HHsearch alignment for GI: 254780858 and conserved domain: TIGR01959

>TIGR01959 nuoF_fam NADH-quinone oxidoreductase, F subunit; InterPro: IPR011537 This entry describes the F chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. ; GO: 0010181 FMN binding, 0016651 oxidoreductase activity acting on NADH or NADPH, 0051287 NAD binding, 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport.
Probab=100.00  E-value=0  Score=1288.94  Aligned_cols=410  Identities=63%  Similarity=1.066  Sum_probs=402.3

Q ss_pred             HHHHHHCC-CCCCCHHHHHHCC---CHHHHHHHHHC--CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCC-CCCEE
Q ss_conf             36755178-7677989999779---98999999826--989999999983977687571124556874235656-88619
Q gi|254780858|r    7 RIFTNLYG-LQGKSLSDSMSRG---HWDNVDKILEK--GRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCS-DRPHY   79 (425)
Q Consensus         7 r~~~~~~~-~~~~~l~~y~~~g---gy~~l~~~l~~--~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~-~~~~y   79 (425)
T Consensus         1 ~l~~~~~~D~~~~~L~~Y~~~gryrgY~~l~KaL~~~~~~ddii~~VK~SGLRGRGGAGFpTGlKWSFmPK~~sg~~pkY   80 (420)
T TIGR01959         1 VLTTNLDDDPESWTLEEYEKRGRYRGYDALRKALEEKMSPDDIIEEVKDSGLRGRGGAGFPTGLKWSFMPKDDSGPKPKY   80 (420)
T ss_pred             CCEEEEECCCCCCCHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             95144324888510788963487024799999985267812588998743798788887643442233567878888536


Q ss_pred             EEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCC
Q ss_conf             9985767784860048999862589999999999971836389981555178999999999999868997767-678866
Q gi|254780858|r   80 LVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYD  158 (425)
Q Consensus        80 vv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~  158 (425)
T Consensus        81 LvCNADE~EPGTcKDR~lm~~~PH~LIEGm~IaayA~ga~~gYiYiRGEf~~~~~~l~~Ai~EA~~~G~LGkNIlGsGFD  160 (420)
T TIGR01959        81 LVCNADEGEPGTCKDRDLMEFDPHQLIEGMIIAAYAIGAKRGYIYIRGEFIKEAENLEAAIAEAYAAGLLGKNILGSGFD  160 (420)
T ss_pred             EEEECCCCCCCCHHHHHHHHCCCCCEEHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             88727779777131489986288703057888778752531047861301678899999999999759820033788620


Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCC-CCCC
Q ss_conf             406997457510011078899863089998688899862278303785000289999999999605688863389-8774
Q gi|254780858|r  159 VDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGR-ENNR  237 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~-~~~~  237 (425)
T Consensus       161 f~l~~H~GAGAYICGEETALleSLEGkrGqPRlKPPFPA~~GLYG~PT~iNNVETla~VP~I~~~G~~Wy~~~G~~~~~~  240 (420)
T TIGR01959       161 FELFVHRGAGAYICGEETALLESLEGKRGQPRLKPPFPAVFGLYGKPTVINNVETLASVPAILRRGADWYSKLGKSEKSP  240 (420)
T ss_pred             EEEEEECCCCCEECHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             57634338885050478974531057668455221787455566788436463233345788721689998507888888


Q ss_pred             CEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Q ss_conf             30476426788787268935898799999986155678711004898524565653210024563342201103873466
Q gi|254780858|r  238 GTKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGT  317 (425)
Q Consensus       238 Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGs  317 (425)
T Consensus       241 GtKLfs~SGhV~kPG~yE~plG~pl~ELledyAGG~r~G~~NLKaviPGGsS~P~L~~~~~~~~~MDydsl~~~GSmLGt  320 (420)
T TIGR01959       241 GTKLFSVSGHVNKPGNYELPLGIPLRELLEDYAGGVRGGWKNLKAVIPGGSSTPVLPAEEHLDVPMDYDSLAAAGSMLGT  320 (420)
T ss_pred             CCEEEEEEEEEECCCEEEEECCCCHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHCCCE
T ss_conf             85487531066579447700677689999986789888725454572687677761645540246677889864411220


Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC-CCCCCCCHH
Q ss_conf             5179942865289999999999987627998852302899999999998289998999999999986223-666776502
Q gi|254780858|r  318 AAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEG-RTICALGDA  396 (425)
Q Consensus       318 g~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~-~S~C~lG~~  396 (425)
T Consensus       321 g~~iv~D~~tc~V~~~~Rl~~Fy~hESCGqCTPCREGt~W~~~il~rie~G~G~~~Did~L~~v~~~i~GG~TiCAlgda  400 (420)
T TIGR01959       321 GAVIVMDESTCIVKAVRRLSEFYAHESCGQCTPCREGTGWLVKILERIEEGEGKKEDIDLLLSVCKQIEGGKTICALGDA  400 (420)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             32687747834889999999973025787857875762459999999971789843589999997434889333678656


Q ss_pred             HHHHHHHHHHHCHHHHHHHH
Q ss_conf             47999999863889999998
Q gi|254780858|r  397 AAWPIQGLIKNFRPLIEERI  416 (425)
Q Consensus       397 a~~pv~s~l~~F~dEfe~hI  416 (425)
T Consensus       401 Aa~P~~~~ikhFR~EFe~~i  420 (420)
T TIGR01959       401 AAWPVQSAIKHFRDEFEAHI  420 (420)
T ss_pred             HHHHHHHHHHHHHHHHHCCC
T ss_conf             65654778887789983379