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)