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