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