HHsearch alignment for GI: 254780866 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=462.95 Aligned_cols=464 Identities=21% Similarity=0.304 Sum_probs=420.6
Q ss_pred CCCCHHHHHHHHH---HHHHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCC
Q ss_conf 9830789999999---99999998720---35530357999999999999999999998630888818999863134854
Q gi|254780866|r 1 MNLPFLSIVTFLP---FLGVFVILFSS---YLGCGRRSFFGVALGISTINFIFSLFVWSVFDKGRSSFQMIEYYHWIDYF 74 (499)
Q Consensus 1 m~~p~l~lii~lP---ll~~li~~~~~---~~~~~~~~~~~i~~~~~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (499)
T Consensus 1 M~~fL~~t~W~vP~Y~L~G~~L~lPWs~G~~R~TGPRPAaY~N~lmT~vaf~Hsl~~l~~iw~~p~~~l~~~WL~~AdL~ 80 (613)
T TIGR01960 1 MLQFLLETSWLVPFYALIGALLALPWSPGIVRKTGPRPAAYFNLLMTFVAFVHSLLALQAIWSQPPEELVFTWLQAADLD 80 (613)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCC
T ss_conf 91347889889888999999998444438402688984789999999999999999999972799544863320579998
Q ss_pred EEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCHH--HHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHCCCCCEEEE
Q ss_conf 0546652258899999999999999975201121002--35678999863024302654043311123431034312355
Q gi|254780866|r 75 CSYHLGVDGISILLVVLTTFLTPFCILSSWKSIQENF--REYMIAFLVLESMVIGAFLSLDMLLFYIFFEASLIPMFVII 152 (499)
Q Consensus 75 ~~~~l~iD~ls~~f~~l~~~i~~l~~~ys~~~~~~~~--~~f~~llll~~~~~~~~~~s~dl~~l~v~~El~~l~~~~Li 152 (499)
T Consensus 81 L~~~leIS~v~~gAl~liTGLnllAQIfAlGYmEkDWglARFf~LLglFEAaL~glvl~dSLFlSYvlLEiLTLsTYLLv 160 (613)
T TIGR01960 81 LSFALEISSVSTGALVLITGLNLLAQIFALGYMEKDWGLARFFALLGLFEAALSGLVLSDSLFLSYVLLEILTLSTYLLV 160 (613)
T ss_pred CCCEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 54201211167999999999999999987543433324799999999999999999999878888999999998899998
Q ss_pred EECC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH---HHHCCCHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 3123-433232100011355445567766655443210001003443---210133037899998541034445540002
Q gi|254780866|r 153 GVWG-GSERIYAAYKFFLYTFFGSIFMLFAIVVMCWEKKTSSIIDLY---AMSKFPFSIQYWMWIAFFCSFAIKIPMFPF 228 (499)
Q Consensus 153 ~~~~-~~~~~~aa~ky~i~~~~~s~~lL~g~~~l~~~~gs~~~~~~~---~~~~~~~~~~~~~~~ll~~g~~~K~~~~Pf 228 (499)
T Consensus 161 GfWfaQPLVVtaARDAFLTKRVGDl~LLMGVvaL~pLAGs~ny~~L~~WA~tA~l~~~~~TLlgLaLIAGP~GKCAQFPL 240 (613)
T TIGR01960 161 GFWFAQPLVVTAARDAFLTKRVGDLLLLMGVVALSPLAGSWNYDDLAEWAATANLDPTTATLLGLALIAGPTGKCAQFPL 240 (613)
T ss_pred HHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 88870230331442110234788999998999984214678827799998205898268888889997401322246875
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCEECCCCCCCCCCCC
Q ss_conf 32010100022223443333232233321110000111223310000000001222221221110000244322332100
Q gi|254780866|r 229 HTWLPNAHVQAPTAGSVFLAGIMLKMGGYGCIRFLLPLFPLASQYFAPVIFFLSLIAIIYASLVSMVQTDIKKLIAYSSI 308 (499)
Q Consensus 229 H~WlP~~y~~ap~~~salls~~~~k~g~~~l~r~~~~l~~~~~~~~~~~l~~l~~~t~~~g~l~al~q~d~KrllAySsi 308 (499)
T Consensus 241 HLWLDEA-MEGP~PAsIlRNsvVVA~GAyvLiK-LQPvL~-LSPvA~~~li~IG~VTAig~SLiaIAQiDIKR~LSysvS 317 (613)
T TIGR01960 241 HLWLDEA-MEGPNPASILRNSVVVAAGAYVLIK-LQPVLT-LSPVALTVLIAIGSVTAIGASLIAIAQIDIKRALSYSVS 317 (613)
T ss_pred CCHHHHH-CCCCCCHHHHHHHHHHHHHHHHHHH-HCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4100021-4788842678778988864422100-210542-115899999898557888788999999879889989999
Q ss_pred CCCCHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCHHHHHHHHCCCHH
Q ss_conf 13540233310487542210234555421023330356777764200111100235565420233201345555301024
Q gi|254780866|r 309 AHMGYVTIGIFSGMKSGVEGAMFQMLSHGLVSSALFFCVGVIYDRLHTRDIFAYGGLVHNMPRYAVVMMVFTMANMGLPG 388 (499)
Q Consensus 309 ~~~G~i~~~l~~~~~~~~~~~~~~~~~h~~~k~~lFl~~g~i~~~~g~~~l~~l~Gl~~~~P~~~~~~~i~~lsl~G~Pp 388 (499)
T Consensus 318 aYmGLVFIAVG~~q~---~~Al~lllTha~A~AlL~MS~GsiI~n~~tQDlT~lGGLWsRrPisg~sFvVGsagLia~~P 394 (613)
T TIGR01960 318 AYMGLVFIAVGLGQG---ELALLLLLTHAIAKALLFMSIGSIIFNTVTQDLTELGGLWSRRPISGLSFVVGSAGLIALPP 394 (613)
T ss_pred HHHHHHHHEECCCCC---CHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 876365621137886---43578889999999998510575655177622131388746661334469999679987453
Q ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 44311228999999986599999999999999999999999997288987655568788912689999999999999772
Q gi|254780866|r 389 TSGFIGEFLVIMSVFQNSNTVAVLASFGVVLSALYSLWLYRKVVFGVSKCEKVQQLKDLSLRERCMVYPIAVLTVFFGIY 468 (499)
Q Consensus 389 ~~GF~~k~~i~~~~~~~~~~~~~~~~~~~~ls~~~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~l~~~~i~lGi~ 468 (499)
T Consensus 395 LG~FWa~~~l~d~~~~~~PwlvGvll~VN~ltA~nLtR~F~LvF~G~akp-kT~RsPEV~Wpm~lPMv~l~il~LllPl~ 473 (613)
T TIGR01960 395 LGSFWAWLKLADGLWATSPWLVGVLLLVNLLTAFNLTRVFRLVFGGKAKP-KTRRSPEVLWPMALPMVVLIILVLLLPLI 473 (613)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 12589999986245544159999999999998765420024454178888-74568787763145339999999999999
Q ss_pred HHH
Q ss_conf 488
Q gi|254780866|r 469 PVP 471 (499)
Q Consensus 469 p~~ 471 (499)
T Consensus 474 l~~ 476 (613)
T TIGR01960 474 LQQ 476 (613)
T ss_pred HHH
T ss_conf 998