RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780617|ref|YP_003065030.1| F0F1 ATP synthase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (509 letters) >gnl|CDD|30405 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy production and conversion]. Length = 504 Score = 775 bits (2002), Expect = 0.0 Identities = 334/509 (65%), Positives = 411/509 (80%), Gaps = 8/509 (1%) Query: 1 MDIHAAEISDILRKRIKDFGNDSEFSEIGRVLSIGDGIARVYGLNNIRAGEMVQFSHGVY 60 M ++ EIS +++++I++F ++E E+G V+S+GDGIARV GL N+ AGE+V+F GV Sbjct: 1 MQLNPTEISSLIKQQIENFDVEAEVKEVGTVISVGDGIARVSGLENVMAGELVEFPGGVK 60 Query: 61 GMALNLEVDNVGVVILGSYKEISEGDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGP 120 GMALNLE D+VG VILG Y +I EGD VKRTGRI++VPVG ELLGRVVDALGNPIDGKGP Sbjct: 61 GMALNLEEDSVGAVILGDYSDIKEGDEVKRTGRILEVPVGEELLGRVVDALGNPIDGKGP 120 Query: 121 IKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIIL 180 I + E APG++ R+SV EPL TGIKAID+LIPIGRGQRELIIGDR+TGKT+I + Sbjct: 121 IDATKTRPVEKKAPGVMDRKSVNEPLQTGIKAIDALIPIGRGQRELIIGDRQTGKTAIAI 180 Query: 181 DTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPA 240 DT +NQK S V CIYVAIGQKRS+VA V+ LE+ GA+ Y+IVV ASASD A Sbjct: 181 DTIINQKGS--------GVKCIYVAIGQKRSTVANVVRTLEEHGAMDYTIVVAASASDSA 232 Query: 241 PMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFY 300 P+Q LAP+AGCAM EYFRDNG LI YDDL KHAVAYR++SLLLRRPPGREAYPGDVFY Sbjct: 233 PLQYLAPYAGCAMAEYFRDNGKDVLIVYDDLSKHAVAYREISLLLRRPPGREAYPGDVFY 292 Query: 301 LHSRLLERAAKMSDALGAGSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQG 360 LHSRLLERAAK+SD LG GS+TALP+IETQ DVSAYIPTNVISITDGQIFLET+LF G Sbjct: 293 LHSRLLERAAKLSDELGGGSITALPIIETQAGDVSAYIPTNVISITDGQIFLETDLFNAG 352 Query: 361 IRPAINIGLSVSRVGSAAQVKAMKQVSGAVKGELAQYREMSSFSKFSSDLDSSTQKFLSK 420 IRPAIN+GLSVSRVGSAAQ+KAMK+V+G+++ LAQYRE+ +FS+F SDLD +T+K L + Sbjct: 353 IRPAINVGLSVSRVGSAAQIKAMKKVAGSLRLILAQYRELEAFSQFGSDLDKATRKQLER 412 Query: 421 GERLTELLKQPQFSPLAMEEQVVMIFAGISGCLDEVAVSQVRKFETNFLSHMRVSSQDIL 480 G+RLTELLKQPQ+SPL++EEQV++++AG +G LD+V V +V FE L+++R +++L Sbjct: 413 GKRLTELLKQPQYSPLSVEEQVLILYAGTNGYLDDVPVEKVADFEKELLAYLRSDHKELL 472 Query: 481 EDIRKQKVLTDDIRSKLINEIKVFLEDFN 509 E+IR K L D+I +KL IK F + F Sbjct: 473 EEIRTTKELDDEIEAKLKAAIKEFKKTFA 501 >gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit. Length = 485 Score = 722 bits (1865), Expect = 0.0 Identities = 283/483 (58%), Positives = 350/483 (72%), Gaps = 8/483 (1%) Query: 26 SEIGRVLSIGDGIARVYGLNNIRAGEMVQFSHGVYGMALNLEVDNVGVVILGSYKEISEG 85 G VL +GDGIAR+YGL+ + AGE+V+F G G+ALNLE +NVGVV++G I EG Sbjct: 5 VNTGTVLQVGDGIARIYGLDEVMAGELVEFEDGTIGIALNLESNNVGVVLMGDGLMIQEG 64 Query: 86 DIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEP 145 VK TG+I +PV LGRVV+AL PIDGKG I + E+ APGII R+SV EP Sbjct: 65 SSVKATGKIAQIPVSEAYLGRVVNALAKPIDGKGEISASESRLIESPAPGIISRRSVYEP 124 Query: 146 LSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVA 205 L TG+ AIDS+IPIGRGQRELIIGDR+TGKT++ DT LNQK V C+YVA Sbjct: 125 LQTGLIAIDSMIPIGRGQRELIIGDRQTGKTAVATDTILNQKGQ--------NVICVYVA 176 Query: 206 IGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHAL 265 IGQK SSVA+ V L++RGA+ Y+IVV +A PA +Q LAP+ G A+ EYF G H L Sbjct: 177 IGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAPYTGAALAEYFMYRGRHTL 236 Query: 266 IAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALP 325 I YDDL K A AYRQ+SLLLRRPPGREAYPGDVFYLHSRLLERAAK+S LG GS+TALP Sbjct: 237 IIYDDLSKQAQAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKLSSQLGEGSMTALP 296 Query: 326 VIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAMKQ 385 ++ETQ DVSAYIPTNVISITDGQIFL +LF GIRPAIN+G+SVSRVGSAAQ+KAMKQ Sbjct: 297 IVETQAGDVSAYIPTNVISITDGQIFLSADLFNAGIRPAINVGISVSRVGSAAQIKAMKQ 356 Query: 386 VSGAVKGELAQYREMSSFSKFSSDLDSSTQKFLSKGERLTELLKQPQFSPLAMEEQVVMI 445 V+G +K ELAQ+ E+ +F++F+SDLD +TQ L++G+RL ELLKQ Q +PL +EEQV I Sbjct: 357 VAGKLKLELAQFAELEAFAQFASDLDKATQNQLARGQRLRELLKQSQSAPLTVEEQVATI 416 Query: 446 FAGISGCLDEVAVSQVRKFETNFLSHMRVSSQDILEDIRKQKVLTDDIRSKLINEIKVFL 505 + G +G LD + + QVRKF ++++ + E I K T++ + L I+ L Sbjct: 417 YTGTNGYLDSLEIGQVRKFLVELRTYLKTNKPQFQEIISSTKTFTEEAEALLKEAIQEQL 476 Query: 506 EDF 508 E F Sbjct: 477 ELF 479 >gnl|CDD|29998 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.. Length = 274 Score = 501 bits (1291), Expect = e-142 Identities = 215/282 (76%), Positives = 241/282 (85%), Gaps = 8/282 (2%) Query: 94 IVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAI 153 I DVPVG LLGRVVDALGNPIDGKGPI+ ++R E+ APGII R+SV EPL TGIKAI Sbjct: 1 IADVPVGEALLGRVVDALGNPIDGKGPIETKERRPIESKAPGIIPRKSVNEPLQTGIKAI 60 Query: 154 DSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSV 213 D++IPIGRGQRELIIGDR+TGKT+I +DT +NQK KVYCIYVAIGQK S+V Sbjct: 61 DAMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGK--------KVYCIYVAIGQKASTV 112 Query: 214 ARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQK 273 A+ VK LE+ GA+ Y+IVV A+ASDPAP+Q LAP+ GCAMGEYF DNG HALI YDDL K Sbjct: 113 AQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAPYTGCAMGEYFMDNGKHALIIYDDLSK 172 Query: 274 HAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVND 333 AVAYRQ+SLLLRRPPGREAYPGDVFYLHSRLLERAAK++D LG GSLTALP+IETQ D Sbjct: 173 QAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKLNDELGGGSLTALPIIETQAGD 232 Query: 334 VSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVG 375 VSAYIPTNVISITDGQIFLET+LF +GIRPAIN+GLSVSRVG Sbjct: 233 VSAYIPTNVISITDGQIFLETDLFNKGIRPAINVGLSVSRVG 274 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 300 bits (771), Expect = 6e-82 Identities = 104/225 (46%), Positives = 136/225 (60%), Gaps = 12/225 (5%) Query: 148 TGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIG 207 TGI+AID L+PIG+GQR I G TGKT ++ N K+ V +YV IG Sbjct: 1 TGIRAIDLLLPIGKGQRIGIFGGSGTGKTVLLGMIARNAKA---------DVVEVYVLIG 51 Query: 208 QKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIA 267 ++ VA F++ L GAL ++VV A++ +P + LAP+ + EYFRD G L+ Sbjct: 52 ERGREVAEFIEELLGEGALKRTVVVAATSDEPPAERYLAPYTALTIAEYFRDQGKDVLLL 111 Query: 268 YDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVI 327 D L + A A R++SLLL PPGRE YPG +F +RLLERA K+ G GS+TALP + Sbjct: 112 LDSLTRFARALREISLLLGEPPGREGYPGSLFSDLARLLERAGKVE---GGGSITALPTV 168 Query: 328 ETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVS 372 D++ IP N ISITDGQI L EL +GI PAI+I LSVS Sbjct: 169 LVPGGDITDPIPDNTISITDGQIVLSRELAERGIYPAIDILLSVS 213 >gnl|CDD|36567 KOG1353, KOG1353, KOG1353, F0F1-type ATP synthase, alpha subunit [Energy production and conversion]. Length = 340 Score = 295 bits (757), Expect = 1e-80 Identities = 139/282 (49%), Positives = 176/282 (62%), Gaps = 11/282 (3%) Query: 8 ISDILRKRIKDFGNDSEFSEIGRVLSIGDGIARVYGLNNIRAGEMVQFSHGVYGMALNLE 67 +S I +RI ++ E GRVLSIGDGIARVYGL N++A EMV+FS G+ GMALNLE Sbjct: 1 MSSIFEERIVGDNTSADLEETGRVLSIGDGIARVYGLTNVQAEEMVEFSSGLKGMALNLE 60 Query: 68 VDNVGVVILGSYKEISEGDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRS 127 +NVGVV+ G I EGD VKRT I DVP LLGRV ALG PIDG G I ++R Sbjct: 61 GENVGVVVFGEDSLIKEGDTVKRTAAISDVPPLKALLGRVGCALGEPIDGNGKISAKERR 120 Query: 128 CTEADAPGIIQRQSVCEPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQK 187 II R SV EP+ TG+KA+DSL+PIGRGQRELIIGDR+TGKTS+ +DT LNQK Sbjct: 121 --------IIPRASVDEPMQTGLKAVDSLVPIGRGQRELIIGDRQTGKTSLAIDTILNQK 172 Query: 188 SSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAP 247 ++ EK K+YC+YVAIGQKRS+VA+ V+ LE+ A+ YSIVV A+AS + P Sbjct: 173 RGNECLDEKKKIYCVYVAIGQKRSTVAQLVQRLEEADAMEYSIVVAATASQAGDVSAYIP 232 Query: 248 FAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPP 289 ++ + Y ++ +S + Sbjct: 233 TNVISI---DGQIFLETELFYKGIRPAINVGLSVSRVGSAAQ 271 Score = 208 bits (531), Expect = 3e-54 Identities = 108/263 (41%), Positives = 148/263 (56%), Gaps = 43/263 (16%) Query: 228 YSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHAL--------IAYDDLQKHAVAYR 279 ++ A+ SD P++ L GCA+GE NG + + D+ + + Sbjct: 79 DTVKRTAAISDVPPLKALLGRVGCALGEPIDGNGKISAKERRIIPRASVDEPMQTGLKAV 138 Query: 280 QLSLLLRRPP----------GREAYPGDVFYLHSRLLERA-------------------- 309 + + R G+ + D R E Sbjct: 139 DSLVPIGRGQRELIIGDRQTGKTSLAIDTILNQKRGNECLDEKKKIYCVYVAIGQKRSTV 198 Query: 310 ----AKMSDALGAGSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAI 365 ++ +A + +Q DVSAYIPTNVISI DGQIFLETELFY+GIRPAI Sbjct: 199 AQLVQRLEEADAMEYSIVVAATASQAGDVSAYIPTNVISI-DGQIFLETELFYKGIRPAI 257 Query: 366 NIGLSVSRVGSAAQVKAMKQVSGAVKGELAQYREMSSFSKFSSDLDSSTQKFLSKGERLT 425 N+GLSVSRVGSAAQ KAMKQV+G++K ELAQYRE+++F++F SDLD++TQ+ L++G RLT Sbjct: 258 NVGLSVSRVGSAAQTKAMKQVAGSLKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLT 317 Query: 426 ELLKQPQFSPLAMEEQVVMIFAG 448 ELLKQ Q++PLA+EEQV +I+AG Sbjct: 318 ELLKQGQYAPLAIEEQVAVIYAG 340 >gnl|CDD|31351 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 441 Score = 210 bits (535), Expect = 9e-55 Identities = 125/420 (29%), Positives = 196/420 (46%), Gaps = 23/420 (5%) Query: 29 GRVLSIGDGIARVYGLNNIRAGEMVQFSHGVYGMALNLEV-----DNVGVVILGSYKEIS 83 GR+ + + G R GE+ + + EV + V ++ + +S Sbjct: 26 GRLTRVTGLLLEAVGPQ-ARIGELCKIERSRGSEKVLAEVVGFNEERVLLMPFEPVEGVS 84 Query: 84 EGDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVC 143 G V TGR + VPVG LLGRV+D LG P+DG G +R +A P ++R+ + Sbjct: 85 PGAEVVPTGRPLSVPVGDALLGRVLDGLGRPLDGGGLPDGTERRPLDAPPPNPLKRRPIE 144 Query: 144 EPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIY 203 EPL TG++AID L+ G+GQR I GK++++ + +E D + Sbjct: 145 EPLDTGVRAIDGLLTCGKGQRIGIFAGSGVGKSTLL--------GMIARNTEADVN--VI 194 Query: 204 VAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYH 263 IG++ V F++ L S+VVVA++ + A M+L A F + EYFRD G Sbjct: 195 ALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIAEYFRDQGKR 254 Query: 264 ALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTA 323 L+ D L + A+A R++ L PP + YP VF RLLERA GS+TA Sbjct: 255 VLLIMDSLTRFAMAQREIGLAAGEPPATKGYPPSVFSELPRLLERAGNG----DKGSITA 310 Query: 324 LPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAM 383 + + +D++ I V SI DG I L L G PAI++ S+SRV + Sbjct: 311 FYTVLVEGDDMNDPIADEVRSILDGHIVLSRALAEAGHYPAIDVLASISRVMPQIVSEEH 370 Query: 384 KQVSGAVKGELAQYREMSSFSK---FSSDLDSSTQKFLSKGERLTELLKQPQFSPLAMEE 440 ++ + ++ L++Y E + + D K + ++ + LKQ + EE Sbjct: 371 RKAARRLRQLLSRYEENEDLIRIGAYQKGSDPELDKAIKLYPKIEQFLKQGIDEKSSFEE 430 >gnl|CDD|30002 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.. Length = 326 Score = 183 bits (466), Expect = 1e-46 Identities = 107/339 (31%), Positives = 169/339 (49%), Gaps = 17/339 (5%) Query: 95 VDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAID 154 + VPVG LLGRV+DA G P+DGKGP+ E R P ++R+ + E L TG++AID Sbjct: 2 LSVPVGDALLGRVLDAFGEPLDGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAID 61 Query: 155 SLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVA 214 L+ +G+GQR I GK++++ +G+ D + IG++ V Sbjct: 62 GLLTVGKGQRLGIFAGSGVGKSTLL--------GMIARGTTADVN--VIALIGERGREVR 111 Query: 215 RFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQKH 274 F++ L S+VVVA++ + +++ A + A+ EYFRD G L+ D L + Sbjct: 112 EFIEKDLGEEGLKRSVVVVATSDESPLLRVKAAYTATAIAEYFRDQGKDVLLLMDSLTRF 171 Query: 275 AVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVNDV 334 A+A R++ L PP + YP VF L RLLERA GS+TA + + +D+ Sbjct: 172 AMAQREIGLAAGEPPTTKGYPPSVFALLPRLLERAGNSDK----GSITAFYTVLVEGDDL 227 Query: 335 SAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAMKQVSGAVKGEL 394 + I V SI DG I L L G PAI++ S+SR+ +A K+ + ++ L Sbjct: 228 NEPIADAVRSILDGHIVLSRALAAAGHYPAIDVLKSISRLMNAVVTPEHKEAARKLRELL 287 Query: 395 AQYREMS---SFSKFSSDLDSSTQKFLSKGERLTELLKQ 430 + Y+E+ + D + + ++ LKQ Sbjct: 288 SAYQEVEDLIRIGAYKKGSDPEVDEAIKLLPKIEAFLKQ 326 >gnl|CDD|31350 COG1156, NtpB, Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion]. Length = 463 Score = 149 bits (379), Expect = 1e-36 Identities = 107/416 (25%), Positives = 183/416 (43%), Gaps = 24/416 (5%) Query: 41 VYGLNNIRAGEMVQ----FSHGVYGMALNLEVDNVGVVILGSYKEISEGD-IVKRTGRIV 95 V G+ GE+V+ G L + D V + + V+ TG + Sbjct: 20 VEGVEGASYGELVEIETPDGEVRRGQVLEVRGDKAVVQVFEGTSGLDTKGTTVRFTGETL 79 Query: 96 DVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAIDS 155 +PV +LLGR+ + G PIDG I E R R E + TGI AID Sbjct: 80 KIPVSEDLLGRIFNGSGKPIDGGPEIVPEDRLDINGAPINPYARIYPEEFIQTGISAIDG 139 Query: 156 LIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVAR 215 + + RGQ+ I +G L + ++++ D E+ V ++ A+G Sbjct: 140 MNTLVRGQKLPIFS--GSGLPHNELAAQIARQATVDGEEEEFAV--VFAAMGITHEEALF 195 Query: 216 FVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFR-DNGYHALIAYDDLQKH 274 F+ E+ GAL +++ + A DPA +++ P + EY + H L+ D+ + Sbjct: 196 FMDEFEETGALDRAVLFLNLADDPAVERIITPRMALTVAEYLAFEKDMHVLVILTDMTNY 255 Query: 275 AVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVNDV 334 A R++S PGR YPG ++ + + ERA ++ GS+T +P++ +D+ Sbjct: 256 CEALREISAAREEVPGRRGYPGYMYTDLATIYERAGRIRGR--KGSITQIPILTMPGDDI 313 Query: 335 SAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAAQVKAM-----KQVSGA 389 + IP IT+GQI L +L +GI P IN+ S+SR+ + VS Sbjct: 314 THPIPDLTGYITEGQIVLSRDLHRKGIYPPINVLPSLSRLMKDGIGEGKTREDHGDVSNQ 373 Query: 390 VKGELAQYRE----MSSFSKFS-SDLDSSTQKFLSKGERLTELLKQPQFSPLAMEE 440 + A+ R+ ++ + + S+ D KF E+ +KQ ++ ++EE Sbjct: 374 LYAAYAEGRDLRELVAVVGEEALSERDRKYLKFADLFEQ--RFIKQGRYENRSIEE 427 >gnl|CDD|30001 cd01135, V_A-ATPase_B, V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.. Length = 276 Score = 139 bits (351), Expect = 2e-33 Identities = 81/281 (28%), Positives = 133/281 (47%), Gaps = 7/281 (2%) Query: 94 IVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAI 153 + VPV ++LGR+ + G PIDG I E+ + R E + TGI AI Sbjct: 1 TLKVPVSEDMLGRIFNGSGKPIDGGPEILAEEYLDINGPPINPVARIYPEEMIQTGISAI 60 Query: 154 DSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSV 213 D + + RGQ+ I +G L + +++ E V ++ A+G Sbjct: 61 DGMNTLVRGQKIPIFSG--SGLPHNELAAQIARQAGVVGEEENFAV--VFAAMGITMEDA 116 Query: 214 ARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFR-DNGYHALIAYDDLQ 272 F E+ GAL ++ + A+DP +++ P EY + G H L+ D+ Sbjct: 117 RFFKDDFEETGALERVVLFLNLANDPTIERIITPRMALTTAEYLAYEKGKHVLVILTDMT 176 Query: 273 KHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVN 332 +A A R++S PGR YPG ++ + + ERA ++ GS+T +P++ + Sbjct: 177 NYAEALREISAAREEVPGRRGYPGYMYTDLATIYERAGRVEGR--NGSITQIPILTMPND 234 Query: 333 DVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSR 373 D++ IP IT+GQI L+ +L +GI P IN+ S+SR Sbjct: 235 DITHPIPDLTGYITEGQIVLDRQLHNRGIYPPINVLPSLSR 275 >gnl|CDD|30404 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy production and conversion]. Length = 468 Score = 122 bits (307), Expect = 3e-28 Identities = 100/386 (25%), Positives = 163/386 (42%), Gaps = 31/386 (8%) Query: 19 FGNDSEFSEIGRVLSIGDGIARVYGLNNIRAGEMVQFSHGVYGMALNLEVDNVGVVILGS 78 F + E EI L + +G V +A +L + V + +GS Sbjct: 18 FPEEDELPEIYNALEVQNGNQGTL----------------VLEVAQHLGDNVVRTIAMGS 61 Query: 79 YKEISEGDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCE--QRSCTEADAPGI 136 + G V TG+ + VPVG LGR+ + LG PID KGPIK E ++ AP Sbjct: 62 TDGLVRGLEVIDTGKPISVPVGKGTLGRIFNVLGEPIDEKGPIKAEDFEKWPIHRKAPSF 121 Query: 137 IQRQSVCEPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEK 196 + + E L TGIK ID L P +G + + G GKT +I + N H Sbjct: 122 EELSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEHG----- 176 Query: 197 DKVYCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEY 256 Y ++ +G++ +++ G L + +V ++P ++ G M EY Sbjct: 177 --GYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRVALTGLTMAEY 234 Query: 257 FRD-NGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDA 315 FRD G L+ D++ + A ++S LL R P Y + +L ER Sbjct: 235 FRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTKK- 293 Query: 316 LGAGSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVG 375 GS+T++ + +D++ P + D L ++ GI PA++ S SR Sbjct: 294 ---GSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRQIAALGIYPAVDPLDSTSRAL 350 Query: 376 SAAQV-KAMKQVSGAVKGELAQYREM 400 V + +V+ V+ L +Y+E+ Sbjct: 351 DPKIVGEEHYEVAREVQSILQRYKEL 376 >gnl|CDD|29999 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.. Length = 274 Score = 113 bits (284), Expect = 1e-25 Identities = 78/279 (27%), Positives = 127/279 (45%), Gaps = 12/279 (4%) Query: 97 VPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLSTGIKAIDSL 156 VPVG E LGR+ + LG PID +GPIK ++ +AP +++ + E L TGIK ID L Sbjct: 4 VPVGPETLGRIFNVLGEPIDERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVIDLL 63 Query: 157 IPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARF 216 P +G + + G GKT +I++ N +H Y ++ +G++ Sbjct: 64 APYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGG-------YSVFAGVGERTREGNDL 116 Query: 217 VKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRD-NGYHALIAYDDLQKHA 275 +++ G LS + +V ++P + G M EYFRD G L+ D++ + Sbjct: 117 YHEMKESGVLSKTALVYGQMNEPPGARARVALTGLTMAEYFRDEEGQDVLLFIDNIFRFT 176 Query: 276 VAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVNDVS 335 A ++S LL R P Y + L ER GS+T++ + +D++ Sbjct: 177 QAGSEVSALLGRMPSAVGYQPTLATEMGALQERITSTKK----GSITSVQAVYVPADDLT 232 Query: 336 AYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRV 374 P + D L + GI PA++ S SR+ Sbjct: 233 DPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRI 271 >gnl|CDD|36565 KOG1351, KOG1351, KOG1351, Vacuolar H+-ATPase V1 sector, subunit B [Energy production and conversion]. Length = 489 Score = 108 bits (272), Expect = 3e-24 Identities = 81/305 (26%), Positives = 137/305 (44%), Gaps = 12/305 (3%) Query: 87 IVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPL 146 V+ TG I+ PV ++LGR+ + G PID P+ E R E + Sbjct: 88 TVEFTGEILRTPVSEDMLGRIFNGSGKPIDKGPPVLAEDYLDINGQPINPYARIYPEEMI 147 Query: 147 STGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTF-------LNQKSSHDKGSEKDKV 199 TGI AID + I RGQ+ I I +K HD +D Sbjct: 148 QTGISAIDVMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKRPEKDVHD--GHEDNF 205 Query: 200 YCIYVAIGQKRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFR- 258 ++ A+G + F + E+ G++ + + A+DP +++ P E+ Sbjct: 206 AIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLANDPTIERIITPRLALTTAEFLAY 265 Query: 259 DNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGA 318 H L+ D+ +A A R++S PGR YPG ++ + + ERA ++ Sbjct: 266 QCEKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLATIYERAGRVEGR--N 323 Query: 319 GSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSAA 378 GS+T +P++ +D++ IP IT+GQI+++ +L + I P IN+ S+SR+ +A Sbjct: 324 GSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSA 383 Query: 379 QVKAM 383 + M Sbjct: 384 IGEGM 388 >gnl|CDD|36564 KOG1350, KOG1350, KOG1350, F0F1-type ATP synthase, beta subunit [Energy production and conversion]. Length = 521 Score = 108 bits (270), Expect = 5e-24 Identities = 93/379 (24%), Positives = 159/379 (41%), Gaps = 29/379 (7%) Query: 85 GDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCE 144 G V TG + +PVG E LGR+++ +G PID +GPIK ++ S A+AP ++ E Sbjct: 114 GQKVLDTGYPISIPVGPETLGRIMNVIGEPIDERGPIKSKKYSPIHAEAPEFVEMSVEQE 173 Query: 145 PLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYV 204 L TGIK +D L P +G + + G GKT +I++ N +H Y ++ Sbjct: 174 ILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGG-------YSVFA 226 Query: 205 AIGQKRSSVARFVKALEDRGAL------SYSIVVVASASDPAPMQLLAPFAGCAMGEYFR 258 +G++ + + G + S +V ++P + G + EYFR Sbjct: 227 GVGERTREGNDLYHEMIESGVINLEGETSKVALVYGQMNEPPGARARVALTGLTVAEYFR 286 Query: 259 D-NGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSDALG 317 D G L+ D++ + A ++S LL R P Y + + ER Sbjct: 287 DQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKK--- 343 Query: 318 AGSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSRVGSA 377 GS+T++ + +D++ P + D L + GI PA++ S SR+ Sbjct: 344 -GSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRGIAELGIYPAVDPLDSTSRIMDP 402 Query: 378 AQV-KAMKQVSGAVKGELAQYREMSSFSKF--SSDLDSSTQKFLSKGERLTELLKQPQFS 434 V + V+ V+ L Y+ + +L + +++ ++ L QP Sbjct: 403 NIVGEEHYNVARGVQKTLQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPF-- 460 Query: 435 PLAMEEQVVMIFAGISGCL 453 QV +F G G L Sbjct: 461 ------QVAEVFTGHPGKL 473 >gnl|CDD|144044 pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal domain. Length = 110 Score = 83.5 bits (207), Expect = 1e-16 Identities = 31/111 (27%), Positives = 55/111 (49%), Gaps = 10/111 (9%) Query: 384 KQVSGAVKGELAQYREMSSFSKF--SSDLDSSTQKFLSKGERLTELLKQPQFSPLAMEEQ 441 KQV+G +K ELAQYRE+ + + L + L + R+ E LKQ Q+SP +E+Q Sbjct: 1 KQVAGQLKLELAQYRELQAIVQLVGEDALSEEDKLTLERARRIEEFLKQNQYSPEPVEKQ 60 Query: 442 VVMIF-------AGISGCLDEVAVSQVRKFETNFLSHMRVSSQDILEDIRK 485 V + A + G D++ + + T L+ + ++ + ++K Sbjct: 61 YVPVEETIDLFYALLRGKFDDLPEDALYRIGTIDLAKYK-DLEEKFKKLKK 110 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 77.5 bits (190), Expect = 9e-15 Identities = 52/194 (26%), Positives = 78/194 (40%), Gaps = 34/194 (17%) Query: 164 RELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALEDR 223 L+ G +GKT++ L LN + K +YV I ++ + + + Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGK--------VVYVDIEEEIEELTERLIGESLK 52 Query: 224 GALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSL 283 GAL I+V A+A DPA +LL+ E R+ G LI D+L + A R+ Sbjct: 53 GALDNLIIVFATADDPAAARLLS------KAERLRERGGDDLIILDELTRLVRALRE--- 103 Query: 284 LLRRPPGREAYPGDVFYLHSRLLERAAKMSDALGAGSLTALPVIETQVNDVSAY----IP 339 RE YPG++ LLERA K G +T + ++ D Sbjct: 104 ------IREGYPGELDEELRELLERARK-------GGVTVIFTLQVPSGDKGDPRLTRGA 150 Query: 340 TNVISITDGQIFLE 353 N+ I D I L Sbjct: 151 QNLEDIADTVIVLS 164 >gnl|CDD|145823 pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. Length = 69 Score = 76.0 bits (188), Expect = 2e-14 Identities = 30/67 (44%), Positives = 40/67 (59%) Query: 26 SEIGRVLSIGDGIARVYGLNNIRAGEMVQFSHGVYGMALNLEVDNVGVVILGSYKEISEG 85 IG V+ + GI R+ GL N E+V+F +G+ G LNL D V VV++G +S G Sbjct: 3 QVIGPVVDVEFGIGRLPGLYNALEVELVEFGNGLLGEVLNLGGDKVRVVVMGGTDGLSRG 62 Query: 86 DIVKRTG 92 D VKRTG Sbjct: 63 DEVKRTG 69 >gnl|CDD|30000 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.. Length = 369 Score = 74.1 bits (182), Expect = 8e-14 Identities = 70/246 (28%), Positives = 115/246 (46%), Gaps = 32/246 (13%) Query: 144 EPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIY 203 EPL TG + +D+L P+ +G I G GKT I + S K S D V IY Sbjct: 139 EPLLTGQRVLDTLFPVVKGGTAAIPGPFGCGKTVI--------QQSLSKYSNSDIV--IY 188 Query: 204 VAIGQKRSSVARFVK---ALED----RGALSYSIVVVASASDPAPMQLLAPFAGCAMGEY 256 V G++ + + ++ L D + ++++ +++ P + + + G + EY Sbjct: 189 VGCGERGNEMTEVLEEFPELTDPVTGEPLMKRTVLIANTSNMPVAAREASIYTGITIAEY 248 Query: 257 FRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRL---LERAAKMS 313 FRD GY+ + D + A A R++S L PG E YP YL +RL ERA ++ Sbjct: 249 FRDMGYNVALMADSTSRWAEALREISGRLEEMPGEEGYPA---YLGARLASFYERAGRVK 305 Query: 314 DALGA----GSLTALPVIETQVNDVSAYIPTNVISITDGQIF--LETELFYQGIRPAINI 367 LG+ GS+T + + D S + + I Q+F L+ +L + P+IN Sbjct: 306 -CLGSPGREGSVTIVGAVSPPGGDFSEPVTQATLRIV--QVFWGLDKKLAQRRHFPSINW 362 Query: 368 GLSVSR 373 +S S+ Sbjct: 363 LISYSK 368 >gnl|CDD|31349 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion]. Length = 588 Score = 74.1 bits (182), Expect = 9e-14 Identities = 73/328 (22%), Positives = 136/328 (41%), Gaps = 49/328 (14%) Query: 138 QRQSVCEPLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKD 197 ++ PL TG + ID+L P+ +G + G +GKT + K ++ D Sbjct: 200 RKLPPEIPLVTGQRVIDTLFPVAKGGTAAVPGPFGSGKTVSQ--------HTLSKLADGD 251 Query: 198 KVYCIYVAIGQKRSSVARFVKA---LED----RGALSYSIVVVASASDPAPMQLLAPFAG 250 V IYV G++ + + ++ L+D + + ++++ +++ P + + + G Sbjct: 252 IV--IYVGCGERGNEMTEVLQEFPELKDPNTGQPLMDRTVLIANTSNMPVAAREASIYTG 309 Query: 251 CAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRL---LE 307 + EY+RD GY + D + A A R++S L PG E YP YL SRL E Sbjct: 310 ITIAEYYRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPA---YLGSRLAEFYE 366 Query: 308 RAAKMSDALGA----GSLTALPVIETQVNDVSAYIPTNVISITDGQIF--LETELFYQGI 361 RA ++ + GS+T + + D S + N + + ++F L+ L + Sbjct: 367 RAGRVR-LVSPEERFGSITVIGAVSPPGGDFSEPVTQNTLRVV--RVFWALDAALANRRH 423 Query: 362 RPAINIGLSVSRVGSAAQVKAMKQVSGAVKGELAQYREMSSFSKFSSDLDSSTQKFLSKG 421 P+IN S S + V E R+ + + L + Sbjct: 424 FPSINWLNSYSLYTEDLR----SWYDENVSPEWGALRDQA-------------MEILQRE 466 Query: 422 ERLTELLKQPQFSPLAMEEQVVMIFAGI 449 L E+++ + L +E+ ++ A I Sbjct: 467 SELQEIVQLVGYDALPEKEKSILDVARI 494 Score = 32.1 bits (73), Expect = 0.33 Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 1/89 (1%) Query: 29 GRVLSIGDGIARVYGLNNIRAGEMVQFSH-GVYGMALNLEVDNVGVVILGSYKEISEGDI 87 G+++ I + G+ + ++V+ G+ G + +E + + + I G+ Sbjct: 3 GKIIRISGPVVVAEGMEGAKMYDVVKVGEMGLIGEIIRIEGNRATIQVYEDTAGIRPGEK 62 Query: 88 VKRTGRIVDVPVGLELLGRVVDALGNPID 116 V+ TGR + V +G LL + D + P+D Sbjct: 63 VENTGRPLSVELGPGLLKSIYDGIQRPLD 91 >gnl|CDD|36566 KOG1352, KOG1352, KOG1352, Vacuolar H+-ATPase V1 sector, subunit A [Energy production and conversion]. Length = 618 Score = 63.4 bits (154), Expect = 1e-10 Identities = 82/323 (25%), Positives = 142/323 (43%), Gaps = 52/323 (16%) Query: 145 PLSTGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYV 204 PL TG + +D+L P +G I G GKT I S K S D + IYV Sbjct: 228 PLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVI--------SQSLSKYSNSDAI--IYV 277 Query: 205 AIGQKRSSVAR----FVKALEDRGALSYSI----VVVASASD-PAPMQLLAPFAGCAMGE 255 G++ + ++ F + + + SI +VA+ S+ P + + + G + E Sbjct: 278 GCGERGNEMSEVLMDFPELTMEVDGKTESIMKRTALVANTSNMPVAAREASIYTGITLSE 337 Query: 256 YFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRL---LERAAKM 312 YFRD GY+ + D + A A R++S L P YP YL +RL ERA ++ Sbjct: 338 YFRDMGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPA---YLGARLASFYERAGRV 394 Query: 313 SDALGA----GSLTALPVIETQVNDVSAYIPTNVISITDGQIF--LETELFYQGIRPAIN 366 LG+ GS++ + + D S + + + I Q+F L+ +L + P+IN Sbjct: 395 K-CLGSPDREGSVSIVGAVSPPGGDFSDPVTSATLGIV--QVFWGLDKKLAQRKHFPSIN 451 Query: 367 IGLSVSRVGSAAQVKAMKQVSGAVKGELAQYREMSSFSKFSSDLDSSTQKFLSKGERLTE 426 +S S+ A L + E ++ +F L + ++ L + E L+E Sbjct: 452 WLISYSKYMRA----------------LDPFYE-KNYPEFVV-LRTKAKEILQEEEDLSE 493 Query: 427 LLKQPQFSPLAMEEQVVMIFAGI 449 +++ S LA +++ + A + Sbjct: 494 IVQLVGKSALAETDKITLEVAKL 516 >gnl|CDD|177000 CHL00060, atpB, ATP synthase CF1 beta subunit. Length = 494 Score = 61.6 bits (150), Expect = 5e-10 Identities = 89/336 (26%), Positives = 133/336 (39%), Gaps = 48/336 (14%) Query: 88 VKRTGRIVDVPVGLELLGRVVDALGNPIDGKGPIKCEQRSCTEADAPGIIQRQSVCEPLS 147 V TG + VPVG LGR+ + LG P+D GP+ S AP IQ + Sbjct: 87 VIDTGAPLSVPVGGATLGRIFNVLGEPVDNLGPVDTRTTSPIHRSAPAFIQLDTKLSIFE 146 Query: 148 TGIKAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIG 207 TGIK +D L P RG + + G GKT +I++ N +H S ++ +G Sbjct: 147 TGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGVS-------VFGGVG 199 Query: 208 Q------------KRSSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGE 255 + K S V E + AL Y ++P ++ M E Sbjct: 200 ERTREGNDLYMEMKESGVINEQNIAESKVALVY-----GQMNEPPGARMRVGLTALTMAE 254 Query: 256 YFRD-NGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSD 314 YFRD N L+ D++ + A ++S LL R P Y + L ER + Sbjct: 255 YFRDVNKQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITSTKE 314 Query: 315 ALGAGSLTALPVIETQVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSR- 373 GS+T++ + +D++ P + D L L +GI PA++ S S Sbjct: 315 ----GSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVDPLDSTSTM 370 Query: 374 -----VG----SAAQVKAMKQVSGAVKGELAQYREM 400 VG AQ VK L +Y+E+ Sbjct: 371 LQPRIVGEEHYETAQ---------RVKQTLQRYKEL 397 >gnl|CDD|29994 cd01128, rho_factor, Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.. Length = 249 Score = 40.2 bits (94), Expect = 0.001 Identities = 51/231 (22%), Positives = 97/231 (41%), Gaps = 32/231 (13%) Query: 151 KAIDSLIPIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKR 210 + +D PIG+GQR LI+ K GKT+++ Q ++ +VY I + I ++ Sbjct: 5 RVVDLFAPIGKGQRGLIVAPPKAGKTTLL------QSIANAITKNHPEVYLIVLLIDERP 58 Query: 211 SSVARFVKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDD 270 V ++++ V+ ++ +P + + ++G +I D Sbjct: 59 EEVTDMQRSVK-------GEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDS 111 Query: 271 LQKHAVAYRQLSLLLRRPPGREAYPGDV----FYLHSRLLERAAKMSDALGAGSLT--AL 324 + + A AY + PP + G V + R A + + GSLT A Sbjct: 112 ITRLARAYNTVV-----PPSGKILSGGVDANALHKPKRFFGAARNIEE---GGSLTIIAT 163 Query: 325 PVIET--QVNDVSAYIPTNVISITDGQIFLETELFYQGIRPAINIGLSVSR 373 +++T +++DV I + ++ L+ L + I PAI+I S +R Sbjct: 164 ALVDTGSRMDDV---IFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTR 211 >gnl|CDD|31352 COG1158, Rho, Transcription termination factor [Transcription]. Length = 422 Score = 37.5 bits (87), Expect = 0.010 Identities = 14/29 (48%), Positives = 21/29 (72%) Query: 151 KAIDSLIPIGRGQRELIIGDRKTGKTSII 179 + ID + PIG+GQR LI+ K GKT+++ Sbjct: 162 RVIDLISPIGKGQRGLIVAPPKAGKTTLL 190 >gnl|CDD|30041 cd01298, ATZ_TRZ_like, TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are catalyzed by atrazine chlorohydrolase (AtzA), hydroxyatrazine ethylaminohydrolase (AtzB), and N-isopropylammelide N-isopropylaminohydrolase (AtzC). All three enzymes belong to the superfamily of metal dependent hydrolases. AtzA and AtzB, beside other related enzymes are represented in this CD.. Length = 411 Score = 30.5 bits (69), Expect = 1.2 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 3/50 (6%) Query: 70 NVGVVILGSYKEISEGDIVKRTGRIVDVPVGLELLGRVVDALGNPIDGKG 119 N +V + + +GD++ GRIV V L L D ID KG Sbjct: 5 NGTIVTTDPRRVLEDGDVLVEDGRIVAVGPALPLPAYPADE---VIDAKG 51 >gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]. Length = 260 Score = 29.7 bits (66), Expect = 2.2 Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 10/74 (13%) Query: 144 EPLSTGIKAIDSLIPIG--RGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYC 201 E + TGI +D ++ G RG LI G TGKT I FL + + + Sbjct: 3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKT-IFALQFLYEGAREGEP-------V 54 Query: 202 IYVAIGQKRSSVAR 215 +YV+ + + Sbjct: 55 LYVSTEESPEELLE 68 >gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 169 Score = 28.3 bits (64), Expect = 4.8 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 13/84 (15%) Query: 167 IIGDRKTGKTSIILDTFLNQK-SSHDKGSEKDKVYCI---YVAIGQKRSSVARFVKALED 222 ++G + +GK++ +L FL + S + Y + V GQ++ + R V E Sbjct: 9 VLGAKGSGKSA-LLRAFLGRSFSLNAYSPTIKPRYAVNTVEVY-GQEKYLILREVGEDEV 66 Query: 223 RGALSYS-------IVVVASASDP 239 L+ + +V +SDP Sbjct: 67 AILLNDAELAACDVACLVYDSSDP 90 >gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction only]. Length = 814 Score = 28.3 bits (63), Expect = 4.9 Identities = 15/48 (31%), Positives = 24/48 (50%) Query: 158 PIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVA 205 I G+ LII +GKT +N+ S KG +D +Y +Y++ Sbjct: 33 EIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYIS 80 >gnl|CDD|133307 cd04107, Rab32_Rab38, Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 201 Score = 28.4 bits (64), Expect = 5.4 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 166 LIIGDRKTGKTSII 179 L+IGD GKTSII Sbjct: 4 LVIGDLGVGKTSII 17 >gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).. Length = 166 Score = 27.8 bits (62), Expect = 6.7 Identities = 10/21 (47%), Positives = 12/21 (57%) Query: 159 IGRGQRELIIGDRKTGKTSII 179 I G R LI G TGK+S+ Sbjct: 24 IKPGDRLLITGPSGTGKSSLF 44 >gnl|CDD|146700 pfam04198, Sugar-bind, Putative sugar-binding domain. This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates. Length = 255 Score = 27.9 bits (63), Expect = 7.3 Identities = 10/43 (23%), Positives = 20/43 (46%) Query: 218 KALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDN 260 + L+++ L +IVV A +P ++ L A + +D Sbjct: 11 QRLKEKFGLKEAIVVPDDADEPDTLEALGRAAAQYLSSLLKDG 53 >gnl|CDD|119430 cd05170, PIKKc_SMG1, Suppressor of morphogenetic effect on genitalia-1 (SMG-1), catalytic domain; The SMG-1 catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. SMG-1 is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). In addition to its catalytic domain, SMG-1 contains a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. SMG-1 plays a critical role in the mRNA surveillance mechanism known as non-sense mediated mRNA decay (NMD). NMD protects the cells from the accumulation of aberrant mRNAs with premature termination codons (PTCs) generated by genome mutations and by errors during transcription and splicing. SMG-1 phosphorylates Upf1, another central component of NMD, at the C-terminus upon recognition of PTCs. The phosphorylation/dephosphorylation cycle of Upf1 is essential for promoting NMD.. Length = 307 Score = 27.8 bits (62), Expect = 7.3 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 8/70 (11%) Query: 354 TELFYQGIRPAI---NIGLSVSRVGSAAQVKAMKQVSGAVKGELAQY---REMSSFSKFS 407 ++LFY I PA+ + L VSR V ++QV + E + RE+ S S Sbjct: 130 SDLFYNKITPALKAHGLSLDVSRRDWPLSV--LRQVLDELMQETPKDLLARELWCSSTTS 187 Query: 408 SDLDSSTQKF 417 S+ S TQ++ Sbjct: 188 SEWWSVTQRY 197 >gnl|CDD|133325 cd04125, RabA_like, RabA-like subfamily. RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 188 Score = 27.8 bits (62), Expect = 7.4 Identities = 7/20 (35%), Positives = 12/20 (60%) Query: 166 LIIGDRKTGKTSIILDTFLN 185 +IIGD GK+S++ + Sbjct: 4 VIIGDYGVGKSSLLKRFTED 23 >gnl|CDD|48401 cd02799, tRNA_bind_EMAP-II_like, tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.. Length = 105 Score = 27.4 bits (61), Expect = 8.5 Identities = 14/39 (35%), Positives = 21/39 (53%) Query: 217 VKALEDRGALSYSIVVVASASDPAPMQLLAPFAGCAMGE 255 +K + RG S +V+ AS +D ++LL P G GE Sbjct: 64 LKPRKMRGVKSQGMVLCASNADHEKVELLEPPEGAKPGE 102 >gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 166 Score = 27.7 bits (62), Expect = 8.9 Identities = 8/17 (47%), Positives = 13/17 (76%) Query: 164 RELIIGDRKTGKTSIIL 180 R ++IGD GK+S+I+ Sbjct: 2 RIVLIGDEGVGKSSLIM 18 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.137 0.380 Gapped Lambda K H 0.267 0.0628 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,826,235 Number of extensions: 312437 Number of successful extensions: 943 Number of sequences better than 10.0: 1 Number of HSP's gapped: 909 Number of HSP's successfully gapped: 43 Length of query: 509 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 411 Effective length of database: 4,146,055 Effective search space: 1704028605 Effective search space used: 1704028605 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 60 (27.1 bits)