HHsearch alignment for GI: 254780182 and conserved domain: TIGR01063

>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 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 A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=2802.17  Aligned_cols=854  Identities=51%  Similarity=0.842  Sum_probs=810.7

Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             66600999998767877799886313754000897367899999998789999981134042556643668870478999
Q gi|254780182|r   16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD   95 (910)
Q Consensus        16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~   95 (910)
T Consensus         1 i~pv~ie~E~k~SYLdYAMSVIVsRALPDvRDGLKPVHRRiLYaM~~~Gl~~d~~~kKsARIVGDV~GkYHPHGD~aiYD   80 (864)
T TIGR01063         1 IVPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVLGKYHPHGDSAIYD   80 (864)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCEEEEEECCCCCCCCCCHHHH
T ss_conf             94565788999998644111322211541003688504577667766278998866002428741047824898734676


Q ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH
Q ss_conf             99971220111561314788708877697201357899978999999863076840533068988548503432273211
Q gi|254780182|r   96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL  175 (910)
Q Consensus        96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL  175 (910)
T Consensus        81 ~LVRMAQDFSlRYpLvDGQGNFGSiDGD~pAAMRYTEaRl~k~a~~ll~DIdKeTVdF~~NYDg~~~EP~VLPs~fPnLL  160 (864)
T TIGR01063        81 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPPAAMRYTEARLTKIAEELLRDIDKETVDFVPNYDGSEKEPTVLPSRFPNLL  160 (864)
T ss_pred             HHHHHCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             77650587100354416888647888882676521788888999999862043631654488886258820751241456


Q ss_pred             HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             01676101013317898547899999988761877688888863458668874434475889999870120389999886
Q gi|254780182|r  176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH  255 (910)
Q Consensus       176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~  255 (910)
T Consensus       161 vNGSsGIAVGMATNIPPHNL~Eiida~~~~i~Np~~~i~eLl~~i~GPDFPTgg~I~G~~GI~~AY~TGRG~i~~Rar~~  240 (864)
T TIGR01063       161 VNGSSGIAVGMATNIPPHNLGEIIDAILAYIDNPDISIEELLEVIKGPDFPTGGIILGRSGIREAYETGRGSIVIRARAE  240 (864)
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCHHHHHCCCCCHHHHHHCCCCEEEEEEEEE
T ss_conf             13247600022257887336899999999871899886799560771137105643050013777335881389999899


Q ss_pred             EEECCC--CCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCEEEEEEECCCCCHHHHHHHHHHHCC
Q ss_conf             543367--845999924644352899999999998716650144587303-74655799994798877899999997610
Q gi|254780182|r  256 IEKTSG--DREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDES-DRQGYRVVIELKRGASADVILNQLYRYTS  332 (910)
Q Consensus       256 ie~~~~--~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeS-dr~giRivielKr~~~~~~vln~Lyk~T~  332 (910)
T Consensus       241 iE~~~~~~gR~~IIvTE~PYqVNKa~LiekIAeLv~ek~ieGIsdiRDESSDr~GiRiVIE~KRD~~a~VvLN~LYk~T~  320 (864)
T TIGR01063       241 IEEDSKKGGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESSDREGIRIVIELKRDAVAEVVLNNLYKQTQ  320 (864)
T ss_pred             EEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHCCCC
T ss_conf             98648899862488862888520268889999874000000321244256687743799997428983015421211264


Q ss_pred             HHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             11000000245541663000299999999999999999999999999988877899999987406999999861899789
Q gi|254780182|r  333 LQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPET  412 (910)
Q Consensus       333 Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~e  412 (910)
T Consensus       321 lQ~~Fg~NmLALv~G~Pk~lnLk~~l~~f~~HR~~Vi~RRT~feLrKA~eRaHiL~GL~~AL~niDevI~lIr~S~~~~~  400 (864)
T TIGR01063       321 LQVSFGINMLALVDGLPKVLNLKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIALDNIDEVIALIRASQNTEE  400 (864)
T ss_pred             CCEECCEEEEEEECCCCCEECHHHHHHHHHHCCEEEEEEEHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             50014812321107897501788999999842313355210001022655789999999999721289999742789889


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             87877631269788999997402211122234452369999999998789999888799999989999999998875304
Q gi|254780182|r  413 ARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILS  492 (910)
Q Consensus       413 Ak~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~  492 (910)
T Consensus       401 Ak~~L~e~~W~l~di~~ll~~~--~~~~l~~~g~F~l~E~QA~AILdMrL~rLTgLE~~Kl~~E~~~L~~~I~~l~~iL~  478 (864)
T TIGR01063       401 AKTRLVERQWELLDILPLLKLV--LEVELGERGTFSLSEIQAQAILDMRLQRLTGLEREKLEEEYKELLELIADLEDILA  478 (864)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH--HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9988421686078999999887--67532888865448899999999887677888899999999999999999997503


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCEEECC-CCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9899999999989999984056883310013-434530101456781899907970523310000023345652110001
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTPRRTRIVEG-LLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVM  571 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~RRT~I~~~-~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~  571 (910)
T Consensus       479 ~~~r~~~iireEL~~i~~~Fgd~RRT~I~~~~~~~~D~EDLI~~E~vVvt~s~~GYvKR~p~~~Y~~Q~RGGkG~~g~~~  558 (864)
T TIGR01063       479 SEERVLEIIREELEEIKEQFGDPRRTEIVAEESEDIDIEDLIARENVVVTLSHKGYVKRVPVSAYRSQKRGGKGVSGADL  558 (864)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCHHHHCCCCEEEEEECCCEEEECCHHHHHCCCCCCCCCCCCCC
T ss_conf             77689999999999999973885321222024322450344147878999716864786030133257666646432531


Q ss_pred             CC-CCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEE
Q ss_conf             46-41010113323777399995489399982000432244456554124545-36556200256630125666871799
Q gi|254780182|r  572 RD-EDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVV  649 (910)
Q Consensus       572 ke-~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lv  649 (910)
T Consensus       559 ~~G~D~i~~~lvasTHD~~Lfftn~G~vY~lK~Y~iP~~~R~akG~pIvNLL~G~~~dE~I~ai~~v~~f~d~~~~~yl~  638 (864)
T TIGR01063       559 KDGDDFIEQLLVASTHDYLLFFTNRGKVYRLKVYQIPEASRTAKGKPIVNLLEGLQKDERITAILSVKEFEDEAYDLYLF  638 (864)
T ss_pred             CCCCCEEEEEEEEECCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEE
T ss_conf             23685056778830776078881888268645441787775678712888605787676688873566668552661799


Q ss_pred             EEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCE-EEEEECCCEEEEEEHH--HCCCCCCCCCCCEEE
Q ss_conf             9947991898423686204777227866158985788896189826-9999369859997587--623547866553576
Q gi|254780182|r  650 FATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEND-ILLTTKLGQCVRFPIS--AIRVFAGRNSVGVRG  726 (910)
Q Consensus       650 l~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~-Iil~T~~G~~lrF~~~--evr~~~GR~a~GVkg  726 (910)
T Consensus       639 ~aTk~G~vKk~~L~~F~~~rs~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~m-gR~~~GV~G  717 (864)
T TIGR01063       639 LATKNGVVKKTSLTEFSNIRSNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREM-GRATRGVRG  717 (864)
T ss_pred             EECCCCEEEEEECHHHHHHHHCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCC-CCCCCCEEE
T ss_conf             9726743887400144354527869999708968999999607886588651488479836885311002-455676013


Q ss_pred             EECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-EEEEEEC
Q ss_conf             752899869998973366654200000122233333334555444444443332222232001110125686-7999975
Q gi|254780182|r  727 ISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQ-FILTVSE  805 (910)
Q Consensus       727 IkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~-~IL~vTe  805 (910)
T Consensus       718 i~L~~~~~v~~~~~~~~i~~~~~D~-------------------------~~~~L~~NlD~vv~~~~~~e~~~~lL~vt~  772 (864)
T TIGR01063       718 IKLKNEDSVISMTVLKGINSIKEDR-------------------------NLEELGVNLDFVVSLEVVSEESQKLLIVTE  772 (864)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHH-------------------------HHHHCCCCEEEEEEEEEECCCCCEEEEEEE
T ss_conf             5406777400013443212002222-------------------------465437424344777862499837899830


Q ss_pred             CCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEE
Q ss_conf             99345301788486675774148876067777686899997289964999945998999990105544515687388980
Q gi|254780182|r  806 KGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFST  885 (910)
Q Consensus       806 ~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L  885 (910)
T Consensus       773 nGyGKRt~~~~yr~~~RGg~Gv~~~~~~~r--~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~~GR~t~GVrL~~l  850 (864)
T TIGR01063       773 NGYGKRTSIEEYRLQSRGGKGVKSIKITDR--NGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSIQGRNTQGVRLIRL  850 (864)
T ss_pred             CCCCEECCHHHCCCCCCCCCEEEEEEEECC--CCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCCCCCCCCCEEEEEE
T ss_conf             684200426257632656623788998646--896878987458740001010883799761032115653565589851


Q ss_pred             CCCCEEEEEEEECC
Q ss_conf             89987999998356
Q gi|254780182|r  886 AKDERVVSVERIRE  899 (910)
Q Consensus       886 ~~~D~Vv~va~i~~  899 (910)
T Consensus       851 ~e~d~vv~v~~~~~  864 (864)
T TIGR01063       851 DEDDKVVSVSLVAK  864 (864)
T ss_pred             CCCCCEEEEEECCC
T ss_conf             78763564220279