HHsearch alignment for GI: 254780867 and conserved domain: TIGR01960
>TIGR01960 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family; InterPro: IPR010217 This family represents NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=100.00 E-value=0 Score=441.81 Aligned_cols=457 Identities=17% Similarity=0.221 Sum_probs=378.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH-----H--HHCCCCHH--------HHHH
Q ss_conf 7786299999999999999999998640230158999999999999999999-----9--71322100--------3167
Q gi|254780867|r 5 SFINDLRLCIPEIIIAFGILFLLLMGVFSRRKNAFHLVVFPVCLLSIALFFL-----L--IMPYEGIG--------LGGA 69 (478)
Q Consensus 5 ~~~~~l~lllP~i~l~~~~l~~l~~~~~~~~~~~~~~~~~~~~~l~i~l~~~-----~--~~~~~~~~--------~~~~ 69 (478)
T Consensus 3 ~fL~~t~W~vP~Y~L~G~~L~lPWs~G~~R~TGPRPAaY~N~lmT~vaf~Hsl~~l~~iw~~p~~~l~~~WL~~AdL~L~ 82 (613)
T TIGR01960 3 QFLLETSWLVPFYALIGALLALPWSPGIVRKTGPRPAAYFNLLMTFVAFVHSLLALQAIWSQPPEELVFTWLQAADLDLS 82 (613)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC
T ss_conf 34788988988899999999844443840268898478999999999999999999997279954486332057999854
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 641007999999999999999999999963210022-4206679999999999873146102212457778877776653
Q gi|254780867|r 70 YISDRFSYFIKAILLMSSIIIFIKMFSCIYVKPFSC-FEFPVIMLMAVLGMLCMISANDMISFYMSLELQSFALYVLIAM 148 (478)
Q Consensus 70 ~~~D~~s~~~~~l~~~~~l~~~~~~~~~~~~~~~~~-~~f~~l~l~~~~g~~~~~~s~~l~~~~v~~E~~~i~~~~LI~~ 148 (478)
T Consensus 83 ~~leIS~v~~gAl~liTGLnllAQIfAlGYmEkDWglARFf~LLglFEAaL~glvl~dSLFlSYvlLEiLTLsTYLLvGf 162 (613)
T TIGR01960 83 FALEISSVSTGALVLITGLNLLAQIFALGYMEKDWGLARFFALLGLFEAALSGLVLSDSLFLSYVLLEILTLSTYLLVGF 162 (613)
T ss_pred CEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 20121116799999999999999998754343332479999999999999999999987888899999999889999888
Q ss_pred HHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHH--HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 20001344555554014620467998898853001000001222211--1013431000012222112344444321100
Q gi|254780867|r 149 NRKSVFSIEAALKYFVLGAFSSAFLLYGISFIYGFTGCTGFSQIATS--LFIGHRSFVLIVGVVLILVGLFFKMALVPFH 226 (478)
Q Consensus 149 ~~~~~~~~~aa~ky~~~~~~g~~~ll~g~~~~y~~~gs~~~~~l~~~--~~~~~~~~~~~~~~~ll~~g~~~K~~~fPfH 226 (478)
T Consensus 163 WfaQPLVVtaARDAFLTKRVGDl~LLMGVvaL~pLAGs~ny~~L~~WA~tA~l~~~-~~TLlgLaLIAGP~GKCAQFPLH 241 (613)
T TIGR01960 163 WFAQPLVVTAARDAFLTKRVGDLLLLMGVVALSPLAGSWNYDDLAEWAATANLDPT-TATLLGLALIAGPTGKCAQFPLH 241 (613)
T ss_pred HHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCH-HHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 87023033144211023478899999899998421467882779999820589826-88888899974013222468754
Q ss_pred HHHHHHHHHHCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 01210122100123333210000023211111244000112221000001222102222000001244544356421112
Q gi|254780867|r 227 MWIPDVYEGSPMFMTAFLATIPKFATTMALCRITSVFWPMLSGLLPIFMCVSIGSMVLGSVVAIRQKDLKRLMAYSSIGH 306 (478)
Q Consensus 227 ~Wlp~a~~~ap~~~salls~~~~~~~~~~l~r~~~~~~~~~~~~~~~l~~~g~~t~i~g~~~al~q~d~KrllAySsi~q 306 (478)
T Consensus 242 LWLDEAMEG-P~PAsIlRNsvVVA~GAyvLiKLQPvL-~LSPvA~~~li~IG~VTAig~SLiaIAQiDIKR~LSysvSaY 319 (613)
T TIGR01960 242 LWLDEAMEG-PNPASILRNSVVVAAGAYVLIKLQPVL-TLSPVALTVLIAIGSVTAIGASLIAIAQIDIKRALSYSVSAY 319 (613)
T ss_pred CHHHHHCCC-CCCHHHHHHHHHHHHHHHHHHHHCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 100021478-884267877898886442210021054-211589999989855788878899999987988998999987
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHCCCCCHHCCCCHHHHHHHHHCCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHCCCCCHH
Q ss_conf 44211111121577888864300232010011000026787408764550210466523211478999986530366500
Q gi|254780867|r 307 AGYALIGFSTGMLGIVAMVRYMVIYLIMMIGFFSCILSLRRKDGNNIQNISDLAGLSRQDIFLTCALTIFLFSLAGIPPF 386 (478)
Q Consensus 307 ~G~i~~~l~~~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~i~~l~gl~~~~P~~~~~~~i~~lsl~GlPp~ 386 (478)
T Consensus 320 mGLVFIAVG~~q~~--~Al~lllTha~A~AlL~MS~GsiI~n--~~tQDlT~lGGLWsRrPisg~sFvVGsagLia~~PL 395 (613)
T TIGR01960 320 MGLVFIAVGLGQGE--LALLLLLTHAIAKALLFMSIGSIIFN--TVTQDLTELGGLWSRRPISGLSFVVGSAGLIALPPL 395 (613)
T ss_pred HHHHHHEECCCCCC--HHHHHHHHHHHHHHHHHHHCCCEEEC--CCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCH
T ss_conf 63656211378864--35788899999999985105756551--776221313887466613344699996799874531
Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 00675999999999628499999999999999999999999996499877865567332189999999999999997676
Q gi|254780867|r 387 AGFFGKYFLLISAVKREFYVLAIVALLSSVISAYYYLRVISIMWFDQSTECVVVVAKEMRLFIFGSILFVTGYFLIENIL 466 (478)
Q Consensus 387 ~GF~sK~~i~~~~~~~~~~~~~~~~~~~s~~s~~y~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 466 (478)
T Consensus 396 G~FWa~~~l~d~~~~~-~PwlvGvll~VN~ltA~nLtR~F~LvF~G~akpkT~RsPEV~Wpm~lPMv~l~il~LllPl~l 474 (613)
T TIGR01960 396 GSFWAWLKLADGLWAT-SPWLVGVLLLVNLLTAFNLTRVFRLVFGGKAKPKTRRSPEVLWPMALPMVVLIILVLLLPLIL 474 (613)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 2589999986245544-159999999999998765420024454178888745687877631453399999999999999
Q ss_pred HHH
Q ss_conf 589
Q gi|254780867|r 467 NSS 469 (478)
Q Consensus 467 ~~~ 469 (478)
T Consensus 475 ~~~ 477 (613)
T TIGR01960 475 QQW 477 (613)
T ss_pred HHH
T ss_conf 987