HHsearch alignment for GI: 254780684 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=952.22  Aligned_cols=415  Identities=26%  Similarity=0.373  Sum_probs=392.7

Q ss_pred             HHHHHHHHHHHHCCCCE-EEEEEEEEEECCEEEEECCCCCCCCCCEEEEECCCCCEEEEEEEECCCEEEEEECCCCCCCC
Q ss_conf             69999999974133421-20128999952589998268888735189995699607999997419979999804855746
Q gi|254780684|r    4 NLETLAQLAEDYSKNLV-VQGGYISSITSVYYTVTCLSQYVCLGDFVVHQGKNSDNLGQVIRINLDIVYICPVGIGEEIS   82 (438)
Q Consensus         4 ~l~~l~~~~~~~~~~l~-~~~G~V~~V~G~ii~v~Gl~~~v~iGelv~i~~~~~~v~geVi~~~~~~~~l~~~~~~~gI~   82 (438)
T Consensus         7 i~~~I~~~I~~f~~~~~~~evG~V~sVgDGiArv~GL~-~vm~~El~eF~~G---~~GiAlNLEedsVG~vi~Gd~~~i~   82 (520)
T TIGR00962         7 ISELIKQQIKNFEKDIEVEEVGTVVSVGDGIARVYGLE-NVMSGELVEFEGG---VQGIALNLEEDSVGAVILGDYSNIR   82 (520)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCEEEEECCCEEEEEECH-HHHHCCEEECCCC---CEEEEEEECCCCEEEEEECCCCCCC
T ss_conf             99999998626251013303627998338789996011-0140100255789---5899997135862489978866653


Q ss_pred             CCCEEEECCC-CEEECCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             7888997288-555246668865430776304788777555301211254333000133110011124587520022358
Q gi|254780684|r   83 LGDLVFHWGR-FRISPSACWCGRVINALGKPIDGDDSLGKGDLSMEIMSKVPPAMNRQRVEKGFKTGIRVIDIFTPLCHG  161 (438)
Q Consensus        83 ~G~~V~~~g~-~~i~vG~~lLGRViD~lG~PlDg~~~l~~~~~~~~i~~~~p~p~~R~~i~e~L~TGIr~ID~l~pig~G  161 (438)
T Consensus        83 EG~~VKRTg~il~vPVG~~llGRvVn~LG~PiDGkGpI~~~~-~~~~E~~APGv~~RkSV~ePlQTGIkAIDAliPIGRG  161 (520)
T TIGR00962        83 EGSTVKRTGRILKVPVGDGLLGRVVNALGQPIDGKGPIESDE-FRPIEKIAPGVIERKSVHEPLQTGIKAIDALIPIGRG  161 (520)
T ss_pred             CCCCCCCCCHHCCCCCCCEEEEEEECCCCCCCCCCCCCCCCC-CCCCCCCCCCEEECCCCCCCCHHHHHHHHCCCCCCCC
T ss_conf             265032032000324575688326845778657777677666-3432145885521466787300005576414689876


Q ss_pred             CEEEEECCCCCCHHHHH--HHHHHHC--------CCCCEEEEECCCCCHHHHHHHHHHHCC-CCCCEEEEEECCCCCHHH
Q ss_conf             50375266788999999--9987407--------898389931246522388999986427-755328984157788034
Q gi|254780684|r  162 QRIGVFAGSGIGKSTLL--SMFARSD--------CFDKVIISLVGERGREVREFIEDYLGD-NLKKSVVVVATSDESPIL  230 (438)
Q Consensus       162 QR~gIfg~~GvGKt~Ll--~~i~~~~--------~~dv~V~alIGeR~rev~efi~~~~~~-~l~~tvvv~~t~d~~~~~  230 (438)
T Consensus       162 QRELIIGDRqTGKTavAIDtIiNQk~~~~~~~~~~dv~CvYVAIGQK~StvA~vv~~LE~~GAM~YTiVV~A~ASdsA~l  241 (520)
T TIGR00962       162 QRELIIGDRQTGKTAVAIDTIINQKDSGELGDEKKDVYCVYVAIGQKASTVAQVVRKLEEHGAMDYTIVVAASASDSASL  241 (520)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHH
T ss_conf             22234232666730565577773057765678655648999620753568999999975348711103367416772124


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCHHHHHHHCC--C-------
Q ss_conf             4444456777888864267988999709899999987665404778432366324554200444443113--6-------
Q gi|254780684|r  231 RKMAPLTAVTIAEYFSSKGDNVLLILDSITRFAHSIREIATNSGELPVARGYPTSVFSELPRLLERIGPS--E-------  301 (438)
Q Consensus       231 r~~a~~~a~~iAEyfr~~G~~Vll~~Ds~tr~a~A~reis~~~ge~P~~~gyp~~~~~~~~~l~ERag~~--~-------  301 (438)
T Consensus       242 qYLAPY~G~tmaEyF~d~GkhaLIiYDDLSKqA~AYR~iSLLLRRPPGREAyPGDVFYLHSRLLERAAKLsdeYve~Ftk  321 (520)
T TIGR00962       242 QYLAPYTGCTMAEYFRDNGKHALIIYDDLSKQAVAYRQISLLLRRPPGREAYPGDVFYLHSRLLERAAKLSDEYVEKFTK  321 (520)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHC
T ss_conf             54206889999999986597379997474078999999998718865871699740145456899986407888854305


Q ss_pred             ---CCC-CCEEEEEEEEECCCCCCCHHHHHHHHHCCCEEEEEHHHHHCCCCCCCCCCCCCCCCCHHCCCHHHHHHHHHHH
Q ss_conf             ---788-5235543334216764202789998612608987042775897131144564000221208999999999999
Q gi|254780684|r  302 ---KEK-GNITAVISVLVDGDNHNDPIADSVRSILDGHIVLNRSLAEEGRYPPVDPLASVSRLADKAWSADEKKLVSSLT  377 (438)
Q Consensus       302 ---~~~-GSiT~~~~v~~~~dd~~~pi~~~~~~i~DG~i~L~r~la~~g~~Paid~~~S~SR~~~~~~~~~~~~~~~~~~  377 (438)
T Consensus       322 GevkGgtGSlTALPIIETQAGDvSAYIPTNVISITDGQIFLesdLFn~GiRPAINvGlSVSRVGgAAQiKAmK~vaG~Lr  401 (520)
T TIGR00962       322 GEVKGGTGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLESDLFNSGIRPAINVGLSVSRVGGAAQIKAMKQVAGSLR  401 (520)
T ss_pred             CCCCCCCCCCCCCCCEEECCCCEEEECCCCEEECCCCHHHHHHHHHCCCCCCCEECCEEEEECCHHHHHHHHHHHCCCHH
T ss_conf             63246653523677225214878663078713524551121020110689871417566744203577665554235224


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9999999999999852344699989999999999999983599888999
Q gi|254780684|r  378 HLIHRFEETRDIRLIGGYRPGVDLILDKAVHQVPIIYDFLKQSPSDLSS  426 (438)
Q Consensus       378 ~~l~~y~~~~~l~~~g~y~~g~d~~~d~~i~~~~~i~~fl~Q~~~e~~~  426 (438)
T Consensus       402 LeLAQYRELeAFsQFaS---DLD~ATk~qLerG~R~vElLKQ~~~~P~p  447 (520)
T TIGR00962       402 LELAQYRELEAFSQFAS---DLDEATKAQLERGKRLVELLKQPQYKPLP  447 (520)
T ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHCCCCEEEEEECCCCCCCC
T ss_conf             55754889988864012---23489999986067234200068865885