HHsearch alignment for GI: 254780991 and conserved domain: COG1197

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription].
Probab=100.00  E-value=3.6e-36  Score=289.42  Aligned_cols=270  Identities=27%  Similarity=0.442  Sum_probs=229.6

Q ss_pred             CCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             73379986337646999999999719978999316346899999999867898389986213444421015554321022
Q gi|254780991|r  168 EKVQLLLGVTGSGKTFTMAKVIEAMQRPAIVMAPNKILAAQLYSEFKNFFPHNAVEYFVSYYDYYQPEAYVPRTDTYIEK  247 (805)
Q Consensus       168 ~~~qlL~GVTGSGKTevya~lI~~~gr~aLvLvPei~La~QL~~rfk~~Fp~n~V~~f~S~~~~yqpEay~p~~d~~i~k  247 (805)
T Consensus         9 ~~~~~l~gl~~~~~a~~~a~l~~~~~~~~~~vt~~~~~a~~l~~~L~-~~~~~~v~~~-------------P~~e~lpyd   74 (1139)
T COG1197           9 GDPLLLGGLSGGAKALLIAALAEEKPNPVLLVTADLQEADRLAEDLR-FFPDQPVLLL-------------PDWETLPYD   74 (1139)
T ss_pred             CCCEEEECCCCHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHH-HCCCCCEEEC-------------CCCCCCCCC
T ss_conf             77557506781367999999986368882899589999999999998-5788735877-------------774456564


Q ss_pred             HCCCCHHHHHHHHHHHHHHHCCCCEEEECCHHHHCCCCCHHH-HHCCEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             103588999999999999854998499827789616898347-7225799941981117875323431176563387754
Q gi|254780991|r  248 ESSINEQIDRMRHSATRSLLERNDCIVVSSVSCIYGIGSVES-YSQMIVQLKIGDSVEQKELLSSLVKQQYKRQDIGIIR  326 (805)
Q Consensus       248 ~~s~n~~i~~~R~~a~~~l~~~~~~IVVgsrSAIfgl~~P~~-~lglIIvdEehd~~~~~~~~~~l~~~~Y~R~D~a~~R  326 (805)
T Consensus        75 ~~sp~~d~~~~Rl~~L~~L~~~~~~i~v~~~~all~~lpp~~~~~~~~l~l~~G~~~d~~~l~~~L~~~GY~~v~~V~~~  154 (1139)
T COG1197          75 RFSPSQDIVSSRLEALRRLAQGKKGIVVVPVNALLQKLPPPDFLEENSLTLKVGEELDLDDLEARLVRAGYERVDMVMEP  154 (1139)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCEEEEEHHHHHHHCCCHHHHHHCEEEEECCCCCCHHHHHHHHHHHCCCEEEEECCC
T ss_conf             46887047999999999987279988998879953346996676335389624872689999999998097003320245


Q ss_pred             HHHCCCCEEEECCCCCHHHHHHHHCCCCCCHHHHHCCCCCCCCHHHHCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             53318724783178887788873104442002221016664001110000100000000256367887545589989989
Q gi|254780991|r  327 GTFRVCGDSIEIFPSHLEDVAWRVSMFGNDIEEISEFYPLTGQKIRNVETIKIYANSHYVTPRPTLNTAMKYIKEELKMR  406 (805)
Q Consensus       327 G~f~~rg~ILdsatps~Es~~~Rie~f~deIe~I~~fDplT~~~~~~~~~~~i~Pa~~~v~~~e~l~~a~~~i~~el~~r  406 (805)
T Consensus       155 GEfsvRG~IlDIfp~~~e-~P~RieffgdeIesIR~Fd~~tQrS~~~v~~i~l~Pa~e~~l~~~~~~~~~~~~~~~----  229 (1139)
T COG1197         155 GEFAVRGGILDIFPPGSE-EPYRIEFFGDEIESIRSFDPETQRSLEEVEEIELLPASEFILDEEAIEAFRKQYLET----  229 (1139)
T ss_pred             CCEEECCCEEEECCCCCC-CCEEEEECCCCEEEEECCCHHHCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHH----
T ss_conf             624511654786048988-867999658701024525856514524554499746211466978999999988764----


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCHHHHHCCCCCCEEEECC
Q ss_conf             988754433211001244447777533211201451011333114465556202330265442132101
Q gi|254780991|r  407 LIELEKEGRLLEAQRLEQRITYDLEMLETTGSCQSIENYSRYLTGRNPGEPPPTLFEYIPEDSLLFVDE  475 (805)
Q Consensus       407 l~~~~~~~~~~ea~rL~qR~~~dle~l~e~G~~~gienyS~~L~~r~~ge~P~tL~dY~p~d~ll~ide  475 (805)
T Consensus       230 ---f--~-----~~~----~~~~~~~~~~g~~~~g~e~~lplfy-----~~~~~l~dylp~~~~i~~d~  279 (1139)
T COG1197         230 ---F--E-----PKR----DDALYEALSSGRRFAGLEYFLPLFY-----EDLATLFDYLPKNTLIVVDE  279 (1139)
T ss_pred             ---C--C-----CCC----CHHHHHHHHCCCCCCCHHHHHHHHH-----CCCHHHHHHCCCCCCEEEHH
T ss_conf             ---0--5-----664----2378999855898542898768775-----45078998556688176656