HHsearch alignment for GI: 254780364 and conserved domain: TIGR01941
>TIGR01941 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit; InterPro: IPR010205 This entry represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0051537 2 iron 2 sulfur cluster binding, 0006814 sodium ion transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=99.97 E-value=3e-30 Score=204.86 Aligned_cols=199 Identities=18% Similarity=0.317 Sum_probs=160.0
Q ss_pred CCCCHHCCCCCE-----EEEEEEEEECCCCEEEEEEECCC--CCCCCCCCEEEECCCCCC--------------------
Q ss_conf 544322073421-----17898998479986999980789--997389857880314586--------------------
Q gi|254780364|r 2 CDVSSELAADVY-----CESVISVKHYTDRLFRFCITRPK--SFRFRSGEFVMLGLIVNG-------------------- 54 (224)
Q Consensus 2 ~~~~~~ip~~~~-----~~~V~~~~~~T~~~~~l~l~~p~--~~~f~aGQ~~~l~~~~~g-------------------- 54 (224)
T Consensus 114 ~Dm~i~~~Ee~fgvk~WeC~V~SN~N~ATFIKEL~l~~p~g~~v~FkaGgY~Qi~~P~~~v~y~Dfd~~~~~~Yr~DW~k 193 (425)
T TIGR01941 114 QDMSIEIPEEVFGVKKWECEVISNDNVATFIKELVLKLPDGESVPFKAGGYIQIEVPAHKVKYADFDQTIQPEYRGDWEK 193 (425)
T ss_pred CCCEEEECEEEECCCCEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCEEEEEECCCEEECCCCCCCCCHHHCCCHHH
T ss_conf 48778732034231101347877798513678988887888830435786478861672331231011012123166325
Q ss_pred ---------------CCEEEEEEECCCCCCCCCEEEEEE-----------------ECCCCCCCCCCCCCCCCCCEECCC
Q ss_conf ---------------110556432056677760179996-----------------157676531000022222100168
Q gi|254780364|r 55 ---------------RPIFRAYSIASPCRDDKLEFCSIK-----------------VDKGFFTTYLQNIQPGDTILLHKK 102 (224)
Q Consensus 55 ---------------~~~~R~ySiaS~p~~~~~~~~i~~-----------------~~~g~~s~~l~~~~~gd~~~~~~~ 102 (224)
T Consensus 194 f~~f~~~~~~~~lpae~~~rAYSmAnYP~E~~~i~lNvRIAtPP~~n~~~~~w~~~~p~G~~SSYifsLKpGDKv~~s-G 272 (425)
T TIGR01941 194 FNLFDLVSKVDQLPAEETVRAYSMANYPEEKGIIKLNVRIATPPFDNGKANKWNSDIPPGIMSSYIFSLKPGDKVTVS-G 272 (425)
T ss_pred CCCEEEEEEECCCCCCCHHHHHCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEE-C
T ss_conf 062547774033564102433202347241787799988418888767643234678987213337744798777997-7
Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHH-HHHHCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 875335644676881799965868088999999-8653088633899994058645430488899887533210124687
Q gi|254780364|r 103 STGDLILDSLIPGNRLYLFSMGTGIAPFASMIR-DPETYKKFDEVIITHTCGRVAELQYGIDVMHEISQDEILKDLIGQK 181 (224)
Q Consensus 103 p~g~f~~~~~~~~~~lvlIAgGtGiaP~~silr-~~~~~~~~~~i~l~~g~R~~~dl~~~~el~~l~~~~~~~~~~~~~~ 181 (224)
T Consensus 273 PfGefF~kDt--daemvFigGGAGmap~RshIld~L~~lks~Rk~sfWYGARS~~E~fY~edf~~L~~e~p--------N 342 (425)
T TIGR01941 273 PFGEFFAKDT--DAEMVFIGGGAGMAPMRSHILDLLKRLKSKRKISFWYGARSKREIFYEEDFDQLEAENP--------N 342 (425)
T ss_pred CCCCCEEEEC--CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHCC--------C
T ss_conf 8885302457--86438973373540368999999860023650245536521244322444788986489--------9
Q ss_pred EEEEEEECCC--CCCCCC----------CCHHHHHCCCHHHH
Q ss_conf 5999810578--877667----------21687858606996
Q gi|254780364|r 182 LKFYRTVTQE--DYLYKG----------RITNHILSGEFYRN 211 (224)
Q Consensus 182 ~~~~~~isre--~~~~~G----------rIt~~i~~g~l~~~ 211 (224)
T Consensus 343 F~~H~aLSdP~PEDnw~Gwdkddp~~tgFih~vl~~nyLk~h 384 (425)
T TIGR01941 343 FKWHVALSDPQPEDNWTGWDKDDPTYTGFIHNVLYENYLKDH 384 (425)
T ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 379998548688510067776786102477877764232137