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