HHsearch alignment for GI: 254780991 and conserved domain: TIGR00614

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family; InterPro: IPR004589 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: 0008026 ATP-dependent helicase activity, 0006310 DNA recombination.
Probab=99.62  E-value=1.1e-12  Score=113.46  Aligned_cols=328  Identities=16%  Similarity=0.181  Sum_probs=218.5

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf             47751888888438999999998873973379986337646999999999719978999316346899999999867898
Q gi|254780991|r  141 FQMQTDYHPSGDQPAAIAQLLKGIHSREKVQLLLGVTGSGKTFTMAKVIEAMQRPAIVMAPNKILAAQLYSEFKNFFPHN  220 (805)
Q Consensus       141 f~l~~~~~P~gdQ~~Ai~~L~~~l~~g~~~qlL~GVTGSGKTevya~lI~~~gr~aLvLvPei~La~QL~~rfk~~Fp~n  220 (805)
T Consensus         7 FG~-~~Frp~--Q~e~I~~~L~----g~RD~~vvMpTG~GKSLCYQ~Pa~~~~G~t~VIsPLiSLm~DQV~~L~~-~~i~   78 (497)
T TIGR00614         7 FGL-SSFRPV--QLEVINAVLE----GRRDCLVVMPTGGGKSLCYQLPALYSDGLTLVISPLISLMEDQVLQLKA-SGIP   78 (497)
T ss_pred             CCC-CCCCHH--HHHHHHHHHC----CCCCEEEEECCCCCHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHH-CCCC
T ss_conf             574-445514--8999998754----8975699815898603676405675089649973636568999999874-4863


Q ss_pred             EEEEEEECCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHH--HCCCCEEEECCHHHHC---CCCCHH------H
Q ss_conf             3899862134444210155543210221035889999999999998--5499849982778961---689834------7
Q gi|254780991|r  221 AVEYFVSYYDYYQPEAYVPRTDTYIEKESSINEQIDRMRHSATRSL--LERNDCIVVSSVSCIY---GIGSVE------S  289 (805)
Q Consensus       221 ~V~~f~S~~~~yqpEay~p~~d~~i~k~~s~n~~i~~~R~~a~~~l--~~~~~~IVVgsrSAIf---gl~~P~------~  289 (805)
T Consensus        79 A~-~L~-------------------------s~~s~~~~~~v~~~~~~k~g~~kllYvtPE~~~~~~~ll~~Le~~Y~~~  132 (497)
T TIGR00614        79 AT-FLN-------------------------SSQSKEQQKEVLTDLSKKDGKLKLLYVTPEKISKSKSLLQTLEKLYERK  132 (497)
T ss_pred             EE-CCC-------------------------CCCCHHHHHHHHHHHHHHCCCEEEEEECHHHHHCCHHHHHHHHHHHHHC
T ss_conf             01-044-------------------------3257789999999987307975899716346534647899999988644


Q ss_pred             HHCCEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCCCCCHHHHHCCCCCCCC
Q ss_conf             72257999419811178753234311765633877545331872478317888778887310444200222101666400
Q gi|254780991|r  290 YSQMIVQLKIGDSVEQKELLSSLVKQQYKRQDIGIIRGTFRVCGDSIEIFPSHLEDVAWRVSMFGNDIEEISEFYPLTGQ  369 (805)
Q Consensus       290 ~lglIIvdEehd~~~~~~~~~~l~~~~Y~R~D~a~~RG~f~~rg~ILdsatps~Es~~~Rie~f~deIe~I~~fDplT~~  369 (805)
T Consensus       133 ~~~~iAvDEAHCiSqWGHDFR~~----Y~~--LG~Lk~~fP~vP~~ALTATA~~~~------------------------  182 (497)
T TIGR00614       133 GITLIAVDEAHCISQWGHDFRPD----YKA--LGSLKQKFPNVPIMALTATASPSV------------------------  182 (497)
T ss_pred             CCEEEEEECEEEECCCCCCCCHH----HHH--HHHHHHHCCCCCEEEEECCCCHHH------------------------
T ss_conf             96699983215435888874079----999--657888548874364340578678------------------------


Q ss_pred             HHHHCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf             11100001000000002563678875455899899899887544332110012444477775332112014510113331
Q gi|254780991|r  370 KIRNVETIKIYANSHYVTPRPTLNTAMKYIKEELKMRLIELEKEGRLLEAQRLEQRITYDLEMLETTGSCQSIENYSRYL  449 (805)
Q Consensus       370 ~~~~~~~~~i~Pa~~~v~~~e~l~~a~~~i~~el~~rl~~~~~~~~~~ea~rL~qR~~~dle~l~e~G~~~gienyS~~L  449 (805)
T Consensus       183 ------------------------------~~Di~~~L---~---------------------l~~------p~~~~~SF  202 (497)
T TIGR00614       183 ------------------------------REDILRIL---N---------------------LKN------PQVFITSF  202 (497)
T ss_pred             ------------------------------HHHHHHHH---C---------------------CCC------CCEEEECC
T ss_conf             ------------------------------99999872---2---------------------136------62464046


Q ss_pred             CCCCCCCCCHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC
Q ss_conf             14465556202330265442132101234475445432456541333235766554443222111010012155545444
Q gi|254780991|r  450 TGRNPGEPPPTLFEYIPEDSLLFVDESHVTIPQISGMYRGDFHRKATLAEYGFRLPSCMDNRPLRFEEWNCLRPTTIVVS  529 (805)
Q Consensus       450 ~~r~~ge~P~tL~dY~p~d~ll~idesh~~~pqi~~~~~~d~~RK~~l~~~gfrlp~~~~n~pl~f~e~~~~~~~~~~~s  529 (805)
T Consensus       203 ------dRPNl~y~v~~K---------------------------~----------------------------------  215 (497)
T TIGR00614       203 ------DRPNLYYEVRRK---------------------------T----------------------------------  215 (497)
T ss_pred             ------CCCCCEEEEECC---------------------------C----------------------------------
T ss_conf             ------687630340057---------------------------8----------------------------------


Q ss_pred             CCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEECCCCCHHHHHHHHHHH----HHHCCCCC-CCCCHHHHHHHHHHHHHHH
Q ss_conf             686754201322002343201244677200001331016889999998----63023212-4662147899999999863
Q gi|254780991|r  530 ATPGSWELEQCQGIIVEQIIRPTGLVDPPVEIRSARTQVEDVYDEINL----AAQQGLRI-LLTVLTKRMAEDLTEYLYE  604 (805)
Q Consensus       530 atPg~~e~e~~~~~~~eqi~rptg~idp~ieir~~~~qvddl~~ei~~----~~~~~~R~-l~~~~tkr~~e~l~~~~~~  604 (805)
T Consensus       216 --------------------------------~n~~~~~~dl~~f~~~~~~s~~~~~G~sGIIYC~SR~~~e~~a~~L~~  263 (497)
T TIGR00614       216 --------------------------------SNTKKILEDLLRFIVKKASSAWEFKGKSGIIYCPSRKKSEQVAAELQK  263 (497)
T ss_pred             --------------------------------CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCHHHHHHHHHHHH
T ss_conf             --------------------------------970258999999987520356524588302752872348999999975


Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHH-CCCCCEEEEHHHHHCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHCC-CC
Q ss_conf             5966873257645789999999973-189869998458753578777117999628856744460137766543127-99
Q gi|254780991|r  605 RNIRVRYMHSEVKTLERIEIIRDLR-LGKFDVLVGINLLREGLDIPECGLVAILDADKEGFLRSKTSLIQTIGRAAR-NV  682 (805)
Q Consensus       605 ~~i~~~~~h~~~~~~~r~~il~~~~-~g~~diLvgt~~~akGlD~p~v~lV~i~dAD~~~f~~~~~~~~q~~GRagR-~~  682 (805)
T Consensus       264 ~G~~a~aYHAGl~~~~R~~V~~~f~nrD~~QvVvATvAFGMGInKpdvRfViH~~-----~Pk~~EsYYQE~GRAGRDgl  338 (497)
T TIGR00614       264 LGIAAGAYHAGLEISARKEVQHKFQNRDEIQVVVATVAFGMGINKPDVRFVIHYS-----LPKSMESYYQESGRAGRDGL  338 (497)
T ss_pred             CCCEEEHHHCCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCEEEEEC-----CCCCCCCCCCCCCCCCCCCC
T ss_conf             5861002402688647789999875038857999872126888763536788507-----88562110135555678973


Q ss_pred             CCEEEEEECCCCHH
Q ss_conf             86699982489889
Q gi|254780991|r  683 NSKVILYADTITKS  696 (805)
Q Consensus       683 ~G~~il~ad~~t~~  696 (805)
T Consensus       339 ~s~c~lfy~~aD~~  352 (497)
T TIGR00614       339 PSECVLFYAPADIA  352 (497)
T ss_pred             CCCEEEEECHHHHH
T ss_conf             20102330435699