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)