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