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