HHsearch alignment for GI: 254780947 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=97.04  E-value=0.037  Score=35.36  Aligned_cols=243  Identities=21%  Similarity=0.292  Sum_probs=178.6

Q ss_pred             HHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCEEE-EECHHHHCCCC----CCCCCCEEEEECHH-------HHHHH
Q ss_conf             98606789833541066630256777753122576089-85206542785----20236569972223-------30088
Q gi|254780947|r  695 SERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIV-IGTHALLNPKI----TFANLGLIIIDEEQ-------HFGVK  762 (1187)
Q Consensus       695 ~~Rf~~~pv~i~~lsRf~~~~e~~~i~~~l~~G~idiv-iGTH~ll~~~v----~f~~LgLliiDEEq-------rFGV~  762 (1187)
T Consensus        70 Vd~L~~~Gv~Aa~lNSt~s~~E~~~i~~~~~~G~~~LLYvAPERL~~~~Fl~~L~~~~i~L~AvDEAHCvSQWGHDFRPe  149 (607)
T TIGR01389        70 VDQLRAAGVAAAYLNSTLSAKEQQEIEKALVNGELKLLYVAPERLEQDYFLNMLKRLTIALLAVDEAHCVSQWGHDFRPE  149 (607)
T ss_pred             HHHHHHCCCEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHH
T ss_conf             99998607014520377888899999999841981577516713211899988731993089983250216688887565


Q ss_pred             HH--HHHHHCCCCCC-EEEEECCCCCHHHH--HHHHCCCCCCEEECCCCCCCCEEEEEEECCHHHHHHHHHHHH--HHCC
Q ss_conf             89--98863167884-89995353408899--997122254122015788775379998579789899999898--7188
Q gi|254780947|r  763 HK--EALKETHTGVH-VLTLSATPIPRTLQ--LAITGVRELSLISMPPINRIACRTSISIFDPLVVRETLMREY--YRGG  835 (1187)
Q Consensus       763 ~K--e~lk~~~~~vd-vLtlsATPIPRTL~--msl~g~rd~S~i~tpP~~R~~v~T~v~~~~~~~i~~ai~rEl--~RgG  835 (1187)
T Consensus       150 Y~~L~~l~~~fp~~P~~iALTATAd~~t~~DI~~~L~L~~~~~f~~-SFdRpNl~~~v~~k~n~--~~~l~~yl~~~~~G  226 (607)
T TIGR01389       150 YRRLGELAERFPQVPTRIALTATADAETRQDIVELLRLKDANEFIS-SFDRPNLRFSVVKKNNK--KKFLLEYLKKHREG  226 (607)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCCCCCC-CCCCHHHHHHHHHHCCC--CHHHHHHHHCCCCC
T ss_conf             8999999986789866998724899878999999708898654125-67751143343120378--13689997507999


Q ss_pred             EEEEEECC-CCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCEECCCCCCCCCEEEEECHH
Q ss_conf             59998264-46928899999861654648886134674789999999963887579761020036332233266762502
Q gi|254780947|r  836 QSFYVCPR-LSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRAD  914 (1187)
Q Consensus       836 Qvf~v~nr-v~~i~~~~~~l~~l~p~~~i~vaHGqm~~~~le~~m~~F~~~~~dvLv~TtIiEsGlDip~aNTiii~~ad  914 (1187)
T Consensus       227 ~SGIIYa~sR~~VE~~~~~L~s~--G~~A~~YHAGL~~~~R~e~Q~~Fl~d~~~vmVAT~AFGMGIdKpnVR--FViH~d  302 (607)
T TIGR01389       227 QSGIIYASSRKKVEELAERLESQ--GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVR--FVIHAD  302 (607)
T ss_pred             CCEEEECCCHHHHHHHHHHHHHC--CCCEEECCCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCC--EEEEEC
T ss_conf             53478767704589999999747--96204036798776899997544462554888871235874787654--888636


Q ss_pred             HCC-CCHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf             358-860455322103567673699996688
Q gi|254780947|r  915 MFG-LAQLYQLRGRVGRSKIASFALFLLPEN  944 (1187)
Q Consensus       915 ~~G-LaqlyQlrGRVGRs~~~ayayl~~~~~  944 (1187)
T Consensus       303 ~P~~~EsYYQE~GRAGRDGlpae~~lly~~~  333 (607)
T TIGR01389       303 MPKNIESYYQEAGRAGRDGLPAEAILLYSLA  333 (607)
T ss_pred             CCCCHHHHHCCCCCCCCCCCHHHHHHHCCHH
T ss_conf             8742111310355468875267786724777