 2.80A {Staphylococcus aureus} Length = 514 Score = 485 bits (1249), Expect = e-137 Identities = 179/488 (36%), Positives = 299/488 (61%), Gaps = 10/488 (2%) Query: 13 VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAF 72 V E ++ +SL L +R+ Y+ I+ERA+PD+RDG KPV RRI++AM G F Sbjct: 24 VSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNF 83 Query: 73 KKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYT 132 +KSA+ VG+VIG+ HPHGD SVY+++VRL+Q + R+ LI GN G+ID D AA RYT Sbjct: 84 RKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYT 143 Query: 133 EARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIP 192 EA+++ +AE +L+ ++++ V F Y++ EP+V PS+FPNLL NG++GI+ G AT IP Sbjct: 144 EAKLSLLAEELLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIP 203 Query: 193 SHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRV 252 HN+ E+ +A L IDNP+I++ +L++YI GPDFPTGGII + + I ++Y G+G V Sbjct: 204 PHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGII-QGIDGIKKAYESGKGRIIV 262 Query: 253 RARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIV 312 R++ E + G +++TEIPY+V KS L+++I EL K++ + ++RDE+ + Sbjct: 263 RSKVEEETLRNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGLRI 322 Query: 313 LFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVL 372 + ++ + + ++ SD++ + NM +S GR P++M + I+ +L H+ EV+ Sbjct: 323 AIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGR-PKLMGIRQIIDSYLNHQIEVV 381 Query: 373 FRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKP---KPVMVSRFSLTENQVD 429 R+ F + ++R+ I++GL+ A +D++I +IR+ K ++ + TE Q + Sbjct: 382 ANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEVYEFTEEQAE 441 Query: 430 AILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS 489 AI+ L+L L + ++ E L A +++ +L++ N I E+ E+K+ F Sbjct: 442 AIVMLQLYRLTNTDIVALEGEHKELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKS- 500 Query: 490 TDLGRRRT 497 R + Sbjct: 501 ----ERLS 504 >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 = 480 bits (1238), Expect = e-136 Identities = 213/489 (43%), Positives = 323/489 (66%), Gaps = 13/489 (2%) Query: 14 EENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFK 73 + + ++ + E +L YA+S I RA+PD+RDG KPVHRRI++ ++E G+ ++K Sbjct: 207 QSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYK 266 Query: 74 KSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTE 133 KSARIVG+V+GK HPHGD S+Y+++VR+AQ F RYPL+ GQGNFG++DGD AAA R+TE Sbjct: 267 KSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTE 326 Query: 134 ARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPS 193 ARMT++ +L+ +++D +DF D Y+ + EP V P++FPNLLANG SGIAVGMAT+IP Sbjct: 327 ARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPP 386 Query: 194 HNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVR 253 HN+ E+ L+L NP+ISI +L+E I GPDFPT G+I+ + I +Y GRG ++R Sbjct: 387 HNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLIL-GKSGIRRAYETGRGSIQMR 445 Query: 254 ARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAED--VRI 311 +R +EE G G IVVTEIP+QV K+R+IEKIAEL+ K+I + D+RDE++ VR+ Sbjct: 446 SRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRV 505 Query: 312 VLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREV 371 V+ + + + +++ +++ + ++T F +NM L GR P+++ L L +L H++ V Sbjct: 506 VIDVR-KDANASVILNNLYKQTPLQTSFGVNMIALVNGR-PKLINLKEALVHYLEHQKTV 563 Query: 372 LFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVM---VSRFSLTENQV 428 + RR+ + ++ R IL+GL IA +IDEII+ IR D K M RF L+E Q Sbjct: 564 VRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQA 623 Query: 429 DAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSK 488 AIL++RLR L LE +I++E + LL +++++L + + E+ E+++ F Sbjct: 624 QAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGD 683 Query: 489 STDLGRRRT 497 RRT Sbjct: 684 D-----RRT 687 >2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter baumannii} PDB: 2xkk_A* Length = 767 Score = 468 bits (1205), Expect = e-132 Identities = 211/519 (40%), Positives = 325/519 (62%), Gaps = 14/519 (2%) Query: 3 VDNISNSNTLVEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMS 62 V++ +L + S+ E+ YL YA+ I +RA+P + DG KPV RRI++AMS Sbjct: 259 VEDKLTMTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMS 318 Query: 63 EMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNID 122 E+GL KKSAR VG+V+GK HPHGD + Y+++V +AQPF RYPLI GQGN+G+ D Sbjct: 319 ELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPD 378 Query: 123 G-DSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTS 181 S AA RYTEA+++ +EL+L + + +++D ++ EP+ P++ PN+L NGT+ Sbjct: 379 DPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTT 438 Query: 182 GIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVE 241 GIAVGMAT IP HN++E+ + +ALI NP+ S EKL EYI PD PT I+ E +++ Sbjct: 439 GIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLK 498 Query: 242 SYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDI 301 GRG +R+RA + +E+ IV+TE+PYQV S++I +IA+ + AK++PL+ D+ Sbjct: 499 IQTTGRGSYRMRAVYTIEK-----NEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDV 553 Query: 302 RDESAE--DVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDG 359 RDES R+V+ ++ +D + +M +F +D+E+ + +N+N++ PQV + Sbjct: 554 RDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRR 613 Query: 360 ILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMVS 419 IL EW+ R++ + RR + + I++R+ IL GLLIAYL+ID +I IIR ED+PKPV++ Sbjct: 614 ILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLME 673 Query: 420 RFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEI 479 F++ E Q +AIL L+LR L KLEE +I+ E D L A+ I L + + N I E+ Sbjct: 674 HFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISEL 733 Query: 480 REVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKE 518 +E + F RR+ + A + +Q ++ E Sbjct: 734 KEDAKKFGDE-----RRSPIVARAEAVQIK-EQDLMPAE 766 >3ilw_A DNA gyrase subunit A; DNA topology, topoisomerase, antibiotic resistance, breakage-reunion domain, structural genomics; HET: DNA; 1.60A {Mycobacterium tuberculosis} Length = 470 Score = 434 bits (1118), Expect = e-122 Identities = 182/471 (38%), Positives = 285/471 (60%), Gaps = 17/471 (3%) Query: 36 STIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVY 95 S I RA+P++RDG KPVHRR+++AM + G + KSAR V E +G HPHGD S+Y Sbjct: 4 SVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIY 63 Query: 96 DSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFR 155 DSLVR+AQP+ RYPL+ GQGNFG+ D AA RYTEAR+T +A +L+ +DE+ VDF Sbjct: 64 DSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFI 123 Query: 156 DTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIE 215 Y+ EP V PS+FPNLLANG+ GIAVGMAT+IP HN++E+ +A ++N + E Sbjct: 124 PNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEE 183 Query: 216 K----LLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVT 271 + ++ + GPDFPT G+IV + ++Y+ GRG R+R VEE RG +V+T Sbjct: 184 ETLAAVMGRVKGPDFPTAGLIV-GSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVIT 242 Query: 272 EIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESA--EDVRIVLFPKNRSLDPDLLMESI 329 E+PYQV I IAE + ++ + +I D+S+ +RIV+ K R +++ ++ Sbjct: 243 ELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIK-RDAVAKVVINNL 301 Query: 330 FMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEI 389 + + ++T F NM + G P+ + LD +++ ++ H+ +V+ RR+++R++ + R I Sbjct: 302 YKHTQLQTSFGANMLAIVDGV-PRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHI 360 Query: 390 LKGLLIAYLNIDEIIAIIR---NEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQ 446 L+GL+ A +DE+IA+IR D + ++ + E Q AIL+++LR L LE + Sbjct: 361 LRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQR 420 Query: 447 IKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRT 497 I +L + AE ++ +L ++Q + E+ E+ + RRT Sbjct: 421 IIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDD-----RRT 466 >2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV, GRAM-positive bacteria, quinolone target, DNA binding, DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae} PDB: 3foe_A* 3fof_A* Length = 496 Score = 429 bits (1104), Expect = e-120 Identities = 170/493 (34%), Positives = 301/493 (61%), Gaps = 10/493 (2%) Query: 16 NVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKS 75 N++ +SL + ER+ Y+ I++RA+PD+RDG KPV RRI+++M++ F +++KS Sbjct: 3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKS 62 Query: 76 ARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEAR 135 A+ VG ++G HPHGD S+YD++VR++Q + R L+ GN G++DGD AA RYTEAR Sbjct: 63 AKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEAR 122 Query: 136 MTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHN 195 ++++A +LQ +++ V F +++ + EP V P+ FPNLL NG++GI+ G AT IP HN Sbjct: 123 LSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHN 182 Query: 196 VQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRAR 255 + E+ +AA+ +ID+P I+KL+E++ GPDFPTG II R+ I ++Y G+G VR++ Sbjct: 183 LAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQ-GRDEIKKAYETGKGRVVVRSK 241 Query: 256 WCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFP 315 +E++ G IV+TEIPY++ K+ L++KI ++ + ++ + ++RDES D + Sbjct: 242 TEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIE 301 Query: 316 KNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRR 375 + + +L++ +F +D++ + NM + QV + + ++AHRREV+ R Sbjct: 302 LKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPIL-SSYIAHRREVILAR 360 Query: 376 SSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRN---EDKPKPVMVSRFSLTENQVDAIL 432 S F + ++R+ I++GL+ +DE+IA+IR + K + + TE Q +AI+ Sbjct: 361 SRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIV 420 Query: 433 NLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDL 492 L+L L + ++ E L + + +++ + +N + E+REVK+ F+ Sbjct: 421 TLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATP--- 477 Query: 493 GRRRTTFCEVSRA 505 R ++ + ++A Sbjct: 478 --RLSSLEDTAKA 488 >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 = 290 bits (744), Expect = 5e-79 Identities = 96/541 (17%), Positives = 198/541 (36%), Gaps = 90/541 (16%) Query: 8 NSNTLVEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLD 67 T+++ +K + + + + + ++L+ R+IP++ DGFKP R++++ + L Sbjct: 238 EPGTVLDPTLKEIPISDFINKELILFSLADN-IRSIPNVLDGFKPGQRKVLYGCFKKNLK 296 Query: 68 FGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFV--QRYPLISGQGNFGN--IDG 123 + A V E + HG+QS+ +++ LAQ FV L+ G FG G Sbjct: 297 SELKVAQLAPYVSECTA--YHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGG 354 Query: 124 DSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGI 183 AAA RY + ++ I D+ + + EP + P +L NG GI Sbjct: 355 KDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKT-VEPEWYLPILPMILVNGAEGI 413 Query: 184 AVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESY 243 G +T IP N EI + L+++ E +E++ + G I Sbjct: 414 GTGWSTYIPPFNPLEIIKNIRHLMNDEE--LEQMHPWFRGWTGTIEEI------------ 459 Query: 244 RLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKR--IPLLEDI 301 R R +E++G + +TE+P + S + E + + P ++D+ Sbjct: 460 ----EPLRYRMYGRIEQIGD--NVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDM 513 Query: 302 RDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVL-SMGRVPQVMPLDGI 360 ++ ++++ ++ + + + +NM G++ + ++ I Sbjct: 514 EEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEI 573 Query: 361 LKEWLAHRREVLFRRSSFRMQAIDRRVEILKG------------LLIAYLNIDEIIAIIR 408 L E+ R E +R + + VE L + + II + Sbjct: 574 LSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELE 633 Query: 409 NEDKPK----------------------------------------PVMVSRFSLTENQV 428 N P+ +++ Sbjct: 634 NLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTY 693 Query: 429 DAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLN-SGKQQWNQIACEIREVKEIFS 487 + +L +R+ SL K ++ + E +++LL S K WN +++ + + Sbjct: 694 EYLLGMRIWSLTKERYQKLLKQKQEKETE---LENLLKLSAKDIWNT---DLKAFEVGYQ 747 Query: 488 K 488 + Sbjct: 748 E 748 >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 = 230 bits (586), Expect = 1e-60 Identities = 93/539 (17%), Positives = 193/539 (35%), Gaps = 90/539 (16%) Query: 10 NTLVEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFG 69 T+++ +K + + + + + ++L+ R+IP++ DGFKP R++++ + L Sbjct: 252 GTVLDPTLKEIPISDFINKELILFSLADN-IRSIPNVLDGFKPGQRKVLYGCFKKNLKSE 310 Query: 70 AAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQR----YPLISGQGNFGNIDGDS 125 + A V E + HG+QS+ +++ LAQ FV L +G G Sbjct: 311 LKVAQLAPYVSECTA--YHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKD 368 Query: 126 AAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAV 185 AAA RY + ++ I D+ + + EP + P +L NG GI Sbjct: 369 AAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKT-VEPEWYLPILPMILVNGAEGIGT 427 Query: 186 GMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRL 245 G +T IP N EI + L+++ E+ + P F Sbjct: 428 GWSTYIPPFNPLEIIKNIRHLMNDEELE-------QMHPWFRGWT-----------GTIE 469 Query: 246 GRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKR--IPLLEDIRD 303 R R +E++G + +TE+P + S + E + + P ++D+ + Sbjct: 470 EIEPLRYRMYGRIEQIGD--NVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEE 527 Query: 304 ESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVL-SMGRVPQVMPLDGILK 362 + ++++ ++ + + + +NM G++ + ++ IL Sbjct: 528 QHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILS 587 Query: 363 EWLAHRREVLFRRSSFRMQAIDRRVEILKG------------LLIAYLNIDEIIAIIRNE 410 E+ R E +R + + VE L + + II + N Sbjct: 588 EFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENL 647 Query: 411 DKPK----------------------------------------PVMVSRFSLTENQVDA 430 P+ +++ + Sbjct: 648 GFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEY 707 Query: 431 ILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLN-SGKQQWNQIACEIREVKEIFSK 488 +L +R+ SL K ++ + E +++LL S K WN +++ + + + Sbjct: 708 LLGMRIWSLTKERYQKLLKQKQEKETE---LENLLKLSAKDIWNT---DLKAFEVGYQE 760 >1zvt_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling, decatenation, DNA binding, DNA topology; 1.70A {Escherichia coli} Length = 256 Score = 162 bits (412), Expect = 2e-40 Identities = 59/242 (24%), Positives = 111/242 (45%), Gaps = 11/242 (4%) Query: 518 EPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPA 577 EP+T+V+S GW+RS K H +D L++K GDS K A+ + ++ + + G++Y + Sbjct: 2 EPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDP 61 Query: 578 GNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRK 637 L S RG GE + + L + + KLL+ S G F+ ++++A R Sbjct: 62 ITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRA 121 Query: 638 GKTFLKVSSEEKMKLVVKVTG--DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKDG 695 GK + + + V + D + + + ++L+F + +P++S+GKG ++ + Sbjct: 122 GKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPSA 181 Query: 696 -------GISDVICFKICEGLTWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKGFPRSG 748 G++ + LT R +L G+RG G+L +G R Sbjct: 182 EAARGEDGLAQLYVLPPQSTLTIH-VGKRKIKLRPEELQKVTGERGRRGTL-MRGLQRID 239 Query: 749 KF 750 + Sbjct: 240 RV 241 >3ku8_A GYRA14, DNA gyrase subunit A; alpha+beta, SH3 domain, topoisomerase, toxin-isomerase compl; HET: DNA; 1.93A {Escherichia coli} PDB: 1x75_A* 3kua_A* Length = 156 Score = 99.0 bits (246), Expect = 4e-21 Identities = 36/142 (25%), Positives = 54/142 (38%), Gaps = 37/142 (26%) Query: 363 EWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMVSR-- 420 L R + RR+ F ++ R IL+ L +A NID II +IR+ P + Sbjct: 12 SGLVPRGSHMTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVA 71 Query: 421 -----------------------------------FSLTENQVDAILNLRLRSLRKLEEY 445 + LTE Q AIL+LRL+ L LE Sbjct: 72 NPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHE 131 Query: 446 QIKSELDNLLAEKEKIDSLLNS 467 ++ E LL + ++ +L S Sbjct: 132 KLLDEYKELLDQIAELLRILGS 153 >3l6v_A GYRA, DNA gyrase subunit A; gyrase A C-terminal domain, GYRA C-terminal domain, DNA wrapping, beta-strand-bearing proline, ATP-binding; HET: DNA; 2.19A {Xanthomonas campestris PV} Length = 370 Score = 84.1 bits (207), Expect = 9e-17 Identities = 45/227 (19%), Positives = 77/227 (33%), Gaps = 17/227 (7%) Query: 514 MIEKEPITVVISNRGWI--------RSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILL 565 +I E + V +S+ G+ R+ + SA KE D + +T D +L Sbjct: 3 LIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLLT 62 Query: 566 LSTDGKAYTLPAGNL--LSGRGHGEAIQLLIDLNHNQDIVTAFV---YDSTCKLLVVSSK 620 ++ GK + LP L G I I L + + Y + + + Sbjct: 63 FTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFMATRN 122 Query: 621 GNAFIVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTGD-HVAVVGENRKLLIFSIDQIP 679 G SE +GK + + + + V GD V + N K + F + Sbjct: 123 GTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVR 182 Query: 680 EMSR-GKGVRLQSYKDGGISDVICFKICEGLTWIDSAGRSYNRSEND 725 M R GVR G +V+ + E ++ + E Sbjct: 183 SMGRTATGVRGIRLAKG--EEVVSLIVSERAGGVEDEVEDESAEEVV 227 Score = 35.5 bits (81), Expect = 0.044 Identities = 31/196 (15%), Positives = 60/196 (30%), Gaps = 43/196 (21%) Query: 542 ALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLS-GRGHGEAIQLLIDLNHNQ 600 A++ EGD+L +LL +++GK + S GR I L + Sbjct: 143 AINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVRSMGRTATGVR--GIRLAKGE 200 Query: 601 DIVTAFV-----------------------------------YDSTCKLLVVSSKGNAFI 625 ++V+ V +L + G Sbjct: 201 EVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDVADNGDVAYILTATENGYGKR 260 Query: 626 VEESEIIANTRKGKTFLKVSSEEKMKLVVKVT----GDHVAVVGENRKLLIFSIDQIPEM 681 +E R + + + + E+ +V+ D V ++ + L+ +I + Sbjct: 261 TPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVMLISDGGTLVRTRGSEISRV 320 Query: 682 SR-GKGVRLQSYKDGG 696 R +GV L G Sbjct: 321 GRNTQGVTLIRLSKGE 336 Score = 33.6 bits (76), Expect = 0.16 Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 4/100 (4%) Query: 560 TDRILLLSTDGKAYTLPAGNL-LSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVS 618 IL + +G P GRG I + N +V A + ST +++++S Sbjct: 246 VAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTT-ERNGKLVRAVLLGSTDEVMLIS 304 Query: 619 SKGNAFIVEESEIIANTR--KGKTFLKVSSEEKMKLVVKV 656 G SEI R +G T +++S EK++ V ++ Sbjct: 305 DGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERL 344 >1zi0_A DNA gyrase subunit A; beta pinwheel, topoisomerase, spiralling beta pinwheel, DNA wrapping, isomerase, DNA bindng protein; HET: DNA; 2.60A {Escherichia coli} Length = 307 Score = 67.1 bits (163), Expect = 1e-11 Identities = 44/211 (20%), Positives = 80/211 (37%), Gaps = 17/211 (8%) Query: 517 KEPITVVISNRGWI--------RSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLST 568 +E + V +S++G++ + + SA KE D + L A+T D IL S+ Sbjct: 2 QEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSS 61 Query: 569 DGKAYTLPAGNLLSG--RGHGEAIQLLIDLNHNQDIVTAFVYDSTC---KLLVVSSKGNA 623 G+ Y++ L G I L+ L ++ I K+ + ++ G Sbjct: 62 RGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTV 121 Query: 624 FIVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMS 682 +E GK +K+ +++ V +G D V + K++ F + M Sbjct: 122 KKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMG 181 Query: 683 -RGKGVRLQSYKDGGISDVICFKICEGLTWI 712 GVR +G V+ + G I Sbjct: 182 CNTTGVRGIRLGEG--DKVVSLIVPRGDGAI 210 Score = 49.7 bits (118), Expect = 2e-06 Identities = 29/162 (17%), Positives = 59/162 (36%), Gaps = 6/162 (3%) Query: 540 LSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHN 599 A+ +GD L D ++L S +GK ++ + + ++ I L Sbjct: 137 KVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRG-IRLGEG 195 Query: 600 QDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKLVVKV--- 656 +V+ V +L + G +E +R K + + E+ LVV Sbjct: 196 DKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQV 255 Query: 657 -TGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGG 696 D + ++ + L+ + +I + R +GV L + Sbjct: 256 DDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDE 297 Score = 30.5 bits (68), Expect = 1.5 Identities = 19/118 (16%), Positives = 44/118 (37%), Gaps = 4/118 (3%) Query: 542 ALHFKEGDSLKIALHAHTTDRILLLSTDGKA-YTLPAGNLLSGRGHGEAIQLLIDLNHNQ 600 + EGD + ++L D +L +T + + + + N Sbjct: 189 GIRLGEGDKV-VSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNG 247 Query: 601 DIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTR--KGKTFLKVSSEEKMKLVVKV 656 +V A D ++++++ G SEI R +G ++ + +E + + +V Sbjct: 248 LVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRV 305 >1wp5_A Topoisomerase IV; broken beta-propeller, hairpin-invaded beta-propeller, six- bladed beta-propeller; 1.79A {Geobacillus stearothermophilus} SCOP: b.68.10.1 Length = 323 Score = 64.6 bits (156), Expect = 7e-11 Identities = 31/180 (17%), Positives = 58/180 (32%), Gaps = 8/180 (4%) Query: 514 MIEKEPITVVISNRGWIRSLKSHSV---DLSALHFKEGDSLKIALHAHTTDRILLLSTDG 570 M+ E + V ++ G+++ S + K+ D L L +T D +LL + G Sbjct: 1 MVASEDVIVTVTKDGYVKRTSLRSYAASNGQDFAMKDTDRLLAMLEMNTKDVLLLFTNKG 60 Query: 571 KAYTLPAGNLLSGRGH--GEAIQLLIDLNHNQDIVTAFVYDST---CKLLVVSSKGNAFI 625 P L R G+ I +I ++ +++I+ A + L V+ G Sbjct: 61 NYLYCPVHELPDIRWKDLGQHIANIIPIDRDEEIIKAIPINDFELNGYFLFVTRNGMVKK 120 Query: 626 VEESEIIANTRKGKTFLKVSSEEKMKLVVKVTGDHVAVVGENRKLLIFSIDQIPEMSRGK 685 E A + + V +T + D+ G Sbjct: 121 TELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGMNELFLVTHNGYALWFDESEVSIVGV 180 Score = 33.8 bits (76), Expect = 0.16 Identities = 18/184 (9%), Positives = 45/184 (24%), Gaps = 8/184 (4%) Query: 514 MIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAY 573 K S +LK+ + + L + H ++ Sbjct: 121 TELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGMNELFLVTHNGYALWFDE--SEVSIV 178 Query: 574 TLPAGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIA 633 + A + + L ++D + ++ + ++ Sbjct: 179 GVRAAGVKGMNLKEGDYIVSGQLITSKDESIVVATQRGAVKKMKLTEFEKATRAKRGVVI 238 Query: 634 NTRKGKTFLKVSSEEKMKLVVKVTGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSY 692 ++S VV D + + E + + I R G + Sbjct: 239 LRELKANPHRISG-----FVVAQDSDTIYLQTEKSFIETIKVGDIRFSDRYSNGSFVLDE 293 Query: 693 KDGG 696 ++ G Sbjct: 294 EENG 297 >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 = 61.5 bits (149), Expect = 7e-10 Identities = 69/470 (14%), Positives = 134/470 (28%), Gaps = 199/470 (42%) Query: 29 RYLAYALSTIKERAIPDLRDGFKPV----HRRI-----IHAM-SEMGLDFGAAFKKSARI 78 ++L Y S ++ + IHA+ +++ + K+ + Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122 Query: 79 VG------EVIGKLHPHGDQSVYDSLVRLAQ-PFVQRYPLISGQGNFGNIDGDSAAAYRY 131 + + + S +L R Q + GQ GN D Y + Sbjct: 123 IKNYITARIMAKRPFDKKSNS---ALFRAVGEGNAQLVAIFGGQ---GNTDD-----Y-F 170 Query: 132 TEARMTQ------VAELI------LQGVDEDAVDFRDTY-----------NEE---DSE- 164 E R V +LI L + +D + N D + Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY 230 Query: 165 ----PVVFP---------------------SKFPNLLANGTSG------IAVGMA----- 188 P+ P + + L G +G AV +A Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLK-GATGHSQGLVTAVAIAETDSW 289 Query: 189 ---------------------------TSIPSHNVQEICEAA-------LALIDNPEISI 214 TS+P +++ E L++ + ++ Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN---LTQ 346 Query: 215 EKLLEYIIGPD-----FPTG---GI-IVESRESIV-----ES-YRLGRGGFRVRARWCVE 259 E++ +Y+ + P G I +V +++V +S Y L +R Sbjct: 347 EQVQDYV---NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL---TLRKAKAPS 400 Query: 260 EVGRGSWCIVVTEIPYQVQK---------------SRLIEKIAELIIAKRIPLLEDIRDE 304 + + + IP+ +K S L+ ++LI +D+ Sbjct: 401 GLDQ-------SRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLI-------NKDLVKN 446 Query: 305 ----SAEDVRIVLFP-------KN-RSLDPDLLMESIFMLSDMETRFPLN 342 +A+D++I P + R L + E I D R P+ Sbjct: 447 NVSFNAKDIQI---PVYDTFDGSDLRVLSGSIS-ERIV---DCIIRLPVK 489 Score = 49.2 bits (117), Expect = 3e-06 Identities = 50/300 (16%), Positives = 88/300 (29%), Gaps = 126/300 (42%) Query: 14 EENV-KAVSLRFALEER-YLAYALSTIKERAIPD-LRDGF-KPVHRRIIHAMSEM----G 65 +V KA+++ F + R Y AY +++ + D L + P S M Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVP---------SPMLSISN 343 Query: 66 LDFGAAFKKSARIVGEVIGKLHPH--GDQSVYDSLV--------------------RLA- 102 L + V + + K + H + V SLV L Sbjct: 344 L------TQEQ--VQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRK 395 Query: 103 --------Q---PFVQRYPLISGQGNFGNIDGDSAAAYR--YTEARMTQVAELILQGVDE 149 Q PF +R S + F + A+ + ++LI + + + Sbjct: 396 AKAPSGLDQSRIPFSERKLKFSNR--FLPV----ASPFHSHLLVP----ASDLINKDLVK 445 Query: 150 DAVDFR---------DTYNEED----SEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNV 196 + V F DT++ D S + + V +P Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS-----ERI---------VDCIIRLPVK-- 489 Query: 197 QEICEAALALIDNPEISIEKLLEYIIGPDFPTGGI----IVESRESIVESYRLGRGGFRV 252 E + + +I+ DF GG ++ R + G G RV Sbjct: 490 ---WETTT----QFKAT------HIL--DFGPGGASGLGVLTHR--NKD----GT-GVRV 527 Score = 43.4 bits (102), Expect = 2e-04 Identities = 70/466 (15%), Positives = 140/466 (30%), Gaps = 189/466 (40%) Query: 303 DESAED------VRIVL-F---------PKNRSLDPDLLMESIFMLSDMETRFPLNMNVL 346 + A D +V F P +L L++ E + ++ Sbjct: 46 EGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNL---CLTEFENCYLEGNDIH 102 Query: 347 SMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEII-- 404 ++ L L +E++ ++ + + +R D+ Sbjct: 103 AL-----AAKLLQENDTTLVKTKELI--KNYITARIMAKR------------PFDKKSNS 143 Query: 405 AIIR--NEDKPKPVMVSRF---SLTENQVDAILNLRLRSLRKLEEYQI-KSELDNLLAEK 458 A+ R E + V + F T++ + LR L YQ + +L+ Sbjct: 144 ALFRAVGEGNAQLVAI--FGGQGNTDDYFE-----ELRDL-----YQTYHVLVGDLIKF- 190 Query: 459 EKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKE 518 L+ ++ + +++F++ ++ L+ Sbjct: 191 --SAETLS-------ELIRTTLDAEKVFTQGLNI--------------LEWLENP--SNT 225 Query: 519 P-----ITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAH--TTDRILLLSTDGK 571 P +++ IS L + I L AH T ++L + Sbjct: 226 PDKDYLLSIPIS------------CPLIGV---------IQL-AHYVVTAKLLGFT---- 259 Query: 572 AYTLPAGNL---LSG-RGHGEAIQLLIDLNHNQDIVTA-----------FVYDS---TCK 613 P G L L G GH +Q +VTA F + S Sbjct: 260 ----P-GELRSYLKGATGH------------SQGLVTAVAIAETDSWESF-FVSVRKAIT 301 Query: 614 LL----VVSSKGNAF--------IVEESEIIANTRKGKTF----LKVS--SEEKMKLVVK 655 +L V A+ I+E+S + N + L +S ++E+++ V Sbjct: 302 VLFFIGVRCY--EAYPNTSLPPSILEDS--LEN---NEGVPSPMLSISNLTQEQVQDYVN 354 Query: 656 VTGDHVAVVGENRKL---LIFSIDQI----PEMS-RGKGVRLQSYK 693 T H+ +++ L+ + P S G + L+ K Sbjct: 355 KTNSHLP---AGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397 Score = 30.3 bits (68), Expect = 1.4 Identities = 41/280 (14%), Positives = 75/280 (26%), Gaps = 102/280 (36%) Query: 524 ISNRGWIRSLKS--HSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAY----TLPA 577 S R S S H + + F L+ + L T+G A T PA Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKI-----LPEPTEGFAADDEPTTPA 58 Query: 578 GNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRK 637 L+ + + + L + +D L + F E+ + Sbjct: 59 E-LVG-----KFLGYVSSLVEPSKVGQ---FDQVLNLCL-----TEF---ENCYLEGN-- 99 Query: 638 GKTFLKVSSEEKMKLVVKVTGDHVAVVGENRKLL-------IFSIDQIPEMSR------- 683 + + L K+ ++ + + ++L+ I + + S Sbjct: 100 -----DIHA-----LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV 149 Query: 684 --GKGVRL------QSYKDGGISDVICFKICEGL-----TW-------IDSAGRSYNR-S 722 G +L Q G D F E L T+ I + + + Sbjct: 150 GEGN-AQLVAIFGGQ----GNTDD--YF---EELRDLYQTYHVLVGDLIKFSAETLSELI 199 Query: 723 EN------------DLLGWL---GKRGGVGSL--VPKGFP 745 ++L WL L +P P Sbjct: 200 RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239 >1suu_A DNA gyrase subunit A; topoisomerase,DNA gyrase, beta-propeller, beta-pinwheel; HET: DNA; 1.75A {Borrelia burgdorferi} SCOP: b.68.10.1 Length = 312 Score = 49.5 bits (117), Expect = 3e-06 Identities = 34/150 (22%), Positives = 72/150 (48%), Gaps = 13/150 (8%) Query: 514 MIEKEPITVVISNRGWI--------RSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILL 565 +++KE I V+++ +G++ + + LS+ +GD + IAL +T D + + Sbjct: 4 LMQKENIVVMLTKKGFLKRLSQNEYKLQGTGGKGLSSFDLNDGDEIVIALCVNTHDYLFM 63 Query: 566 LSTDGKAYTLPAGNLL--SGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCK---LLVVSSK 620 +S +GK Y + A + S G+ I LI+L ++I+T LL+ ++ Sbjct: 64 ISNEGKLYLINAYEIKDSSRASKGQNISELINLGDQEEILTIKNSKDLTDDAYLLLTTAS 123 Query: 621 GNAFIVEESEIIANTRKGKTFLKVSSEEKM 650 G E ++ A +G +K++ ++ + Sbjct: 124 GKIARFESTDFKAVKSRGVIVIKLNDKDFV 153 Score = 36.0 bits (82), Expect = 0.029 Identities = 28/170 (16%), Positives = 62/170 (36%), Gaps = 9/170 (5%) Query: 539 DLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNL-LSGRGHGEAIQLLIDLN 597 + + + D + A ++++ LS G A+ + ++ L+ RG + + Sbjct: 141 GVIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIFNSRDVRLTNRGTQGVCGMKLKEG 200 Query: 598 HNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIA-NTRKGKTFLKVSSEEKMKLVVKV 656 V + + LL+VS G + S+I S++K VV Sbjct: 201 DLFVKVLSVKENPY--LLIVSENGYGKRLNMSKISELKRGATGYTSYKKSDKKAGSVVDA 258 Query: 657 ----TGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVI 701 D + +V + K L ++ E + +G+++ + + V Sbjct: 259 IAVSEDDEILLVSKRSKALRTVAGKVSEQGKDARGIQVLFLDNDSLVSVS 308 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 45.6 bits (107), Expect = 4e-05 Identities = 113/500 (22%), Positives = 182/500 (36%), Gaps = 144/500 (28%) Query: 33 YALSTIKERAI----PDLRDGFKPVHRRIIH-AMSEMGLDFGAAFKKSARIVGEVIGKLH 87 Y S ++ I P+L +G+ P + +I + E L+ A K++A H Sbjct: 894 YETSILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLEPFEASKETAEQFK------H 947 Query: 88 PHGDQ-SVYD---------SLVRLAQ---PFVQRYP-LISGQGNFGNI-DGDSAAAYRYT 132 HGD+ +++ L++ A P R+ L++GQ I G +A Y + Sbjct: 948 QHGDKVDIFEIPETGEYSVKLLKGATLYIPKALRFDRLVAGQ-----IPTGWNAKTYGIS 1002 Query: 133 EARMTQVAEL---ILQGVDED--AVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAV-- 185 + ++QV + +L V E A D Y + V S+ N +G G++ Sbjct: 1003 DDIISQVDPITLFVLVSVVEAFIASGITDPY---EMYKYVHVSEVGNCSGSGMGGVSALR 1059 Query: 186 GMATSI----PSHN--VQEICEAALALIDNPEISIEKLLEYIIGP-DFPTGGII--VESR 236 GM P N +QE + I+ + LL GP P G VES Sbjct: 1060 GMFKDRFKDEPVQNDILQE------SFINTMSAWVNMLLISSSGPIKTPVGACATSVESV 1113 Query: 237 ESIVESYRLGRGGFRVRARWCVEEVG-------RGSWCIVVTEIPYQVQKSRLIEKIAEL 289 + VE+ G+ AR C+ VG GS+ E S +E+ Sbjct: 1114 DIGVETILSGK------ARICI--VGGYDDFQEEGSF-----EFGNMKATSNTLEEFEH- 1159 Query: 290 IIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRF--PLNMNVLS 347 R P AE R +N ++ I M +D+ + P+ +++ Sbjct: 1160 ---GRTP---------AEMSRPATTTRNGFMEAQGAGIQIIMQADLALKMGVPI-YGIVA 1206 Query: 348 M--------GR-VPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYL 398 M GR VP P GIL H V + + M+ R+ Sbjct: 1207 MAATATDKIGRSVPA--PGKGILTTAREHHSSVKYASPNLNMKYRKRQ------------ 1252 Query: 399 NIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDN--LLA 456 ++ E + K EN+++A+ KLE +I SE N LL Sbjct: 1253 -------LVTREAQIK-------DWVENELEAL---------KLEAEEIPSEDQNEFLLE 1289 Query: 457 EKEKI----DSLLNSGKQQW 472 +I +S L + +QQW Sbjct: 1290 RTREIHNEAESQLRAAQQQW 1309 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 35.7 bits (81), Expect = 0.039 Identities = 28/97 (28%), Positives = 38/97 (39%), Gaps = 35/97 (36%) Query: 427 QVDAILNLRL----RSLRKLEEYQIK--SELD---NLLAE--KEKIDSLLNSGKQQWNQI 475 Q D RL S+RK E Q K ELD ++ + +EK L ++WNQ Sbjct: 76 QAD-----RLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL----EEWNQR 126 Query: 476 ACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQ 512 E E +I ++ ADKA QQ Sbjct: 127 QSEQVEKNKINNRI---------------ADKAFYQQ 148 Score = 28.0 bits (61), Expect = 8.6 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 26/86 (30%) Query: 206 LIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVE---SYRLGRGGFRVRARWCVEEVG 262 L PE SI K E E R+ + E + ++ +R +A+ +EE Sbjct: 80 LTQEPE-SIRKWRE--------------EQRKRLQELDAASKVMEQEWREKAKKDLEE-- 122 Query: 263 RGSWCIVVTEIPYQVQKSRLIEKIAE 288 W +E QV+K+++ +IA+ Sbjct: 123 ---WNQRQSE---QVEKNKINNRIAD 142 >2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 3.00A {Aquifex aeolicus VF5} Length = 425 Score = 32.4 bits (73), Expect = 0.44 Identities = 22/144 (15%), Positives = 41/144 (28%), Gaps = 22/144 (15%) Query: 399 NIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEK 458 D + + DK +V + L L R+ +I L+ L +E+ Sbjct: 10 KPDYVKERLATRDKELVSLVDKV------------LELDKRRR----EIIKRLEALRSER 53 Query: 459 EKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKE 518 K+ + K++ VKE+ + L E + + Sbjct: 54 NKLSKEIGKLKREGKDTTEIQNRVKELKEEIDRLEEELRKVEEELKNTLLWIPNLPHPSV 113 Query: 519 PIT------VVISNRGWIRSLKSH 536 P+ V + G R Sbjct: 114 PVGEDEKDNVEVRRWGEPRKFDFE 137 >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 = 30.4 bits (67), Expect = 1.6 Identities = 7/22 (31%), Positives = 14/22 (63%), Gaps = 3/22 (13%) Query: 201 EAALAL-IDN--PEISIEKLLE 219 +A+L L D+ P ++I+ +E Sbjct: 26 QASLKLYADDSAPALAIKATME 47 >2j0w_A Lysine-sensitive aspartokinase 3; feedback inhibition, allosteric regulation, ACT domain, transferase, amino acid biosynthesis; HET: ADP; 2.5A {Escherichia coli} SCOP: c.73.1.3 d.58.18.10 d.58.18.10 PDB: 2j0x_A* Length = 449 Score = 29.2 bits (64), Expect = 3.6 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%) Query: 400 IDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNL-----RLRSLRKLEEYQ--IKSELD 452 ++ I+ ++ + V++S + N + A+ R L + Q I L Sbjct: 20 MNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLR 79 Query: 453 NLLAEKEKIDSLLNSGKQQWNQIACE 478 +E+I+ LL + A Sbjct: 80 YPNVIREEIERLLENITVLAEAAALA 105 >1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X* Length = 758 Score = 28.5 bits (63), Expect = 5.4 Identities = 37/227 (16%), Positives = 79/227 (34%), Gaps = 28/227 (12%) Query: 251 RVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAE-LIIAKRIPLLEDIRDESAEDV 309 RA E GS+ P V K+ + ++++ L I + + + Sbjct: 476 MARAGLGHEHKPVGSFLFAG---PTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVS- 531 Query: 310 RIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHR- 368 R++ + + + +L+D + P + +L + +L+ Sbjct: 532 RLI-----GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNILLQVMDNGTL 586 Query: 369 -----REVLFRRSSFRMQ--AIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPK-----PV 416 R+ FR M A R E LI N + + I+ P+ Sbjct: 587 TDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDN 646 Query: 417 MVSRFSLTENQVDAILNLRLRSLRK-LEEYQIKSELD----NLLAEK 458 ++ L+ + + +++ + L+ L++ + E+ N LAEK Sbjct: 647 IIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEK 693 >3bho_A Cleavage and polyadenylation specificity factor subunit 5; CPSF5, RNA processing, cleavage factor, diadenosine tetraphosphate, mRNA processing; HET: B4P; 1.80A {Homo sapiens} PDB: 3bap_A 2cl3_A 2j8q_A Length = 208 Score = 28.5 bits (64), Expect = 5.6 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 2/53 (3%) Query: 556 HAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLID--LNHNQDIVTAF 606 H H +LLL + LP G L G E ++ L+ L ++ + Sbjct: 68 HEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDW 120 >2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256 Score = 28.5 bits (62), Expect = 6.1 Identities = 16/109 (14%), Positives = 29/109 (26%), Gaps = 28/109 (25%) Query: 527 RGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGH 586 G + L+ +S L+ + EG + K L L G Sbjct: 19 TGLLEYLRWNSKYLTDSAYTEGSTGKTCLMKAV--------------------LNLQDGV 58 Query: 587 GEAIQLLIDLNHNQDIVTAFVYDSTCK--------LLVVSSKGNAFIVE 627 I L+ ++ + V L + K + V+ Sbjct: 59 NACIMPLLQIDKDSGNPKPLVNAQCTDEFYQGHSALHIAIEKRSLQCVK 107 >2aaz_A TS, tsase, thymidylate synthase; methyl transferase, nucleotide biosynthesis, transferase; HET: UMP CB3; 2.08A {Filobasidiella neoformans} Length = 317 Score = 28.1 bits (62), Expect = 7.4 Identities = 11/65 (16%), Positives = 18/65 (27%), Gaps = 6/65 (9%) Query: 254 ARWCVEEVGRGSWCIVVTEI------PYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAE 307 A E + + P + Q R +L A+ + DI E Sbjct: 239 ALITDTEPHEFILQMGDAHVYRDHVEPLKTQLEREPRDFPKLKWARSKEEIGDIDGFKVE 298 Query: 308 DVRIV 312 D + Sbjct: 299 DFVVE 303 >3glk_A Acetyl-COA carboxylase 2; ATP binding, alternative splicing, ATP-binding, biotin, fatty acid biosynthesis, ligase, lipid synthesis, manganese; 2.10A {Homo sapiens} PDB: 3gid_A 2hjw_A Length = 540 Score = 27.9 bits (61), Expect = 8.0 Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 1/31 (3%) Query: 396 AYLNIDEIIAIIRNEDKPKPVMVSRFSLTEN 426 Y N++ I+ I + + V +EN Sbjct: 108 NYANVELIVDIAKRI-PVQAVWAGWGHASEN 137 >3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori} Length = 256 Score = 27.8 bits (61), Expect = 9.5 Identities = 9/53 (16%), Positives = 27/53 (50%), Gaps = 1/53 (1%) Query: 432 LNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKE 484 L+ + SL L + + +LD L +KE + + + +++ + ++ + ++ Sbjct: 16 LDKEIDSLEPLIR-EKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQ 67 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 0.319 0.137 0.389 Gapped Lambda K H 0.267 0.0673 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 6,474,710 Number of extensions: 317102 Number of successful extensions: 1063 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1004 Number of HSP's successfully gapped: 58 Length of query: 753 Length of database: 5,693,230 Length adjustment: 100 Effective length of query: 653 Effective length of database: 3,268,830 Effective search space: 2134545990 Effective search space used: 2134545990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 60 (27.0 bits)