HHsearch alignment for GI: 254780810 and conserved domain: TIGR00962

>TIGR00962 atpA ATP synthase F1, alpha subunit; InterPro: IPR005294 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the alpha subunit found in the F1 complex of F-ATPases. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha-subunit contains a highly conserved adenine-specific non-catalytic nucleotide-binding domain, with a conserved amino acid sequence of Gly-X-X-X-X-Gly-Lys. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex.
Probab=100.00  E-value=0  Score=627.72  Aligned_cols=398  Identities=17%  Similarity=0.137  Sum_probs=363.4

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCEEEEECCCC----CCCCCCCCEEEC
Q ss_conf             0998999999998389885766678999999987520587489999985404770267504548----666655604601
Q gi|254780810|r   11 NKSPTKLLAFAESLEIENANVMRKQELMFSILKVLSGRDVEIIGEGVIEVLQDGFGFLRSPDAN----YLAGPDDIYVSP   86 (423)
Q Consensus        11 ~~~l~EL~eiAkelgIe~~~~l~K~eLI~~Il~~~~~~~g~~~~eGvLEIl~dGyGFLR~~~~~----yl~~~~DiyVs~   86 (423)
T Consensus         1 ~l~~~Ei~~~I~~-~I~~f~~~~~~---~evG~V~sVgDGiArv~GL~~vm~---~El~eF~~G~~GiAlNLEedsVG~v   73 (520)
T TIGR00962         1 QLKLEEISELIKQ-QIKNFEKDIEV---EEVGTVVSVGDGIARVYGLENVMS---GELVEFEGGVQGIALNLEEDSVGAV   73 (520)
T ss_pred             CCCHHHHHHHHHH-HHHCCCCEEEE---ECCCEEEEECCCEEEEEECHHHHH---CCEEECCCCCEEEEEEECCCCEEEE
T ss_conf             9877799999999-86262510133---036279983387899960110140---1002557895899997135862489


Q ss_pred             CCCCCCCCCCCCEEEEEEEECCCCCCCCCCEEECCCCCCCHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             00001221259879998862468887630002222556887885124430002000112234324778653213688899
Q gi|254780810|r   87 SQIKSFSLKTGDTVEGSIRAPREGERYFALLKVNAINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVID  166 (423)
Q Consensus        87 slir~f~Lr~GD~V~g~~r~~~~~~~~~~L~rV~~vnG~~~d~~~~~~~f~~l~p~~p~~~i~le~~~~~p~~~~~~~id  166 (423)
T Consensus        74 i~Gd~~~i~EG~~VKRTg~il~vPVG~~llGRvVn~LG~PiDGkGpI~~~~~~~~E~~APGv~~RkSV~ePlQTGIkAID  153 (520)
T TIGR00962        74 ILGDYSNIREGSTVKRTGRILKVPVGDGLLGRVVNALGQPIDGKGPIESDEFRPIEKIAPGVIERKSVHEPLQTGIKAID  153 (520)
T ss_pred             EECCCCCCCCCCCCCCCCHHCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
T ss_conf             97886665326503203200032457568832684577865777767766634321458855214667873000055764


Q ss_pred             HHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCC------CCCEEEEEECCCCHHHHHHHHHHH-------CCEEEEC
Q ss_conf             886551023122204877878999999999986118------864699995087878999999840-------3427823
Q gi|254780810|r  167 LIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNH------PECYLIVLLIDERPEEVTDMQRSV-------QGEVISS  233 (423)
Q Consensus       167 ~~~pig~gqr~~i~~~~~~gkt~ll~~ia~~~~~~~------~~v~~i~~ligEr~~ev~e~~~~~-------~~~vv~s  233 (423)
T Consensus       154 AliPIGRGQRELIIGDRqTGKTavAIDtIiNQk~~~~~~~~~~dv~CvYVAIGQK~StvA~vv~~LE~~GAM~YTiVV~A  233 (520)
T TIGR00962       154 ALIPIGRGQRELIIGDRQTGKTAVAIDTIINQKDSGELGDEKKDVYCVYVAIGQKASTVAQVVRKLEEHGAMDYTIVVAA  233 (520)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEE
T ss_conf             14689876222342326667305655777730577656786556489996207535689999999753487111033674


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHCCC-----CCCCCCCCCCCCHHHHHHCHHHHHCCC
Q ss_conf             667888899999999999999999779928999816389877620013-----667776777520246650468752257
Q gi|254780810|r  234 TFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLM-----PSSGKILTGGVDANALQRPKRFFGAAR  308 (423)
Q Consensus       234 t~d~~~~~~~~~a~~a~~~a~~~~e~G~dVll~~DslTR~ArA~~~~~-----~~~g~~~~gg~~~~~l~~~~~~~~~ar  308 (423)
T Consensus       234 ~ASdsA~lqYLAPY~G~tmaEyF~d~GkhaLIiYDDLSKqA~AYR~iSLLLRRPPGREAyPGDVFYL---HSRLLERAAK  310 (520)
T TIGR00962       234 SASDSASLQYLAPYTGCTMAEYFRDNGKHALIIYDDLSKQAVAYRQISLLLRRPPGREAYPGDVFYL---HSRLLERAAK  310 (520)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHH---HHHHHHHHHH
T ss_conf             1677212454206889999999986597379997474078999999998718865871699740145---4568999864


Q ss_pred             CCCC----------CCC-CEEEEEEEECCCC-CCCCHHHHHHHHCCCCEEEEEHHHHHCCCCCCCCCCCCCCCCHHHCCC
Q ss_conf             7777----------785-0012112012676-554138898852266078980878847999740533542210155199
Q gi|254780810|r  309 NIKE----------GGS-LTIIGTALVDTGS-RMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVE  376 (423)
Q Consensus       309 ~~~~----------~Gs-~T~~~t~lvetg~-~~d~~i~~~~~~~~d~~i~L~r~la~~~~~PAId~~~S~sR~~~~l~~  376 (423)
T Consensus       311 LsdeYve~FtkGevkGgtGSlTALPIIETQAGDvSAYIPTNVISITDGQIFLesdLFn~GiRPAINvGlSVSRVGgAAQi  390 (520)
T TIGR00962       311 LSDEYVEKFTKGEVKGGTGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLESDLFNSGIRPAINVGLSVSRVGGAAQI  390 (520)
T ss_pred             CCHHHHHHHHCCCCCCCCCCCCCCCCEEECCCCEEEECCCCEEECCCCHHHHHHHHHCCCCCCCEECCEEEEECCHHHHH
T ss_conf             07888854305632466535236772252148786630787135245511210201106898714175667442035776


Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHH--------HHHHCCCCHHHHHHH
Q ss_conf             999999999999961269378999999--------984028998999986
Q gi|254780810|r  377 RQDLQKVFMLRRIVSSMNSSDAIEFLI--------DKLKQTKDNKDFFYS  418 (423)
Q Consensus       377 ~~~~~~~~~~r~~l~~~~~~e~~~~l~--------~~~~~~~~n~e~l~~  418 (423)
T Consensus       391 KAmK~vaG~LrLeLAQYRELeAFsQFaSDLD~ATk~qLerG~R~vElLKQ  440 (520)
T TIGR00962       391 KAMKQVAGSLRLELAQYRELEAFSQFASDLDEATKAQLERGKRLVELLKQ  440 (520)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             65554235224557548899888640122348999998606723420006