HHsearch alignment for GI: 254780814 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=2598.85  Aligned_cols=789  Identities=52%  Similarity=0.851  Sum_probs=756.8

Q ss_pred             CCHHHCEECCCCCHHCCCCCCEECCCCCC-CHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEECCCCCCCCCC
Q ss_conf             78655123135420004587154327996-32544565675557886860779757999838983999976844536407
Q gi|254780814|r   10 YDADSIQILKGLDAVKKRPSMYIGDTDGE-SGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLH   88 (803)
Q Consensus        10 Y~~~~i~~L~gle~vrkRP~mYiG~t~~~-~Gl~hlv~EiidNsvDe~~~g~~~~I~V~i~~dgsisV~dnGrGIPv~~h   88 (803)
T Consensus         1 Y~A~sIkVLeGLEAVRKRPGMYIGdTg-~G~GLHHlvyEVVDNaIDEAlAGyC~~I~v~i~~dgsv~V~DnGRGIPVdIH   79 (818)
T TIGR01059         1 YDASSIKVLEGLEAVRKRPGMYIGDTG-EGTGLHHLVYEVVDNAIDEALAGYCDTINVTINDDGSVTVEDNGRGIPVDIH   79 (818)
T ss_pred             CCCCCEEEEECCCCCCCCCCCEECCCC-CCCCCEEEEEEEECCHHHHHHCCCCCEEEEEEECCCEEEEEECCCCCCCCCC
T ss_conf             983300433147775378883011248-7897238999984340442006612414899962876999858858874306


Q ss_pred             CCCC------CCEEEEEEEEECCCCCCCCCCCEEECCCCCCEEEEEEECCCEEEEEEEECCEEEEEEEECCEECCCCEEE
Q ss_conf             7788------5001256425011323289860483116752037786326449999997895999998898364631387
Q gi|254780814|r   89 KEEG------ISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVT  162 (803)
Q Consensus        89 ~~~~------~~~~E~i~t~L~ag~kfd~~~yk~sgGlhGvG~s~vNalS~~~~v~v~rdgk~~~q~f~~g~~~~~l~~~  162 (803)
T Consensus        80 p~eGakqGRe~SA~EvVlT~LHAGGKFD~~sYKVSGGLHGVGvSVVNALS~~L~v~v~RdGk~y~q~F~~G~P~~~L~~~  159 (818)
T TIGR01059        80 PEEGAKQGREISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVKRDGKIYRQEFERGIPVGPLEVV  159 (818)
T ss_pred             CCCCCCCCCCCCCEEEEEEEECCCEEECCCCEEEECCEEECCEEEEEECCCEEEEEEEECCEEEEEEECCCCEECCEEEE
T ss_conf             76878788856600012200057500158804786756503279996117289999998692999998487220530681


Q ss_pred             CCCCCCCCEEEEEEECHHHHH-HHHCCHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCEEEECCCCCCHHHHHHHCCCCC
Q ss_conf             327788870899987788854-2100089999999973114641699999635864210100126883577653003565
Q gi|254780814|r  163 GSAGNDTGTEVTFLPSSDIFS-VQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKK  241 (803)
Q Consensus       163 ~~~~~~~GT~I~F~PD~~iF~-~~~~~~d~l~~R~~~~A~Ln~gl~i~l~Der~~~~~~~~f~~~~Gi~~fv~~l~~~~~  241 (803)
T Consensus       160 G~~~~~~GT~V~F~PD~~iF~~~~efd~~~l~~RLrELAFLN~Gv~I~l~D~R~~~~k~~~F~YeGGI~~fV~YLn~~K~  239 (818)
T TIGR01059       160 GEETKKTGTTVRFVPDPEIFEETTEFDFDILAKRLRELAFLNSGVKISLEDERLGKVKKVEFHYEGGIKSFVKYLNRNKE  239 (818)
T ss_pred             CCCCCCCCCEEEEEECHHHHCCCCEECHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEEEEECCCHHHHHHHHCCCCC
T ss_conf             34656667678996071321443033278899999888871897269998732567520378735618999999537882


Q ss_pred             CCCCCCEE----EEEEEE----EEEEEEEEEECCCCCCEEEEEECCCCCCCCCCEEHHHHHHHHHHHHHHHHHCCCCC-C
Q ss_conf             56885203----642003----69997334531775412122224621666772103568889999999998624200-0
Q gi|254780814|r  242 PLMQSPIR----IQGSRD----NISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSK-K  312 (803)
Q Consensus       242 ~~~~~~i~----~~~~~~----~~~veval~~~~~~~e~i~SfvN~I~T~~GGtHv~gf~~al~~~i~~y~~~~~~~K-k  312 (803)
T Consensus       240 ~l~~~ii~ektt~~g~~~~~~~~i~VEvALQwnd~Y~e~i~sF~NNI~T~eGGTHl~GFr~aLTr~~n~y~~~~~l~Ki~  319 (818)
T TIGR01059       240 PLHEEIIYEKTTISGEKEDDDGGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKKNKLLKIE  319 (818)
T ss_pred             CCCCCCCCCCCEEEEEECCCCCEEEEEEEEEEECCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             24788642343157775167760799999876268551037885675567886117788657899999999736875324


Q ss_pred             CCCCCCHHHHHCCCEEEEEEECCCCCCCCCCHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             12357613430572156665213763357210020261111032111026899998740035799987789998877554
Q gi|254780814|r  313 DKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAA  392 (803)
Q Consensus       313 ~k~~~~~~Diregl~~visvki~nP~F~gQTK~kL~s~~v~~~v~~~v~~~l~~~l~~n~~~ak~i~~k~~~a~~ar~~a  392 (803)
T Consensus       320 ~~~~l~GeD~REGLtAViSvKvP~PqFEGQTK~KLGNsEVr~~V~~~v~e~l~~f~eeNP~~Ak~Iv~K~~~AA~AReAA  399 (818)
T TIGR01059       320 SKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPTEAKAIVEKAIEAARAREAA  399 (818)
T ss_pred             CCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             45567657710223899998148789788322346464167778888799999997529068999999999999998875


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCC-CCCCCCCCCCEEEEECCCCCCCHHHCCHHHHHCC
Q ss_conf             553211001100124676676666555555521799982557543-2233465443023300562033443058766323
Q gi|254780814|r  393 RRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGG-SAKQGRSRENQAILPLRGKILNVERARFDKMLSS  471 (803)
Q Consensus       393 ~kar~~~rrK~~~~~~~lpgKL~Dc~~k~~~~~eL~ivEGDSAgg-sak~gRdr~~qai~PLrGKilNv~~a~~~~i~~n  471 (803)
T Consensus       400 rkARELtRRKSaLd~~~LPGKLADC~~kDP~~sElYiVEGDSAGGcSAKqGRDR~fQAILPLrGKILNVEKaR~dK~l~N  479 (818)
T TIGR01059       400 RKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGCSAKQGRDRKFQAILPLRGKILNVEKARLDKILSN  479 (818)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEECEECCCHHHHHHH
T ss_conf             66443001667423245886302578888123126687345277765444678654342332455210001204553212


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCEEEEECCCEEEEEECCCEE
Q ss_conf             66788887625787753321235673738998508888532899999999963077874895999438337887267179
Q gi|254780814|r  472 QEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQ  551 (803)
Q Consensus       472 ~Ei~~l~~~lG~~~g~~~~~~~~lrY~kiiimtDaD~DG~HI~~Llltff~~~~~~li~~g~~yia~ppl~~~~~~K~E~  551 (803)
T Consensus       480 ~Ei~~~ItALG~GI~~d~Fdl~KLRYHKIIIMTDADVDGSHIRTLLLTFFYR~M~~LIE~GyvYIAqPPLYKvk~gk~~~  559 (818)
T TIGR01059       480 DEIQAIITALGCGIGKDEFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKER  559 (818)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCHHHHCCCCCC
T ss_conf             53388899736886766787232464436884067878368999999988740158874587265078602120465511


Q ss_pred             EEECHHHHHHHHHHHCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCHH--H
Q ss_conf             981457898999850011000014577654354689999999999999---99864344579999988742113511--2
Q gi|254780814|r  552 YVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDK---LIKDFYPNHDKTFIEQAVISGVFNCE--S  626 (803)
Q Consensus       552 YikDD~EL~~~Ll~~gl~~~~l~~~~~~~~l~ge~L~~li~~~~~~~~---~l~~l~~~~~~~lle~l~~~~~l~~~--~  626 (803)
T Consensus       560 Yikdd~e~d~yll~~~~~~~~l~--~~~~~L~~~~Le~~~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  637 (818)
T TIGR01059       560 YIKDDKELDHYLLNLGINEAELV--ITKRELVGELLEDLVNAYLELEKRKNLINRLERKAIRFSEELLIYQDLLEKELLE  637 (818)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEE--ECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHC
T ss_conf             22277899889887532420265--3478999999999999999886314479999874043557888755530222200


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC-----CCCEECCCCCCCEEEEEEECCCCEEEEECHHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             35778999999998876531000-----0110024456705999995185302664667741642789999888877511
Q gi|254780814|r  627 DQEINVSLASKLANRLNFIAEKS-----EKSWHGSINNSDILVKRIARGVQEQFVLEGSSIFSFGSKYKRIFSNRIEENY  701 (803)
Q Consensus       627 d~~~~~~~~~~l~~~l~~~~~~~-----~~~~~~~~~~~~i~~~~~~~Gv~~~~~l~~~~~~s~~~~~~~~~~~~l~~~~  701 (803)
T Consensus       638 ~~~~~~~~~~~~~y~~~~~E~~~~~~~~~~~~~~~~~~f~~~v-vR-~G~~~~~~L~~~q~~~~e~~~~~~~~~~~~~~~  715 (818)
T TIGR01059       638 YESAVKYWLQGALYIYSDKEKEEAKTQLPVHKNAEKELFESSV-VR-HGLDTDYILEKEQLELFEYGEIISLELSLQGLF  715 (818)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHE-EE-CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             1468888999999887556578888742235677887541211-44-377632001666643323454344211034554


Q ss_pred             CCCEEEEECCCEEEECCHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHCCCCHHHCEEEEEEHHHHHHHHHHHHHHC
Q ss_conf             45502765582587399899999999863067628603777788955722303896134021236798898887865641
Q gi|254780814|r  702 LTILSLICNGDKIKITGPCSLLDTIFSIGRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLM  781 (803)
Q Consensus       702 ~~~~~l~~~~~~~~i~s~~el~~~i~~~gkKG~sIQRYKGLGEMNPeQLWETTMDP~tRtLLqV~IeDa~~Ad~iF~~LM  781 (803)
T Consensus       716 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~iQRYKGLGEMna~QLWETTMdP~~R~L~~V~~~DA~~AD~~F~~LM  795 (818)
T TIGR01059       716 ETRAKLIRKNKKFEINSLEEALDKLVELGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLM  795 (818)
T ss_pred             HHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHCCCCCCCEEEEEEHHHHHHHHHHCCCCC
T ss_conf             43432100122310025899999998407898604543166667822203342884644487745799988654320006


Q ss_pred             CCCCCCHHHHHHHHHHHC-CCCC
Q ss_conf             899876289988524412-3669
Q gi|254780814|r  782 GDEVEPRREFIQENSLPS-ALDI  803 (803)
Q Consensus       782 GD~VEPRReFIe~NAL~v-NLDI  803 (803)
T Consensus       796 Gd~VePRR~FIE~nAl~v~nLDv  818 (818)
T TIGR01059       796 GDEVEPRREFIEANALDVKNLDV  818 (818)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             89865307899999998852489