HHsearch alignment for GI: 254780382 and conserved domain: PRK10689
>PRK10689 transcription-repair coupling factor; Provisional.
Probab=100.00 E-value=1.2e-37 Score=261.69 Aligned_cols=334 Identities=20% Similarity=0.261 Sum_probs=248.0
Q ss_pred CCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHC------CCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf 6988899999997-8798789899999999976------99799982798517899999999998606521478279998
Q gi|254780382|r 6 LGLSPKVVCAVLD-AGYVKPTPIQIKTIPLVLQ------RHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLIL 78 (465)
Q Consensus 6 l~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~l~------g~dvi~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~lil 78 (465)
T Consensus 583 f~~d~~~~~eFe~~Fpye-ET~DQl~AI~eV~~DMes~~PMDRLiCGDVGfGKTEVA~RAAFkav~------~gkQVavl 655 (1148)
T PRK10689 583 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE------NHKQVAVL 655 (1148)
T ss_pred CCCCHHHHHHHHHCCCCC-CCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHH------CCCEEEEE
T ss_conf 789849999999609997-87689999999987763886774156768888779999999999996------39808998
Q ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC---CCCH-HHHHHCCCCHHHHHHHCCCCCCCCCEEECCCC
Q ss_conf 2858999999999874102333221000012222222222---2101-12210221023333200000012100102551
Q gi|254780382|r 79 EPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK---LERG-ADVLICTPGRILDHFNRGKLLMNNIEILVIDE 154 (465)
Q Consensus 79 ~PtreLa~Qi~~~~~~~~~~~~l~~~~~~gg~~~~~~~~~---l~~~-~~IiV~TP~rl~~~l~~~~~~l~~~~~lViDE 154 (465)
T Consensus 656 vPTTiLA~QH~~tF~~Rf~~~pv~i~~LsRf~s~ke~~~i~~~l~~G~idIvIGT-----H~ll~~dv~f~~LGLlIiDE 730 (1148)
T PRK10689 656 VPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGT-----HKLLQSDVKWKDLGLLIVDE 730 (1148)
T ss_pred ECCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEEEHH-----HHHHCCCCCCCCCCEEEECC
T ss_conf 3662237999999998764157337750388889999999999866998776204-----88866986546664378601
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 00000001003578875431022222333432112222111122222100134443212346421111122221102444
Q gi|254780382|r 155 ADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCAL 234 (465)
Q Consensus 155 ah~l~~~gf~~~i~~i~~~~~~~~q~i~~SAT~~~~v~~l~~~~l~~~~~i~v~~~~~~~~~i~~~~~~~~~~~~~k~~~ 234 (465)
T Consensus 731 Eqr-----FGV~~KE~lk~l~~~vdvLtltATPIPRTL~msl~G~rdlS~i~tpP~~R~~--v~-T~v~~~~----~~~i 798 (1148)
T PRK10689 731 EHR-----FGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLA--VK-TFVREYD----SLVV 798 (1148)
T ss_pred CHH-----CCHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCCCCCCCC--CE-EEEECCC----HHHH
T ss_conf 021-----3799999997228998789762556446999988077330221369998987--08-9983587----2999
Q ss_pred HHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCC--CCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEHHHHHHHHCCC
Q ss_conf 321012234565067762134432222222222--332222234542033323444420135523888846646440788
Q gi|254780382|r 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEK--QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIP 312 (465)
Q Consensus 235 l~~l~~~~~~~~k~iIF~~t~~~~~~l~~~L~~--~g~~v~~lhg~l~~~~R~~~~~~F~~g~~~vLV~Td~~~~GiDip 312 (465)
T Consensus 799 ~eai~re~~rggq~~~~~~~~~~i~~~~~~~~~~~p~~~~~~~hg~m~~~~~e~~m~~f~~~~~~~l~~ttiie~g~dip 878 (1148)
T PRK10689 799 REAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIP 878 (1148)
T ss_pred HHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCEEECCCCCC
T ss_conf 99999999818808999532541999999999748777189998999989999999999759988999897876586677
Q ss_pred CCCEEEEECCCC-CHHHHHHHHHCCCCCCCCEEEEEEECHH------HHHHHHHHHHH
Q ss_conf 765002002467-7899887521024588853999977888------99999999999
Q gi|254780382|r 313 DVGHVFNFDVPN-RAENYIHRIGRTGRAGRHGKAFTLVAKE------DIKHIDAIEKL 363 (465)
Q Consensus 313 ~v~~VI~~d~P~-~~~~y~hR~GR~gR~g~~G~~i~~~~~~------d~~~~~~i~~~ 363 (465)
T Consensus 879 ~ant~ii~~a~~~gl~ql~qlrgrvgr~~~~ayaYll~~~~~~lt~~A~kRL~ai~~~ 936 (1148)
T PRK10689 879 TANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASL 936 (1148)
T ss_pred CCCEEEEECHHHCCHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf 8847999753214557777543655778870799998678777898999999999970