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