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)