HHsearch alignment for GI: 254780222 and conserved domain: TIGR01059
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=100.00 E-value=0 Score=1996.34 Aligned_cols=632 Identities=46% Similarity=0.740 Sum_probs=602.2
Q ss_pred CCHHHEEECCCCHHHHCCCCEEECCCCC-CCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCEEEEEECCCCCCCCCCC
Q ss_conf 6975602311210343269815467775-502202443666678777618997699998289839999669843444176
Q gi|254780222|r 44 YDASSIRILEGLEPVRMRPGMYIGGTDE-KALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNGRGIPVENHP 122 (686)
Q Consensus 44 Y~~~~i~~L~glE~VrkRP~mYIGst~~-~GL~~i~~EIldNavDe~~~g~~~~I~V~i~~dg~IsV~ddGrGIPv~~h~ 122 (686)
T Consensus 1 Y~A~sIkVLeGLEAVRKRPGMYIGdTg~G~GLHHlvyEVVDNaIDEAlAGyC~~I~v~i~~dgsv~V~DnGRGIPVdIHp 80 (818)
T TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGDTGEGTGLHHLVYEVVDNAIDEALAGYCDTINVTINDDGSVTVEDNGRGIPVDIHP 80 (818)
T ss_pred CCCCCEEEEECCCCCCCCCCCEECCCCCCCCCEEEEEEEECCHHHHHHCCCCCEEEEEEECCCEEEEEECCCCCCCCCCC
T ss_conf 98330043314777537888301124878972389999843404420066124148999628769998588588743067
Q ss_pred CCCC------CEEEEEEEEEEECCCCCCCCCEEEECCCCCHHHHHHHHEEEEEEEEEECCCEEEEEEEECCCEECCCEEC
Q ss_conf 6578------7012345452002477777741563144538898762032126999941883899997279451131121
Q gi|254780222|r 123 KFPN------KSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTVARQNTIFSQKFSRGIPLSPLEKK 196 (686)
Q Consensus 123 k~~~------~~~~Elif~~L~aggnfdd~~yk~sgGlnGvGaklvNalS~~f~Vev~r~gk~y~q~f~~g~~~~~~~~i 196 (686)
T Consensus 81 ~-eGakqGRe~SA~EvVlT~LHAGGKFD~~sYKVSGGLHGVGvSVVNALS~~L~v~v~RdGk~y~q~F~~G~P~~~L~~~ 159 (818)
T TIGR01059 81 E-EGAKQGREISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVKRDGKIYRQEFERGIPVGPLEVV 159 (818)
T ss_pred C-CCCCCCCCCCCEEEEEEEECCCEEECCCCEEEECCEEECCEEEEEECCCEEEEEEEECCEEEEEEECCCCEECCEEEE
T ss_conf 6-878788856600012200057500158804786756503279996117289999998692999998487220530681
Q ss_pred CCCCCCCCEEEEEEECHHHEECCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCEEEEEECCCCHHHHHCC
Q ss_conf 67677885399999842432001222289999988887530577359995164532224554112343158612221002
Q gi|254780222|r 197 EKVRNKRGTRITFRPDPKIFGDKAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTK 276 (686)
Q Consensus 197 ~~~~~k~GT~ItF~PD~~iFg~~~~~d~~~l~~rl~~~A~L~~gl~i~~~~~~~~~~~~~~~~~~~f~~~~Gi~dyv~~~ 276 (686)
T Consensus 160 G~~~~~~GT~V~F~PD~~iF~~~~efd~~~l~~RLrELAFLN~Gv~I~l~D~R~-----~~~k~~~F~YeGGI~~fV~YL 234 (818)
T TIGR01059 160 GEETKKTGTTVRFVPDPEIFEETTEFDFDILAKRLRELAFLNSGVKISLEDERL-----GKVKKVEFHYEGGIKSFVKYL 234 (818)
T ss_pred CCCCCCCCCEEEEEECHHHHCCCCEECHHHHHHHHHHHHHHCCCCEEEEEECCC-----CCCCEEEEEECCCHHHHHHHH
T ss_conf 346566676789960713214430332788999998888718972699987325-----675203787356189999995
Q ss_pred CCCCCCCCCCCEE----EEEEEC-CCEEEEEEEEEEECCCCCC-EEEEEEECCCCCCCEEECCHHHHHHHHHHHHHHHCC
Q ss_conf 4677666775203----333214-8015589998541467774-278883000655752413046789999998763018
Q gi|254780222|r 277 LENRSLISSEIFT----GKTEKK-GTHRGTVEWAIAWCEENPE-ITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQ 350 (686)
Q Consensus 277 ~~~~~~~~~~~~~----~~~~~~-~~~~~~veval~~~~~~~~-~~SFVN~I~T~~GGTHv~g~~~ai~k~i~~~~~~~~ 350 (686)
T Consensus 235 n~~K~~l~~~ii~ektt~~g~~~~~~~~i~VEvALQwnd~Y~e~i~sF~NNI~T~eGGTHl~GFr~aLTr~~n~y~~~~~ 314 (818)
T TIGR01059 235 NRNKEPLHEEIIYEKTTISGEKEDDDGGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKKNK 314 (818)
T ss_pred CCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEEEEECCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 37882247886423431577751677607999998762685510378856755678861177886578999999997368
Q ss_pred --C-CCCCCCCCCCCCCCEEEEEEEEEEHHHCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf --8-3322233222236426999977634560764466202523200001210158899977401356889999999999
Q gi|254780222|r 351 --N-KRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERSE 427 (686)
Q Consensus 351 --~-kk~~~i~~~dIk~~L~~~Isv~I~nP~FesQTKekL~s~~~~~~v~~~i~~~l~~~l~~n~~~a~~I~~~~~~~a~ 427 (686)
T Consensus 315 l~Ki~~~~~l~GeD~REGLtAViSvKvP~PqFEGQTK~KLGNsEVr~~V~~~v~e~l~~f~eeNP~~Ak~Iv~K~~~AA~ 394 (818)
T TIGR01059 315 LLKIESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPTEAKAIVEKAIEAAR 394 (818)
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 75324455676577102238999981487897883223464641677788887999999975290689999999999999
Q ss_pred HHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCC-CHHHCCCCCCEEEEEECCEECCHHHHHHH
Q ss_conf 65454433444-22110024565333567765655403799732767642-10010112220122112313144541087
Q gi|254780222|r 428 ERLRRRKQREV-NRKTAIRKLRLPGKLADCSQNIAHGTELFIVEGDSAGG-SAKQARNRSNQAVLPLRGKILNVASAGSE 505 (686)
Q Consensus 428 ~r~~~~k~k~~-~rk~~~~~~~lpgKL~Da~~~~~~~~eL~lvEGDSA~g-sAk~grdr~~qgi~PLRGKiLNv~~as~~ 505 (686)
T Consensus 395 AReAArkARELtRRKSaLd~~~LPGKLADC~~kDP~~sElYiVEGDSAGGcSAKqGRDR~fQAILPLrGKILNVEKaR~d 474 (818)
T TIGR01059 395 AREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGCSAKQGRDRKFQAILPLRGKILNVEKARLD 474 (818)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECEECCCHH
T ss_conf 98875664430016674232458863025788881231266873452777654446786543423324552100012045
Q ss_pred HHHCCHHHHHHHHHHCCCCCCC-CCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEE
Q ss_conf 7632288999998825665433-333465525189997798771468899999999870888633938993099699974
Q gi|254780222|r 506 KIRNNQQIMDLVQALGCRTRSQ-YREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISPPLFRITQ 584 (686)
Q Consensus 506 ki~~N~Ei~~l~~~lGl~~g~~-~~~~~LRYgkIiImTDaD~DGsHI~~Lll~ff~~~~p~Li~~g~v~~~~tPl~kv~~ 584 (686)
T Consensus 475 K~l~N~Ei~~~ItALG~GI~~d~Fdl~KLRYHKIIIMTDADVDGSHIRTLLLTFFYR~M~~LIE~GyvYIAqPPLYKvk~ 554 (818)
T TIGR01059 475 KILSNDEIQAIITALGCGIGKDEFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKK 554 (818)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCHHHHC
T ss_conf 53212533888997368867667872324644368840678783689999999887401588745872650786021204
Q ss_pred CCEEEEECCHHHHHHHH---------------------------------------------------------------
Q ss_conf 89799937899999999---------------------------------------------------------------
Q gi|254780222|r 585 GTKSVYAHDEEHKQKIL--------------------------------------------------------------- 601 (686)
Q Consensus 585 g~~~~y~~~e~e~~~~~--------------------------------------------------------------- 601 (686)
T Consensus 555 gk~~~Yikdd~e~d~yll~~~~~~~~l~~~~~~L~~~~Le~~~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 634 (818)
T TIGR01059 555 GKKERYIKDDKELDHYLLNLGINEAELVITKRELVGELLEDLVNAYLELEKRKNLINRLERKAIRFSEELLIYQDLLEKE 634 (818)
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCHH
T ss_conf 65511222778998898875324202653478999999999999999886314479999874043557888755530222
Q ss_pred ----------------------------HH--------------------------------------------------
Q ss_conf ----------------------------98--------------------------------------------------
Q gi|254780222|r 602 ----------------------------EE-------------------------------------------------- 603 (686)
Q Consensus 602 ----------------------------~~-------------------------------------------------- 603 (686)
T Consensus 635 ~~~~~~~~~~~~~~~~y~~~~~E~~~~~~~~~~~~~~~~~~f~~~vvR~G~~~~~~L~~~q~~~~e~~~~~~~~~~~~~~ 714 (818)
T TIGR01059 635 LLEYESAVKYWLQGALYIYSDKEKEEAKTQLPVHKNAEKELFESSVVRHGLDTDYILEKEQLELFEYGEIISLELSLQGL 714 (818)
T ss_pred HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf 20014688889999998875565788887422356778875412114437763200166664332345434421103455
Q ss_pred -------------------------HHHCCCCCEEEEEEECCCCCCHHHHHHHCCCCCCEEEEEEEECCCCCCHHHHHHH
Q ss_conf -------------------------7741788607868506778898899886039400079999866410267989999
Q gi|254780222|r 604 -------------------------FKKHGKGKIEISRFKGLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDS 658 (686)
Q Consensus 604 -------------------------~~~~~~~k~~i~ryKGLGe~~~~e~~et~~~p~~r~l~~v~~~~~~~~~~~~~~~ 658 (686)
T Consensus 715 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~iQRYKGLGEMna~QLWETTMdP~~R~L~~V~~~D----A~~AD~~ 790 (818)
T TIGR01059 715 FETRAKLIRKNKKFEINSLEEALDKLVELGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIED----AVEADRI 790 (818)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHCCCCCCCEEEEEEHHH----HHHHHHH
T ss_conf 443432100122310025899999998407898604543166667822203342884644487745799----9886543
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 998807981689999997524677517
Q gi|254780222|r 659 INKLMGTKADERFKFIQERASFIDDVG 685 (686)
Q Consensus 659 f~~lmG~~~~~RK~wi~~~~~~~~~ld 685 (686)
T Consensus 791 F~~LMGd~VePRR~FIE~nAl~v~nLD 817 (818)
T TIGR01059 791 FSTLMGDEVEPRREFIEANALDVKNLD 817 (818)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf 200068986530789999999885248