HHsearch alignment for GI: 254780306 and conserved domain: TIGR01057

>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739 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. This entry describes topoisomerase I from archaea, which is more closely related to bacterial than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. 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=100.00  E-value=0  Score=1017.61  Aligned_cols=585  Identities=32%  Similarity=0.498  Sum_probs=488.7

Q ss_pred             EECCHHHHHHHHHHHCCC----------------------CEEEEEECCCEECCCCCC---CCCC--CCCCCEEEEECCC
Q ss_conf             977904787788750899----------------------899994251100786557---8676--6674406887765
Q gi|254780306|r    5 IVESPAKAKTISKYLGSN----------------------YKVLSSFGHIRDLPAKKG---SVLP--EKEFEMIWNIDPS   57 (837)
Q Consensus         5 IvEsP~kak~I~~~Lg~~----------------------y~V~as~GHirdLp~~~~---~v~~--~~~f~p~y~v~~~   57 (837)
T Consensus         1 iaEKP~~A~KIA~AL~~~~G~~kks~~gVpYye~~rdGk~i~vasavGHLfgL~~~~~k~Fg~~PvFD~eW~Pi~~~dkg   80 (637)
T TIGR01057         1 IAEKPKVAKKIAGALSDDRGVLKKSLYGVPYYEVVRDGKKIIVASAVGHLFGLAPKSRKVFGEYPVFDIEWVPIFEIDKG   80 (637)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCEEECCCCCCEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf             98871158999862056777302116875407898779179985153315688865554358877321123305676067


Q ss_pred             H---HHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC-CCCHH
Q ss_conf             4---8999999999870998999469970257999999999755125788716999980379899999986226-46989
Q gi|254780306|r   58 S---QKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR-DINLD  133 (837)
Q Consensus        58 ~---kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r-~~d~~  133 (837)
T Consensus        81 kgY~~~Y~~~L~~l~~~a~~y~~AcDYDiEG~lIGf~alky~C---g~~~~~A~RMkFStLt~~di~rAy~n~e~~~dyg  157 (637)
T TIGR01057        81 KGYVKKYIKALSKLAKGADEYIVACDYDIEGELIGFKALKYAC---GVEKLKAKRMKFSTLTKKDIRRAYKNPEIEIDYG  157 (637)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHHC---CCCCHHCCCCCCCCCCHHHHHHHHHCCCCEECHH
T ss_conf             1368999999998512354356762103565307678987508---8640001334300023799999973889443032


Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHC---CCC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEE
Q ss_conf             999999999989874011378988641---467---65342268999999999999641376544001223315799654
Q gi|254780306|r  134 LVNAYLARRALDYLVGFNLSPILWQKL---PGA---RSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKF  207 (837)
Q Consensus       134 Lv~A~~aRr~lD~lvG~~lSp~L~rk~---~~~---lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f  207 (837)
T Consensus       158 ~v~AG~ARhiLDw~fGvN~SRALm~A~r~a~gr~v~LS~GRVQ~PtL~~l~eRe~EI~~F~P~pywvi~~~~~~-gG~~~  236 (637)
T TIGR01057       158 MVDAGAARHILDWYFGVNLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREIKKFVPKPYWVIKALLEK-GGGVF  236 (637)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC-CCCEE
T ss_conf             21113056777888534287899999999729989995176520799999988999852899830267785406-88558


Q ss_pred             EEEEEEECCEEECCCCHHHHHHHHHHHHHHCCC-CCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             223310358330331011356667776420015-6301000023322246852103799999887608889999999987
Q gi|254780306|r  208 TAHLTDFNGQRIEKKSISNKKEADDLISFVKKA-TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQK  286 (837)
Q Consensus       208 ~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~  286 (837)
T Consensus       237 ~A~~--------~~~K~~~~e~a~~i~~~~~~~~~~~V~~v~~~~~~~~PP~pFdLGtLQ~EAy~~fG~sPk~Tq~IAq~  308 (637)
T TIGR01057       237 KAES--------EKEKIWKEEEAKSILEEVKKSKSAKVEEVRVKRSILKPPPPFDLGTLQREAYRVFGFSPKKTQEIAQE  308 (637)
T ss_pred             EEEC--------CCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             7522--------57874124655568886167988423324553111683259875525899998607996446899999


Q ss_pred             HHCCCCCCCHHHHHHHHCCCCCCCCCHHH--HHHHHHHHHH--HCCC--CCCC---C--CCCCCCCCCCCCCCCCCCEEE
Q ss_conf             62135567212245531475544443056--8999976552--0011--2376---3--111125566688777652477
Q gi|254780306|r  287 LYEGIDVNGEIVGLITYMRTDGVHMSPDA--LEAVRRSITS--HYGD--HYLP---E--KPRIYSSKSKNAQEAHEAIRP  355 (837)
Q Consensus       287 LYE~~~~~~~~~GlITYpRTDS~~ls~ea--~~~~r~~i~~--~~g~--~~l~---~--~~r~y~~k~k~aQeAHeAIrP  355 (837)
T Consensus       309 LY~--------~al~SYPRT~SQKLP~~i~Y~~il~nLakn~P~yr~~~e~L~~~G~~LkPve-GkKe---DpAHPAIhp  376 (637)
T TIGR01057       309 LYE--------EALISYPRTSSQKLPKSINYRKILKNLAKNNPLYREYAERLLEKGGELKPVE-GKKE---DPAHPAIHP  376 (637)
T ss_pred             HHH--------CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCC-CCCC---CCCCCCCCC
T ss_conf             864--------2351588787667888778799999997248984689999871678878857-8779---667886005


Q ss_pred             EECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHH-CCCCCC
Q ss_conf             3023464000001999999999999999999852221100100136774079639999987488058856763-267776
Q gi|254780306|r  356 NDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVW-ENQYDQ  434 (837)
Q Consensus       356 T~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy-~~~~~~  434 (837)
T Consensus       377 tG~--~P~~--G~LSk~e~~vYdLIvrRfLA~F~~~Ai~~~~~V~l~~~~G---~~F~~sG~Rv~k~GWl~~YG~Y~k~-  448 (637)
T TIGR01057       377 TGE--IPSE--GELSKDEKKVYDLIVRRFLAVFSEEAIREKLKVELRIGEG---EKFKLSGKRVVKKGWLEVYGKYSKF-  448 (637)
T ss_pred             CCC--CCCC--CCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCC---EEEEECCCCEEECCCCCCCCCCCCC-
T ss_conf             678--8888--8777788999989987887511510214334378982387---0698415612103630017666888-


Q ss_pred             CCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEEC
Q ss_conf             32100101488645688211001101112346431017899874332102566551578999997322022147712220
Q gi|254780306|r  435 EKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQ  514 (837)
Q Consensus       435 ~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT  514 (837)
T Consensus       449 -----~e~~lPel~~Gd~~~V~~v~~~~~~t~pP~Ry~~ASlir~lE~~glGTkaTRA~Ii~~Ly~RgY~eG-~~~~~Vt  522 (637)
T TIGR01057       449 -----EEKELPELKRGDKIKVVRVKVEKKETKPPARYDKASLIRELEKRGLGTKATRAEIIEKLYKRGYIEG-KKSIKVT  522 (637)
T ss_pred             -----CCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCEEEC-CCEEEEC
T ss_conf             -----8754888888886899998864540686876657789899872588841038999998711731541-8634652


Q ss_pred             CHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             11420000223366556898899999999999862601347899998676766557667755666776556766410245
Q gi|254780306|r  515 NTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFP  594 (837)
Q Consensus       515 ~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~  594 (837)
T Consensus       523 PLG~~vi~tl~~y~peii~~~LTR~fE~~lE~I~~Gr~~k~~Videa~~~~~kiLe~f~~~-~~~ig~el~~~----~~~  597 (637)
T TIGR01057       523 PLGEAVIETLKRYCPEIISEELTREFEKKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKR-LEDIGIELAKS----LDS  597 (637)
T ss_pred             CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH----HCC
T ss_conf             4505899999873410068132389999988875078666789999899999988999988-99998998887----312


Q ss_pred             CC-CCCCCCEECCCCCCCCEEEEEECCC-CCCCCCCCCCCC
Q ss_conf             55-5676611433467773136871577-611123434323
Q gi|254780306|r  595 PK-ENNEDSRTCPECHTHSLSLKLSSKY-GAFVGCTNYPEC  633 (837)
Q Consensus       595 ~~-~~~~~~~~Cp~C~~g~L~~k~~gK~-G~FigCSnyPeC  633 (837)
T Consensus       598 ~~e~K~~vvg~CP~CGG-~lv~ky~~~~~~rFvgCS~yp~c  637 (637)
T TIGR01057       598 SEEKKAKVVGKCPKCGG-KLVVKYAKKGRKRFVGCSNYPEC  637 (637)
T ss_pred             CCCCCCEEEECCCCCCC-CEEEEEECCCCCEEECCCCCCCC
T ss_conf             23324505523778887-34898606888412115788899