RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780810|ref|YP_003065223.1| transcription termination
factor Rho [Candidatus Liberibacter asiaticus str. psy62]
(423 letters)
>gnl|CDD|181809 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 810 bits (2096), Expect = 0.0
Identities = 300/418 (71%), Positives = 362/418 (86%), Gaps = 2/418 (0%)
Query: 4 MKLQELKNKSPTKLLAFAESLEIENANVMRKQELMFSILKVLSGRDVEIIGEGVIEVLQD 63
M L ELKNKS ++LL AE L IENA+ +RKQEL+F+ILK + + +I GEGV+E+L D
Sbjct: 1 MNLSELKNKSLSELLELAEELGIENASRLRKQELIFAILKAQAEKGGDIFGEGVLEILPD 60
Query: 64 GFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYFALLKVNAIN 123
GFGFLRSPDANYL GPDDIYVSPSQI+ F+L+TGDTVEG IR P+EGERYFALLKV +N
Sbjct: 61 GFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGKIRPPKEGERYFALLKVETVN 120
Query: 124 FDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPP 183
+ PE+ RN+ F+NLTPLYP++R +E NPE D+S+R+IDLIAPIGKGQR LIVAPP
Sbjct: 121 GEDPEKARNRPLFENLTPLYPNERLRLETGNPE--DLSTRIIDLIAPIGKGQRGLIVAPP 178
Query: 184 RTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTFDESAARHV 243
+ GKT+LLQNIA+SI NHPE +LIVLLIDERPEEVTDMQRSV+GEV++STFDE A RHV
Sbjct: 179 KAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHV 238
Query: 244 QVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANALQRPKRF 303
QVAEMVI KAK LVE+G DVVILLDSITRL RAYN ++PSSGK+L+GGVDANAL RPKRF
Sbjct: 239 QVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSGGVDANALHRPKRF 298
Query: 304 FGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDI 363
FGAARNI+EGGSLTII TAL+DTGSRMDEVIFEEFKGTGN E+ L+RK+A+KRIFPA+DI
Sbjct: 299 FGAARNIEEGGSLTIIATALIDTGSRMDEVIFEEFKGTGNMELHLDRKLAEKRIFPAIDI 358
Query: 364 IKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDAIEFLIDKLKQTKDNKDFFYSMNK 421
+SGTRKE+LL+ ++LQKV++LR+I+S M+ +A+EFL+DKLK+TK N++FF SMN+
Sbjct: 359 NRSGTRKEELLLSPEELQKVWILRKILSPMDEVEAMEFLLDKLKKTKTNEEFFDSMNR 416
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. Members of
this family differ in the specificity of RNA binding.
Length = 415
Score = 693 bits (1791), Expect = 0.0
Identities = 280/418 (66%), Positives = 351/418 (83%), Gaps = 3/418 (0%)
Query: 4 MKLQELKNKSPTKLLAFAESLEIENANVMRKQELMFSILKVLSGRDVEIIGEGVIEVLQD 63
++ELKN +L AE L +EN + ++KQEL+F+ILK + + I GEGV+E+L D
Sbjct: 1 YNIEELKNMPLEELRKLAEQLGVENTSSLKKQELIFAILKAHAEQGGLIFGEGVLEILPD 60
Query: 64 GFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYFALLKVNAIN 123
GFGFLRSPD++YL GPDDIYVSPSQI+ F+L+TGDT+EG IR+P+EGERYFALLKV ++N
Sbjct: 61 GFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRTGDTIEGQIRSPKEGERYFALLKVESVN 120
Query: 124 FDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPP 183
D PE+ +N++ F+NLTPLYP++R +E +D+S+RV+DL APIGKGQR LIVAPP
Sbjct: 121 GDDPEKAKNRVLFENLTPLYPNERLRLET---STEDLSTRVLDLFAPIGKGQRGLIVAPP 177
Query: 184 RTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTFDESAARHV 243
+ GKT+LLQ IA +I +NHPE LIVLLIDERPEEVTDMQRSV+GEV++STFDE A+RHV
Sbjct: 178 KAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHV 237
Query: 244 QVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANALQRPKRF 303
QVAEMVI KAK LVE+ DVVILLDSITRL RAYN + P+SGK+L+GGVDANAL RPKRF
Sbjct: 238 QVAEMVIEKAKRLVEHKKDVVILLDSITRLARAYNTVTPASGKVLSGGVDANALHRPKRF 297
Query: 304 FGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDI 363
FGAARNI+EGGSLTII TAL+DTGSRMDEVIFEEFKGTGN E+ L+RK+AD+RIFPA+DI
Sbjct: 298 FGAARNIEEGGSLTIIATALIDTGSRMDEVIFEEFKGTGNMELHLDRKLADRRIFPAIDI 357
Query: 364 IKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDAIEFLIDKLKQTKDNKDFFYSMNK 421
KSGTRKE+LL+ ++LQK+++LR+I+S M+S +A+EFLI KLK+TK N++F SM +
Sbjct: 358 KKSGTRKEELLLTPEELQKIWVLRKIISPMDSIEAMEFLISKLKKTKTNEEFLESMKR 415
>gnl|CDD|183675 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 566 bits (1462), Expect = e-162
Identities = 213/373 (57%), Positives = 285/373 (76%), Gaps = 12/373 (3%)
Query: 56 GVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGER--- 112
G+++VL D + F+R + YL GP+D+YVS +Q++ L+ GD V G++RAPREGE+
Sbjct: 298 GILDVL-DNYAFVR--TSGYLPGPNDVYVSMNQVRKNGLRKGDAVTGAVRAPREGEQGNQ 354
Query: 113 ---YFALLKVNAINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIA 169
+ L++++++N PE + + F LTPLYP++R +E E K +++RVIDLI
Sbjct: 355 RQKFNPLVRLDSVNGMSPEEAKKRPEFGKLTPLYPNERLRLE---TEPKKLTTRVIDLIM 411
Query: 170 PIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGE 229
PIGKGQR LIV+PP+ GKT +LQNIA++I N+PEC+L+V+L+DERPEEVTDMQRSV+GE
Sbjct: 412 PIGKGQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERPEEVTDMQRSVKGE 471
Query: 230 VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILT 289
VI+STFD + H VAE+ I +AK LVE G DVV+LLDSITRL RAYN+ P+SG+IL+
Sbjct: 472 VIASTFDRPPSDHTTVAELAIERAKRLVELGKDVVVLLDSITRLGRAYNLAAPASGRILS 531
Query: 290 GGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLE 349
GGVD+ AL PKRFFGAARNI+ GGSLTII TALV+TGS+MDEVIFEEFKGTGN E+ L+
Sbjct: 532 GGVDSTALYPPKRFFGAARNIENGGSLTIIATALVETGSKMDEVIFEEFKGTGNMELKLD 591
Query: 350 RKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDAIEFLIDKLKQT 409
RK+ADKRIFPA+D+ SGTRKE+LL+ +L V LRR++S ++S AI+ LI +LK+T
Sbjct: 592 RKLADKRIFPAVDVNASGTRKEELLLSPDELAIVHKLRRVLSGLDSQQAIDLLISRLKKT 651
Query: 410 KDNKDFFYSMNKQ 422
K N +F ++K
Sbjct: 652 KSNYEFLMQVSKT 664
>gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 538 bits (1389), Expect = e-154
Identities = 225/366 (61%), Positives = 289/366 (78%), Gaps = 6/366 (1%)
Query: 55 EGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYF 114
GV+E+L DGFGFLRS NYL PDD++V P+ I+ F+L+TGD VEG R ERY
Sbjct: 20 LGVLEILGDGFGFLRSARRNYLPSPDDVFVPPALIRRFNLRTGDVVEGVARPR---ERYR 76
Query: 115 ALLKVNAINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKG 174
L++V+++N PE++ + HFD+LTPL+P +R +E + D+S RV+DL+APIGKG
Sbjct: 77 VLVRVDSVNGTDPEKLARRPHFDDLTPLHPRERLRLETGS---DDLSMRVVDLVAPIGKG 133
Query: 175 QRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISST 234
QR LIVAPPR GKT+LLQ IA ++ NHPE +L+VLLIDERPEEVTDM+RSV+GEV +ST
Sbjct: 134 QRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYAST 193
Query: 235 FDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDA 294
FD H++VAE+V+ +AK LVE G DVVILLDS+TRL RAYN + SSG+ L+GGVDA
Sbjct: 194 FDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLARAYNNEVESSGRTLSGGVDA 253
Query: 295 NALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIAD 354
ALQRPKR FGAARNI+EGGSLTII TALVDTGSRMDEVIFEEFKGTGN EIVL+R++AD
Sbjct: 254 RALQRPKRLFGAARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNMEIVLDRELAD 313
Query: 355 KRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSSMNSSDAIEFLIDKLKQTKDNKD 414
KR+FPA+DI KSGTR+E+LL++ ++L+KV LRR ++S +A+E L++KL++T DN +
Sbjct: 314 KRVFPAIDIAKSGTRREELLLDSKELEKVRRLRRALASRKPVEAMEALLEKLRETPDNAE 373
Query: 415 FFYSMN 420
F S+
Sbjct: 374 FLNSVQ 379
>gnl|CDD|148864 pfam07497, Rho_RNA_bind, Rho termination factor, RNA-binding
domain. The Rho termination factor disengages newly
transcribed RNA from its DNA template at certain,
specific transcripts. It it thought that two copies of
Rho bind to RNA and that Rho functions as a hexamer of
protomers.
Length = 78
Score = 151 bits (384), Expect = 3e-37
Identities = 59/78 (75%), Positives = 68/78 (87%)
Query: 52 IIGEGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGE 111
I GEGV+E+L DGFGFLRSPDANYL GPDDIYVSPSQI+ F+L+TGDT+EG IR P+EGE
Sbjct: 1 IFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTIEGKIRPPKEGE 60
Query: 112 RYFALLKVNAINFDVPER 129
RYFALLKV IN + PE+
Sbjct: 61 RYFALLKVETINGEPPEK 78
>gnl|CDD|162913 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase.
Length = 422
Score = 97.4 bits (243), Expect = 7e-21
Identities = 73/254 (28%), Positives = 121/254 (47%), Gaps = 25/254 (9%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
R ID + G+GQR I A GK+ LL IA + V+ LI ER EV +
Sbjct: 134 RAIDGLLTCGEGQRIGIFAGAGVGKSTLLGMIA-----RGASADVNVIALIGERGREVRE 188
Query: 222 ----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
+RSV ++ ST D + ++ A A A+ + G V++++DS+T
Sbjct: 189 FIEHHLGEEGRKRSV---LVVSTSDRPSLERLKAAYTATAIAEYFRDQGKRVLLMMDSLT 245
Query: 272 RLCRAYNVLMPSSGKILT-GGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRM 330
R RA + ++G+ GG + R A N E GS+T + T LV+ G M
Sbjct: 246 RFARALREIGLAAGEPPARGGYPPSVFSSLPRLLERAGN-GEKGSITALYTVLVE-GDDM 303
Query: 331 DEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIV 390
++ I +E + + IVL R +A++ +PA+D++ S +R +V + + LRR++
Sbjct: 304 NDPIADEVRSILDGHIVLSRALAERNHYPAIDVLASLSRVMSQVVSTEHRRAAGKLRRLL 363
Query: 391 SSMNSSDAIEFLID 404
++ +E LI
Sbjct: 364 ATY---KEVELLIR 374
>gnl|CDD|162162 TIGR01026, fliI_yscN, ATPase FliI/YscN family. This family of
ATPases demonstrates extensive homology with ATP
synthase F1, beta subunit. It is a mixture of members
with two different protein functions. The first group is
exemplified by Salmonella typhimurium FliI protein. It
is needed for flagellar assembly, its ATPase activity is
required for flagellation, and it may be involved in a
specialized protein export pathway that proceeds without
signal peptide cleavage. The second group of proteins
function in the export of virulence proteins;
exemplified by Yersinia sp. YscN protein an ATPase
involved in the type III secretory pathway for the
antihost Yops proteins.
Length = 440
Score = 92.8 bits (231), Expect = 1e-19
Identities = 76/272 (27%), Positives = 123/272 (45%), Gaps = 36/272 (13%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
R ID + +GKGQR I A GK+ LL IA + E + V+ LI ER EV +
Sbjct: 152 RSIDGLLTVGKGQRIGIFAGSGVGKSTLLGMIAR-----NTEADVNVIALIGERGREVRE 206
Query: 222 ----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
++RSV V+ +T D+S ++ A + A A+ + G DV++L+DS+T
Sbjct: 207 FIEHDLGEEGLKRSV---VVVATSDQSPLLRLKGAYVATAIAEYFRDQGKDVLLLMDSVT 263
Query: 272 RLCRAYNVLMPSSGKI-LTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRM 330
R A + ++G+ T G + R A GS+T T LV+ G M
Sbjct: 264 RFAMAQREIGLAAGEPPATKGYTPSVFSTLPRLLERA-GASGKGSITAFYTVLVE-GDDM 321
Query: 331 DEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIV 390
+E I + +G + IVL R +A + +PA+D++ S +R +V + + R ++
Sbjct: 322 NEPIADSVRGILDGHIVLSRALAQRGHYPAIDVLASISRLMTAIVSEEHRRAARKFRELL 381
Query: 391 SS--------------MNSSDAIEFLIDKLKQ 408
S S ++F I K +
Sbjct: 382 SKYKDNEDLIRIGAYQRGSDRELDFAIAKYPK 413
>gnl|CDD|163293 TIGR03498, FliI_clade3, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 418
Score = 90.8 bits (226), Expect = 6e-19
Identities = 68/222 (30%), Positives = 111/222 (50%), Gaps = 26/222 (11%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
RVID P+ +GQR I A GK+ LL +A +N +++ L+ ER EV +
Sbjct: 129 RVIDTFLPLCRGQRLGIFAGSGVGKSTLLSMLA----RNTDADVVVIALVGERGREVREF 184
Query: 222 ---------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITR 272
++RSV V+ +T DES Q A A A+ + G DV++L+DS+TR
Sbjct: 185 LEDDLGEEGLKRSV---VVVATSDESPLMRRQAAYTATAIAEYFRDQGKDVLLLMDSVTR 241
Query: 273 LCRAYNVLMPSSG-----KILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTG 327
A + ++G + T V + + P+ A + GS+T I T LVD G
Sbjct: 242 FAMAQREIGLAAGEPPVARGYTPSVFS---ELPRLLERAGPGAEGKGSITGIFTVLVD-G 297
Query: 328 SRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
+E + + +G + IVL+R IA++ +PA++++ S +R
Sbjct: 298 DDHNEPVADAVRGILDGHIVLDRAIAERGRYPAINVLASVSR 339
>gnl|CDD|136438 PRK07594, PRK07594, type III secretion system ATPase SsaN;
Validated.
Length = 433
Score = 85.4 bits (211), Expect = 2e-17
Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 32/246 (13%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
R ID +A G+GQR I + P GK+ LL ++ N P+ VL LI ER EV +
Sbjct: 144 RAIDSVATCGEGQRVGIFSAPGVGKSTLL-----AMLCNAPDADSNVLVLIGERGREVRE 198
Query: 222 M----------QRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
+R V ++ +T D A V+ + A+ + G VV+L DS+T
Sbjct: 199 FIDFTLSEETRKRCV---IVVATSDRPALERVRALFVATTIAEFFRDNGKRVVLLADSLT 255
Query: 272 RLCRAYNVLMPSSGKILTGGVDANALQRPKRFFGA------ARNIKEGGSLTIIGTALVD 325
R RA + ++G+ G + P F A + E GS+T T LV+
Sbjct: 256 RYARAAREIALAAGETAVSG------EYPPGVFSALPRLLERTGMGEKGSITAFYTVLVE 309
Query: 326 TGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFM 385
G M+E + +E + + IVL R++A++ +PA+D++ + +R ++ + Q +
Sbjct: 310 -GDDMNEPLADEVRSLLDGHIVLSRRLAERGHYPAIDVLATLSRVFPVVTSHEHRQLAAI 368
Query: 386 LRRIVS 391
LRR ++
Sbjct: 369 LRRCLA 374
>gnl|CDD|181092 PRK07721, fliI, flagellum-specific ATP synthase; Validated.
Length = 438
Score = 84.4 bits (209), Expect = 6e-17
Identities = 86/290 (29%), Positives = 136/290 (46%), Gaps = 49/290 (16%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
R ID + +GKGQR I A GK+ L+ IA +N ++ LI ER EV +
Sbjct: 147 RAIDSLLTVGKGQRVGIFAGSGVGKSTLMGMIA----RNTSADLNVIALIGERGREVREF 202
Query: 222 ---------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITR 272
++RS+ V+ +T D+ A ++ A A A+ + GL+V++++DS+TR
Sbjct: 203 IERDLGPEGLKRSI---VVVATSDQPALMRIKGAYTATAIAEYFRDQGLNVMLMMDSVTR 259
Query: 273 LCRAYN-----VLMPSSGKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTG 327
+ A V P + K T V A PK N GS+T T LVD G
Sbjct: 260 VAMAQREIGLAVGEPPTTKGYTPSVFA---ILPKLLERTGTN--ASGSITAFYTVLVD-G 313
Query: 328 SRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLR 387
M+E I + +G + VL+R++A+K +PA++++KS +R + +V + + R
Sbjct: 314 DDMNEPIADTVRGILDGHFVLDRQLANKGQYPAINVLKSVSRVMNHIVSPEHKEAANRFR 373
Query: 388 RIVSS-MNSSD-----------------AIEF---LIDKLKQTKDNKDFF 416
++S+ NS D AI+F +I LKQ D K F
Sbjct: 374 ELLSTYQNSEDLINIGAYKRGSSREIDEAIQFYPQIISFLKQGTDEKATF 423
>gnl|CDD|132536 TIGR03497, FliI_clade2, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 413
Score = 80.4 bits (199), Expect = 8e-16
Identities = 77/257 (29%), Positives = 124/257 (48%), Gaps = 31/257 (12%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
+ ID + IGKGQR I A GK+ LL IA +N ++ LI ER EV D
Sbjct: 126 KAIDGLLTIGKGQRVGIFAGSGVGKSTLLGMIA----RNAKADINVIALIGERGREVRDF 181
Query: 222 ---------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITR 272
++RSV V+ +T D+ A ++ A A A+ + G DV++++DS+TR
Sbjct: 182 IEKDLGEEGLKRSV---VVVATSDQPALMRLKAAFTATAIAEYFRDQGKDVLLMMDSVTR 238
Query: 273 LCRA-----YNVLMPSSGKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTG 327
A V P + + T V + PK + + + GS+T T LVD G
Sbjct: 239 FAMAQREIGLAVGEPPTTRGYTPSVFS---LLPKLLERSGNS--QKGSITGFYTVLVD-G 292
Query: 328 SRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLR 387
M+E I + +G + IVL R++A K +PA+D++ S +R + +V + + LR
Sbjct: 293 DDMNEPIADAVRGILDGHIVLSRELAAKNHYPAIDVLASVSRVMNEIVSEEHKELAGKLR 352
Query: 388 RIVSSMNSSDAIEFLID 404
+++ + E LI+
Sbjct: 353 ELLAVYKEA---EDLIN 366
>gnl|CDD|181583 PRK08927, fliI, flagellum-specific ATP synthase; Validated.
Length = 442
Score = 80.4 bits (199), Expect = 9e-16
Identities = 68/227 (29%), Positives = 111/227 (48%), Gaps = 28/227 (12%)
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPE 217
D+ R ++ +GQR I A GK++LL +A + + + V+ LI ER
Sbjct: 143 DLGVRALNTFLTCCRGQRMGIFAGSGVGKSVLLSMLAR-----NADADVSVIGLIGERGR 197
Query: 218 EVTD----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILL 267
EV + + RSV V+ +T DE A Q A + +A A+ + G DV+ L+
Sbjct: 198 EVQEFLQDDLGPEGLARSV---VVVATSDEPALMRRQAAYLTLAIAEYFRDQGKDVLCLM 254
Query: 268 DSITRLCRAYNVLMPSSG-----KILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTA 322
DS+TR A + S+G K T V A + P+ A G++T + T
Sbjct: 255 DSVTRFAMAQREIGLSAGEPPTTKGYTPTVFA---ELPRLLERAGPGPIGEGTITGLFTV 311
Query: 323 LVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
LVD G +E + + +G + IV+ER IA++ +PA++++KS +R
Sbjct: 312 LVD-GDDHNEPVADAVRGILDGHIVMERAIAERGRYPAINVLKSVSR 357
>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
Length = 440
Score = 80.2 bits (198), Expect = 9e-16
Identities = 70/253 (27%), Positives = 109/253 (43%), Gaps = 25/253 (9%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
R ID I G+GQR I A GK+ LL + ++VL LI ER EV +
Sbjct: 152 RAIDGILSCGEGQRIGIFAAAGVGKSTLLGMLC-----ADSAADVMVLALIGERGREVRE 206
Query: 222 M----------QRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
R+V V+ +T D A ++ A+ + G V+++ DS+T
Sbjct: 207 FLEQVLTPEARARTV---VVVATSDRPALERLKGLSTATTIAEYFRDRGKKVLLMADSLT 263
Query: 272 RLCRAYNVLMPSSGKI-LTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRM 330
R RA + ++G+ G + R N + GS+T T LV+ G M
Sbjct: 264 RYARAAREIGLAAGEPPAAGSFPPSVFANLPRLLERTGN-SDRGSITAFYTVLVE-GDDM 321
Query: 331 DEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIV 390
+E + +E + + IVL R++A +PA+DI S +R +V L LRR+
Sbjct: 322 NEPVADEVRSLLDGHIVLSRRLAGAGHYPAIDIAASVSRIMPQIVSAGQLAMAQKLRRM- 380
Query: 391 SSMNSSDAIEFLI 403
+ IE L+
Sbjct: 381 --LACYQEIELLV 391
>gnl|CDD|169656 PRK09099, PRK09099, type III secretion system ATPase; Provisional.
Length = 441
Score = 77.9 bits (192), Expect = 4e-15
Identities = 70/246 (28%), Positives = 123/246 (50%), Gaps = 26/246 (10%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYL-IVLLIDERPEEVTD 221
R++D + +G+GQR I AP GK+ L+ A +C + ++ LI ER EV +
Sbjct: 152 RIVDGLMTLGEGQRMGIFAPAGVGKSTLMGMFARGT-----QCDVNVIALIGERGREVRE 206
Query: 222 ----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
M RSV V+ +T D S+ + A + A A+ + GL V++++DS+T
Sbjct: 207 FIELILGEDGMARSV---VVCATSDRSSIERAKAAYVATAIAEYFRDRGLRVLLMMDSLT 263
Query: 272 RLCRAYNVLMPSSGKILT-GGVDANALQRPKRFFGAARNIKEGGSLTIIGTALV--DTGS 328
R RA + ++G+ G + R A + E GS+T + T L ++GS
Sbjct: 264 RFARAQREIGLAAGEPPARRGFPPSVFAELPRLLERA-GMGETGSITALYTVLAEDESGS 322
Query: 329 RMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRR 388
+ I EE +G + ++L R+IA + +PA+D++ S +R +V R+ +Q LR+
Sbjct: 323 ---DPIAEEVRGILDGHMILSREIAARNQYPAIDVLGSLSRVMPQVVPREHVQAAGRLRQ 379
Query: 389 IVSSMN 394
+++
Sbjct: 380 LLAKHR 385
>gnl|CDD|180696 PRK06793, fliI, flagellum-specific ATP synthase; Validated.
Length = 432
Score = 77.3 bits (190), Expect = 6e-15
Identities = 73/273 (26%), Positives = 131/273 (47%), Gaps = 28/273 (10%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
+ ID + IG GQ+ I A GK+ LL IA + K + ++ L+ ER EV D
Sbjct: 145 KSIDSMLTIGIGQKIGIFAGSGVGKSTLLGMIAKNAKAD----INVISLVGERGREVKDF 200
Query: 223 QRSVQGE-------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCR 275
R GE V+ +T DES ++ A++ + A+ + G +V++++DS+TR
Sbjct: 201 IRKELGEEGMRKSVVVVATSDESHLMQLRAAKLATSIAEYFRDQGNNVLLMMDSVTRFAD 260
Query: 276 AYNVL------MPSSGK-ILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGS 328
A + +P GK +L L+R + + GS+T I T LVD G
Sbjct: 261 ARRSVDIAVKELPIGGKTLLMESYMKKLLERSGK--------TQKGSITGIYTVLVD-GD 311
Query: 329 RMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRR 388
++ + + +G + IVL+R++A +PA+ ++ S +R + +V Q +R+
Sbjct: 312 DLNGPVPDLARGILDGHIVLKRELATLSHYPAISVLDSVSRIMEEIVSPNHWQLANEMRK 371
Query: 389 IVSSMNSSDAIEFLIDKLKQTKDNKDFFYSMNK 421
I+ S+ + + F + +++ +N F NK
Sbjct: 372 IL-SIYKENELYFKLGTIQENAENAYIFECKNK 403
>gnl|CDD|180526 PRK06315, PRK06315, type III secretion system ATPase; Provisional.
Length = 442
Score = 75.7 bits (186), Expect = 2e-14
Identities = 71/267 (26%), Positives = 125/267 (46%), Gaps = 25/267 (9%)
Query: 144 PDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHP 203
PD +L + + R ID + + +GQR I A GK+ LL IA +N
Sbjct: 136 PDPLHRAKLRTILSTGV--RCIDGMLTVARGQRIGIFAGAGVGKSSLLGMIA----RNAE 189
Query: 204 ECYL-IVLLIDERPEEVTD----------MQRSVQGEVISSTFDESAARHVQVAEMVIAK 252
E + ++ LI ER EV + M+RSV ++ ST D+S+ + A + A
Sbjct: 190 EADVNVIALIGERGREVREFIEGDLGEEGMKRSV---IVVSTSDQSSQLRLNAAYVGTAI 246
Query: 253 AKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKI-LTGGVDANALQR-PKRFFGAARNI 310
A+ + G VV+++DS+TR RA + ++G+ G + PK + +
Sbjct: 247 AEYFRDQGKTVVLMMDSVTRFARALREVGLAAGEPPARAGYTPSVFSTLPKLLERSGASD 306
Query: 311 KEGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRK 370
K G++T T LV G M+E + +E K + IVL +A +PA+D++ S +R
Sbjct: 307 K--GTITAFYTVLV-AGDDMNEPVADEVKSILDGHIVLSNALAQAYHYPAIDVLASISRL 363
Query: 371 EDLLVERQDLQKVFMLRRIVSSMNSSD 397
+V + + + R +++ +++
Sbjct: 364 LTAIVPEEQRRIIGKAREVLAKYKANE 390
>gnl|CDD|163292 TIGR03496, FliI_clade1, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 411
Score = 74.4 bits (184), Expect = 5e-14
Identities = 77/300 (25%), Positives = 127/300 (42%), Gaps = 75/300 (25%)
Query: 137 DNLTPLYPDKRFNMELN--NPENK-------DISSRVIDLIAPIGKGQRSLIVAPPRTGK 187
D PL +R + NP + D+ R I+ + +G+GQR I A GK
Sbjct: 91 DGKGPLDAGERVPLYAPPINPLKRAPIDEPLDVGVRAINGLLTVGRGQRMGIFAGSGVGK 150
Query: 188 TILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD----------MQRSVQGEVISSTFD 236
+ LL +A + E ++V+ LI ER EV + + RSV V+++T D
Sbjct: 151 STLLGMMAR-----YTEADVVVVGLIGERGREVKEFIEDILGEEGLARSV---VVAATAD 202
Query: 237 ESAARHVQVAE--MVIAKAKCLVEY----GLDVVILLDSITRLC---------------- 274
ES ++ A IA EY G DV++L+DS+TR
Sbjct: 203 ESPLMRLRAAFYATAIA------EYFRDQGKDVLLLMDSLTRFAMAQREIALAIGEPPAT 256
Query: 275 RAYNVLMPSS--GKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDE 332
+ Y P S K+ ++R A + GS+T T LV+ G +
Sbjct: 257 KGY----PPSVFAKL------PQLVER------AGNGEEGKGSITAFYTVLVE-GDDQQD 299
Query: 333 VIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVSS 392
I + + + IVL R++A++ +PA+DI+ S +R +V + Q ++++S
Sbjct: 300 PIADAARAILDGHIVLSRELAEQGHYPAIDILASISRVMPDVVSPEHRQAARRFKQLLSR 359
>gnl|CDD|180762 PRK06936, PRK06936, type III secretion system ATPase; Provisional.
Length = 439
Score = 73.2 bits (180), Expect = 1e-13
Identities = 66/242 (27%), Positives = 121/242 (50%), Gaps = 24/242 (9%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPEEVTD 221
RVID + G+GQR I A GK+ LL ++ I+ E + VL LI ER EV +
Sbjct: 151 RVIDGLLTCGEGQRMGIFAAAGGGKSTLLASL---IR--SAEVDVTVLALIGERGREVRE 205
Query: 222 ----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
++++V ++ +T D + + + + A+ + G V++L+DS+T
Sbjct: 206 FIESDLGEEGLRKAV---LVVATSDRPSMERAKAGFVATSIAEYFRDQGKRVLLLMDSVT 262
Query: 272 RLCRAYNVLMPSSGKILT--GGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSR 329
R RA + ++G+ T G + P+ A ++ K GS+T + T LV+ G
Sbjct: 263 RFARAQREIGLAAGEPPTRRGYPPSVFAALPRLMERAGQSDK--GSITALYTVLVE-GDD 319
Query: 330 MDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRI 389
M E + +E + + I+L RK+A +PA+D+++S +R + +V ++ LR +
Sbjct: 320 MTEPVADETRSILDGHIILSRKLAAANHYPAIDVLRSASRVMNQIVSKEHKTWAGRLREL 379
Query: 390 VS 391
++
Sbjct: 380 LA 381
>gnl|CDD|180875 PRK07196, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 73.0 bits (179), Expect = 1e-13
Identities = 65/219 (29%), Positives = 110/219 (50%), Gaps = 13/219 (5%)
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEE 218
D+ I+ + IGKGQR ++A GK++LL I + + ++V LI ER E
Sbjct: 140 DVGVNAINGLLTIGKGQRVGLMAGSGVGKSVLLGMITRYTQAD----VVVVGLIGERGRE 195
Query: 219 VTD-MQRSVQGE------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
V + ++ S+Q V+++ DES ++ E+ A A + G DV++L+DS+T
Sbjct: 196 VKEFIEHSLQAAGMAKSVVVAAPADESPLMRIKATELCHAIATYYRDKGHDVLLLVDSLT 255
Query: 272 RLCRAYNVLMPSSGK-ILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRM 330
R A + S G+ T G +A R +A N G++T I T L + +
Sbjct: 256 RYAMAQREIALSLGEPPATKGYPPSAFSIIPRLAESAGNSSGNGTMTAIYTVLAEGDDQQ 315
Query: 331 DEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
D ++ + + + IVL RK+A+ +PA+DI +S +R
Sbjct: 316 DPIV-DCARAVLDGHIVLSRKLAEAGHYPAIDISQSISR 353
>gnl|CDD|168339 PRK06002, fliI, flagellum-specific ATP synthase; Validated.
Length = 450
Score = 68.9 bits (169), Expect = 3e-12
Identities = 60/220 (27%), Positives = 110/220 (50%), Gaps = 23/220 (10%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECY--LIVLLIDERPEEVT 220
RVID+ P+ GQR I A GK+ LL +A + + + +++ L+ ER EV
Sbjct: 154 RVIDIFTPLCAGQRIGIFAGSGVGKSTLLAMLARA------DAFDTVVIALVGERGREVR 207
Query: 221 D---------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
+ ++++V + +T DES A A+ + G +V++++DS+T
Sbjct: 208 EFLEDTLADNLKKAV---AVVATSDESPMMRRLAPLTATAIAEYFRDRGENVLLIVDSVT 264
Query: 272 RLCRAYNVLMPSSGK--ILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSR 329
R A + ++G+ + G + + P+ A + GGS+T I + LVD G
Sbjct: 265 RFAHAAREVALAAGEPPVARGYPPSVFSELPRLLERAGPGAEGGGSITGIFSVLVD-GDD 323
Query: 330 MDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
++ + + +GT + IVL+R IA++ +PA+D + S +R
Sbjct: 324 HNDPVADSIRGTLDGHIVLDRAIAEQGRYPAVDPLASISR 363
>gnl|CDD|128651 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 68.8 bits (169), Expect = 3e-12
Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 55 EGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKS--FSLKTGDTVEGSIRAPREGER 112
GV++ GFGF+R D G D++V PSQI+ SL+ GD VE + +PR G +
Sbjct: 1 TGVVKWFNKGFGFIRPDD-----GGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGK 55
Query: 113 YFALLKV 119
A V
Sbjct: 56 PEAENVV 62
>gnl|CDD|181253 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 68.5 bits (168), Expect = 3e-12
Identities = 70/251 (27%), Positives = 111/251 (44%), Gaps = 46/251 (18%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILL-QNIAHSIKKNHPECYLIVLLIDERPEEVTD 221
R ID + G GQR I A GKT L+ I HS + ++I L I ER EVT+
Sbjct: 140 RAIDGLLTCGVGQRMGIFASAGCGKTSLMNMLIEHS----EADVFVIGL-IGERGREVTE 194
Query: 222 ----MQRSVQGE---VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLC 274
++ S + E ++ +T D S+ A + A+ + G VV+ +DS+TR
Sbjct: 195 FVESLRASSRREKCVLVYATSDFSSVDRCNAALVATTVAEYFRDQGKRVVLFIDSMTRYA 254
Query: 275 RAYNVLMPSSGKI-LTGGVDANA-------LQRPKRFFGAARNIKEGGSLTIIGTALVDT 326
RA + ++G++ G A+ L+RP GS+T T L+++
Sbjct: 255 RALRDVALAAGELPARRGYPASVFDSLPRLLERPGAT--------LAGSITAFYTVLLES 306
Query: 327 GSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRK---------------- 370
D I +E + + I L RK+A K +PA+D++KS +R
Sbjct: 307 EEEPD-PIGDEIRSILDGHIYLSRKLAAKGHYPAIDVLKSVSRVFGQVTDPKHRQLAAAF 365
Query: 371 EDLLVERQDLQ 381
LL ++LQ
Sbjct: 366 RKLLTRLEELQ 376
>gnl|CDD|181599 PRK08972, fliI, flagellum-specific ATP synthase; Validated.
Length = 444
Score = 60.5 bits (147), Expect = 8e-10
Identities = 72/276 (26%), Positives = 128/276 (46%), Gaps = 29/276 (10%)
Query: 137 DNLTPLYPDKR--FNMELNNP-------ENKDISSRVIDLIAPIGKGQRSLIVAPPRTGK 187
D L P+Y D+R + NP E D+ R I+ + +GKGQR + A GK
Sbjct: 116 DGLGPIYTDQRASRHSPPINPLSRRPITEPLDVGVRAINAMLTVGKGQRMGLFAGSGVGK 175
Query: 188 TILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM----------QRSVQGEVISSTFDE 237
++LL + + ++V L+ ER EV + RSV V+++ D
Sbjct: 176 SVLLGMMTRGTTAD----VIVVGLVGERGREVKEFIEEILGEEGRARSV---VVAAPADT 228
Query: 238 SAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKI-LTGGVDANA 296
S ++ E A+ + GL+V++L+DS+TR +A + + G+ T G +
Sbjct: 229 SPLMRLKGCETATTIAEYFRDQGLNVLLLMDSLTRYAQAQREIALAVGEPPATKGYPPSV 288
Query: 297 LQRPKRFFGAARNIKEG-GSLTIIGTALVDTGSRMDEVIFEEFKGTGNSEIVLERKIADK 355
+ A N G GS+T T L + G + + I + + + IVL R++AD
Sbjct: 289 FAKLPALVERAGNGGPGQGSITAFYTVLTE-GDDLQDPIADASRAILDGHIVLSRELADS 347
Query: 356 RIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVS 391
+PA+DI S +R +++ + L+ + ++++ S
Sbjct: 348 GHYPAIDIEASISRVMPMVISEEHLEAMRRVKQVYS 383
>gnl|CDD|181182 PRK07960, fliI, flagellum-specific ATP synthase; Validated.
Length = 455
Score = 60.6 bits (147), Expect = 9e-10
Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 14/243 (5%)
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEE 218
D R I+ + +G+GQR + A GK++LL +A + + ++V LI ER E
Sbjct: 160 DTGVRAINALLTVGRGQRMGLFAGSGVGKSVLLGMMARYTQAD----VIVVGLIGERGRE 215
Query: 219 VTDMQRSVQGE-------VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSIT 271
V D ++ G VI++ D S +Q A A+ + G V++++DS+T
Sbjct: 216 VKDFIENILGAEGRARSVVIAAPADVSPLLRMQGAAYATRIAEDFRDRGQHVLLIMDSLT 275
Query: 272 RLCRAYNVLMPSSGKI-LTGGVDANALQR-PKRFFGAARNIKEGGSLTIIGTALVDTGSR 329
R A + + G+ T G + + P A I GGS+T T L + +
Sbjct: 276 RYAMAQREIALAIGEPPATKGYPPSVFAKLPALVERAGNGISGGGSITAFYTVLTEGDDQ 335
Query: 330 MDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRI 389
D I + + + IVL R++A+ +PA+DI S +R L++ Q +V +++
Sbjct: 336 QDP-IADSARAILDGHIVLSRRLAEAGHYPAIDIEASISRAMTALIDEQHYARVRQFKQL 394
Query: 390 VSS 392
+SS
Sbjct: 395 LSS 397
>gnl|CDD|148865 pfam07498, Rho_N, Rho termination factor, N-terminal domain. The
Rho termination factor disengages newly transcribed RNA
from its DNA template at certain, specific transcripts.
It it thought that two copies of Rho bind to RNA and
that Rho functions as a hexamer of protomers. This
domain is found to the N-terminus of the RNA binding
domain (pfam07497).
Length = 43
Score = 58.1 bits (142), Expect = 4e-09
Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 8 ELKNKSPTKLLAFAESLEIENANVMRKQELMFSILK 43
ELK K+ +L A+ L IEN + +RKQEL+F+ILK
Sbjct: 1 ELKEKTLAELREIAKELGIENYSRLRKQELIFAILK 36
>gnl|CDD|168181 PRK05688, fliI, flagellum-specific ATP synthase; Validated.
Length = 451
Score = 55.1 bits (133), Expect = 3e-08
Identities = 64/237 (27%), Positives = 117/237 (49%), Gaps = 22/237 (9%)
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVL-LIDERPE 217
D+ R I+ + +G+GQR + A GK++LL + E +IV+ LI ER
Sbjct: 153 DVGIRSINGLLTVGRGQRLGLFAGTGVGKSVLL-----GMMTRFTEADIIVVGLIGERGR 207
Query: 218 EVTD----------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILL 267
EV + ++RSV V++S D++ ++ A A+ + G +V++L+
Sbjct: 208 EVKEFIEHILGEEGLKRSV---VVASPADDAPLMRLRAAMYCTRIAEYFRDKGKNVLLLM 264
Query: 268 DSITRLCRAYNVLMPSSGKI-LTGGVDANALQRPKRFFGAARNIKEG-GSLTIIGTALVD 325
DS+TR +A + + G+ T G + + + A N + G GS+T T L +
Sbjct: 265 DSLTRFAQAQREIALAIGEPPATKGYPPSVFAKLPKLVERAGNAEPGGGSITAFYTVLSE 324
Query: 326 TGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQK 382
G + I + +G + IVL R++A++ +PA+DI S +R +V+ + L++
Sbjct: 325 -GDDQQDPIADSARGVLDGHIVLSRRLAEEGHYPAIDIEASISRVMPQVVDPEHLRR 380
>gnl|CDD|181439 PRK08472, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 54.3 bits (131), Expect = 5e-08
Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 12/234 (5%)
Query: 165 IDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD-MQ 223
ID + GKGQ+ I A GK+ L+ I K +V LI ER E+ + ++
Sbjct: 148 IDGLLTCGKGQKLGIFAGSGVGKSTLMGMIV----KGCLAPIKVVALIGERGREIPEFIE 203
Query: 224 RSVQGE-----VISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYN 278
+++ G+ ++ +T D+S A ++ A+ GLDV+ ++DS+TR A
Sbjct: 204 KNLGGDLENTVIVVATSDDSPLMRKYGAFCAMSVAEYFKNQGLDVLFIMDSVTRFAMAQR 263
Query: 279 VLMPSSGKILTG-GVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEVIFEE 337
+ + G+ T G + L + A + GS+T T LV+ G M + I ++
Sbjct: 264 EIGLALGEPPTSKGYPPSVLSLLPQLMERAGKEEGKGSITAFFTVLVE-GDDMSDPIADQ 322
Query: 338 FKGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLVERQDLQKVFMLRRIVS 391
+ + IVL R++ D I+P ++I+ S +R + ++ + +R+ S
Sbjct: 323 SRSILDGHIVLSRELTDFGIYPPINILNSASRVMNDIISPEHKLAARKFKRLYS 376
>gnl|CDD|130111 TIGR01039, atpD, ATP synthase, F1 beta subunit. The sequences of
ATP synthase F1 alpha and beta subunits are related and
both contain a nucleotide-binding site for ATP and ADP.
They have a common amino terminal domain but vary at the
C-terminus. The beta chain has catalytic activity, while
the alpha chain is a regulatory subunit. Proton
translocating ATP synthase, F1 beta subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), A subunit.
Length = 461
Score = 53.6 bits (129), Expect = 9e-08
Identities = 71/270 (26%), Positives = 113/270 (41%), Gaps = 47/270 (17%)
Query: 137 DNLTPLYPDKRFNMELNNPENKDISSR---------VIDLIAPIGKGQRSLIVAPPRTGK 187
D P+ +R+ + P ++ S++ VIDL+AP KG + + GK
Sbjct: 97 DEKGPIPAKERWPIHRKAPSFEEQSTKVEILETGIKVIDLLAPYAKGGKIGLFGGAGVGK 156
Query: 188 TILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSV-QGEVISST------FDESAA 240
T+L+Q + ++I K H Y + + ER E D+ + + VI T +E
Sbjct: 157 TVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPG 215
Query: 241 RHVQVAEMVIAKAKCLVEY-----GLDVVILLDSITRLCRAYNVL------MPSS-GKIL 288
++VA + A EY G DV++ +D+I R +A + + MPS+ G
Sbjct: 216 ARMRVALTGLTMA----EYFRDEQGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQP 271
Query: 289 TGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMD---EVIFEEFKGTGNSE 345
T + LQ +R GS+T + V D F T
Sbjct: 272 TLATEMGELQ--ERITSTK-----TGSITSVQAVYVPADDLTDPAPATTFAHLDAT---- 320
Query: 346 IVLERKIADKRIFPAMDIIKSGTRKEDLLV 375
VL RKIA+ I+PA+D + S +R D V
Sbjct: 321 TVLSRKIAELGIYPAVDPLDSTSRLLDPSV 350
>gnl|CDD|102061 PRK05922, PRK05922, type III secretion system ATPase; Validated.
Length = 434
Score = 53.8 bits (129), Expect = 9e-08
Identities = 37/137 (27%), Positives = 63/137 (45%), Gaps = 17/137 (12%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD- 221
+ ID +GKGQR + + P +GK+ LL IA K ++ LI ER EV +
Sbjct: 146 KAIDAFLTLGKGQRIGVFSEPGSGKSSLLSTIAKGSKST----INVIALIGERGREVREY 201
Query: 222 ---------MQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITR 272
QR++ +I+S E+A V + A+ + G V+ ++DS++R
Sbjct: 202 IEQHKEGLAAQRTI---IIASPAHETAPTKVIAGRAAMTIAEYFRDQGHRVLFIMDSLSR 258
Query: 273 LCRAYNVLMPSSGKILT 289
A + + G+ L+
Sbjct: 259 WIAALQEVALARGETLS 275
>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 45.1 bits (106), Expect = 3e-05
Identities = 27/147 (18%), Positives = 42/147 (28%), Gaps = 12/147 (8%)
Query: 173 KGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVIS 232
G+ LIV PP +GKT L + +A + I E E Q +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDG---EDILEEVLDQLLLIIVGGK 57
Query: 233 STFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGV 292
R + A L V++LD IT L A +
Sbjct: 58 KASGSGELR--------LRLALALARKLKPDVLILDEITSLLDA-EQEALLLLLEELRLL 108
Query: 293 DANALQRPKRFFGAARNIKEGGSLTII 319
++ + K+ G +
Sbjct: 109 LLLKSEKNLTVILTTNDEKDLGPALLR 135
>gnl|CDD|180863 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
Length = 507
Score = 43.0 bits (102), Expect = 2e-04
Identities = 23/51 (45%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 152 LNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKT-ILLQNIAHSIKKN 201
LN I + IDL+ PIGKGQR LI+ +TGKT I L I + N
Sbjct: 123 LNEQLYTGIIA--IDLLIPIGKGQRELIIGDRQTGKTHIALNTIINQKNTN 171
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 40.5 bits (95), Expect = 0.001
Identities = 40/134 (29%), Positives = 61/134 (45%), Gaps = 27/134 (20%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKT-ILLQNIAHSIKKNHPECYLIVLLIDERPEEVTD 221
+VID + PIG+GQR LI+ +TGKT I + I + +N I I +R V
Sbjct: 151 KVIDALIPIGRGQRELILGDRQTGKTAIAIDTILNQKGRN---VLCIYCAIGQRASAV-- 205
Query: 222 MQRSVQGEVISSTFDESAARH--VQVAE-------MVIAK------AKCLVEYGLDVVIL 266
+V+++ + A + V V E IA + +E G DV+I+
Sbjct: 206 ------AKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPYAATSIGEHFMEQGRDVLIV 259
Query: 267 LDSITRLCRAYNVL 280
D +T+ RAY L
Sbjct: 260 YDDLTQHARAYREL 273
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 39.4 bits (93), Expect = 0.002
Identities = 65/277 (23%), Positives = 108/277 (38%), Gaps = 61/277 (22%)
Query: 137 DNLTPLYPDKRFNMELNNPENKDISSR---------VIDLIAPIGKGQRSLIVAPPRTGK 187
D PL ++R + P + + VIDL+ PI KG ++ + GK
Sbjct: 97 DGGPPLPAEERRPIHSTIPPLAEQDTSTEILETGIKVIDLLCPIAKGGKTGLFGGAGVGK 156
Query: 188 TILLQNIAHSIKKNHPECYLIVLLIDERPEE----VTDMQRSVQGEVISST------FDE 237
T+L+ + +I K H + + ER E +M+ S V+ T +E
Sbjct: 157 TVLMMELIFNISKQH-SGSSVFAGVGERSREGHELYHEMKES---GVLDKTVMVYGQMNE 212
Query: 238 SAARHVQVAEMVIAKAKCLVEY-----GLDVVILLDSITRLCRAYNVLMPSSGKI-LTGG 291
++V + A EY DV++ +D+I R +A + + G++ G
Sbjct: 213 PPGARMRVVLTGLTIA----EYLRDEEKEDVLLFIDNIFRFVQAGSEVSGLLGRMPSRVG 268
Query: 292 ------VDANALQRPKRFFGAARNIKEGGSLTIIGTALVDTGSRMDEV-------IFEEF 338
+ LQ +R + GS+T I V D++ IF
Sbjct: 269 YQPTLASEVAELQ--ERIA---ST--KNGSITSIQAVYVP----ADDLTDPAAVAIFSHL 317
Query: 339 KGTGNSEIVLERKIADKRIFPAMDIIKSGTRKEDLLV 375
+S +VL R A K I+PA+D + S + D LV
Sbjct: 318 ----DSTVVLSRAQAAKGIYPAIDPLASSSNLLDPLV 350
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 39.1 bits (92), Expect = 0.002
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 141 PLYPDKRFNMELNNPENKDISS---------RVIDLIAPIGKGQRSLIVAPPRTGKT 188
PL R +E P + +V+D + PIG+GQR LI+ +TGKT
Sbjct: 120 PLQATARRPLERPAPAIIERDFVTEPLQTGIKVVDALIPIGRGQRELIIGDRQTGKT 176
>gnl|CDD|162134 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit.
Length = 501
Score = 37.4 bits (87), Expect = 0.008
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 165 IDLIAPIGKGQRSLIVAPPRTGKT 188
ID + PIG+GQR LI+ +TGKT
Sbjct: 152 IDAMIPIGRGQRELIIGDRQTGKT 175
>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit beta.
A small number of taxonomically diverse prokaryotic
species have what appears to be a second ATP synthase,
in addition to the normal F1F0 ATPase in bacteria and
A1A0 ATPase in archaea. These enzymes use ion gradients
to synthesize ATP, and in principle may run in either
direction. This model represents the F1 beta subunit of
this apparent second ATP synthase.
Length = 449
Score = 37.1 bits (86), Expect = 0.010
Identities = 55/225 (24%), Positives = 97/225 (43%), Gaps = 30/225 (13%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
+ ID++ P+ +G ++ + GKT+LL + H++ H + I I ER E ++
Sbjct: 127 KAIDVLVPLERGGKAGLFGGAGVGKTVLLTEMIHNMVGQH-QGVSIFCGIGERCREGEEL 185
Query: 223 QRSVQGEVISSTFDESAARHVQVAEMVIAK------AKCLVEY-----GLDVVILLDSIT 271
R ++ + D + Q+ E A+ A + EY DV++L+D+I
Sbjct: 186 YREMKE---AGVLDNTVMVFGQMNEPPGARFRVGHTALTMAEYFRDDEKQDVLLLIDNIF 242
Query: 272 RLCRAYNV------LMPSS-GKILTGGVDANALQRPKRFFGAARNIKEGGSLTIIGTALV 324
R +A + MPS G T G + L+ +R G++T I V
Sbjct: 243 RFIQAGSEVSGLLGQMPSRLGYQPTLGTELAELE--ERI-----ATTSDGAITSIQAVYV 295
Query: 325 DTGSRMDEVIFEEFKGTGNSEIVLERKIADKRIFPAMDIIKSGTR 369
D F S +VL RK A + ++PA+D ++S ++
Sbjct: 296 PADDFTDPAAVHTFSHLSAS-LVLSRKRASEGLYPAIDPLQSTSK 339
>gnl|CDD|140212 PTZ00185, PTZ00185, ATPase alpha subunit; Provisional.
Length = 574
Score = 36.6 bits (84), Expect = 0.012
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 3/57 (5%)
Query: 149 NMELNNPENKDISS--RVIDLIAPIGKGQRSLIVAPPRTGKT-ILLQNIAHSIKKNH 202
N+ +P N ++ + + +D + PIG+GQR LIV +TGKT I + I + ++ N
Sbjct: 162 NIVSRSPVNYNLLTGFKAVDTMIPIGRGQRELIVGDRQTGKTSIAVSTIINQVRINQ 218
>gnl|CDD|149329 pfam08206, OB_RNB, Ribonuclease B OB domain. This family includes
the N-terminal OB domain found in ribonuclease B
proteins in one or two copies.
Length = 58
Score = 36.7 bits (86), Expect = 0.012
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 56 GVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGER 112
G + + GFGFL PD DDI++ P Q+K GD V I R
Sbjct: 1 GTVRGHKKGFGFLI-PD----DEEDDIFIPPEQMK--KAMHGDRVLVRITKGDRRGR 50
>gnl|CDD|181753 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 36.6 bits (86), Expect = 0.013
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 164 VIDLIAPIGKGQRSLIVAPPRTGKT 188
ID + PIG+GQR LI+ +TGKT
Sbjct: 152 AIDAMIPIGRGQRELIIGDRQTGKT 176
>gnl|CDD|163043 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation.
Length = 270
Score = 36.2 bits (84), Expect = 0.016
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 156 ENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSI-----KKNHPECYLIVL 210
E + +++ + + +LI++PP+ GKT LL+++A + + V
Sbjct: 93 EKLGAADKLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKK--VG 150
Query: 211 LIDERPE 217
++DER E
Sbjct: 151 IVDERSE 157
>gnl|CDD|172578 PRK14088, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 440
Score = 34.0 bits (78), Expect = 0.082
Identities = 20/72 (27%), Positives = 33/72 (45%)
Query: 139 LTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSI 198
LTPL PD F + P N +++ G+ I GKT LLQ+I + +
Sbjct: 95 LTPLNPDYTFENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYV 154
Query: 199 KKNHPECYLIVL 210
+N P+ ++ +
Sbjct: 155 VQNEPDLRVMYI 166
>gnl|CDD|179776 PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
Length = 586
Score = 33.6 bits (78), Expect = 0.10
Identities = 38/139 (27%), Positives = 59/139 (42%), Gaps = 48/139 (34%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIA-HSIKKNHPECYLIVLLI--DERPEEV 219
RVID P+ KG + I P +GKT+ +A + IV+ + ER E+
Sbjct: 216 RVIDTFFPVAKGGTAAIPGPFGSGKTVTQHQLAKWADAD-------IVIYVGCGERGNEM 268
Query: 220 TD-----------------MQRSVQGEVISSTFDES----AARHVQV-AEMVIAKAKCLV 257
T+ M+R+V +I++T S AAR + + IA
Sbjct: 269 TEVLEEFPELIDPKTGRPLMERTV---LIANT---SNMPVAAREASIYTGITIA------ 316
Query: 258 EY----GLDVVILLDSITR 272
EY G DV+++ DS +R
Sbjct: 317 EYYRDMGYDVLLMADSTSR 335
>gnl|CDD|130115 TIGR01043, ATP_syn_A_arch, ATP synthase archaeal, A subunit.
Archaeal ATP synthase shares extensive sequence
similarity with eukaryotic and prokaryotic V-type
(H+)-ATPases.
Length = 578
Score = 31.6 bits (72), Expect = 0.41
Identities = 69/254 (27%), Positives = 106/254 (41%), Gaps = 68/254 (26%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLI--DERPEEVT 220
R++D PI KG + I P +GKT+ +A K + + IV+ I ER E+T
Sbjct: 211 RILDTFFPIAKGGTAAIPGPFGSGKTVTQHQLA---KWSDAD---IVVYIGCGERGNEMT 264
Query: 221 D-----------------MQRSVQGEVISSTFD-ESAARHVQVAEMVIAKAKCLVEY--- 259
D M+R+V +I++T + AAR E I + EY
Sbjct: 265 DVLEEFPELKDPKTGKPLMERTV---LIANTSNMPVAAR-----EASIYTGITIAEYFRD 316
Query: 260 -GLDVVILLDSITRLCRAYNVL------MPSSGKILTGGVDANALQRPKRFFGAARNIK- 311
G DV ++ DS +R A + MP G A R F+ A +K
Sbjct: 317 MGYDVALMADSTSRWAEAMREISGRLEEMPGE-----EGYPAYLASRLAEFYERAGRVKT 371
Query: 312 -----EGGSLTIIGTALVDTGSRMDEVIFEEFKGTGNS-EIV-----LERKIADKRIFPA 360
GS+T+IG A+ G E + T N+ IV L+ +A +R FPA
Sbjct: 372 LGGEERVGSVTVIG-AVSPPGGDFSEPV------TQNTLRIVKVFWALDADLAQRRHFPA 424
Query: 361 MDIIKSGTRKEDLL 374
++ ++S + DL+
Sbjct: 425 INWLQSYSLYVDLV 438
>gnl|CDD|181752 PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
Length = 463
Score = 31.3 bits (72), Expect = 0.46
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 346 IVLERKIADKRIFPAMDIIKSGTR 369
VL R+IA+ I+PA+D + S +R
Sbjct: 322 TVLSRQIAELGIYPAVDPLDSTSR 345
Score = 29.3 bits (67), Expect = 1.8
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 164 VIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNH 202
VIDL+AP KG + + GKT+L+Q + ++I K H
Sbjct: 134 VIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEH 172
>gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases.
Length = 654
Score = 30.8 bits (70), Expect = 0.64
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 55 EGVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYF 114
+GV++ GFGFLR D + D ++ P Q+K + GD VE + + R+
Sbjct: 18 KGVVKAHNKGFGFLRPDDDD----KKDYFIPPPQMK--KVMHGDLVEACPLSQPQRGRFE 71
Query: 115 A 115
A
Sbjct: 72 A 72
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 29.7 bits (67), Expect = 1.4
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 18/94 (19%)
Query: 105 RAPREGERYFALLKVN------AINFDVPERVRNKIHFDNLTPLYPDKRFNMELNNPENK 158
RA ER LL+ A +P +R +I F+ + YP + P+
Sbjct: 303 RAAGAAERLIELLQAEPDIKAPAHPKTLPVPLRGEIEFEQVNFAYPAR--------PDQP 354
Query: 159 DISSRVIDLIAPIGKGQRSLIVAPPRTGKTILLQ 192
+ ++L + G+ +V P GK+ L Q
Sbjct: 355 ALDG--LNLT--VRPGETVALVGPSGAGKSTLFQ 384
>gnl|CDD|162678 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans.
Length = 709
Score = 29.5 bits (67), Expect = 1.5
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 56 GVIEVLQDGFGFLRSPDANYLAGPDDIYVSPSQIKSFSLKTGDTVEGSI-RAPREGER 112
G + +DGFGFLR D DDI++ P Q+ GD V I P G+R
Sbjct: 71 GTVIAHRDGFGFLRPED----DDEDDIFIPPRQMN--GAMHGDRVLVRITGKPDGGDR 122
>gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 450
Score = 29.4 bits (67), Expect = 1.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 186 GKTILLQNIAHSIKKNHPE 204
GKT LL I + I + +P
Sbjct: 160 GKTHLLHAIGNYILEKNPN 178
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 29.0 bits (65), Expect = 2.6
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 134 IHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIA---PIGKG---QRSLIVAPPRTGK 187
+ + L PL F L PEN D+ R++ GKG + P +GK
Sbjct: 99 MKYGELDPLMTFANF---LVTPEN-DLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGK 154
Query: 188 TILLQNIAHSIKKNH 202
T L+Q H+++++
Sbjct: 155 THLMQAAVHALRESG 169
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes.
Length = 571
Score = 28.5 bits (64), Expect = 3.1
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 126 VPERVRNKIHFDNLTPLYPDKRFNMELNNPENKDISSRVIDLIAPIGKGQRSLIVAPPRT 185
ER R + F N+T YP + + + S I L+ G+ +V +
Sbjct: 323 AIERARGDVEFRNVTFRYPGR---------DRPALDS--ISLVIE--PGETVALVGRSGS 369
Query: 186 GKTIL 190
GK+ L
Sbjct: 370 GKSTL 374
>gnl|CDD|183253 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 28.6 bits (64), Expect = 3.4
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 62 QDGFGFLRSPDANYLAGPDDIYVSPSQIK 90
+DG+GFLR DD+Y+S Q+K
Sbjct: 93 RDGYGFLRVEGRK-----DDLYLSSEQMK 116
>gnl|CDD|130530 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA family. This
subfamily is closely related to, yet is distinct from,
uroporphyrinogen decarboxylase (EC 4.1.1.37). It
includes two isozymes from Methanosarcina barkeri of
methylcobalamin--coenzyme M methyltransferase. It also
includes a chloromethane utilization protein, CmuA,
which transfers the methyl group of chloromethane to a
corrinoid protein.
Length = 340
Score = 28.3 bits (63), Expect = 3.9
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 11/75 (14%)
Query: 246 AEMVIAKAKCLVEYGLDVVILLDSITRLCRAYNVLMPSSGKILTGGVDANALQRPKRFFG 305
+ VIA AK +VE G DV+ + D + +++ P + K L KR F
Sbjct: 179 LDFVIAYAKAMVEAGADVIAIADPFA----SSDLISPETYKEF-------GLPYQKRLFA 227
Query: 306 AARNIKEGGSLTIIG 320
+ I L I G
Sbjct: 228 YIKEIGGITVLHICG 242
>gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006).
Length = 405
Score = 28.3 bits (64), Expect = 4.1
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 186 GKTILLQNIAHSIKKNHPE 204
GKT LL I + I +N+P
Sbjct: 148 GKTHLLHAIGNEILENNPN 166
>gnl|CDD|131256 TIGR02201, heptsyl_trn_III, lipopolysaccharide heptosyltransferase
III, putative. This family consists of examples of the
putative ADP-heptose:LPS heptosyltransferase III, an
enzyme of LPS inner core region biosynthesis. LPS,
composed of lipid A, a core region, and O antigen, is
found in the outer membrane of Gram-negative bacteria.
This enzyme may be less widely distributed than
heptosyltransferases I and II.
Length = 344
Score = 27.9 bits (62), Expect = 5.3
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 176 RSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDE 214
R L++ G +L + S+KKN+P+ + VLL E
Sbjct: 1 RILLIKLRHHGDMLLTTPVISSLKKNYPDAKIDVLLYQE 39
>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 529
Score = 27.7 bits (62), Expect = 5.4
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 163 RVIDLIAPIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM 222
+ L P G+ R I+ P +GK+ LL + + E V L + D
Sbjct: 352 DGVSLDLPPGE--RVAILGPSGSGKSTLLMLLTGLLDPLQGE----VTLDGVSVSSLQDE 405
Query: 223 QRSV 226
R
Sbjct: 406 LRRR 409
>gnl|CDD|161977 TIGR00649, MG423, conserved hypothetical protein. Contains an
ATP-binding domain at the N-terminal end of the protein.
Possibly part of a superfamily of beta-lactmases.
Length = 422
Score = 27.7 bits (62), Expect = 6.2
Identities = 14/57 (24%), Positives = 28/57 (49%)
Query: 217 EEVTDMQRSVQGEVISSTFDESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRL 273
E++ D+ ++ +G VI +TF + R Q+ ++ + + YG + L RL
Sbjct: 208 EQLNDIFKNAKGRVIVATFASNIHRVQQLIQIARKQGRKFAVYGRSMEHLFGIARRL 264
>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
Length = 497
Score = 27.5 bits (62), Expect = 6.7
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 160 ISSRVIDLIAPIGKGQRS--LIVAP-PRTGKTILLQNIAHSIKKNH 202
IS+ + DL + +G S +I+A P GKT L NIA + K +
Sbjct: 200 ISTGLRDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAY 245
>gnl|CDD|165190 PHA02852, PHA02852, putative virion structural protein;
Provisional.
Length = 153
Score = 27.6 bits (61), Expect = 6.9
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 132 NKIHFDNLTPLYPDKRFNMELNNPENKDI-----SSRVI--DLIAP--IGKGQRSLIVAP 182
N F++L PL P K N+ NN N D+ S+++I +L GK L+ P
Sbjct: 79 NNSFFESLEPLLPVKTINLSYNNTINDDLQDNTLSTKMILLELFNSFKFGKKSNYLVKYP 138
>gnl|CDD|178901 PRK00148, PRK00148, Maf-like protein; Reviewed.
Length = 194
Score = 27.5 bits (62), Expect = 7.7
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 229 EVISSTFDESAARHVQVAEMV----IAKAKCLVEYGLDVVIL-LDSI 270
V+ S DE A +E+V AKA+ + E D V+L DS+
Sbjct: 24 LVVVSHVDEDAIAASSPSELVQALARAKAEAVAENAPDAVVLGCDSM 70
>gnl|CDD|147823 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 27.2 bits (61), Expect = 9.0
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 179 IVAPPRTGKTILLQN-IAHSI 198
+ + GKT LL N I + I
Sbjct: 38 FMKSAQVGKTELLLNWIGYFI 58
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.318 0.136 0.375
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,971,943
Number of extensions: 474501
Number of successful extensions: 1107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1056
Number of HSP's successfully gapped: 86
Length of query: 423
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 327
Effective length of database: 3,920,105
Effective search space: 1281874335
Effective search space used: 1281874335
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: 58 (26.1 bits)