HHsearch alignment for GI: 254780353 and conserved domain: TIGR01062

>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742 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 negative 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=1661.97  Aligned_cols=733  Identities=41%  Similarity=0.737  Sum_probs=703.8

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 iE~~~l~~~~~~~YL~Y~~~~IM~RaLP~i~DGLKPV~RR~~YAM~~L~L~a~a~yKKsAR~VGDVlGKyHPHGD~A~Y~   80 (747)
T TIGR01062         1 IENLDLRNFTEEAYLNYSLYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDVLGKYHPHGDSAVYE   80 (747)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEECCCCCCCCCCCCHHHHH
T ss_conf             97651578988888888888887423772025775146899888887164767775200102102124605896248999


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHH
Q ss_conf             999610013216613267887088677-9710024689985599999984218786175216799632422312345267
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDG-DSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNL  175 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~-d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~l  175 (753)
T Consensus        81 ~~V~~AQ~FS~RYPLvDGQGN~Ga~DdP~~~AAMRYTESRl~~~s~lLl~~l~~~TvD~~~~fD~~~~EP~~lPA~lP~~  160 (747)
T TIGR01062        81 ALVLLAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISELLLEELGQGTVDFRPNFDGTLLEPKILPARLPNI  160 (747)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             99986211123476201677868898742123433246678999999998618872133457887424644253112055


Q ss_pred             HHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEE
Q ss_conf             64266504677775167778899999999987286532013443203677887760106988999898503341599999
Q gi|254780353|r  176 LANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRAR  255 (753)
Q Consensus       176 L~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k  255 (753)
T Consensus       161 L~NG~~GIAVGMAT~IPPHNl~E~adA~~~LiD~P~agl~d~l~~v~GPDfPT~a~II~~~~~I~~~Y~~GRGS~r~Ra~  240 (747)
T TIGR01062       161 LLNGTTGIAVGMATDIPPHNLRELADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKKEEIRKIYETGRGSVRMRAR  240 (747)
T ss_pred             HCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHCCCCEEEEEEE
T ss_conf             60688724752217888623799999999985288321689999734857898765747189999998569833897226


Q ss_pred             EEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCC--EEEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             99864378840799952420021689999999986402221345776406766--0588985045458899999875420
Q gi|254780353|r  256 WCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAED--VRIVLFPKNRSLDPDLLMESIFMLS  333 (753)
Q Consensus       256 ~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~--~~~vi~~~~r~~~~~~vl~~Lyk~T  333 (753)
T Consensus       241 W~KE~~syGty~ivi~~lP~Q~~~sk~i~QIA~~~~~KKlP~~~~iRDEsDH~~~iR~Vi~PR~~~~D~~~vM~~LF~~T  320 (747)
T TIGR01062       241 WKKEDGSYGTYQIVISALPHQISKSKVIEQIAIQLKDKKLPLISDIRDESDHENPIRVVIVPRSNRVDPDIVMEHLFATT  320 (747)
T ss_pred             EEECCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             53014666502676522775354015889999999717887024203423677856899843887768799999986542


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             00012233113331268972204999999899998999999999999999999999999998641078999975200001
Q gi|254780353|r  334 DMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKP  413 (753)
Q Consensus       334 ~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~~  413 (753)
T Consensus       321 ~LE~~~~~N~N~IG~~~~P~V~nlLEIL~E~L~fR~~~v~RR~~Y~L~Kv~~RL~IL~~L~i~fLN~DEvIEIIR~EDeP  400 (747)
T TIGR01062       321 DLEKSYRLNMNMIGLDNKPAVKNLLEILQEWLVFRRNTVIRRLTYRLNKVLKRLHILEGLLIAFLNIDEVIEIIREEDEP  400 (747)
T ss_pred             CHHHHEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC
T ss_conf             20011233224640698960454899999999855888787888779999989988764755202100101222379984


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       401 K~~lM~RF~ls~~Q~e~IL~~rLR~L~KLEE~~i~~E~~~L~K~~~~L~~IL~~~~~l~~l~KKEi~~~~~~yg~ntiiG  480 (747)
T TIGR01062       401 KTILMERFKLSEIQAEAILNLRLRHLAKLEEHKIKDEQSELEKERAILEKILKSERKLNQLVKKEIQADAKKYGLNTIIG  480 (747)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEC
T ss_conf             28998550635899999986555565457788887656677899999999987568999999899999998740242203


Q ss_pred             CCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEE
Q ss_conf             55420000110000001100245667059987101020256554455322345555540121111478178980688278
Q gi|254780353|r  494 RRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAY  573 (753)
Q Consensus       494 ~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY  573 (753)
T Consensus       481 ~R~~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~D~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y  560 (747)
T TIGR01062       481 ARRSSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDIDLSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSY  560 (747)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEE
T ss_conf             55451356788888876653036788179982777355046656671435413686123345512775179997288526


Q ss_pred             EEEHHHCCCCCCCCCCCCCCCCCCCC-CEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCEEE
Q ss_conf             75511212123444422223576765-30789998579985999974897899638874023335627885368980568
Q gi|254780353|r  574 TLPAGNLLSGRGHGEAIQLLIDLNHN-QDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKL  652 (753)
Q Consensus       574 ~l~a~~Ips~~~kG~pI~~ll~l~~~-EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~li~  652 (753)
T Consensus       561 ~l~~~~l~~a~g~G~Pl~~KL~l~~Gn~~i~~~l~~~~~Q~LL~AS~~G~GF~~~~~~liA~~k~GK~l~~lPE~~~~~~  640 (747)
T TIGR01062       561 ALDPLNLPSARGQGEPLTGKLLLPIGNATIENILMESENQKLLLASDAGYGFLVKFNDLIARNKAGKALINLPENASVLA  640 (747)
T ss_pred             EECCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCEEEECHHHHHHCHHCHHHCCCCCCCEEEC
T ss_conf             63112043456778722688732688623107776358853210001686247400433331100402001788861104


Q ss_pred             EEECCCCE--EEEEECCCCEEEEEHHHCCCCCHHHCCEEEECCC-------CCEEEEEEEECCCCCEEEEECCCCCCCCC
Q ss_conf             89618980--9999569938995578778336121413342187-------87568999733888369994177566451
Q gi|254780353|r  653 VVKVTGDH--VAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKD-------GGISDVICFKICEGLTWIDSAGRSYNRSE  723 (753)
Q Consensus       653 v~~~~~d~--iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lkd-------~~~~~~~~~~~~e~~~il~~t~~g~~k~~  723 (753)
T Consensus       641 p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~KG~G~~~~~~~~a~A~~~~~~L~~l~~~~~Q~~L~~~-~Gk~KI~L~~  719 (747)
T TIGR01062       641 PLVVNDDSDLIVAITEAGRLLVFPIDDLPELSKGKGNKLIRIPAANAKDREELLLDLKILNKQDGLSFN-DGKRKIKLKP  719 (747)
T ss_pred             CEEECCCCCEEEEECCCCEEEEECHHHCCCCCCCCCCEEEEECCHHHCCCCCCCEEEEEECCCCCEEEC-CCCEEEEECH
T ss_conf