HHsearch alignment for GI: 254780327 and conserved domain: TIGR01054

>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=97.46  E-value=0.0036  Score=45.26  Aligned_cols=346  Identities=20%  Similarity=0.243  Sum_probs=199.5

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-------HCCCCCCHHHHHHHHHHCCCC--EEEECCCCCHH-HHHHHHHH
Q ss_conf             999999973998889669999999999576-------608768447999999970794--50673368068-99999999
Q gi|254780327|r   51 SEFKERINNGETLDDLLVPAFAVVREVARR-------TLGMRPFDVQLLGGMILHKGC--VAEMKTGEGKT-LAAVLPVY  120 (890)
Q Consensus        51 ~~~~~~~~~g~~l~~~l~eafa~~rea~~R-------~lg~~~~dvQl~g~~~l~~g~--iaem~TGEGKT-L~a~l~~~  120 (890)
T Consensus        44 ~~vc~~Lr~~~TL~~~-~K~~~~~~~~~k~f~~FF~~~~G~~pws~Qk~WAKRv~~~~SFai~APTGVGKttFG~~mslf  122 (1843)
T TIGR01054        44 LKVCRALRKEKTLKAY-LKEYCSLDEELKEFEEFFKKAVGSEPWSIQKSWAKRVLKGDSFAIVAPTGVGKTTFGLVMSLF  122 (1843)
T ss_pred             HHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             9999999605872112-155433789999999999997188843567999999641796489805887677999999999


Q ss_pred             HHHHCCCCCEEECCCCHHHHHHHHHHHHHHHHHCCC----EEEECCCCCHHHHHHH------CCCCCCCCCCCCCCCCCC
Q ss_conf             986079995697469277387599999999882943----6763598798899740------256353344343211122
Q gi|254780327|r  121 LNALSGKGVHVVTVNDYLARRDSNTMSAIYKFLGLS----TGVVFHDLSDDKRRAA------YACDITYITNNELGFDYL  190 (890)
Q Consensus       121 lnal~g~~vhvvTvNdyLA~RDa~~m~~~y~~lgls----vg~~~~~~~~~~r~~~------Y~~di~Y~t~~e~gfDyL  190 (890)
T Consensus       123 lA~kKGkR~y~ilPT~lLv~Qv~~kl~~~~~k~g~~~~~l~~~yhS~L~~~~kke~~Eri~~GDfdilitT~~FL-----  197 (1843)
T TIGR01054       123 LAKKKGKRSYIILPTTLLVKQVAEKLSSLAEKEGVGIVRLLGAYHSKLSTKEKKEVKERIENGDFDILITTSMFL-----  197 (1843)
T ss_pred             HHHHCCCEEEEEECHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCEEEEHHHHHHH-----
T ss_conf             865429878999470788999999987520025750000222101126545678899987318917861224688-----


Q ss_pred             HHHHHHCHHHHC-CCCCCEEEEECCHHHHHHHHCC---CEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEC--CCC-CCC
Q ss_conf             143200002210-2667438861203545643024---215238876524787874345443013551441--444-432
Q gi|254780327|r  191 RDNMQYRRVDMV-QRGHNFAIVDEVDSIFIDEART---PLIISGPVEDHSDLYRTIDSIIIQLHPSDYEID--EKQ-RTV  263 (890)
Q Consensus       191 rDnm~~~~~~~v-~r~~~~aivDEvDSiLiDeart---PLiIsg~~~~~~~~~~~~~~~~~~l~~~dy~id--~~~-~~v  263 (890)
T Consensus       198 ~----K~~~~L~~~y~F~liFVDDVDa~Lk~-skNVD~~L~LlGF~eE---~i~~a~~~i~L~~k~-~k~~~~~~~~~~~  268 (1843)
T TIGR01054       198 S----KNFDKLKNQYKFDLIFVDDVDALLKA-SKNVDKILKLLGFSEE---LIEKAYELIKLKLKE-NKLEEDLAREKIV  268 (1843)
T ss_pred             H----HHHHHCCCCCEEEEEEEECHHHHHHC-CCCHHHHHHHHCCCHH---HHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_conf             8----76651789851448997153676316-5556677755178899---999999999998876-4357788888886


Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEECCCCCCCCCCCCCHHH
Q ss_conf             20146799998631016884524757600133899999999999985269731610893789755458515686211234
Q gi|254780327|r  264 HFSEKGTERIEELLHGENLLKSGGLYSFENVAIVHLINNALKSHTLFLRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQ  343 (890)
Q Consensus       264 ~lt~~G~~~~e~~~~~~~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~~Yiv~~~~v~ivDe~TGr~~~gr~~~~Gl  343 (890)
T Consensus       269 ~R~E~~~~~LE~----------------------~~r~~~~~a~~~~krGr~------g~LivsSATG~prG~r------  314 (1843)
T TIGR01054       269 VRLEARKKLLEA----------------------KRRLEKLEAEIKKKRGRK------GVLIVSSATGKPRGKR------  314 (1843)
T ss_pred             HHHHHHHHHHHH----------------------HHHHHHHHHHHHHCCCCC------EEEEEEECCCCCCCCH------
T ss_conf             467888999999----------------------999898776474324886------4699985148887613------


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHCCC-CCCHHHHHHHHHHHCC-CEEEECCCCCEEEEECHHHHCCCH
Q ss_conf             89999997302484312566434889983032000013-4305489999987199-679807899622430203422377
Q gi|254780327|r  344 HQALEAKERVKIQPENQTLSSITFQNYFLKYRKLSGMT-GTASTEAEELANIYNL-DVIEVPTNVPVIRIDEHDEIYRTS  421 (890)
Q Consensus       344 hQaieaKe~v~i~~e~~t~a~it~qn~Fr~y~kl~GmT-GTa~te~~Ef~~iY~l-~v~~iPtnkp~~r~d~~d~v~~t~  421 (890)
T Consensus       315 ---------------------------~~LFR~LL~FevG~~~~--------~GLRnvvD~y~~~~d-------------  346 (1843)
T TIGR01054       315 ---------------------------VKLFRELLGFEVGKGSD--------TGLRNVVDVYEEDED-------------  346 (1843)
T ss_pred             ---------------------------HHHHHHHCCCCCCCCCC--------CCCCCEEEEEECCCC-------------
T ss_conf             ---------------------------36536552710057642--------233213885114888-------------


Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEHHH---HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC
Q ss_conf             8899999999999974099079861116---7899999999860771022310224778888875305587048875024
Q gi|254780327|r  422 EEKYAAIIAEIIDSHKKGQPVLVGTPSI---EKSEYLASQLRKHKFTKFQILNALYHEKEAYIISQAGIPGAVTIATNMA  498 (890)
Q Consensus       422 ~~k~~ai~~~i~~~~~~grpvLvgt~sv---e~Se~ls~~L~~~~~~~h~vLNAk~~~~Ea~Iia~AG~~g~vTiATNMA  498 (890)
T Consensus       347 -~v~E~~~~sve~v~~LG~GGlVyvs~~yG~e~a~ei~~~L~~~Gv-~A~~~~~~k~~~~~~~F----~~GE~dVliG~a  420 (1843)
T TIGR01054       347 -GVKEKLLESVELVKKLGKGGLVYVSIDYGKEKAEEIKEFLREHGV-KAVAYHAKKPKEDLEKF----AEGEIDVLIGVA  420 (1843)
T ss_pred             -CHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCC-EEEEEEECCCCCCHHHH----HCCCEEEEEEEE
T ss_conf             -446889999999998479439997122255899999999985794-79998403773203466----348513687710


Q ss_pred             C
Q ss_conf             4
Q gi|254780327|r  499 G  499 (890)
Q Consensus       499 G  499 (890)
T Consensus       421 ~  421 (1843)
T TIGR01054       421 S  421 (1843)
T ss_pred             C
T ss_conf             1