HHsearch alignment for GI: 254780619 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=93.46  E-value=0.39  Score=27.80  Aligned_cols=126  Identities=24%  Similarity=0.407  Sum_probs=77.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH
Q ss_conf             23566543446666883789999999875204896199844753157999999999985146847997152100134455
Q gi|254780619|r  185 PVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILE  264 (731)
Q Consensus       185 ~~~~~~~~~~~~~~Lt~eQ~~a~~~i~~~~~~~f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~  264 (731)
T Consensus       200 ~SFdRPNl~y~v~~K~~n~~~~~~dl~~f~~~---------~~~s~~~-----------~~G~sGIIYC~SR~~~e~~a~  259 (497)
T TIGR00614       200 TSFDRPNLYYEVRRKTSNTKKILEDLLRFIVK---------KASSAWE-----------FKGKSGIIYCPSRKKSEQVAA  259 (497)
T ss_pred             ECCCCCCCEEEEECCCCCHHHHHHHHHHHHHH---------HCCCCCC-----------CCCCCEEEECCCCHHHHHHHH
T ss_conf             04668763034005789702589999999875---------2035652-----------458830275287234899999


Q ss_pred             HHHCCCCCEEEEEECCCCCHHHHHHHHHHH-CCCCEEEEECCHHHH-HHH--CCCEEEEE-EECC-CCCCHHCCC
Q ss_conf             543038976899623557235667899997-199739994001211-001--00013677-4055-321000024
Q gi|254780619|r  265 RFQKRFGVKPAEWHSSLSTSMREKIWRQVA-RGAISVIVGVRSALF-LPF--KKLGLIVI-DEEH-DISYKQEEG  333 (731)
Q Consensus       265 rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~-~G~~~IVIGtRSAif-~P~--~nLglIIv-DEEH-d~sykq~~~  333 (731)
T Consensus       260 ~L~~~-G~~a~aYHAGl~~~~R~~V~~~f~nrD~~QvVvATv--AFGMGInKpdvRfViH~~~Pk~~EsYYQE~G  331 (497)
T TIGR00614       260 ELQKL-GIAAGAYHAGLEISARKEVQHKFQNRDEIQVVVATV--AFGMGINKPDVRFVIHYSLPKSMESYYQESG  331 (497)
T ss_pred             HHHHC-CCEEEHHHCCCCHHHHHHHHHHHHCCCCCEEEEEEE--ECCCCCCCCCCCEEEEECCCCCCCCCCCCCC
T ss_conf             99755-861002402688647789999875038857999872--1268887635367885078856211013555