RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780615|ref|YP_003065028.1| F0F1 ATP synthase subunit beta
[Candidatus Liberibacter asiaticus str. psy62]
(478 letters)
>gnl|CDD|177000 CHL00060, atpB, ATP synthase CF1 beta subunit.
Length = 494
Score = 767 bits (1982), Expect = 0.0
Identities = 308/485 (63%), Positives = 378/485 (77%), Gaps = 12/485 (2%)
Query: 1 MTTKAKTESVGRIQQIMGAVVDVVFVN-SLPPIFSSLETSDKGS-----RIVFEVVQHLG 54
+ + +++GRI QI+G V+DV F +P I+++L + + + EV Q LG
Sbjct: 7 GVSTLEEKNLGRITQIIGPVLDVAFPPGKMPNIYNALVVKGRDTAGQEINVTCEVQQLLG 66
Query: 55 EKTVRCIAMSRTDGLSRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKR 114
VR +AMS TDGL RG VIDTG ++VPVG ATLGRI NV+GEPVD+ G + +
Sbjct: 67 NNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEPVDNLGPVDTRTTS 126
Query: 115 AIHQPSPSYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVA 174
IH+ +P++ + T SI TGIKV+DL++PY++GGKIGLFGGAGVGKTVLIMELINN+A
Sbjct: 127 PIHRSAPAFIQLDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIA 186
Query: 175 KAHGGYSVFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGA 234
KAHGG SVF GVGERTREGNDLY EM +S V I+ + N + SK +L+YGQMNEPPGA
Sbjct: 187 KAHGGVSVFGGVGERTREGNDLYMEMKESGV-IN--EQNIAE--SKVALVYGQMNEPPGA 241
Query: 235 RSRVALTGLTVAEHFRDQG-QDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALE 293
R RV LT LT+AE+FRD QDVL F+DNIFRF QA SE+SALLGR+PSAVGYQ TL+ E
Sbjct: 242 RMRVGLTALTMAEYFRDVNKQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTE 301
Query: 294 MGELQERITTTLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAI 353
MG LQERIT+T +GSITS+QA+YVPADDLTDPAPAT+F HLDATTVLSR ++ KGIYPA+
Sbjct: 302 MGSLQERITSTKEGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAV 361
Query: 354 DPLDSNSSMLEIDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARAR 413
DPLDS S+ML+ IVG+EHY+ A+RV++ LQRYK LQDIIAILG+DELSEED+L VARAR
Sbjct: 362 DPLDSTSTMLQPRIVGEEHYETAQRVKQTLQRYKELQDIIAILGLDELSEEDRLTVARAR 421
Query: 414 KLERFMSQPFHVAESFTGLPGKFVSLEETIRGFKGLVQGEYDHLPELAFYMVGSIDEAVK 473
K+ERF+SQPF VAE FTG PGK+V L ETIRGF+ ++ GE D LPE AFY+VG+IDEA
Sbjct: 422 KIERFLSQPFFVAEVFTGSPGKYVGLAETIRGFQLILSGELDGLPEQAFYLVGNIDEATA 481
Query: 474 KAEVI 478
KA +
Sbjct: 482 KAANL 486
>gnl|CDD|30404 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 758 bits (1958), Expect = 0.0
Identities = 328/474 (69%), Positives = 384/474 (81%), Gaps = 18/474 (3%)
Query: 9 SVGRIQQIMGAVVDVVFVNS--LPPIFSSLETSDKGSR-IVFEVVQHLGEKTVRCIAMSR 65
+ G++ Q++G VVDV F LP I+++LE + +V EV QHLG+ VR IAM
Sbjct: 2 NKGKVVQVIGPVVDVEFPEEDELPEIYNALEVQNGNQGTLVLEVAQHLGDNVVRTIAMGS 61
Query: 66 TDGLSRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISS--EKRAIHQPSPSY 123
TDGL RG VIDTG I+VPVG+ TLGRI NV+GEP+D++G I + EK IH+ +PS+
Sbjct: 62 TDGLVRGLEVIDTGKPISVPVGKGTLGRIFNVLGEPIDEKGPIKAEDFEKWPIHRKAPSF 121
Query: 124 TEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 183
E ST IL TGIKVIDL++PY KGGKIGLFGGAGVGKTVLI ELINN+AK HGGYSVF
Sbjct: 122 EELSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVF 181
Query: 184 AGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGL 243
AGVGERTREGNDLYHEM +S V K +L++GQMNEPPGAR RVALTGL
Sbjct: 182 AGVGERTREGNDLYHEMKESGV------------LDKTALVFGQMNEPPGARMRVALTGL 229
Query: 244 TVAEHFRDQ-GQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERIT 302
T+AE+FRD+ GQDVL F+DNIFRFTQA SE+SALLGR+PSAVGYQ TLA EMG+LQERIT
Sbjct: 230 TMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERIT 289
Query: 303 TTLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSM 362
+T KGSITSVQA+YVPADDLTDPAPAT+F HLDATTVLSRQI+ GIYPA+DPLDS S
Sbjct: 290 STKKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRQIAALGIYPAVDPLDSTSRA 349
Query: 363 LEIDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARARKLERFMSQP 422
L+ IVG+EHY+VAR VQ ILQRYK LQDIIAILGMDELSEEDKL VARARK++RF+SQP
Sbjct: 350 LDPKIVGEEHYEVAREVQSILQRYKELQDIIAILGMDELSEEDKLTVARARKIQRFLSQP 409
Query: 423 FHVAESFTGLPGKFVSLEETIRGFKGLVQGEYDHLPELAFYMVGSIDEAVKKAE 476
F VAE FTG PGK+V L++TIRGFK +++G+YDHLPE AFYMVGSI+EAV+KA+
Sbjct: 410 FFVAEVFTGSPGKYVPLKDTIRGFKRILEGKYDHLPEQAFYMVGSIEEAVEKAK 463
>gnl|CDD|36564 KOG1350, KOG1350, KOG1350, F0F1-type ATP synthase, beta subunit
[Energy production and conversion].
Length = 521
Score = 725 bits (1872), Expect = 0.0
Identities = 338/476 (71%), Positives = 391/476 (82%), Gaps = 7/476 (1%)
Query: 2 TTKAKTESVGRIQQIMGAVVDVVFVNSLPPIFSSLETSDKGSRIVFEVVQHLGEKTVRCI 61
+ A ++ GRI ++GAVVDV F LPPI ++LE + +R+V EV QHLGE TVR I
Sbjct: 44 SKAAAKKNKGRIVAVIGAVVDVQFEEGLPPILNALEVKGRDTRLVLEVAQHLGENTVRTI 103
Query: 62 AMSRTDGLSRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSP 121
AM T+GL RG V+DTG I++PVG TLGRIMNVIGEP+D++G I S + IH +P
Sbjct: 104 AMDGTEGLVRGQKVLDTGYPISIPVGPETLGRIMNVIGEPIDERGPIKSKKYSPIHAEAP 163
Query: 122 SYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS 181
+ E S + IL TGIKV+DL++PY KGGKIGLFGGAGVGKTVLIMELINN+AKAHGGYS
Sbjct: 164 EFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYS 223
Query: 182 VFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALT 241
VFAGVGERTREGNDLYHEMI+S V I+ SK +L+YGQMNEPPGAR+RVALT
Sbjct: 224 VFAGVGERTREGNDLYHEMIESGV-INLEGET-----SKVALVYGQMNEPPGARARVALT 277
Query: 242 GLTVAEHFRDQ-GQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQER 300
GLTVAE+FRDQ GQDVL F+DNIFRFTQA SE+SALLGRIPSAVGYQ TLA +MG +QER
Sbjct: 278 GLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQER 337
Query: 301 ITTTLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNS 360
ITTT KGSITSVQA+YVPADDLTDPAPAT+F HLDATTVLSR I+E GIYPA+DPLDS S
Sbjct: 338 ITTTKKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRGIAELGIYPAVDPLDSTS 397
Query: 361 SMLEIDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARARKLERFMS 420
+++ +IVG+EHY+VAR VQ+ LQ YKSLQDIIAILGMDELSEEDKL VARARK++RF+S
Sbjct: 398 RIMDPNIVGEEHYNVARGVQKTLQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLS 457
Query: 421 QPFHVAESFTGLPGKFVSLEETIRGFKGLVQGEYDHLPELAFYMVGSIDEAVKKAE 476
QPF VAE FTG PGK V LEETIRGFK +++GEYDHLPE AFYMVG I+E V KAE
Sbjct: 458 QPFQVAEVFTGHPGKLVPLEETIRGFKAILEGEYDHLPEQAFYMVGGIEEVVAKAE 513
>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 = 476 bits (1227), Expect = e-135
Identities = 209/284 (73%), Positives = 239/284 (84%), Gaps = 13/284 (4%)
Query: 82 ITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTDASILTTGIKVID 141
I+VPVG TLGRI NV+GEP+D++G I + + IH+ +P + EQST IL TGIKVID
Sbjct: 2 ISVPVGPETLGRIFNVLGEPIDERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVID 61
Query: 142 LISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMI 201
L++PY KGGKIGLFGGAGVGKTVLIMELINN+AKAHGGYSVFAGVGERTREGNDLYHEM
Sbjct: 62 LLAPYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERTREGNDLYHEMK 121
Query: 202 DSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQ-GQDVLFFV 260
+S V SK +L+YGQMNEPPGAR+RVALTGLT+AE+FRD+ GQDVL F+
Sbjct: 122 ESGVL------------SKTALVYGQMNEPPGARARVALTGLTMAEYFRDEEGQDVLLFI 169
Query: 261 DNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERITTTLKGSITSVQAIYVPAD 320
DNIFRFTQA SE+SALLGR+PSAVGYQ TLA EMG LQERIT+T KGSITSVQA+YVPAD
Sbjct: 170 DNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGALQERITSTKKGSITSVQAVYVPAD 229
Query: 321 DLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSMLE 364
DLTDPAPAT+F HLDATTVLSR I+E GIYPA+DPLDS S +L+
Sbjct: 230 DLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRILD 273
>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 = 237 bits (608), Expect = 5e-63
Identities = 90/227 (39%), Positives = 126/227 (55%), Gaps = 15/227 (6%)
Query: 135 TGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 194
TGI+ IDL+ P KG +IG+FGG+G GKTVL+ + N V+ +GER RE
Sbjct: 1 TGIRAIDLLLPIGKGQRIGIFGGSGTGKTVLLGMIARNAKA--DVVEVYVLIGERGREVA 58
Query: 195 DLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQ 254
+ E++ G + ++ +EPP R T LT+AE+FRDQG+
Sbjct: 59 EFIEELL------------GEGALKRTVVVAATSDEPPAERYLAPYTALTIAEYFRDQGK 106
Query: 255 DVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERIT-TTLKGSITSVQ 313
DVL +D++ RF +A EIS LLG P GY +L ++ L ER GSIT++
Sbjct: 107 DVLLLLDSLTRFARALREISLLLGEPPGREGYPGSLFSDLARLLERAGKVEGGGSITALP 166
Query: 314 AIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNS 360
+ VP D+TDP P + + D VLSR+++E+GIYPAID L S S
Sbjct: 167 TVLVPGGDITDPIPDNTISITDGQIVLSRELAERGIYPAIDILLSVS 213
>gnl|CDD|31351 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 235 bits (600), Expect = 3e-62
Identities = 138/447 (30%), Positives = 224/447 (50%), Gaps = 34/447 (7%)
Query: 10 VGRIQQIMGAVVDVVFVNSLPPIFSSLETSDKGSRIVFEVVQHLGEKTVRCIAMSRTDGL 69
GR+ ++ G +++ V + +E S +++ EVV E+ + +G+
Sbjct: 25 RGRLTRVTGLLLEAVGPQARIGELCKIERSRGSEKVLAEVVGFNEERVLLM-PFEPVEGV 83
Query: 70 SRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTD 129
S G V+ TG ++VPVG+A LGR+++ +G P+D G +E+R + P P+ ++
Sbjct: 84 SPGAEVVPTGRPLSVPVGDALLGRVLDGLGRPLDGGGLPDGTERRPLDAPPPNPLKRRPI 143
Query: 130 ASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGER 189
L TG++ ID + KG +IG+F G+GVGK+ L + +I +A +V A +GER
Sbjct: 144 EEPLDTGVRAIDGLLTCGKGQRIGIFAGSGVGKSTL-LGMIARNTEAD--VNVIALIGER 200
Query: 190 TREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHF 249
RE E I+ K+ G + ++ +E R + A T T+AE+F
Sbjct: 201 GREVR----EFIE--------KDLGEEGLKRSVVVVATSDESALMRLKAAFTATTIAEYF 248
Query: 250 RDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERITTTLKGSI 309
RDQG+ VL +D++ RF A EI G P+ GY ++ E+ L ER KGSI
Sbjct: 249 RDQGKRVLLIMDSLTRFAMAQREIGLAAGEPPATKGYPPSVFSELPRLLERAGNGDKGSI 308
Query: 310 TSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSMLEIDIVG 369
T+ + V DD+ DP + LD VLSR ++E G YPAID L S S ++ IV
Sbjct: 309 TAFYTVLVEGDDMNDPIADEVRSILDGHIVLSRALAEAGHYPAIDVLASISRVMP-QIVS 367
Query: 370 QEHYDVARRVQEILQRYKSLQDIIAI----LGMDELSEEDKLVVARARKLERFMSQPFHV 425
+EH ARR++++L RY+ +D+I I G D ++ + K+E+F+ Q
Sbjct: 368 EEHRKAARRLRQLLSRYEENEDLIRIGAYQKGSDPELDK---AIKLYPKIEQFLKQG--- 421
Query: 426 AESFTGLPGKFVSLEETIRGFKGLVQG 452
+ S EET+ + ++
Sbjct: 422 -------IDEKSSFEETLEQLEAILSS 441
>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 = 195 bits (496), Expect = 3e-50
Identities = 110/343 (32%), Positives = 178/343 (51%), Gaps = 23/343 (6%)
Query: 83 TVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTDASILTTGIKVIDL 142
+VPVG+A LGR+++ GEP+D +G + + + + P+ ++ +L TG++ ID
Sbjct: 3 SVPVGDALLGRVLDAFGEPLDGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAIDG 62
Query: 143 ISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMID 202
+ KG ++G+F G+GVGK+ L + +I A +V A +GER RE + + +
Sbjct: 63 LLTVGKGQRLGIFAGSGVGKSTL-LGMIARGTTAD--VNVIALIGERGREVREFIEKDL- 118
Query: 203 SKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQDVLFFVDN 262
G + ++ +E P R + A T +AE+FRDQG+DVL +D+
Sbjct: 119 -----------GEEGLKRSVVVVATSDESPLLRVKAAYTATAIAEYFRDQGKDVLLLMDS 167
Query: 263 IFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERITTTLKGSITSVQAIYVPADDL 322
+ RF A EI G P+ GY ++ + L ER + KGSIT+ + V DDL
Sbjct: 168 LTRFAMAQREIGLAAGEPPTTKGYPPSVFALLPRLLERAGNSDKGSITAFYTVLVEGDDL 227
Query: 323 TDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSMLEIDIVGQEHYDVARRVQEI 382
+P + LD VLSR ++ G YPAID L S S ++ +V EH + AR+++E+
Sbjct: 228 NEPIADAVRSILDGHIVLSRALAAAGHYPAIDVLKSISRLMN-AVVTPEHKEAARKLREL 286
Query: 383 LQRYKSLQDIIAI----LGMDELSEEDKLVVARARKLERFMSQ 421
L Y+ ++D+I I G D +E + K+E F+ Q
Sbjct: 287 LSAYQEVEDLIRIGAYKKGSDPEVDE---AIKLLPKIEAFLKQ 326
>gnl|CDD|31350 COG1156, NtpB, Archaeal/vacuolar-type H+-ATPase subunit B [Energy
production and conversion].
Length = 463
Score = 138 bits (348), Expect = 4e-33
Identities = 101/377 (26%), Positives = 167/377 (44%), Gaps = 26/377 (6%)
Query: 66 TDGLSRGD-CVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYT 124
T GL V TG + +PV E LGRI N G+P+D I+ ++ I+ +
Sbjct: 62 TSGLDTKGTTVRFTGETLKIPVSEDLLGRIFNGSGKPIDGGPEIVPEDRLDINGAPINPY 121
Query: 125 EQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS--- 181
+ + TGI ID ++ +G K+ +F G+G+ L + I A G
Sbjct: 122 ARIYPEEFIQTGISAIDGMNTLVRGQKLPIFSGSGLPHNELAAQ-IARQATVDGEEEEFA 180
Query: 182 -VFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVAL 240
VFA +G E E + G+ + L ++P R
Sbjct: 181 VVFAAMGITHEEALFFMDEF----------EETGAL--DRAVLFLNLADDPAVERIITPR 228
Query: 241 TGLTVAEHFR-DQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQE 299
LTVAE+ ++ VL + ++ + +A EISA +P GY + ++ + E
Sbjct: 229 MALTVAEYLAFEKDMHVLVILTDMTNYCEALREISAAREEVPGRRGYPGYMYTDLATIYE 288
Query: 300 R--ITTTLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLD 357
R KGSIT + + +P DD+T P P + + VLSR + KGIYP I+ L
Sbjct: 289 RAGRIRGRKGSITQIPILTMPGDDITHPIPDLTGYITEGQIVLSRDLHRKGIYPPINVLP 348
Query: 358 SNSSMLEIDI----VGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARAR 413
S S +++ I ++H DV+ ++ + L++++A++G + LSE D+ + A
Sbjct: 349 SLSRLMKDGIGEGKTREDHGDVSNQLYAAYAEGRDLRELVAVVGEEALSERDRKYLKFAD 408
Query: 414 KLE-RFMSQPFHVAESF 429
E RF+ Q + S
Sbjct: 409 LFEQRFIKQGRYENRSI 425
>gnl|CDD|31349 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
production and conversion].
Length = 588
Score = 133 bits (336), Expect = 1e-31
Identities = 99/361 (27%), Positives = 159/361 (44%), Gaps = 26/361 (7%)
Query: 93 RIMNVIGEPVDDQG--AIISSEKRAIHQPSPSYTEQSTDASILTTGIKVIDLISPYQKGG 150
+ +VI + G + + + P + L TG +VID + P KGG
Sbjct: 167 TVEDVIATVSTEGGEVDVQMMTTWPVRKARP-VKRKLPPEIPLVTGQRVIDTLFPVAKGG 225
Query: 151 KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIDSKVNIDPR 210
+ G G GKTV L A G ++ G GER E ++ E + K DP
Sbjct: 226 TAAVPGPFGSGKTVSQHTLSKL---ADGDIVIYVGCGERGNEMTEVLQEFPELK---DPN 279
Query: 211 KNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQAN 270
G + + L+ N P AR TG+T+AE++RD G DV D+ R+ +A
Sbjct: 280 --TGQPLMDRTVLIANTSNMPVAAREASIYTGITIAEYYRDMGYDVALMADSTSRWAEAL 337
Query: 271 SEISALLGRIPSAVGYQSTLALEMGELQER--ITTTL-----KGSITSVQAIYVPADDLT 323
EIS L +P GY + L + E ER + GSIT + A+ P D +
Sbjct: 338 REISGRLEEMPGEEGYPAYLGSRLAEFYERAGRVRLVSPEERFGSITVIGAVSPPGGDFS 397
Query: 324 DPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSMLEI------DIVGQEHYDVAR 377
+P + + L ++ + +P+I+ L+S S E + V E +
Sbjct: 398 EPVTQNTLRVVRVFWALDAALANRRHFPSINWLNSYSLYTEDLRSWYDENVSPEWGALRD 457
Query: 378 RVQEILQRYKSLQDIIAILGMDELSEEDKLVVARARKL-ERFMSQ-PFHVAESFTGLPGK 435
+ EILQR LQ+I+ ++G D L E++K ++ AR + E F+ Q F +++ L +
Sbjct: 458 QAMEILQRESELQEIVQLVGYDALPEKEKSILDVARIIREDFLQQNAFDEIDAYCSLRKQ 517
Query: 436 F 436
+
Sbjct: 518 Y 518
>gnl|CDD|144044 pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal
domain.
Length = 110
Score = 130 bits (330), Expect = 7e-31
Identities = 42/105 (40%), Positives = 64/105 (60%), Gaps = 3/105 (2%)
Query: 373 YDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARARKLERFMSQPFHVAESFTGL 432
VA +++ L +Y+ LQ I+ ++G D LSEEDKL + RAR++E F+ Q + E
Sbjct: 1 KQVAGQLKLELAQYRELQAIVQLVGEDALSEEDKLTLERARRIEEFLKQNQYSPEPV--- 57
Query: 433 PGKFVSLEETIRGFKGLVQGEYDHLPELAFYMVGSIDEAVKKAEV 477
++V +EETI F L++G++D LPE A Y +G+ID A K
Sbjct: 58 EKQYVPVEETIDLFYALLRGKFDDLPEDALYRIGTIDLAKYKDLE 102
>gnl|CDD|30405 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 124 bits (314), Expect = 4e-29
Identities = 104/433 (24%), Positives = 190/433 (43%), Gaps = 41/433 (9%)
Query: 2 TTKAKTESVGRIQQIMGAVVDVVFVNSLPPIFSS--LETSDKGSRIVFEVVQHLGEKTVR 59
+A+ + VG + + + V+ L + + +E V + +L E +V
Sbjct: 20 DVEAEVKEVGTVISVGD---GIARVSGLENVMAGELVEFPGG----VKGMALNLEEDSVG 72
Query: 60 CIAMSRTDGLSRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQP 119
+ + + GD V TG + VPVGE LGR+++ +G P+D +G I +++ R + +
Sbjct: 73 AVILGDYSDIKEGDEVKRTGRILEVPVGEELLGRVVDALGNPIDGKGPIDATKTRPVEKK 132
Query: 120 SPSYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGG 179
+P ++ + L TGIK ID + P +G + + G GKT + ++ I N K G
Sbjct: 133 APGVMDRKSVNEPLQTGIKAIDALIPIGRGQRELIIGDRQTGKTAIAIDTIIN-QKGSGV 191
Query: 180 YSVFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVA 239
++ +G++ ++ + + +G+ ++ ++ +
Sbjct: 192 KCIYVAIGQKRSTVANVVRTL----------EEHGAM--DYTIVVAASASDSAPLQYLAP 239
Query: 240 LTGLTVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGY-------QSTLAL 292
G +AE+FRD G+DVL D++ + A EIS LL R P Y S L
Sbjct: 240 YAGCAMAEYFRDNGKDVLIVYDDLSKHAVAYREISLLLRRPPGREAYPGDVFYLHSRLLE 299
Query: 293 EMGELQERITTTLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPA 352
+L + + GSIT++ I A D++ P + D L + GI PA
Sbjct: 300 RAAKLSDELGG---GSITALPIIETQAGDVSAYIPTNVISITDGQIFLETDLFNAGIRPA 356
Query: 353 IDPLDSNS---SMLEIDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVV 409
I+ S S S +I + + VA ++ IL +Y+ L+ + G D L + + +
Sbjct: 357 INVGLSVSRVGSAAQIKAMKK----VAGSLRLILAQYRELEA-FSQFGSD-LDKATRKQL 410
Query: 410 ARARKLERFMSQP 422
R ++L + QP
Sbjct: 411 ERGKRLTELLKQP 423
>gnl|CDD|36566 KOG1352, KOG1352, KOG1352, Vacuolar H+-ATPase V1 sector, subunit A
[Energy production and conversion].
Length = 618
Score = 115 bits (290), Expect = 2e-26
Identities = 85/324 (26%), Positives = 159/324 (49%), Gaps = 30/324 (9%)
Query: 116 IHQPSPSYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAK 175
+ QP P TE+ L TG +V+D + P +GG + G G GKTV +++
Sbjct: 213 VRQPRP-VTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTV--------ISQ 263
Query: 176 AHGGYS-----VFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNE 230
+ YS ++ G GER E +++ + + + +D + ++ + +L+ N
Sbjct: 264 SLSKYSNSDAIIYVGCGERGNEMSEVLMDFPELTMEVDGKT---ESIMKRTALVANTSNM 320
Query: 231 PPGARSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTL 290
P AR TG+T++E+FRD G +V D+ R+ +A EIS L +P+ GY + L
Sbjct: 321 PVAAREASIYTGITLSEYFRDMGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYL 380
Query: 291 ALEMGELQERITTTL-------KGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQ 343
+ ER +GS++ V A+ P D +DP + + + L ++
Sbjct: 381 GARLASFYERAGRVKCLGSPDREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKK 440
Query: 344 ISEKGIYPAIDPLDSNSS-MLEIDIVGQEHY----DVARRVQEILQRYKSLQDIIAILGM 398
++++ +P+I+ L S S M +D +++Y + + +EILQ + L +I+ ++G
Sbjct: 441 LAQRKHFPSINWLISYSKYMRALDPFYEKNYPEFVVLRTKAKEILQEEEDLSEIVQLVGK 500
Query: 399 DELSEEDKLVVARARKL-ERFMSQ 421
L+E DK+ + A+ + + F+ Q
Sbjct: 501 SALAETDKITLEVAKLIKDDFLQQ 524
>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 = 111 bits (278), Expect = 7e-25
Identities = 78/286 (27%), Positives = 126/286 (44%), Gaps = 20/286 (6%)
Query: 82 ITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTDASILTTGIKVID 141
+ VPV E LGRI N G+P+D I++ E I+ P + + ++ TGI ID
Sbjct: 2 LKVPVSEDMLGRIFNGSGKPIDGGPEILAEEYLDINGPPINPVARIYPEEMIQTGISAID 61
Query: 142 LISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS----VFAGVGERTREGNDLY 197
++ +G KI +F G+G+ L ++ A G VFA +G +
Sbjct: 62 GMNTLVRGQKIPIFSGSGLPHNELAAQIARQ-AGVVGEEENFAVVFAAMGITMEDARFFK 120
Query: 198 HEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFR-DQGQDV 256
+ + G+ + L N+P R LT AE+ ++G+ V
Sbjct: 121 DDF----------EETGAL--ERVVLFLNLANDPTIERIITPRMALTTAEYLAYEKGKHV 168
Query: 257 LFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQER--ITTTLKGSITSVQA 314
L + ++ + +A EISA +P GY + ++ + ER GSIT +
Sbjct: 169 LVILTDMTNYAEALREISAAREEVPGRRGYPGYMYTDLATIYERAGRVEGRNGSITQIPI 228
Query: 315 IYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNS 360
+ +P DD+T P P + + VL RQ+ +GIYP I+ L S S
Sbjct: 229 LTMPNDDITHPIPDLTGYITEGQIVLDRQLHNRGIYPPINVLPSLS 274
>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 = 106 bits (265), Expect = 2e-23
Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 18/253 (7%)
Query: 116 IHQPSPSYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAK 175
+ QP P E+ L TG +V+D + P KGG + G G GKTV+ L +K
Sbjct: 125 VRQPRP-VKEKLPPNEPLLTGQRVLDTLFPVVKGGTAAIPGPFGCGKTVIQQSL----SK 179
Query: 176 -AHGGYSVFAGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGA 234
++ ++ G GER GN++ + + DP G + + L+ N P A
Sbjct: 180 YSNSDIVIYVGCGER---GNEMTEVLEEFPELTDPVT--GEPLMKRTVLIANTSNMPVAA 234
Query: 235 RSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEM 294
R TG+T+AE+FRD G +V D+ R+ +A EIS L +P GY + L +
Sbjct: 235 REASIYTGITIAEYFRDMGYNVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLGARL 294
Query: 295 GELQER--ITTTL-----KGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEK 347
ER L +GS+T V A+ P D ++P + + L ++++++
Sbjct: 295 ASFYERAGRVKCLGSPGREGSVTIVGAVSPPGGDFSEPVTQATLRIVQVFWGLDKKLAQR 354
Query: 348 GIYPAIDPLDSNS 360
+P+I+ L S S
Sbjct: 355 RHFPSINWLISYS 367
>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 = 100 bits (250), Expect = 1e-21
Identities = 75/290 (25%), Positives = 119/290 (41%), Gaps = 41/290 (14%)
Query: 82 ITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTDASILTTGIKVID 141
VPVGEA LGR+++ +G P+D +G I + E+R I +P + + L TGIK ID
Sbjct: 2 ADVPVGEALLGRVVDALGNPIDGKGPIETKERRPIESKAPGIIPRKSVNEPLQTGIKAID 61
Query: 142 LISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMI 201
+ P +G + + G GKT + ++ I N K Y ++ +G++
Sbjct: 62 AMIPIGRGQRELIIGDRQTGKTAIAIDTIIN-QKGKKVYCIYVAIGQK------------ 108
Query: 202 DSKVNIDPRKNNGSAVGSKCSLL--YGQM----------NEPPGARSRVALTGLTVAEHF 249
S V L +G M ++P + TG + E+F
Sbjct: 109 ------------ASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAPYTGCAMGEYF 156
Query: 250 RDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERITTTLK--- 306
D G+ L D++ + A ++S LL R P Y + L ER
Sbjct: 157 MDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKLNDELG 216
Query: 307 -GSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDP 355
GS+T++ I A D++ P + D L + KGI PAI+
Sbjct: 217 GGSLTALPIIETQAGDVSAYIPTNVISITDGQIFLETDLFNKGIRPAINV 266
>gnl|CDD|36565 KOG1351, KOG1351, KOG1351, Vacuolar H+-ATPase V1 sector, subunit B
[Energy production and conversion].
Length = 489
Score = 97.4 bits (242), Expect = 8e-21
Identities = 92/363 (25%), Positives = 158/363 (43%), Gaps = 30/363 (8%)
Query: 78 TGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYTEQSTDASILTTGI 137
TG + PV E LGRI N G+P+D +++ + I+ + + ++ TGI
Sbjct: 92 TGEILRTPVSEDMLGRIFNGSGKPIDKGPPVLAEDYLDINGQPINPYARIYPEEMIQTGI 151
Query: 138 KVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLY 197
ID+++ +G KI +F AG+ + ++ AG+ +R +
Sbjct: 152 SAIDVMNSIARGQKIPIFSAAGLPHNEIAAQICRQ-----------AGLVKRPEKDVHDG 200
Query: 198 HE------MIDSKVNIDPR---KNNGSAVGS--KCSLLYGQMNEPPGARSRVALTGLTVA 246
HE VN++ K + GS + L N+P R LT A
Sbjct: 201 HEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLANDPTIERIITPRLALTTA 260
Query: 247 EHFRDQ-GQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERI--TT 303
E Q + VL + ++ + A E+SA +P GY + ++ + ER
Sbjct: 261 EFLAYQCEKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLATIYERAGRVE 320
Query: 304 TLKGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKGIYPAIDPLDSNSSML 363
GSIT + + +P DD+T P P + + + RQ+ + IYP I+ L S S ++
Sbjct: 321 GRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLM 380
Query: 364 EIDI----VGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKLVVARARKLER-F 418
+ I ++H DV+ ++ K +Q + A++G + LS ED L + K E+ F
Sbjct: 381 KSAIGEGMTRKDHSDVSNQLYACYAIGKDVQAMKAVVGEEALSSEDLLYLEFLDKFEKNF 440
Query: 419 MSQ 421
+SQ
Sbjct: 441 ISQ 443
>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 = 75.1 bits (184), Expect = 4e-14
Identities = 51/196 (26%), Positives = 74/196 (37%), Gaps = 35/196 (17%)
Query: 151 KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIDSKVNIDPR 210
I +FG G GKT L ++L N+A GG V+ + E E +
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEIEELTERLIG----------- 48
Query: 211 KNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQAN 270
+ +++ ++P AR AE R++G D L +D + R +A
Sbjct: 49 -ESLKGALDNLIIVFATADDPAAARLLSK------AERLRERGGDDLIILDELTRLVRAL 101
Query: 271 SEISALLGRIPSAVGYQSTLALEMGELQERITTTLKGSITSVQAIYVPADDLTDP----A 326
EI GY L E+ EL ER KG +T + + VP+ D DP
Sbjct: 102 REI---------REGYPGELDEELRELLERAR---KGGVTVIFTLQVPSGDKGDPRLTRG 149
Query: 327 PATSFTHLDATTVLSR 342
D VLSR
Sbjct: 150 AQNLEDIADTVIVLSR 165
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 70.8 bits (174), Expect = 9e-13
Identities = 81/306 (26%), Positives = 130/306 (42%), Gaps = 43/306 (14%)
Query: 67 DGLS--RGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSYT 124
DGL G V TG +PV EA LGR++N + +P+D +G I +SE R I P+P
Sbjct: 57 DGLMIQEGSSVKATGKIAQIPVSEAYLGRVVNALAKPIDGKGEISASESRLIESPAPGII 116
Query: 125 EQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFA 184
+ + L TG+ ID + P +G + + G GKT + + I N K V+
Sbjct: 117 SRRSVYEPLQTGLIAIDSMIPIGRGQRELIIGDRQTGKTAVATDTILN-QKGQNVICVYV 175
Query: 185 GVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLY--GQM----------NEPP 232
+G++ S+V + L G M + P
Sbjct: 176 AIGQKA------------------------SSVAQVVTTLQERGAMEYTIVVAETADSPA 211
Query: 233 GARSRVALTGLTVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLAL 292
+ TG +AE+F +G+ L D++ + QA ++S LL R P Y +
Sbjct: 212 TLQYLAPYTGAALAEYFMYRGRHTLIIYDDLSKQAQAYRQMSLLLRRPPGREAYPGDVFY 271
Query: 293 EMGELQER---ITTTL-KGSITSVQAIYVPADDLTDPAPATSFTHLDATTVLSRQISEKG 348
L ER +++ L +GS+T++ + A D++ P + D LS + G
Sbjct: 272 LHSRLLERAAKLSSQLGEGSMTALPIVETQAGDVSAYIPTNVISITDGQIFLSADLFNAG 331
Query: 349 IYPAID 354
I PAI+
Sbjct: 332 IRPAIN 337
>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 = 66.4 bits (163), Expect = 2e-11
Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 13 IQQIMGAVVDVVFVN-SLPPIFSSLETSDK-GSRIVFEVVQHLGEKTVRCIAMSRTDGLS 70
I Q++G VVDV F LP ++++LE + V +LG VR + M TDGLS
Sbjct: 1 IVQVIGPVVDVEFGIGRLPGLYNALEVELVEFGNGLLGEVLNLGGDKVRVVVMGGTDGLS 60
Query: 71 RGDCVIDTG 79
RGD V TG
Sbjct: 61 RGDEVKRTG 69
>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 = 53.7 bits (129), Expect = 1e-07
Identities = 59/269 (21%), Positives = 108/269 (40%), Gaps = 36/269 (13%)
Query: 138 KVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGG-YSVFAGVGERTREGNDL 196
+V+DL +P KG + + GKT L+ + N + K H Y + + ER E D+
Sbjct: 5 RVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDM 64
Query: 197 YHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGLTVAEHFRDQGQDV 256
+ K ++ +EPP +VA L A+ + G+DV
Sbjct: 65 QRSV-------------------KGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDV 105
Query: 257 LFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQ--ERITTTLK-----GSI 309
+ +D+I R +A + + G+I S ++ L +R + GS+
Sbjct: 106 VILLDSITRLARAYNTVVPPSGKILSG-------GVDANALHKPKRFFGAARNIEEGGSL 158
Query: 310 TSVQAIYVPADDLTDPAPATSFTHL-DATTVLSRQISEKGIYPAIDPLDSNSSMLEIDIV 368
T + V D F + VL R+++E+ I+PAID L S + E+ ++
Sbjct: 159 TIIATALVDTGSRMDDVIFEEFKGTGNMELVLDRRLAERRIFPAIDILKSGTRKEEL-LL 217
Query: 369 GQEHYDVARRVQEILQRYKSLQDIIAILG 397
E ++ +L ++ + +L
Sbjct: 218 DPEELQRMWLLRRVLSDMDPIEAMEFLLK 246
>gnl|CDD|31352 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 49.5 bits (118), Expect = 2e-06
Identities = 60/241 (24%), Positives = 98/241 (40%), Gaps = 33/241 (13%)
Query: 125 EQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAH-GGYSVF 183
E+ ++ L+T +VIDLISP KG + + GKT L+ + N + H +
Sbjct: 151 ERENGSTDLST--RVIDLISPIGKGQRGLIVAPPKAGKTTLLQNIANAITTNHPECELIV 208
Query: 184 AGVGERTREGNDLYHEMIDSKVNIDPRKNNGSAVGSKCSLLYGQMNEPPGARSRVALTGL 243
+ ER E D+ R G V S +EPP +VA +
Sbjct: 209 LLIDERPEEVTDM------------QRSVKGEVVAST-------FDEPPSRHVQVAEMVI 249
Query: 244 TVAEHFRDQGQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERITT 303
A+ + G+DV+ +D+I R +A + + G++ S G + AL +R
Sbjct: 250 EKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSG-GVDAN-ALHR---PKRFFG 304
Query: 304 TLK-----GSITSVQAIYVPADDLTDPAPATSFTHL-DATTVLSRQISEKGIYPAIDPLD 357
+ GS+T + V D F + L R+++E+ I+PAID
Sbjct: 305 AARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNMELHLDRKLAERRIFPAIDINK 364
Query: 358 S 358
S
Sbjct: 365 S 365
>gnl|CDD|36567 KOG1353, KOG1353, KOG1353, F0F1-type ATP synthase, alpha subunit
[Energy production and conversion].
Length = 340
Score = 46.5 bits (110), Expect = 2e-05
Identities = 36/116 (31%), Positives = 53/116 (45%), Gaps = 8/116 (6%)
Query: 57 TVRCIAMSRTDGLSRGDCVIDTGTQITVPVGEATLGRIMNVIGEPVDDQGAIISSEKRAI 116
V + + GD V T VP +A LGR+ +GEP+D G I + E+R I
Sbjct: 63 NVGVVVFGEDSLIKEGDTVKRTAAISDVPPLKALLGRVGCALGEPIDGNGKISAKERRII 122
Query: 117 HQPSPSYTEQSTDASILTTGIKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINN 172
P S E + TG+K +D + P +G + + G GKT L ++ I N
Sbjct: 123 --PRASVDE------PMQTGLKAVDSLVPIGRGQRELIIGDRQTGKTSLAIDTILN 170
>gnl|CDD|146673 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30
as well as the Vps36 protein. Vps36 is involved in Golgi
to endosome trafficking. EAP30 is a subunit of the ELL
complex. The ELL is an 80-kDa RNA polymerase II
transcription factor. ELL interacts with three other
proteins to form the complex known as ELL complex. The
ELL complex is capable of increasing that catalytic rate
of transcription elongation, but is unable to repress
initiation of transcription by RNA polymerase II as is
the case of ELL. EAP30 is thought to lead to the
derepression of ELL's transcriptional inhibitory
activity.
Length = 219
Score = 32.6 bits (75), Expect = 0.24
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 14/84 (16%)
Query: 353 IDPLDSNSSMLEIDIVGQEHYDVARRVQEILQRYK-------SLQDIIAIL----GMDEL 401
+DPL S VG +Y++A ++ EI SLQD+ A+ G + +
Sbjct: 72 VDPLASKKGFWSGLGVGDFYYELAVQIVEICLATLKENGGIISLQDLYALYNRARGTELV 131
Query: 402 SEEDKLVVARARKLERFMSQPFHV 425
S +D ++ +KLE+ F +
Sbjct: 132 SPDD--LLKACKKLEKLGL-GFKL 152
>gnl|CDD|147324 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyse the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 31.7 bits (73), Expect = 0.51
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 260 VDNIFRFTQANSEISALLGRIPSAVGYQSTLALEMGELQERIT 302
IF EI AL ++P+AV Q L LE+ L R T
Sbjct: 1291 AREIFGLPALWDEIEALDNKVPAAV--QLRLLLELRRLLRRAT 1331
>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 31.3 bits (71), Expect = 0.57
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 125 EQSTDASILTTGIKVID-LISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 183
++ + TG +D + S ++ G I + G+GKT L + + N A
Sbjct: 171 FENGGLIGVPTGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAI 230
Query: 184 AGVGERTREGNDLYHEMIDSKVNIDPRK 211
+ E + E L ++ S+ I+ K
Sbjct: 231 FSL-EMSEE--QLVMRLLSSESGIESSK 255
>gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB..
Length = 226
Score = 30.9 bits (70), Expect = 0.76
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 133 LTTGIKVIDLI--SPYQKGGKIGLFGGAGVGKTVLIMELINNVAK 175
++TG K +D + G +FG G GKT L ++L
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQL 45
>gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 952
Score = 30.8 bits (69), Expect = 0.95
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 141 DLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAH 177
+SP + G I L G G GKT L+ L + +K
Sbjct: 423 QELSPVFRHGNILLNGPKGSGKTNLVKALFDYYSKDL 459
>gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction
mechanisms].
Length = 889
Score = 30.7 bits (69), Expect = 1.0
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 149 GGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 186
G +G++G GVGKT L ++ N + + V
Sbjct: 179 VGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWV 216
>gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 30.3 bits (68), Expect = 1.1
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 125 EQSTDASILTTGIKVIDLISP--YQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSV 182
E+ D ++TG +D +G ++G GKT L ++L+ N K GG +
Sbjct: 34 ERREDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKP-GGKAA 92
Query: 183 F 183
F
Sbjct: 93 F 93
>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 30.0 bits (67), Expect = 1.6
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 141 DLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 183
L+ +++G + L G GVGKT L + + N + KA G SV
Sbjct: 97 SLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKA--GISVL 137
>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 29.7 bits (66), Expect = 1.7
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 133 LTTGIKVIDLISP--YQKGGKIGLFGGAGVGKTVLIMELINNVAKA 176
+ TGI +D I +G + + G G GKT+ ++ + A+
Sbjct: 5 IPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGARE 50
>gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.6 bits (67), Expect = 1.8
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 154 LFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 194
++G GKT L+ E + + + G ++ R E
Sbjct: 25 VYGPRRCGKTALLREFLEEL-RELGYRVIYYDPLRREFEEK 64
>gnl|CDD|147481 pfam05317, Thermopsin, Thermopsin. This family consists of several
thermopsin proteins from archaebacteria. Thermopsin is a
thermostable acid protease which is capable of
hydrolysing the following bonds: Leu-Val, Leu-Tyr,
Phe-Phe, Phe-Tyr, and Tyr-Thr. The specificity of
thermopsin is therefore similar to that of pepsin, that
is, it prefers large hydrophobic residues at both sides
of the scissile bond.
Length = 267
Score = 29.6 bits (67), Expect = 2.0
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 255 DVLFFVDNIFRFTQANSEISAL----LGRIPSAVGYQS 288
+ L F+DN++ FT + +S G I AV Q
Sbjct: 97 NTLTFIDNVWNFTSPFANLSNSSISGNGVIYGAVNGQY 134
>gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 29.5 bits (67), Expect = 2.1
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 154 LFGGAGVGKTVLIMELINNVAKAHG 178
L+G G GK+ L L + G
Sbjct: 3 LYGPPGCGKSTLAKYLARALLDHLG 27
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.2 bits (64), Expect = 2.3
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 146 YQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGND 195
+ K KI + G GVGKT L+ L+ + ++ +T E
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYR 51
>gnl|CDD|34477 COG4868, COG4868, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 493
Score = 29.2 bits (65), Expect = 2.3
Identities = 29/94 (30%), Positives = 41/94 (43%), Gaps = 17/94 (18%)
Query: 343 QISEKGIYPAIDPLDSNSSMLEIDIVGQEHYDVARRVQEILQRY-KSLQDI--------- 392
+I K Y + P D +M+ I E A + QEI++RY K+L D
Sbjct: 267 RILGKSPYAS--PTDMGVNMVGFAITDDEAAREASK-QEIIRRYFKTLVDFKAENVDEEA 323
Query: 393 ---IAILGMD-ELSEEDKLVVARARKLERFMSQP 422
I +L D L+ ED+ VV AR+ QP
Sbjct: 324 VKRIELLMNDLGLTPEDRKVVVFARQKAELTGQP 357
>gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily
includes classical N-Ras, H-Ras, and K-Ras, as well as
R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1,
RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins
regulate cell growth, proliferation and differentiation.
Ras is activated by guanine nucleotide exchange factors
(GEFs) that release GDP and allow GTP binding. Many
RasGEFs have been identified. These are sequestered in
the cytosol until activation by growth factors triggers
recruitment to the plasma membrane or Golgi, where the
GEF colocalizes with Ras. Active GTP-bound Ras
interacts with several effector proteins: among the best
characterized are the Raf kinases, phosphatidylinositol
3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 160
Score = 28.7 bits (65), Expect = 3.4
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 151 KIGLFGGAGVGKTVLIMELINNV 173
K+ + G GVGK+ + ++ +
Sbjct: 1 KVVVLGAGGVGKSAITIQFVKGT 23
>gnl|CDD|33254 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.8 bits (64), Expect = 3.5
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 154 LFGGAGVGKTVLIMELINNVAKAHGGYSVF 183
+ G G GKTVL+ L+ K V
Sbjct: 441 IIGPTGAGKTVLLSFLLAQALKYGNPQIVA 470
>gnl|CDD|73056 cd03297, ABC_ModC_molybdenum_transporter, ModC is an ABC-type
transporter and the ATPase component of a molybdate
transport system that also includes the periplasmic
binding protein ModA and the membrane protein ModB. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 214
Score = 28.6 bits (64), Expect = 3.6
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 148 KGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 186
G+FG +G GK+ L+ I + K GG V G
Sbjct: 22 NEEVTGIFGASGAGKSTLL-RCIAGLEKPDGGTIVLNGT 59
>gnl|CDD|29984 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange..
Length = 325
Score = 28.6 bits (64), Expect = 3.8
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 125 EQSTDASILTTGIKVIDL---ISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS 181
+ D ++ TG +D+ I Y KG I ++G GKT L + I K GG
Sbjct: 28 DAVQDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKL-GGTV 86
Query: 182 VF 183
F
Sbjct: 87 AF 88
>gnl|CDD|35737 KOG0517, KOG0517, KOG0517, Beta-spectrin [Cytoskeleton].
Length = 2473
Score = 28.4 bits (63), Expect = 4.0
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 348 GIYPAIDPLDSNSSMLEIDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSEEDKL 407
+ P + L +++ L+ G + + +R QE+LQ + LQ E +
Sbjct: 1849 ALEPQVQQLQEDAARLQKAYAGDKAEAIQQREQEVLQAWAELQG---------ACEARRD 1899
Query: 408 VVARARKLERFMSQ 421
+A L RF S
Sbjct: 1900 RLADTSDLFRFFSM 1913
>gnl|CDD|100094 cd05801, PGM_like3, This bacterial PGM-like
(phosphoglucomutase-like) protein of unknown function
belongs to the alpha-D-phosphohexomutase superfamily.
The alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Other
members of this superfamily include phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model..
Length = 522
Score = 28.4 bits (64), Expect = 5.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 156 GGAGVGKTVLIMELINNVAKAHG 178
AGVGKT++ +I+ VA A G
Sbjct: 324 KSAGVGKTLVSSSMIDRVAAALG 346
>gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family
within the Ras superfamily. There are at least 60 Rab
genes in the human genome, and a number of Rab GTPases
are conserved from yeast to humans. Rab GTPases are
small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. 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 mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. 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.
Since crystal structures often lack C-terminal
residues, the lipid modification site is not available
for annotation in many of the CDs in the hierarchy, but
is included where possible.
Length = 159
Score = 28.2 bits (64), Expect = 5.6
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 151 KIGLFGGAGVGKTVLIMELINN 172
KI L G +GVGKT L++ ++
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDG 23
>gnl|CDD|33260 COG3457, COG3457, Predicted amino acid racemase [Amino acid
transport and metabolism].
Length = 353
Score = 28.0 bits (62), Expect = 5.9
Identities = 9/39 (23%), Positives = 19/39 (48%)
Query: 365 IDIVGQEHYDVARRVQEILQRYKSLQDIIAILGMDELSE 403
+D+ D AR++ E R + D++ ++ +L E
Sbjct: 94 VDVSTVSELDTARQLSEAAVRMGKVHDVLLMVDYGDLRE 132
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases..
Length = 151
Score = 27.9 bits (62), Expect = 7.1
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 154 LFGGAGVGKTVLIMELINNVAKAHGGYSVFA 184
L+G G GKT L + N + + G
Sbjct: 24 LYGPPGTGKTTLARAIANELFRP--GAPFLY 52
>gnl|CDD|36310 KOG1094, KOG1094, KOG1094, Discoidin domain receptor DDR1 [Signal
transduction mechanisms].
Length = 807
Score = 27.7 bits (61), Expect = 7.5
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 253 GQDVLFFVDNIFRFTQANSEISALLGRIPSAVGYQSTLALE 293
D LFF + F AN+ + AL G P + GYQ L ++
Sbjct: 346 AGDWLFFSEVSFISDAANNSLLALGGTFPESRGYQPVLKVD 386
>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3 Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions..
Length = 144
Score = 27.7 bits (62), Expect = 7.6
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 147 QKGGKIGLFGGAGVGKTVLIMELINNVAKAHGG 179
G +IGL G G GK+ L ++LI + G
Sbjct: 24 NPGDRIGLVGRNGAGKSTL-LKLIAGELEPDEG 55
>gnl|CDD|146048 pfam03223, V-ATPase_C, V-ATPase subunit C.
Length = 371
Score = 27.6 bits (62), Expect = 7.6
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 88 EATLGRIMNVIGEPVDDQGAIISSEKRAIHQPSPSY 123
E L +I ++ E ++DQG +SS R Y
Sbjct: 66 EGVLKKIERILRELLEDQGGKLSSTLRVNDVSLDQY 101
>gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C. This
family is also known as MRP (mulrtidrug
resisitance-associated protein). Some of the MRP
members have five additional transmembrane segments in
their N-terminas, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate..
Length = 204
Score = 27.7 bits (62), Expect = 8.0
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 137 IKVIDLISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVG 187
+K I+L P KG + + G G GK+ L+ L+ + K G SV +
Sbjct: 21 LKDINLEVP--KGELVAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGSIA 69
>gnl|CDD|146436 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerization of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 186
Score = 27.5 bits (62), Expect = 8.6
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 133 LTTGIKVID-LISPYQKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 183
L TG +D L QKG I + +GKT + + N A +F
Sbjct: 2 LPTGFTDLDQLTGGLQKGDLIIIAARPSMGKTAFALNIARNAALKQDKPVLF 53
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
0.317 0.135 0.374
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,409,034
Number of extensions: 287270
Number of successful extensions: 997
Number of sequences better than 10.0: 1
Number of HSP's gapped: 946
Number of HSP's successfully gapped: 70
Length of query: 478
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 381
Effective length of database: 4,167,664
Effective search space: 1587879984
Effective search space used: 1587879984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)