HHsearch alignment for GI: 254780382 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=100.00  E-value=0  Score=414.49  Aligned_cols=327  Identities=25%  Similarity=0.370  Sum_probs=260.7

Q ss_pred             HHHHH-CCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             99997-87987898999999999769979998279851789999999999860652147827999828589999999998
Q gi|254780382|r   14 CAVLD-AGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNF   92 (465)
Q Consensus        14 ~~l~~-~~~~~pt~iQ~~~i~~~l~g~dvi~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~lil~PtreLa~Qi~~~~   92 (465)
T Consensus         3 ~~L~~~FGY~~FR~gQe~II~~vL~g~~~l~vmPTGGGKSlCYQ~PALl--l~G-------lt~VISPLIsLMkDQVd~L   73 (607)
T TIGR01389         3 QVLKETFGYDDFRGGQEEIIEHVLDGRDVLVVMPTGGGKSLCYQVPALL--LKG-------LTVVISPLISLMKDQVDQL   73 (607)
T ss_pred             CHHHHHCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHH--HCC-------CEEEECCHHHHHHHHHHHH
T ss_conf             0204446877677315899999847798589738998512777217887--289-------8799842363147799999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCC---C-CHHHHHHCCCCHHHHHHHCCCCCCCCCEEECCCCCCCCCCCC--CHHH
Q ss_conf             741023332210000122222222222---1-011221022102333320000001210010255100000001--0035
Q gi|254780382|r   93 EKYGKNYNLTVALLIGGIPFEAQNKKL---E-RGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMG--FIPY  166 (465)
Q Consensus        93 ~~~~~~~~l~~~~~~gg~~~~~~~~~l---~-~~~~IiV~TP~rl~~~l~~~~~~l~~~~~lViDEah~l~~~g--f~~~  166 (465)
T Consensus        74 ~~----~Gv~Aa~lNSt~s~~E~~~i~~~~~~G~~~LLYvAPERL~~~~Fl~~L~~~~i~L~AvDEAHCvSQWGHDFRPe  149 (607)
T TIGR01389        74 RA----AGVAAAYLNSTLSAKEQQEIEKALVNGELKLLYVAPERLEQDYFLNMLKRLTIALLAVDEAHCVSQWGHDFRPE  149 (607)
T ss_pred             HH----CCCEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCHH
T ss_conf             86----07014520377888899999999841981577516713211899988731993089983250216688887565


Q ss_pred             HHHHH---HHHCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             78875---4310222223334321122221111222--221001344432123464211111222211024443210122
Q gi|254780382|r  167 IQNIT---SLVPFTRQTLLFSATMTDELQKVSENFL--QNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQS  241 (465)
Q Consensus       167 i~~i~---~~~~~~~q~i~~SAT~~~~v~~l~~~~l--~~~~~i~v~~~~~~~~~i~~~~~~~~~~~~~k~~~l~~l~~~  241 (465)
T Consensus       150 Y~~L~~l~~~fp~~P~~iALTATAd~~t~~DI~~~L~L~~~~~f-~~SF--dRpNl~~~v---~~k~n~~~~l~~yl-~~  222 (607)
T TIGR01389       150 YRRLGELAERFPQVPTRIALTATADAETRQDIVELLRLKDANEF-ISSF--DRPNLRFSV---VKKNNKKKFLLEYL-KK  222 (607)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCCCC-CCCC--CCHHHHHHH---HHHCCCCHHHHHHH-HC
T ss_conf             89999999867898669987248998789999997088986541-2567--751143343---12037813689997-50


Q ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCCCCEEEEEC
Q ss_conf             34565067762134432222222222332222234542033323444420135523888846646440788765002002
Q gi|254780382|r  242 QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFD  321 (465)
Q Consensus       242 ~~~~~k~iIF~~t~~~~~~l~~~L~~~g~~v~~lhg~l~~~~R~~~~~~F~~g~~~vLV~Td~~~~GiDip~v~~VI~~d  321 (465)
T Consensus       223 ~~~G~SGIIYa~sR~~VE~~~~~L~s~G~~A~~YHAGL~~~~R~e~Q~~Fl~d~~~vmVAT~AFGMGIdKpnVRFViH~d  302 (607)
T TIGR01389       223 HREGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHAD  302 (607)
T ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCEEEEEC
T ss_conf             79995347876770458999999974796204036798776899997544462554888871235874787654888636


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCEEEEEEECHHHHHHHHHH
Q ss_conf             467789988752102458885399997788899999999
Q gi|254780382|r  322 VPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAI  360 (465)
Q Consensus       322 ~P~~~~~y~hR~GR~gR~g~~G~~i~~~~~~d~~~~~~i  360 (465)
T Consensus       303 ~P~~~EsYYQE~GRAGRDGlpae~~lly~~~D~~l~~~~  341 (607)
T TIGR01389       303 MPKNIESYYQEAGRAGRDGLPAEAILLYSLADIALLKRF  341 (607)
T ss_pred             CCCCHHHHHCCCCCCCCCCCHHHHHHHCCHHHHHHHHHH
T ss_conf             874211131035546887526778672477789999999