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