HHsearch alignment for GI: 254780619 and conserved domain: PRK10689
>PRK10689 transcription-repair coupling factor; Provisional.
Probab=100.00 E-value=2.2e-41 Score=335.59 Aligned_cols=314 Identities=22% Similarity=0.311 Sum_probs=259.3
Q ss_pred CCCC-CCCHHHHHHHHHHHHHHCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCC-
Q ss_conf 4666-68837899999998752048-96199844753157999999999985146847997152100134455543038-
Q gi|254780619|r 194 FSLP-ILDKNQQDVVEQVVPLCTKG-FAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF- 270 (731)
Q Consensus 194 ~~~~-~Lt~eQ~~a~~~i~~~~~~~-f~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF- 270 (731)
T Consensus 595 ~~FpyeET~DQl~AI~eV~~DMes~~PMDRLiCGDVGfGKTEVA~RAAFkav~~gkQVavlvPTTiLA~QH~~tF~~Rf~ 674 (1148)
T PRK10689 595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA 674 (1148)
T ss_pred HCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 60999787689999999987763886774156768888779999999999996398089983662237999999998764
Q ss_pred --CCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCHHHH---HHHCCCEEEEEEECCCCCCHHCCCCCCCHHHHHHHH
Q ss_conf --976899623557235667899997199739994001211---001000136774055321000024432248999997
Q gi|254780619|r 271 --GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVR 345 (731)
Q Consensus 271 --~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVIGtRSAif---~P~~nLglIIvDEEHd~sykq~~~pry~aRdvA~~R 345 (731)
T Consensus 675 ~~pv~i~~LsRf~s~ke~~~i~~~l~~G~idIvIGTH-~ll~~dv~f~~LGLlIiDEEq----------rFGV~~KE~lk 743 (1148)
T PRK10689 675 NWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTH-KLLQSDVKWKDLGLLIVDEEH----------RFGVRHKERIK 743 (1148)
T ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEHHH-HHHCCCCCCCCCCEEEECCCH----------HCCHHHHHHHH
T ss_conf 1573377503888899999999998669987762048-886698654666437860102----------13799999997
Q ss_pred HHHCCCCEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEE
Q ss_conf 51103210000245432467753212344412432236765433211022223322245479899999988622655179
Q gi|254780619|r 346 GKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTL 425 (731)
Q Consensus 346 a~~~~~~lilgSATPSles~~~~~~g~~~~~~l~~R~~~~~~P~i~ivDm~~~~~~~~~~lS~~l~~~i~~~l~~g~qvl 425 (731)
T Consensus 744 ~l~~~vdvLtltATPIPRTL~msl~G~rdlS~i~tpP~~R-~~v~T~v------~---~~~~~~i~eai~re~~rggq~~ 813 (1148)
T PRK10689 744 AMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR-LAVKTFV------R---EYDSLVVREAILREILRGGQVY 813 (1148)
T ss_pred HCCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCCCCCC-CCCEEEE------E---CCCHHHHHHHHHHHHHHCCEEE
T ss_conf 2289987897625564469999880773302213699989-8708998------3---5872999999999998188089
Q ss_pred EEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHHHHHHC
Q ss_conf 97422200000023565434310146520121135783200002102446555666787411001354289988885204
Q gi|254780619|r 426 LFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEY 505 (731)
Q Consensus 426 l~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e~l~~~ 505 (731)
T Consensus 814 ~~~~~~~-------------------------------------------------------------~i~~~~~~~~~~ 832 (1148)
T PRK10689 814 YLYNDVE-------------------------------------------------------------NIQKAAERLAEL 832 (1148)
T ss_pred EEECCHH-------------------------------------------------------------HHHHHHHHHHHH
T ss_conf 9953254-------------------------------------------------------------199999999974
Q ss_pred CCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 85200010232113586789999986212576579870443023113452012330003443102455789999987543
Q gi|254780619|r 506 FPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQV 585 (731)
Q Consensus 506 fp~~~v~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq~i~kg~~fp~v~lv~il~aD~~l~~pd~ra~E~~~qll~qv 585 (731)
T Consensus 833 ~p~~~~~~~hg~m--~~~~~e~~m~~f~~~~~~~l~~ttiie~g~dip~ant~ii~~a~~~gl-----------~ql~ql 899 (1148)
T PRK10689 833 VPEARIAIGHGQM--RERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGL-----------AQLHQL 899 (1148)
T ss_pred CCCCCEEEEECCC--CHHHHHHHHHHHHCCCCCEEEECCEEECCCCCCCCCEEEEECHHHCCH-----------HHHHHH
T ss_conf 8777189998999--989999999999759988999897876586677884799975321455-----------777754
Q ss_pred HHCCCCCCCCCEEEEEE
Q ss_conf 11025667886899993
Q gi|254780619|r 586 TGRAGRFGLKSLGLIQA 602 (731)
Q Consensus 586 ~gRagr~~~~g~v~iQt 602 (731)
T Consensus 900 rgrvgr~~~~ayaYll~ 916 (1148)
T PRK10689 900 RGRVGRSHHQAYAWLLT 916 (1148)
T ss_pred CCCCCCCCCEEEEEEEE
T ss_conf 36557788707999986