HHsearch alignment for GI: 254780684 and conserved domain: TIGR03324

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=100.00  E-value=0  Score=910.68  Aligned_cols=419  Identities=27%  Similarity=0.399  Sum_probs=397.6

Q ss_pred             CHHHHHHHHHHHHHCCCCE-EEEEEEEEEECCEEEEECCCCCCCCCCEEEEECCCCCEEEEEEEECCCEEEEEECCCCCC
Q ss_conf             2369999999974133421-201289999525899982688887351899956996079999974199799998048557
Q gi|254780684|r    2 QKNLETLAQLAEDYSKNLV-VQGGYISSITSVYYTVTCLSQYVCLGDFVVHQGKNSDNLGQVIRINLDIVYICPVGIGEE   80 (438)
Q Consensus         2 ~~~l~~l~~~~~~~~~~l~-~~~G~V~~V~G~ii~v~Gl~~~v~iGelv~i~~~~~~v~geVi~~~~~~~~l~~~~~~~g   80 (438)
T Consensus         6 ~~~~~~~~~~i~~~~~~~~~~e~G~v~~vgdgia~v~Gl~-~~~~~el~~f~~---~~~g~~~nle~~~vg~v~lg~~~~   81 (497)
T TIGR03324         6 DKAFQQLDQARESFQPQLTVQEVGTVESVSTGIARVHGLP-GVGFEELLRFPG---GLLGIAFNVDEDEVGVVLLGEYSH   81 (497)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCEEEEECCC-CCCCCCEEEECC---CCEEEEEECCCCCEEEEEECCCCC
T ss_conf             9999999999972488752466679999748569997850-104486388089---988999963788379999569877


Q ss_pred             CCCCCEEEECCC-CEEECCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             467888997288-5552466688654307763047887775553012112543330001331100111245875200223
Q gi|254780684|r   81 ISLGDLVFHWGR-FRISPSACWCGRVINALGKPIDGDDSLGKGDLSMEIMSKVPPAMNRQRVEKGFKTGIRVIDIFTPLC  159 (438)
Q Consensus        81 I~~G~~V~~~g~-~~i~vG~~lLGRViD~lG~PlDg~~~l~~~~~~~~i~~~~p~p~~R~~i~e~L~TGIr~ID~l~pig  159 (438)
T Consensus        82 i~~G~~V~~TG~~l~VPVG~~lLGRVvd~LG~PiDGkgpi~~~-~~~pie~~aP~i~~R~~V~epL~TGIkaID~liPIG  160 (497)
T TIGR03324        82 LQAGDEVERTGRVMDVPVGDGLLGRVVDPLGRPLDGGGPLASS-PRLPIERPAPPIMDRAPVTVPLQTGLKVIDALIPIG  160 (497)
T ss_pred             CCCCCEEEECCCCEEEECCHHHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCC
T ss_conf             6899999858982287448887176458885567899998876-410245789896347888871002414554246556


Q ss_pred             CCCEEEEECCCCCCHHHHH--HHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHC-CCCCCEEEEEECCCCCHHHHHHHHH
Q ss_conf             5850375266788999999--998740789838993124652238899998642-7755328984157788034444445
Q gi|254780684|r  160 HGQRIGVFAGSGIGKSTLL--SMFARSDCFDKVIISLVGERGREVREFIEDYLG-DNLKKSVVVVATSDESPILRKMAPL  236 (438)
Q Consensus       160 ~GQR~gIfg~~GvGKt~Ll--~~i~~~~~~dv~V~alIGeR~rev~efi~~~~~-~~l~~tvvv~~t~d~~~~~r~~a~~  236 (438)
T Consensus       161 rGQRelIigdrgtGKTtla~dtIinqk~~~vicVyvaIGqr~seV~~~v~~l~~~gal~~TvVV~Ata~dpa~lr~~Apy  240 (497)
T TIGR03324       161 RGQRELILGDRQTGKTAIAIDTILNQKGRNVLCIYCAIGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPY  240 (497)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEEEHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHH
T ss_conf             77467764588888008899999704566718999973250787999999987487523417999568899899988789


Q ss_pred             HHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCHHHHHHHCCCC--CCCCEEEEEEEE
Q ss_conf             677788886426798899970989999998766540477843236632455420044444311367--885235543334
Q gi|254780684|r  237 TAVTIAEYFSSKGDNVLLILDSITRFAHSIREIATNSGELPVARGYPTSVFSELPRLLERIGPSEK--EKGNITAVISVL  314 (438)
Q Consensus       237 ~a~~iAEyfr~~G~~Vll~~Ds~tr~a~A~reis~~~ge~P~~~gyp~~~~~~~~~l~ERag~~~~--~~GSiT~~~~v~  314 (438)
T Consensus       241 aa~aiAEyFrd~G~dVLlv~DdLTr~A~A~REisLll~rpPgreaYPgdvFylhsrLLERA~~l~~~~ggGSiTalpive  320 (497)
T TIGR03324       241 AATSIGEHFMEQGRDVLIVYDDLTQHARAYRELSLLLRRPPGREAFPGDIFYVHSRLLERSTHLNEELGGGSLTALPIIE  320 (497)
T ss_pred             HHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEE
T ss_conf             99999999996897489999780699999999998648999877889359877078887324778999997723247998


Q ss_pred             ECCCCCCCHHHHHHHHHCCCEEEEEHHHHHCCCCCCCCCCCCCCCCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             21676420278999861260898704277589713114456400022120899999999999999999999999998523
Q gi|254780684|r  315 VDGDNHNDPIADSVRSILDGHIVLNRSLAEEGRYPPVDPLASVSRLADKAWSADEKKLVSSLTHLIHRFEETRDIRLIGG  394 (438)
Q Consensus       315 ~~~dd~~~pi~~~~~~i~DG~i~L~r~la~~g~~Paid~~~S~SR~~~~~~~~~~~~~~~~~~~~l~~y~~~~~l~~~g~  394 (438)
T Consensus       321 t~~~D~sayIptnvisItDGqI~L~~~Lf~~G~~PAIdvg~SVSRVG~~aq~~~~k~vag~lrl~laq~~El~~f~qfgs  400 (497)
T TIGR03324       321 TEAQNISAYIPTNLISITDGQIYLSPTLFELGVLPAVDVGKSVSRVGGKAQLAAYRAVAGDLKLAYAQFEELETFARFGA  400 (497)
T ss_pred             CCCCCCCCCHHHHHHHHCCCEEEECCCHHHCCCCCCCCCCCCEECCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             02886566445422201086799724076579976435687731367243058999874456999998999999987624


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             4469998999999999999998359988899976
Q gi|254780684|r  395 YRPGVDLILDKAVHQVPIIYDFLKQSPSDLSSED  428 (438)
Q Consensus       395 y~~g~d~~~d~~i~~~~~i~~fl~Q~~~e~~~~~  428 (438)
T Consensus       401 ---~ld~~t~~~l~rG~r~~e~lkQ~~~~p~~~~  431 (497)
T TIGR03324       401 ---RLDENTRKTIEHGRRIRACLKQTQSSPLTVP  431 (497)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHCCCCCCCCCHH
T ss_conf             ---4489999999887999998667778996999