HHsearch alignment for GI: 254780353 and conserved domain: TIGR01061

>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741 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 . This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1782.33  Aligned_cols=722  Identities=32%  Similarity=0.543  Sum_probs=682.5

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHH
Q ss_conf             66531999999888888899985104764112897046899999998689998980354053666542768874789999
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYD   96 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~   96 (753)
T Consensus         1 ~~~~~Le~v~g~~F~kYaKYIIQDRALPD~RDGLKPVQRRILYaM~~~G~~fdk~YkKSAr~VGev~GkYHPHGDSSiYd   80 (745)
T TIGR01061         1 IINLPLEEVVGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMSEDGNTFDKPYKKSARTVGEVIGKYHPHGDSSIYD   80 (745)
T ss_pred             CCCCCHHHHHHCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHH
T ss_conf             97875035440000000251340456665111577035778766532378668870012011102226712898644778


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHH
Q ss_conf             99961001321661326788708867797100246899855999999842187861752167996324223123452676
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLL  176 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL  176 (753)
T Consensus        81 AmvRMSQ~WKn~~~lv~mHGNnGSiDGDnaAAMRYTEaRLS~iA~~LL~di~K~~V~F~~NFDDseKEP~vLP~lfPNLL  160 (745)
T TIGR01061        81 AMVRMSQDWKNNLVLVEMHGNNGSIDGDNAAAMRYTEARLSKIASELLKDIDKKTVKFIPNFDDSEKEPTVLPALFPNLL  160 (745)
T ss_pred             HHHHCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             86414746334318998506667889985155432476677999999740477831033687788877742344213456


Q ss_pred             HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             42665046777751677788999999999872865320134432036778877601069889998985033415999999
Q gi|254780353|r  177 ANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARW  256 (753)
Q Consensus       177 ~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~  256 (753)
T Consensus       161 iNGatGIaAGYATnIpPHn~~Ev~Da~i~rId~P~c~v~~L~e~~kgPDFPTGG~i-~~~~~~~~aY~tGkGk~iirak~  239 (745)
T TIGR01061       161 INGATGIAAGYATNIPPHNLNEVIDALIYRIDHPDCSVDKLMEIVKGPDFPTGGII-QGEDGIKKAYETGKGKFIIRAKI  239 (745)
T ss_pred             HHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCEE-ECHHHHHHHHHCCCCEEEEEEEE
T ss_conf             52013320000047788876689999986138988417889854484115887246-14154788985498139998642


Q ss_pred             EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             98643788407999524200216899999999864022213457764067660588985045458899999875420000
Q gi|254780353|r  257 CVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDME  336 (753)
Q Consensus       257 ~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq  336 (753)
T Consensus       240 ~~e~~~ng~~QI~It~IPYE~nKAnlvK~iedi~~d~kv~gi~eVrDeSDr~GlriiI~~Kk~~~~e~v~nyLyK~T~Lq  319 (745)
T TIGR01061       240 EIEVNKNGLNQIVITEIPYETNKANLVKKIEDIIVDKKVAGIEEVRDESDRKGLRIIIELKKDANAEKVLNYLYKKTDLQ  319 (745)
T ss_pred             EEEEECCCCCEEEECCCCHHHHHHHHEEEEEEEEECCEEHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCCCE
T ss_conf             55320588204897457467766764000002676450000010034457575546560545247556787541343543


Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CC
Q ss_conf             122331133312689722049999998999989999999999999999999999999986410789999752000---01
Q gi|254780353|r  337 TRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNED---KP  413 (753)
Q Consensus       337 ~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~---~~  413 (753)
T Consensus       320 i~YN~n~vaI~-nr~P~lv~L~~yLd~yi~h~~evi~~~~~Ydl~ka~~R~~IveGLik~isilDeiI~~IRas~~k~DA  398 (745)
T TIGR01061       320 INYNFNMVAIA-NRTPILVGLLSYLDAYIKHSKEVIINRSLYDLEKAKKRLEIVEGLIKAISILDEIIKLIRASEDKSDA  398 (745)
T ss_pred             EEECCCCEEEC-CCCCEEECHHHHHHHHHHHHHHHEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCH
T ss_conf             86432417840-47633644016888887230232002464238889878898888999999987898877302453360


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             10000002577577889988789999889999766678999988776544203978878999999999987417743345
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLG  493 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~  493 (753)
T Consensus       399 k~~Li~~f~FT~~QAEAIv~LrLY~LTnTDi~~L~~E~~eL~~~~~~l~~~i~~~k~~~~~lk~~l~~~KK~F~~~----  474 (745)
T TIGR01061       399 KENLIDKFEFTENQAEAIVSLRLYRLTNTDIFELKEEEEELEKKIKSLEEIIASEKARKKLLKKKLKELKKKFAQE----  474 (745)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----
T ss_conf             3431011377725799999988603732037777878999999999999987657899999899999872310575----


Q ss_pred             CCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCC-EEECCCCCCCCCC---CCCCCCCCCCEEEEEECCCCCEEEEECC
Q ss_conf             55420000110000001100245667059987101-0202565544553---2234555554012111147817898068
Q gi|254780353|r  494 RRRTTFCEVSRADKATLQQAMIEKEPITVVISNRG-WIRSLKSHSVDLS---ALHFKEGDSLKIALHAHTTDRILLLSTD  569 (753)
Q Consensus       494 ~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~G-yIKr~k~~~~~~~---~~~~KegD~l~~~~~~~t~d~LLffTs~  569 (753)
T Consensus       475 -R~s~l~~~-~~~~~i~~~~li~~~~~~v~itk~GnY~K~~S~~sf~ss~~~d~g~~~~d~l~~~~~~nttd~lL~~Ts~  552 (745)
T TIGR01061       475 -RRSKLEDE-IEKIKINEDELIEKEDLYVVITKDGNYIKRTSKRSFASSKYDDFGLKDDDILFYQTIANTTDKLLIFTSK  552 (745)
T ss_pred             -HHHHHHHH-HHHEECCHHHHHHHCCCEEEEEECCCEEHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCEEEEEECC
T ss_conf             -04567511-6530104678532146407998447630001266762047311577553345354652122537887616


Q ss_pred             CEEEEEEHHHCCCCCCC--CCCCCCCCC-CCCCCEEEEEEEE---C-CCCEEEEEECCCCEEEEEHHHHHCCC---CCCE
Q ss_conf             82787551121212344--442222357-6765307899985---7-99859999748978996388740233---3562
Q gi|254780353|r  570 GKAYTLPAGNLLSGRGH--GEAIQLLID-LNHNQDIVTAFVY---D-STCKLLVVSSKGNAFIVEESEIIANT---RKGK  639 (753)
Q Consensus       570 GkvY~l~a~~Ips~~~k--G~pI~~ll~-l~~~EkIv~~~~~---~-~~~~lll~Tk~G~ikr~~l~~~~~~~---k~Gk  639 (753)
T Consensus       553 g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fdv~~~~L~l~sklg~vKriel~~l~~~~~y~sK~~  632 (745)
T TIGR01061       553 GNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFDVDEAILVLASKLGMVKRIELTELDIKRNYRSKAI  632 (745)
T ss_pred             CCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHH
T ss_conf             66642130314566566899872000110210684899986132257468989987558747876032477865101223


Q ss_pred             EEEEECCCCCEEEEEECCC---CEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEEEEEEECCCCCEEEEEC
Q ss_conf             7885368980568896189---8099995699389955787783361-21413342187875689997338883699941
Q gi|254780353|r  640 TFLKVSSEEKMKLVVKVTG---DHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVICFKICEGLTWIDSA  715 (753)
Q Consensus       640 ~~ikLk~~D~li~v~~~~~---d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~~~~~~~~e~~~il~~t  715 (753)
T Consensus       633 ~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~GvK~mkLK~~D~v~~~~i~~~~~~~vl-l~  711 (745)
T TIGR01061       633 LILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAAGVKGMKLKEDDEVKSGLILEANESLVL-LT  711 (745)
T ss_pred             HHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCCCEEEEECCCCCEEEEEEEECCCCCEEE-EE
T ss_conf             32111789543899984188844189997368357730203323144667311330576763899999827995589-97


Q ss_pred             CCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77566451143225444136660275526776
Q gi|254780353|r  716 GRSYNRSENDLLGWLGKRGGVGSLVPKGFPRS  747 (753)
Q Consensus       716 ~~g~~k~~~~~~~~~~~RggkG~~~~k~~~K~  747 (753)
T Consensus       712 ~~Gs~k~~~~~El~~~sRa~~~~~llRp~kk~  743 (745)
T TIGR01061       712 QRGSVKRLSISELKVTSRAATGVKLLRPLKKK  743 (745)
T ss_pred             ECCCEEEEEHHHHHHHHHHCCCCHHHCCCCCC
T ss_conf             36825651036555534311651111000047