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)