HHsearch alignment for GI: 254780855 and conserved domain: TIGR01962

>TIGR01962 NuoD NADH dehydrogenase I, D subunit; InterPro: IPR010219 This entry recognises specifically the D subunit of NADH dehydrogenase I complex. It excludes the related chain of NAD(P)H-quinone oxidoreductases from chloroplast and Synechocystis, where the quinone may be plastoquinone rather than ubiquinone. This subunit often appears as a subunit C/D fusion.; GO: 0016651 oxidoreductase activity acting on NADH or NADPH, 0006118 electron transport.
Probab=100.00  E-value=0  Score=553.00  Aligned_cols=387  Identities=61%  Similarity=1.081  Sum_probs=375.2

Q ss_pred             CEEEEEECCCCCCCCCCEEEEEEEECCEEEEEEEEECCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             15998406868666775599999839989999988041157889874098987855443121234488899999999999
Q gi|254780855|r    7 RSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEK   86 (396)
Q Consensus         7 ~~~~~~~gp~~~~~~g~l~~~~~v~~~~V~~a~~~~g~~~RGfE~il~Gr~~~da~~it~RICGIC~~aH~~Aa~~AiE~   86 (396)
T Consensus         1 ~~~~lNlGPQHPStHGvLRLiLelDGE~v~~a~P~IGYLHRG~EK~~E~~tY~q~~Py~DRlDYls~~~ne~AY~LAVEK   80 (408)
T TIGR01962         1 EEMILNLGPQHPSTHGVLRLILELDGEQVVRADPHIGYLHRGTEKLAENRTYTQAIPYTDRLDYLSPFSNELAYALAVEK   80 (408)
T ss_pred             CEEEEECCCCCCHHHCCCEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHCCCHHHHHHHHHHHH
T ss_conf             91578458888221111014466058589885267776212578876433333116734325551510100488888787


Q ss_pred             HHC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCC
Q ss_conf             838--857888999999999999999889998743343056418999999999999789975597647633653620007
Q gi|254780855|r   87 LLG--IEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQD  164 (396)
Q Consensus        87 a~g--i~vp~~a~llR~Ll~~~e~i~sH~~h~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~gG~~~Hp~~~vpGGv~~~  164 (396)
T Consensus        81 LlGit~evP~RA~vIRV~l~EL~RI~sHLl~igt~~lD~GAmTp~lyaFr~RE~~~DL~E~~~G~RM~~~y~R~GGV~~D  160 (408)
T TIGR01962        81 LLGITIEVPRRAQVIRVILLELNRISSHLLFIGTHALDLGAMTPFLYAFREREKILDLFEAITGARMHSAYFRIGGVAED  160 (408)
T ss_pred             HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHH
T ss_conf             70761246731589999999988998899999998777877769999888799999999876300246676345871321


Q ss_pred             CC---HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCC
Q ss_conf             89---899999999999999999999999844833344212211230333310235665101367601021017544334
Q gi|254780855|r  165 IP---PELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYS  241 (396)
Q Consensus       165 ~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~~~g~~~~~r~~~~~~~~~  241 (396)
T Consensus       161 LPdf~~n~l~~i~~Fl~~~p~~l~~~e~Ll~~NrIwk~R~~gVGvv~~~~A~~~G~tG~~LRgsGi~~D~RK~~PY~~Y~  240 (408)
T TIGR01962       161 LPDFMENWLEEIREFLEQFPKRLKDYETLLNENRIWKQRTQGVGVVSAKDALDWGLTGPMLRGSGIDWDIRKEEPYEGYD  240 (408)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCEECHHHHHHCCCCCCCHHHCCCCCCCCCCCCCCHHH
T ss_conf             03454338999999998614559999999872616775215763007699984489864521236420256677632020


Q ss_pred             CCCCCCEEECCCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCHH----------------HHHHH
Q ss_conf             67754001012320122110001168758999999962103578672011112303044----------------89999
Q gi|254780855|r  242 ELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPK----------------RADMK  305 (396)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~  305 (396)
T Consensus       241 ~~DFdVp~~~~GDcY~Ry~~r~~E~~ES~kIieQC~~~~~~---~GP~~~~~p~~~~P~Dlq~GPdGlGnsPkhik~~~~  317 (408)
T TIGR01962       241 ELDFDVPVGENGDCYDRYLLRVLEMRESIKIIEQCLEKLRT---PGPIKADNPKLAPPPDLQVGPDGLGNSPKHIKEEMK  317 (408)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             26565431888862045566788899899999998873588---588031788630671002577656777489999986


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             75675430575557776158974899998895117999998799808899983587568688999970880575999897
Q gi|254780855|r  306 RSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILG  385 (396)
Q Consensus       306 ~~~e~l~~~~~~~~~~~~~~~G~GvG~vEAPRG~L~H~~~~~~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iir  385 (396)
T Consensus       318 ~~mEaLI~HF~L~t~G~~vP~GEvY~~~EsPKGElG~yi~SDG~~~PYR~k~RaPSF~hLQ~l~~~~~G~~lAD~ia~~g  397 (408)
T TIGR01962       318 TSMEALIHHFKLVTEGFRVPAGEVYVAIESPKGELGFYIISDGGTKPYRLKIRAPSFAHLQALEAMLVGHYLADLIAILG  397 (408)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEEEEEEECCCCCCEEEEECCCCHHHHHHHHHHHHCHHHHHHHHHHH
T ss_conf             44678888887753377288986000045248730378884188985367763864366888999860206888899876


Q ss_pred             HCCCCCCCCCC
Q ss_conf             60912055359
Q gi|254780855|r  386 SLDIVFGEVDR  396 (396)
Q Consensus       386 SfDpC~sC~dr  396 (396)
T Consensus       398 s~D~V~GeVDR  408 (408)
T TIGR01962       398 SIDIVMGEVDR  408 (408)
T ss_pred             HCCCCCCCCCC
T ss_conf             05733346689