HHsearch alignment for GI: 254780327 and conserved domain: TIGR01389

>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=92.91  E-value=0.87  Score=25.81  Aligned_cols=337  Identities=21%  Similarity=0.319  Sum_probs=187.8

Q ss_pred             HHHCC---CCCCHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             76608---768447999999970794506733680689999999998607999569746927738759999999988294
Q gi|254780327|r   79 RRTLG---MRPFDVQLLGGMILHKGCVAEMKTGEGKTLAAVLPVYLNALSGKGVHVVTVNDYLARRDSNTMSAIYKFLGL  155 (890)
Q Consensus        79 ~R~lg---~~~~dvQl~g~~~l~~g~iaem~TGEGKTL~a~l~~~lnal~g~~vhvvTvNdyLA~RDa~~m~~~y~~lgl  155 (890)
T Consensus         6 ~~~FGY~~FR~gQe~II~~vL~g~~~l~vmPTGGGKSlCYQ~PALl--l~Glt~-VISP---LIsLMkDQVd~-L~~~Gv   78 (607)
T TIGR01389         6 KETFGYDDFRGGQEEIIEHVLDGRDVLVVMPTGGGKSLCYQVPALL--LKGLTV-VISP---LISLMKDQVDQ-LRAAGV   78 (607)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHH--HCCCEE-EECC---HHHHHHHHHHH-HHHCCC
T ss_conf             4446877677315899999847798589738998512777217887--289879-9842---36314779999-986070


Q ss_pred             CEEEECCCCCHHHHHHHC------CCCCCCCCCCCCCCCCCHHHHHHCHHHHCCCCCCEEEEECCHHHHHHHHCCCEEEC
Q ss_conf             367635987988997402------56353344343211122143200002210266743886120354564302421523
Q gi|254780327|r  156 STGVVFHDLSDDKRRAAY------ACDITYITNNELGFDYLRDNMQYRRVDMVQRGHNFAIVDEVDSIFIDEARTPLIIS  229 (890)
Q Consensus       156 svg~~~~~~~~~~r~~~Y------~~di~Y~t~~e~gfDyLrDnm~~~~~~~v~r~~~~aivDEvDSiLiDeartPLiIs  229 (890)
T Consensus        79 ~Aa~lNSt~s~~E~~~i~~~~~~G~~~LLYvAPERL~~~~Fl~~L~~~~-------i~L~A--------vDEAHC---vS  140 (607)
T TIGR01389        79 AAAYLNSTLSAKEQQEIEKALVNGELKLLYVAPERLEQDYFLNMLKRLT-------IALLA--------VDEAHC---VS  140 (607)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCC-------CEEEE--------EECCCC---CC
T ss_conf             1452037788889999999984198157751671321189998873199-------30899--------832502---16


Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             88765247878743454430135514414444322014679999863101688452475760013389999999999998
Q gi|254780327|r  230 GPVEDHSDLYRTIDSIIIQLHPSDYEIDEKQRTVHFSEKGTERIEELLHGENLLKSGGLYSFENVAIVHLINNALKSHTL  309 (890)
Q Consensus       230 g~~~~~~~~~~~~~~~~~~l~~~dy~id~~~~~v~lt~~G~~~~e~~~~~~~~~~~~~l~~~~~~~~~~~i~~al~A~~~  309 (890)
T Consensus       141 QWGHDFRPeY~~L~~l~~~-------------------------------------------------------------  159 (607)
T TIGR01389       141 QWGHDFRPEYRRLGELAER-------------------------------------------------------------  159 (607)
T ss_pred             CCCCCCCHHHHHHHHHHHH-------------------------------------------------------------
T ss_conf             6888875658999999986-------------------------------------------------------------


Q ss_pred             HHCCCCEEEECCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHCCCCCCHHH-H
Q ss_conf             526973161089378975545851568621123489999997302484312566434889983032000013430548-9
Q gi|254780327|r  310 FLRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLSSITFQNYFLKYRKLSGMTGTASTE-A  388 (890)
Q Consensus       310 ~~~d~~Yiv~~~~v~ivDe~TGr~~~gr~~~~GlhQaieaKe~v~i~~e~~t~a~it~qn~Fr~y~kl~GmTGTa~te-~  388 (890)
T Consensus       160 -------------------------------------------------------------fp~~P~~iALTATAd~~t~  178 (607)
T TIGR01389       160 -------------------------------------------------------------FPQVPTRIALTATADAETR  178 (607)
T ss_pred             -------------------------------------------------------------CCCCCEEEEEECCCCHHHH
T ss_conf             -------------------------------------------------------------7898669987248998789


Q ss_pred             HHHH---HHHCCCEEEECCCCCEEEEECHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999---8719967980789962243020342237788999999999999740990798611167899999999860771
Q gi|254780327|r  389 EELA---NIYNLDVIEVPTNVPVIRIDEHDEIYRTSEEKYAAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFT  465 (890)
Q Consensus       389 ~Ef~---~iY~l~v~~iPtnkp~~r~d~~d~v~~t~~~k~~ai~~~i~~~~~~grpvLvgt~sve~Se~ls~~L~~~~~~  465 (890)
T Consensus       179 ~DI~~~L~L~~~~~f~~SFdRpNl~~~v~-----~k~n~~~~l~~yl-~~~~~G~SGIIYa~sR~~VE~~~~~L~s~G~-  251 (607)
T TIGR01389       179 QDIVELLRLKDANEFISSFDRPNLRFSVV-----KKNNKKKFLLEYL-KKHREGQSGIIYASSRKKVEELAERLESQGI-  251 (607)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCHHHHHHHH-----HHCCCCHHHHHHH-HCCCCCCCEEEECCCHHHHHHHHHHHHHCCC-
T ss_conf             99999708898654125677511433431-----2037813689997-5079995347876770458999999974796-


Q ss_pred             HHHHHHHHHHH------HH----HHHHHHCCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             02231022477------88----888753055870488750244665540276755788865113575530089999999
Q gi|254780327|r  466 KFQILNALYHE------KE----AYIISQAGIPGAVTIATNMAGRGTDIQLGGNVAMRIEHELANISDEEIRNKRIKMIQ  535 (890)
Q Consensus       466 ~h~vLNAk~~~------~E----a~Iia~AG~~g~vTiATNMAGRGTDI~Lgg~~~~~~~~~~~~~~~~~~~~~~~~~~~  535 (890)
T Consensus       252 ~A~----~YHAGL~~~~R~e~Q~~Fl~----d~~~vmVAT~AFGMGId--------------------------------  291 (607)
T TIGR01389       252 SAL----AYHAGLSNKVRAENQEDFLY----DDVKVMVATNAFGMGID--------------------------------  291 (607)
T ss_pred             CEE----ECCCCCCHHHHHHHHHHHHH----HCCEEEEEEECCCCCCC--------------------------------
T ss_conf             204----03679877689999754446----25548888712358747--------------------------------


Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHCCCCCCCCCCCCEEEEEECCCHHHHHHCCHHHHHHHHHHCCCCC-CC
Q ss_conf             98776433345407627998267753233554205434566867238998423014542021013445421002566-62
Q gi|254780327|r  536 EEVQSLKEKAIVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQDDLMRIFGSPRMESFLRKIGLKEG-EA  614 (890)
Q Consensus       536 ~~~~~~~~~v~~~GGL~VigterhesrRid~QlrGRagRQGdpG~s~f~~SleD~l~r~Fgsdri~~lm~klg~~eg-ep  614 (890)
T Consensus       292 ------KpnVR-----FViH~d~P~~~EsYYQE~GRAGRDGlpae~~lly~~~D~~l~-------~~~I~~s~~~~~~K~  353 (607)
T TIGR01389       292 ------KPNVR-----FVIHADMPKNIESYYQEAGRAGRDGLPAEAILLYSLADIALL-------KRFIEQSEADEDRKQ  353 (607)
T ss_pred             ------CCCCC-----EEEEECCCCCHHHHHCCCCCCCCCCCHHHHHHHCCHHHHHHH-------HHHHHCCCCCHHHHH
T ss_conf             ------87654-----888636874211131035546887526778672477789999-------999741588488999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             1456799999999
Q gi|254780327|r  615 IIHPWINKAIERA  627 (890)
Q Consensus       615 Ies~~itksIE~A  627 (890)
T Consensus       354 ~e~~KL~~m~~y~  366 (607)
T TIGR01389       354 IEREKLDAMLAYC  366 (607)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999988