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