RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3765
(592 letters)
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 701 bits (1812), Expect = 0.0
Identities = 253/349 (72%), Positives = 310/349 (88%), Gaps = 2/349 (0%)
Query: 1 KTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEI 60
+ + G IFG+G LE+LPDGFGFLRS +NY+ DDIY+SPSQIRRFNL TGD VEG+I
Sbjct: 42 QAEKGGDIFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGKI 101
Query: 61 RVPKNGERYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRI 120
R PK GERYFALLK++ VNGE PE ++NR LF+NLTPL+P + L LE + E+++ RI
Sbjct: 102 RPPKEGERYFALLKVETVNGEDPEKARNRPLFENLTPLYPNERLRLET--GNPEDLSTRI 159
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 180
IDLIAPIGKGQRGL+VA PK+GK+++LQ+IA++ITTNH E +IV+LIDERPEEVT+MQR
Sbjct: 160 IDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQR 219
Query: 181 SVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPAS 240
SV+GEV+ASTFDEPA RHVQVAEMV+EKAKRLVE KDV+ILLDSITRLARAYNTV+P+S
Sbjct: 220 SVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSS 279
Query: 241 GKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNM 300
GKVL+GGVD+NAL RPKRFFGAARNIEEGGSLTIIATALI+TGSRMD+VI+EEFKGTGNM
Sbjct: 280 GKVLSGGVDANALHRPKRFFGAARNIEEGGSLTIIATALIDTGSRMDEVIFEEFKGTGNM 339
Query: 301 EVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSL 349
E+HL+R+LAEKR++PAI++N+SGTR+EELL+ ++LQK+W+LRK+L +
Sbjct: 340 ELHLDRKLAEKRIFPAIDINRSGTRKEELLLSPEELQKVWILRKILSPM 388
Score = 197 bits (503), Expect = 4e-57
Identities = 76/129 (58%), Positives = 94/129 (72%), Gaps = 27/129 (20%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA 548
VA PK+GK+++LQ+IA++ITTNH E +IV+LIDERPEEVT+MQRSV+GEV+ASTFDEPA
Sbjct: 175 VAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPA 234
Query: 549 ---------------------------LSVMCKLARAYNTVIPASGKVLTGGVDSNALQR 581
L + +LARAYNTV+P+SGKVL+GGVD+NAL R
Sbjct: 235 ERHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSGGVDANALHR 294
Query: 582 PKRFFGAAR 590
PKRFFGAAR
Sbjct: 295 PKRFFGAAR 303
Score = 163 bits (416), Expect = 1e-44
Identities = 65/114 (57%), Positives = 83/114 (72%)
Query: 387 IDLEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDD 446
+L + + RLRKQEL+FAI K + + G IFG+G LE+LPDGFGFLRS +NY+ DD
Sbjct: 19 EELGIENASRLRKQELIFAILKAQAEKGGDIFGEGVLEILPDGFGFLRSPDANYLPGPDD 78
Query: 447 IYLSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVNVASPKSGKSIIL 500
IY+SPSQIRRFNL TG +G+IR PK GERYFALLK++ VN P+ ++ L
Sbjct: 79 IYVSPSQIRRFNLRTGDTVEGKIRPPKEGERYFALLKVETVNGEDPEKARNRPL 132
>gnl|CDD|224080 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 657 bits (1696), Expect = 0.0
Identities = 255/363 (70%), Positives = 312/363 (85%), Gaps = 3/363 (0%)
Query: 1 KTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEI 60
+ + GE IFGDG LE+LPDGFGFLRS S+Y+ DDIY+SPSQIRRFNL TGD VEG++
Sbjct: 45 QAEQGEEIFGDGVLEILPDGFGFLRSADSSYLPGPDDIYVSPSQIRRFNLRTGDTVEGKV 104
Query: 61 RVPKNGERYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRI 120
R PK GERYFALLK++ VNG+ PE +KNR LF+NLTPL+P + L LER S +++ R+
Sbjct: 105 RPPKEGERYFALLKVEAVNGDDPEKAKNRVLFENLTPLYPNERLKLERENGS-TDLSTRV 163
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 180
IDLI+PIGKGQRGL+VA PK+GK+ +LQ+IA+AITTNH E +IV+LIDERPEEVT+MQR
Sbjct: 164 IDLISPIGKGQRGLIVAPPKAGKTTLLQNIANAITTNHPECELIVLLIDERPEEVTDMQR 223
Query: 181 SVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPAS 240
SV+GEV+ASTFDEP RHVQVAEMV+EKAKRLVE KDV+ILLDSITRLARAYNTV+P+S
Sbjct: 224 SVKGEVVASTFDEPPSRHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSS 283
Query: 241 GKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNM 300
GKVL+GGVD+NAL RPKRFFGAARNIEEGGSLTIIATAL++TGSRMD+VI+EEFKGTGNM
Sbjct: 284 GKVLSGGVDANALHRPKRFFGAARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNM 343
Query: 301 EVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLTMTSFTVSLFF 360
E+HL+R+LAE+R++PAI++NKSGTR+EELL+ D+LQK+WVLR++L + F
Sbjct: 344 ELHLDRKLAERRIFPAIDINKSGTRKEELLLSPDELQKMWVLRRILSPMDEIDAIE--FL 401
Query: 361 IKR 363
I +
Sbjct: 402 IDK 404
Score = 186 bits (474), Expect = 6e-53
Identities = 76/129 (58%), Positives = 92/129 (71%), Gaps = 27/129 (20%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA 548
VA PK+GK+ +LQ+IA+AITTNH E +IV+LIDERPEEVT+MQRSV+GEV+ASTFDEP
Sbjct: 179 VAPPKAGKTTLLQNIANAITTNHPECELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPP 238
Query: 549 ---------------------------LSVMCKLARAYNTVIPASGKVLTGGVDSNALQR 581
L + +LARAYNTV+P+SGKVL+GGVD+NAL R
Sbjct: 239 SRHVQVAEMVIEKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSGGVDANALHR 298
Query: 582 PKRFFGAAR 590
PKRFFGAAR
Sbjct: 299 PKRFFGAAR 307
Score = 152 bits (386), Expect = 1e-40
Identities = 66/112 (58%), Positives = 84/112 (75%)
Query: 389 LEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIY 448
L + + RLRKQ+L+FAI K + + GE IFGDG LE+LPDGFGFLRS S+Y+ DDIY
Sbjct: 24 LGIENYSRLRKQDLIFAILKAQAEQGEEIFGDGVLEILPDGFGFLRSADSSYLPGPDDIY 83
Query: 449 LSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVNVASPKSGKSIIL 500
+SPSQIRRFNL TG +G++R PK GERYFALLK++ VN P+ K+ +L
Sbjct: 84 VSPSQIRRFNLRTGDTVEGKVRPPKEGERYFALLKVEAVNGDDPEKAKNRVL 135
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. This RNA
helicase, the transcription termination factor Rho,
occurs in nearly all bacteria but is missing from the
Cyanobacteria, the Mollicutes (Mycoplasmas), and various
Lactobacillales including Streptococcus. It is also
missing, of course, from the Archaea, which also lack
Nus factors. Members of this family from Micrococcus
luteus, Mycobacterium tuberculosis, and related species
have a related but highly variable long, highly charged
insert near the amino end. Members of this family differ
in the specificity of RNA binding [Transcription,
Transcription factors].
Length = 415
Score = 615 bits (1589), Expect = 0.0
Identities = 255/363 (70%), Positives = 308/363 (84%), Gaps = 5/363 (1%)
Query: 1 KTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEI 60
+ G IFG+G LE+LPDGFGFLRS S+Y+ DDIY+SPSQIRRFNL TGD +EG+I
Sbjct: 42 HAEQGGLIFGEGVLEILPDGFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRTGDTIEGQI 101
Query: 61 RVPKNGERYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRI 120
R PK GERYFALLK++ VNG+ PE +KNR LF+NLTPL+P + L LE S E+++ R+
Sbjct: 102 RSPKEGERYFALLKVESVNGDDPEKAKNRVLFENLTPLYPNERLRLET---STEDLSTRV 158
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 180
+DL APIGKGQRGL+VA PK+GK+++LQ IA AIT NH E +IV+LIDERPEEVT+MQR
Sbjct: 159 LDLFAPIGKGQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQR 218
Query: 181 SVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPAS 240
SV+GEV+ASTFDEPA RHVQVAEMV+EKAKRLVE KKDV+ILLDSITRLARAYNTV PAS
Sbjct: 219 SVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVVILLDSITRLARAYNTVTPAS 278
Query: 241 GKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNM 300
GKVL+GGVD+NAL RPKRFFGAARNIEEGGSLTIIATALI+TGSRMD+VI+EEFKGTGNM
Sbjct: 279 GKVLSGGVDANALHRPKRFFGAARNIEEGGSLTIIATALIDTGSRMDEVIFEEFKGTGNM 338
Query: 301 EVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLTMTSFTVSLFF 360
E+HL+R+LA++R++PAI++ KSGTR+EELL+ ++LQKIWVLRK++ M S F
Sbjct: 339 ELHLDRKLADRRIFPAIDIKKSGTRKEELLLTPEELQKIWVLRKIIS--PMDSIEAMEFL 396
Query: 361 IKR 363
I +
Sbjct: 397 ISK 399
Score = 293 bits (752), Expect = 1e-93
Identities = 141/293 (48%), Positives = 169/293 (57%), Gaps = 82/293 (27%)
Query: 380 VLAETQTI--DLEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQG 437
L E + + L V + L+KQEL+FAI K + G IFG+G LE+LPDGFGFLRS
Sbjct: 10 PLEELRKLAEQLGVENTSSLKKQELIFAILKAHAEQGGLIFGEGVLEILPDGFGFLRSPD 69
Query: 438 SNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVN--------- 488
S+Y+ DDIY+SPSQIRRFNL TG +G+IR PK GERYFALLK++ VN
Sbjct: 70 SSYLPGPDDIYVSPSQIRRFNLRTGDTIEGQIRSPKEGERYFALLKVESVNGDDPEKAKN 129
Query: 489 --------------------------------------------VASPKSGKSIILQHIA 504
VA PK+GK+++LQ IA
Sbjct: 130 RVLFENLTPLYPNERLRLETSTEDLSTRVLDLFAPIGKGQRGLIVAPPKAGKTVLLQKIA 189
Query: 505 HAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA---------------- 548
AIT NH E +IV+LIDERPEEVT+MQRSV+GEV+ASTFDEPA
Sbjct: 190 QAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKR 249
Query: 549 -----------LSVMCKLARAYNTVIPASGKVLTGGVDSNALQRPKRFFGAAR 590
L + +LARAYNTV PASGKVL+GGVD+NAL RPKRFFGAAR
Sbjct: 250 LVEHKKDVVILLDSITRLARAYNTVTPASGKVLSGGVDANALHRPKRFFGAAR 302
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 529 bits (1365), Expect = 0.0
Identities = 200/344 (58%), Positives = 264/344 (76%), Gaps = 12/344 (3%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGER--- 68
G L+VL D + F+R+ G Y+ +D+Y+S +Q+R+ L GD V G +R P+ GE+
Sbjct: 298 GILDVL-DNYAFVRTSG--YLPGPNDVYVSMNQVRKNGLRKGDAVTGAVRAPREGEQGNQ 354
Query: 69 ---YFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIA 125
+ L+++ VNG PE +K R F LTPL+P + L LE E K +T R+IDLI
Sbjct: 355 RQKFNPLVRLDSVNGMSPEEAKKRPEFGKLTPLYPNERLRLE--TEPK-KLTTRVIDLIM 411
Query: 126 PIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGE 185
PIGKGQRGL+V+ PK+GK+ ILQ+IA+AITTN+ E ++V+L+DERPEEVT+MQRSV+GE
Sbjct: 412 PIGKGQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERPEEVTDMQRSVKGE 471
Query: 186 VIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLT 245
VIASTFD P H VAE+ +E+AKRLVE+ KDV++LLDSITRL RAYN PASG++L+
Sbjct: 472 VIASTFDRPPSDHTTVAELAIERAKRLVELGKDVVVLLDSITRLGRAYNLAAPASGRILS 531
Query: 246 GGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLE 305
GGVDS AL PKRFFGAARNIE GGSLTIIATAL+ETGS+MD+VI+EEFKGTGNME+ L+
Sbjct: 532 GGVDSTALYPPKRFFGAARNIENGGSLTIIATALVETGSKMDEVIFEEFKGTGNMELKLD 591
Query: 306 RRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSL 349
R+LA+KR++PA+++N SGTR+EELL+ D+L + LR++L L
Sbjct: 592 RKLADKRIFPAVDVNASGTRKEELLLSPDELAIVHKLRRVLSGL 635
Score = 198 bits (507), Expect = 1e-55
Identities = 92/256 (35%), Positives = 127/256 (49%), Gaps = 89/256 (34%)
Query: 421 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGER--- 477
G L+VL D + F+R+ G Y+ +D+Y+S +Q+R+ L G G +R P+ GE+
Sbjct: 298 GILDVL-DNYAFVRTSG--YLPGPNDVYVSMNQVRKNGLRKGDAVTGAVRAPREGEQGNQ 354
Query: 478 ---YFALLKIKKVN---------------------------------------------- 488
+ L+++ VN
Sbjct: 355 RQKFNPLVRLDSVNGMSPEEAKKRPEFGKLTPLYPNERLRLETEPKKLTTRVIDLIMPIG 414
Query: 489 -------VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIA 541
V+ PK+GK+ ILQ+IA+AITTN+ E ++V+L+DERPEEVT+MQRSV+GEVIA
Sbjct: 415 KGQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIA 474
Query: 542 STFDEPA---------------------------LSVMCKLARAYNTVIPASGKVLTGGV 574
STFD P L + +L RAYN PASG++L+GGV
Sbjct: 475 STFDRPPSDHTTVAELAIERAKRLVELGKDVVVLLDSITRLGRAYNLAAPASGRILSGGV 534
Query: 575 DSNALQRPKRFFGAAR 590
DS AL PKRFFGAAR
Sbjct: 535 DSTALYPPKRFFGAAR 550
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 498 bits (1283), Expect = e-174
Identities = 209/340 (61%), Positives = 267/340 (78%), Gaps = 6/340 (1%)
Query: 11 DGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGERYF 70
G LE+L DGFGFLRS NY+ S DD+++ P+ IRRFNL TGD VEG R ERY
Sbjct: 20 LGVLEILGDGFGFLRSARRNYLPSPDDVFVPPALIRRFNLRTGDVVEGVARPR---ERYR 76
Query: 71 ALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPIGKG 130
L+++ VNG PE R FD+LTPLHP++ L LE ++++ R++DL+APIGKG
Sbjct: 77 VLVRVDSVNGTDPEKLARRPHFDDLTPLHPRERLRLE---TGSDDLSMRVVDLVAPIGKG 133
Query: 131 QRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIAST 190
QRGL+VA P++GK+++LQ IA A+ NH E ++V+LIDERPEEVT+M+RSV+GEV AST
Sbjct: 134 QRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYAST 193
Query: 191 FDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGGVDS 250
FD P H++VAE+VLE+AKRLVE KDV+ILLDS+TRLARAYN + +SG+ L+GGVD+
Sbjct: 194 FDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLARAYNNEVESSGRTLSGGVDA 253
Query: 251 NALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAE 310
ALQRPKR FGAARNIEEGGSLTIIATAL++TGSRMD+VI+EEFKGTGNME+ L+R LA+
Sbjct: 254 RALQRPKRLFGAARNIEEGGSLTIIATALVDTGSRMDEVIFEEFKGTGNMEIVLDRELAD 313
Query: 311 KRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLT 350
KRV+PAI++ KSGTRREELL+ +L+K+ LR+ L S
Sbjct: 314 KRVFPAIDIAKSGTRREELLLDSKELEKVRRLRRALASRK 353
Score = 196 bits (499), Expect = 5e-57
Identities = 97/252 (38%), Positives = 127/252 (50%), Gaps = 83/252 (32%)
Query: 420 DGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGERYF 479
G LE+L DGFGFLRS NY+ S DD+++ P+ IRRFNL TG + +G R ERY
Sbjct: 20 LGVLEILGDGFGFLRSARRNYLPSPDDVFVPPALIRRFNLRTGDVVEGVARPR---ERYR 76
Query: 480 ALLKIKKVN--------------------------------------------------- 488
L+++ VN
Sbjct: 77 VLVRVDSVNGTDPEKLARRPHFDDLTPLHPRERLRLETGSDDLSMRVVDLVAPIGKGQRG 136
Query: 489 --VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDE 546
VA P++GK+++LQ IA A+ NH E ++V+LIDERPEEVT+M+RSV+GEV ASTFD
Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDR 196
Query: 547 PA---------------------------LSVMCKLARAYNTVIPASGKVLTGGVDSNAL 579
P L + +LARAYN + +SG+ L+GGVD+ AL
Sbjct: 197 PPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLARAYNNEVESSGRTLSGGVDARAL 256
Query: 580 QRPKRFFGAARK 591
QRPKR FGAAR
Sbjct: 257 QRPKRLFGAARN 268
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 456 bits (1176), Expect = e-160
Identities = 174/236 (73%), Positives = 213/236 (90%)
Query: 115 NITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEE 174
++ R++DL APIGKGQRGL+VA PK+GK+ +LQ IA+AIT NH E +IV+LIDERPEE
Sbjct: 1 ELSTRVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEE 60
Query: 175 VTEMQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYN 234
VT+MQRSV+GEVIASTFDEP RHVQVAEMVLEKAKRLVE KDV+ILLDSITRLARAYN
Sbjct: 61 VTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYN 120
Query: 235 TVIPASGKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEF 294
TV+P SGK+L+GGVD+NAL +PKRFFGAARNIEEGGSLTIIATAL++TGSRMDDVI+EEF
Sbjct: 121 TVVPPSGKILSGGVDANALHKPKRFFGAARNIEEGGSLTIIATALVDTGSRMDDVIFEEF 180
Query: 295 KGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLT 350
KGTGNME+ L+RRLAE+R++PAI++ KSGTR+EELL+ ++LQ++W+LR++L +
Sbjct: 181 KGTGNMELVLDRRLAERRIFPAIDILKSGTRKEELLLDPEELQRMWLLRRVLSDMD 236
Score = 174 bits (444), Expect = 1e-50
Identities = 74/130 (56%), Positives = 89/130 (68%), Gaps = 27/130 (20%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA 548
VA PK+GK+ +LQ IA+AIT NH E +IV+LIDERPEEVT+MQRSV+GEVIASTFDEP
Sbjct: 22 VAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPP 81
Query: 549 ---------------------------LSVMCKLARAYNTVIPASGKVLTGGVDSNALQR 581
L + +LARAYNTV+P SGK+L+GGVD+NAL +
Sbjct: 82 ERHVQVAEMVLEKAKRLVEHGKDVVILLDSITRLARAYNTVVPPSGKILSGGVDANALHK 141
Query: 582 PKRFFGAARK 591
PKRFFGAAR
Sbjct: 142 PKRFFGAARN 151
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 230 bits (590), Expect = 2e-72
Identities = 71/217 (32%), Positives = 106/217 (48%), Gaps = 13/217 (5%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEV 175
TG R IDL+ PIGKGQR + +GK+++L IA + + + +LI ER EV
Sbjct: 1 TGIRAIDLLLPIGKGQRIGIFGGSGTGKTVLLGMIARNAKADV---VEVYVLIGERGREV 57
Query: 176 TEMQRSVRGE-------VIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITR 228
E + GE V+A+T DEP L A+ + KDV++LLDS+TR
Sbjct: 58 AEFIEELLGEGALKRTVVVAATSDEPPAERYLAPYTALTIAEYFRDQGKDVLLLLDSLTR 117
Query: 229 LARAYNTVIPASGKV-LTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMD 287
ARA + G+ G + R A +E GGS+T + T L+ G +
Sbjct: 118 FARALREISLLLGEPPGREGYPGSLFSDLARLLERAGKVEGGGSITALPTVLVPGGD-IT 176
Query: 288 DVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGT 324
D I + + ++ L R LAE+ +YPAI++ S +
Sbjct: 177 DPIPDNTISITDGQIVLSRELAERGIYPAIDILLSVS 213
Score = 73.6 bits (182), Expect = 7e-15
Identities = 30/138 (21%), Positives = 48/138 (34%), Gaps = 38/138 (27%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGE-------VIA 541
+GK+++L IA + + + +LI ER EV E + GE V+A
Sbjct: 21 FGGSGTGKTVLLGMIARNAKADV---VEVYVLIGERGREVAEFIEELLGEGALKRTVVVA 77
Query: 542 STFDEP----------ALSV-----------------MCKLARAYNTVIPASGKV-LTGG 573
+T DEP AL++ + + ARA + G+ G
Sbjct: 78 ATSDEPPAERYLAPYTALTIAEYFRDQGKDVLLLLDSLTRFARALREISLLLGEPPGREG 137
Query: 574 VDSNALQRPKRFFGAARK 591
+ R A K
Sbjct: 138 YPGSLFSDLARLLERAGK 155
>gnl|CDD|203651 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 = 144 bits (365), Expect = 1e-41
Identities = 55/77 (71%), Positives = 65/77 (84%)
Query: 8 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGE 67
IFG+G LE+LPDGFGFLRS +NY+ DDIY+SPSQIRRFNL TGD +EG+IR PK GE
Sbjct: 1 IFGEGVLEILPDGFGFLRSPEANYLPGPDDIYVSPSQIRRFNLRTGDTIEGKIRPPKEGE 60
Query: 68 RYFALLKIKKVNGEKPE 84
RYFALLK++ +NGE PE
Sbjct: 61 RYFALLKVEAINGEPPE 77
Score = 127 bits (322), Expect = 1e-35
Identities = 50/76 (65%), Positives = 60/76 (78%)
Query: 417 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGE 476
IFG+G LE+LPDGFGFLRS +NY+ DDIY+SPSQIRRFNL TG +G+IR PK GE
Sbjct: 1 IFGEGVLEILPDGFGFLRSPEANYLPGPDDIYVSPSQIRRFNLRTGDTIEGKIRPPKEGE 60
Query: 477 RYFALLKIKKVNVASP 492
RYFALLK++ +N P
Sbjct: 61 RYFALLKVEAINGEPP 76
>gnl|CDD|239906 cd04459, Rho_CSD, Rho_CSD: Rho protein cold-shock domain (CSD).
Rho protein is a transcription termination factor in
most bacteria. In bacteria, there are two distinct
mechanisms for mRNA transcription termination. In
intrinsic termination, RNA polymerase and nascent mRNA
are released from DNA template by an mRNA stem loop
structure, which resembles the transcription
termination mechanism used by eukaryotic pol III. The
second mechanism is mediated by Rho factor. Rho factor
terminates transcription by using energy from ATP
hydrolysis to forcibly dissociate the transcripts from
RNA polymerase. Rho protein contains an N-terminal
S1-like domain, which binds single-stranded RNA. Rho
has a C-terminal ATPase domain which hydrolyzes ATP to
provide energy to strip RNA polymerase and mRNA from
the DNA template. Rho functions as a homohexamer.
Length = 68
Score = 121 bits (307), Expect = 1e-33
Identities = 49/68 (72%), Positives = 55/68 (80%)
Query: 10 GDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGERY 69
G G LE+LPDGFGFLRS G NY+ DDIY+SPSQIRRFNL TGD V G+IR PK GERY
Sbjct: 1 GSGVLEILPDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPPKEGERY 60
Query: 70 FALLKIKK 77
FALLK++
Sbjct: 61 FALLKVEA 68
Score = 112 bits (283), Expect = 3e-30
Identities = 47/68 (69%), Positives = 53/68 (77%)
Query: 419 GDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGERY 478
G G LE+LPDGFGFLRS G NY+ DDIY+SPSQIRRFNL TG G+IR PK GERY
Sbjct: 1 GSGVLEILPDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPPKEGERY 60
Query: 479 FALLKIKK 486
FALLK++
Sbjct: 61 FALLKVEA 68
>gnl|CDD|238556 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific
ATPase/type III secretory pathway virulence-related
protein. This group of ATPases are responsible for the
export of flagellum and virulence-related proteins. The
bacterial flagellar motor is similar to the F0F1-ATPase,
in that they both are proton driven rotary molecular
devices. However, the main function of the bacterial
flagellar motor is to rotate the flagellar filament for
cell motility. Intracellular pathogens such as
Salmonella and Chlamydia also have proteins which are
similar to the flagellar-specific ATPase, but function
in the secretion of virulence-related proteins via the
type III secretory pathway.
Length = 326
Score = 98.1 bits (245), Expect = 2e-22
Identities = 73/241 (30%), Positives = 114/241 (47%), Gaps = 22/241 (9%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE 177
R ID + +GKGQR + A GKS +L IA + A + ++ LI ER EV E
Sbjct: 58 RAIDGLLTVGKGQRLGIFAGSGVGKSTLLGMIA-----RGTTADVNVIALIGERGREVRE 112
Query: 178 ----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
++RSV V+ +T DE V+ A A+ + KDV++L+DS+T
Sbjct: 113 FIEKDLGEEGLKRSV---VVVATSDESPLLRVKAAYTATAIAEYFRDQGKDVLLLMDSLT 169
Query: 228 RLARAYNTVIPASGKVL-TGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRM 286
R A A + A+G+ T G + R A N + GS+T T L+E G +
Sbjct: 170 RFAMAQREIGLAAGEPPTTKGYPPSVFALLPRLLERAGN-SDKGSITAFYTVLVE-GDDL 227
Query: 287 DDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
++ I + + + + L R LA YPAI++ KS +R ++ + + LR+LL
Sbjct: 228 NEPIADAVRSILDGHIVLSRALAAAGHYPAIDVLKSISRLMNAVVTPEHKEAARKLRELL 287
Query: 347 Y 347
Sbjct: 288 S 288
Score = 36.5 bits (85), Expect = 0.033
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 19/71 (26%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGE 538
A GKS +L IA + A + ++ LI ER EV E ++RSV
Sbjct: 76 AGSGVGKSTLLGMIA-----RGTTADVNVIALIGERGREVREFIEKDLGEEGLKRSV--- 127
Query: 539 VIASTFDEPAL 549
V+ +T DE L
Sbjct: 128 VVVATSDESPL 138
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 94.3 bits (235), Expect = 1e-20
Identities = 75/243 (30%), Positives = 117/243 (48%), Gaps = 21/243 (8%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEE 174
TG R ID + G+GQR + A GKS +L I S + ++ LI ER E
Sbjct: 130 PTGVRAIDGLLTCGEGQRIGIFAGAGVGKSTLL----GMIARGASADVNVIALIGERGRE 185
Query: 175 VTE----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLD 224
V E +RSV ++ ST D P+ ++ A A+ + K V++++D
Sbjct: 186 VREFIEHHLGEEGRKRSV---LVVSTSDRPSLERLKAAYTATAIAEYFRDQGKRVLLMMD 242
Query: 225 SITRLARAYNTVIPASGKVLT-GGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETG 283
S+TR ARA + A+G+ GG + R A N E+ GS+T + T L+E G
Sbjct: 243 SLTRFARALREIGLAAGEPPARGGYPPSVFSSLPRLLERAGNGEK-GSITALYTVLVE-G 300
Query: 284 SRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLR 343
M+D I +E + + + L R LAE+ YPAI++ S +R ++ + + LR
Sbjct: 301 DDMNDPIADEVRSILDGHIVLSRALAERNHYPAIDVLASLSRVMSQVVSTEHRRAAGKLR 360
Query: 344 KLL 346
+LL
Sbjct: 361 RLL 363
Score = 36.1 bits (84), Expect = 0.048
Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 18/83 (21%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE----------MQRSVRGEV 539
A GKS +L I S + ++ LI ER EV E +RSV +
Sbjct: 152 AGAGVGKSTLL----GMIARGASADVNVIALIGERGREVREFIEHHLGEEGRKRSV---L 204
Query: 540 IASTFDEPALSVMCKLARAYNTV 562
+ ST D P+L K A +
Sbjct: 205 VVSTSDRPSL-ERLKAAYTATAI 226
>gnl|CDD|224079 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 93.8 bits (234), Expect = 2e-20
Identities = 77/244 (31%), Positives = 119/244 (48%), Gaps = 23/244 (9%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPE 173
TG R ID + GKGQR + A GKS +L IA ++EA + ++ LI ER
Sbjct: 148 DTGVRAIDGLLTCGKGQRIGIFAGSGVGKSTLLGMIA-----RNTEADVNVIALIGERGR 202
Query: 174 EVTE----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILL 223
EV E ++RSV V+ +T DE A ++ A A+ + K V++++
Sbjct: 203 EVREFIEKDLGEEGLKRSV---VVVATSDESALMRLKAAFTATTIAEYFRDQGKRVLLIM 259
Query: 224 DSITRLARAYNTVIPASGKVL-TGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIET 282
DS+TR A A + A+G+ T G + R A N + GS+T T L+E
Sbjct: 260 DSLTRFAMAQREIGLAAGEPPATKGYPPSVFSELPRLLERAGN-GDKGSITAFYTVLVE- 317
Query: 283 GSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVL 342
G M+D I +E + + + L R LAE YPAI++ S +R ++ ++ + L
Sbjct: 318 GDDMNDPIADEVRSILDGHIVLSRALAEAGHYPAIDVLASISRVMPQIVSEEHRKAARRL 377
Query: 343 RKLL 346
R+LL
Sbjct: 378 RQLL 381
Score = 41.0 bits (97), Expect = 0.001
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 19/72 (26%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGE 538
A GKS +L IA ++EA + ++ LI ER EV E ++RSV
Sbjct: 170 AGSGVGKSTLLGMIA-----RNTEADVNVIALIGERGREVREFIEKDLGEEGLKRSV--- 221
Query: 539 VIASTFDEPALS 550
V+ +T DE AL
Sbjct: 222 VVVATSDESALM 233
>gnl|CDD|233237 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 [Energy metabolism, ATP-proton
motive force interconversion].
Length = 440
Score = 91.7 bits (228), Expect = 1e-19
Identities = 80/284 (28%), Positives = 133/284 (46%), Gaps = 28/284 (9%)
Query: 76 KKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGL 134
K ++G+ L T P++P K + + TG R ID + +GKGQR
Sbjct: 113 KPIDGKGKFLDNVETEGLITAPINPLKRAPIREILS-----TGVRSIDGLLTVGKGQRIG 167
Query: 135 LVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVR 183
+ A GKS +L IA ++EA + ++ LI ER EV E ++RSV
Sbjct: 168 IFAGSGVGKSTLLGMIAR-----NTEADVNVIALIGERGREVREFIEHDLGEEGLKRSV- 221
Query: 184 GEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKV 243
V+ +T D+ ++ A + A+ + KDV++L+DS+TR A A + A+G+
Sbjct: 222 --VVVATSDQSPLLRLKGAYVATAIAEYFRDQGKDVLLLMDSVTRFAMAQREIGLAAGEP 279
Query: 244 -LTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEV 302
T G + R A GS+T T L+E G M++ I + +G + +
Sbjct: 280 PATKGYTPSVFSTLPRLLERA-GASGKGSITAFYTVLVE-GDDMNEPIADSVRGILDGHI 337
Query: 303 HLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
L R LA++ YPAI++ S +R ++ ++ + R+LL
Sbjct: 338 VLSRALAQRGHYPAIDVLASISRLMTAIVSEEHRRAARKFRELL 381
Score = 30.8 bits (70), Expect = 2.1
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 19/67 (28%)
Query: 495 GKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIAST 543
GKS +L IA ++EA + ++ LI ER EV E ++RSV V+ +T
Sbjct: 175 GKSTLLGMIAR-----NTEADVNVIALIGERGREVREFIEHDLGEEGLKRSV---VVVAT 226
Query: 544 FDEPALS 550
D+ L
Sbjct: 227 SDQSPLL 233
>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
Length = 440
Score = 85.6 bits (212), Expect = 9e-18
Identities = 69/240 (28%), Positives = 110/240 (45%), Gaps = 22/240 (9%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE 177
R ID I G+GQR + A+ GKS +L + S A +M++ LI ER EV E
Sbjct: 152 RAIDGILSCGEGQRIGIFAAAGVGKSTLLGMLC-----ADSAADVMVLALIGERGREVRE 206
Query: 178 M----------QRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
R+V V+ +T D PA ++ A+ + K V+++ DS+T
Sbjct: 207 FLEQVLTPEARARTV---VVVATSDRPALERLKGLSTATTIAEYFRDRGKKVLLMADSLT 263
Query: 228 RLARAYNTVIPASGKV-LTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRM 286
R ARA + A+G+ G + R N + GS+T T L+E G M
Sbjct: 264 RYARAAREIGLAAGEPPAAGSFPPSVFANLPRLLERTGNSDR-GSITAFYTVLVE-GDDM 321
Query: 287 DDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
++ + +E + + + L RRLA YPAI++ S +R ++ +L LR++L
Sbjct: 322 NEPVADEVRSLLDGHIVLSRRLAGAGHYPAIDIAASVSRIMPQIVSAGQLAMAQKLRRML 381
Score = 32.5 bits (74), Expect = 0.71
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 19/74 (25%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTEM----------QRSVRGE 538
A+ GKS +L + S A +M++ LI ER EV E R+V
Sbjct: 170 AAAGVGKSTLLGMLC-----ADSAADVMVLALIGERGREVREFLEQVLTPEARARTV--- 221
Query: 539 VIASTFDEPALSVM 552
V+ +T D PAL +
Sbjct: 222 VVVATSDRPALERL 235
>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 = 85.0 bits (211), Expect = 1e-17
Identities = 68/222 (30%), Positives = 110/222 (49%), Gaps = 21/222 (9%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEV 175
TG R+ID P+ +GQR + A GKS +L +A + ++++ L+ ER EV
Sbjct: 126 TGVRVIDTFLPLCRGQRLGIFAGSGVGKSTLLSMLARNTDAD----VVVIALVGERGREV 181
Query: 176 TE----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDS 225
E ++RSV V+ +T DE Q A A+ + KDV++L+DS
Sbjct: 182 REFLEDDLGEEGLKRSV---VVVATSDESPLMRRQAAYTATAIAEYFRDQGKDVLLLMDS 238
Query: 226 ITRLARAYNTVIPASGK--VLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETG 283
+TR A A + A+G+ V G S + P+ A E GS+T I T L++ G
Sbjct: 239 VTRFAMAQREIGLAAGEPPVARGYTPSVFSELPRLLERAGPGAEGKGSITGIFTVLVD-G 297
Query: 284 SRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
++ + + +G + + L+R +AE+ YPAIN+ S +R
Sbjct: 298 DDHNEPVADAVRGILDGHIVLDRAIAERGRYPAINVLASVSR 339
>gnl|CDD|136438 PRK07594, PRK07594, type III secretion system ATPase SsaN;
Validated.
Length = 433
Score = 83.8 bits (207), Expect = 3e-17
Identities = 73/245 (29%), Positives = 121/245 (49%), Gaps = 25/245 (10%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEE 174
+TG R ID +A G+GQR + ++P GKS +L + +A + +++LI ER E
Sbjct: 140 MTGIRAIDSVATCGEGQRVGIFSAPGVGKSTLLAMLCNAPDAD----SNVLVLIGERGRE 195
Query: 175 VTEM-------QRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
V E + R ++ +T D PA V+ + A+ + K V++L DS+T
Sbjct: 196 VREFIDFTLSEETRKRCVIVVATSDRPALERVRALFVATTIAEFFRDNGKRVVLLADSLT 255
Query: 228 RLARAYNTVIPASGKVLTGGVDSNALQRPKRFFGA-ARNIE-----EGGSLTIIATALIE 281
R ARA + A+G+ G + P F A R +E E GS+T T L+E
Sbjct: 256 RYARAAREIALAAGETAVSG------EYPPGVFSALPRLLERTGMGEKGSITAFYTVLVE 309
Query: 282 TGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWV 341
G M++ + +E + + + L RRLAE+ YPAI++ + +R ++ + Q +
Sbjct: 310 -GDDMNEPLADEVRSLLDGHIVLSRRLAERGHYPAIDVLATLSRVFPVVTSHEHRQLAAI 368
Query: 342 LRKLL 346
LR+ L
Sbjct: 369 LRRCL 373
Score = 28.8 bits (64), Expect = 8.3
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEM-------QRSVRGEVIAS 542
++P GKS +L + +A + +++LI ER EV E + R ++ +
Sbjct: 162 SAPGVGKSTLLAMLCNAPDAD----SNVLVLIGERGREVREFIDFTLSEETRKRCVIVVA 217
Query: 543 TFDEPALSVMCKLARA 558
T D PAL + L A
Sbjct: 218 TSDRPALERVRALFVA 233
>gnl|CDD|180875 PRK07196, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 83.4 bits (206), Expect = 5e-17
Identities = 74/253 (29%), Positives = 120/253 (47%), Gaps = 19/253 (7%)
Query: 82 KPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPIGKGQRGLLVASPKS 141
K +L + L L +HP L R +++ ++ I+ + IGKGQR L+A
Sbjct: 111 KGQLGGSTPLQQQLPQIHP----LQRRAVDTPLDVGVNAINGLLTIGKGQRVGLMAGSGV 166
Query: 142 GKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTEMQRSVRGE-------VIASTFDE 193
GKS++L I T +++A +++V LI ER EV E V+A+ DE
Sbjct: 167 GKSVLLGMI-----TRYTQADVVVVGLIGERGREVKEFIEHSLQAAGMAKSVVVAAPADE 221
Query: 194 PAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGK-VLTGGVDSNA 252
++ E+ A + DV++L+DS+TR A A + + G+ T G +A
Sbjct: 222 SPLMRIKATELCHAIATYYRDKGHDVLLLVDSLTRYAMAQREIALSLGEPPATKGYPPSA 281
Query: 253 LQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKR 312
R +A N G++T I T L E G D I + + + + L R+LAE
Sbjct: 282 FSIIPRLAESAGNSSGNGTMTAIYTVLAE-GDDQQDPIVDCARAVLDGHIVLSRKLAEAG 340
Query: 313 VYPAINLNKSGTR 325
YPAI++++S +R
Sbjct: 341 HYPAIDISQSISR 353
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 76.4 bits (188), Expect = 2e-16
Identities = 44/185 (23%), Positives = 73/185 (39%), Gaps = 30/185 (16%)
Query: 132 RGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE-------MQRSVRG 184
L+ SGK+ + +A I T ++ V I+E EE+TE
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVD-IEEEIEELTERLIGESLKGALDNL 58
Query: 185 EVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVL 244
++ +T D+PA + L KA+RL E D +I+LD +TRL RA +
Sbjct: 59 IIVFATADDPAAARL------LSKAERLRERGGDDLIILDELTRLVRALREI-------- 104
Query: 245 TGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMD---DVIYEEFKGTGNME 301
G + + AR G +T+I T + +G + D + + +
Sbjct: 105 REGYPGELDEELRELLERARK----GGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTV 160
Query: 302 VHLER 306
+ L R
Sbjct: 161 IVLSR 165
Score = 30.9 bits (70), Expect = 1.1
Identities = 24/124 (19%), Positives = 43/124 (34%), Gaps = 22/124 (17%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE-------MQRSVRGEVIA 541
SGK+ + +A I T ++ V I+E EE+TE ++
Sbjct: 5 FGPTGSGKTTLALQLALNIAT-KGGKVVYVD-IEEEIEELTERLIGESLKGALDNLIIVF 62
Query: 542 STFDEPALSVM-CKLARAYN------------TVIPASGKVLTGGVDSNALQRPKRFFGA 588
+T D+PA + + K R T + + + + G + +
Sbjct: 63 ATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLER 122
Query: 589 ARKY 592
ARK
Sbjct: 123 ARKG 126
>gnl|CDD|211826 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 [Cellular processes,
Chemotaxis and motility].
Length = 413
Score = 80.8 bits (200), Expect = 3e-16
Identities = 77/263 (29%), Positives = 124/263 (47%), Gaps = 26/263 (9%)
Query: 96 TPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAI 154
P +P L+R TG + ID + IGKGQR + A GKS +L IA
Sbjct: 107 PPPNP-----LKRPRIRDPLETGIKAIDGLLTIGKGQRVGIFAGSGVGKSTLLGMIAR-- 159
Query: 155 TTNHSEAIMIVMLIDERPEEVTE----------MQRSVRGEVIASTFDEPAYRHVQVAEM 204
N I ++ LI ER EV + ++RSV V+ +T D+PA ++ A
Sbjct: 160 --NAKADINVIALIGERGREVRDFIEKDLGEEGLKRSV---VVVATSDQPALMRLKAAFT 214
Query: 205 VLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTG-GVDSNALQRPKRFFGAA 263
A+ + KDV++++DS+TR A A + A G+ T G + + +
Sbjct: 215 ATAIAEYFRDQGKDVLLMMDSVTRFAMAQREIGLAVGEPPTTRGYTPSVFSLLPKLLERS 274
Query: 264 RNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSG 323
N + GS+T T L++ G M++ I + +G + + L R LA K YPAI++ S
Sbjct: 275 GN-SQKGSITGFYTVLVD-GDDMNEPIADAVRGILDGHIVLSRELAAKNHYPAIDVLASV 332
Query: 324 TRREELLIQDDKLQKIWVLRKLL 346
+R ++ ++ + LR+LL
Sbjct: 333 SRVMNEIVSEEHKELAGKLRELL 355
>gnl|CDD|181092 PRK07721, fliI, flagellum-specific ATP synthase; Validated.
Length = 438
Score = 80.2 bits (198), Expect = 5e-16
Identities = 72/252 (28%), Positives = 120/252 (47%), Gaps = 24/252 (9%)
Query: 110 IESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLI 168
I + R ID + +GKGQR + A GKS ++ IA ++ A + ++ LI
Sbjct: 138 IREPMEVGVRAIDSLLTVGKGQRVGIFAGSGVGKSTLMGMIA-----RNTSADLNVIALI 192
Query: 169 DERPEEVTE----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKD 218
ER EV E ++RS+ V+ +T D+PA ++ A A+ + +
Sbjct: 193 GERGREVREFIERDLGPEGLKRSI---VVVATSDQPALMRIKGAYTATAIAEYFRDQGLN 249
Query: 219 VIILLDSITRLARAYNTVIPASGKVLT--GGVDSNALQRPKRFFGAARNIEEGGSLTIIA 276
V++++DS+TR+A A + A G+ T G S PK N GS+T
Sbjct: 250 VMLMMDSVTRVAMAQREIGLAVGEPPTTKGYTPSVFAILPKLLERTGTN--ASGSITAFY 307
Query: 277 TALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKL 336
T L++ G M++ I + +G + L+R+LA K YPAIN+ KS +R ++ +
Sbjct: 308 TVLVD-GDDMNEPIADTVRGILDGHFVLDRQLANKGQYPAINVLKSVSRVMNHIVSPEHK 366
Query: 337 QKIWVLRKLLYS 348
+ R+LL +
Sbjct: 367 EAANRFRELLST 378
Score = 30.5 bits (69), Expect = 2.7
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 19/66 (28%)
Query: 495 GKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIAST 543
GKS ++ IA ++ A + ++ LI ER EV E ++RS+ V+ +T
Sbjct: 170 GKSTLMGMIA-----RNTSADLNVIALIGERGREVREFIERDLGPEGLKRSI---VVVAT 221
Query: 544 FDEPAL 549
D+PAL
Sbjct: 222 SDQPAL 227
>gnl|CDD|168181 PRK05688, fliI, flagellum-specific ATP synthase; Validated.
Length = 451
Score = 79.4 bits (196), Expect = 1e-15
Identities = 74/241 (30%), Positives = 119/241 (49%), Gaps = 22/241 (9%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE 177
R I+ + +G+GQR L A GKS++L + T +EA I++V LI ER EV E
Sbjct: 157 RSINGLLTVGRGQRLGLFAGTGVGKSVLL-----GMMTRFTEADIIVVGLIGERGREVKE 211
Query: 178 ----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
++RSV V+AS D+ ++ A A+ + K+V++L+DS+T
Sbjct: 212 FIEHILGEEGLKRSV---VVASPADDAPLMRLRAAMYCTRIAEYFRDKGKNVLLLMDSLT 268
Query: 228 RLARAYNTVIPASGKV-LTGGVDSNALQRPKRFFGAARNIEEG-GSLTIIATALIETGSR 285
R A+A + A G+ T G + + + A N E G GS+T T L E G
Sbjct: 269 RFAQAQREIALAIGEPPATKGYPPSVFAKLPKLVERAGNAEPGGGSITAFYTVLSE-GDD 327
Query: 286 MDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKL 345
D I + +G + + L RRLAE+ YPAI++ S +R ++ + L++ ++L
Sbjct: 328 QQDPIADSARGVLDGHIVLSRRLAEEGHYPAIDIEASISRVMPQVVDPEHLRRAQRFKQL 387
Query: 346 L 346
Sbjct: 388 W 388
>gnl|CDD|236166 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 78.5 bits (194), Expect = 2e-15
Identities = 71/227 (31%), Positives = 107/227 (47%), Gaps = 31/227 (13%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPE 173
ITG R ID + G GQR + AS GK+ ++ + HSEA + ++ LI ER
Sbjct: 136 ITGVRAIDGLLTCGVGQRMGIFASAGCGKTSLMNML-----IEHSEADVFVIGLIGERGR 190
Query: 174 EVTE----MQRSVRGE---VIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSI 226
EVTE ++ S R E ++ +T D + A + A+ + K V++ +DS+
Sbjct: 191 EVTEFVESLRASSRREKCVLVYATSDFSSVDRCNAALVATTVAEYFRDQGKRVVLFIDSM 250
Query: 227 TRLARAYNTVIPASGK--VLTGGVDS------NALQRPKRFFGAARNIEEGGSLTIIATA 278
TR ARA V A+G+ G S L+RP GS+T T
Sbjct: 251 TRYARALRDVALAAGELPARRGYPASVFDSLPRLLERPGAT--------LAGSITAFYTV 302
Query: 279 LIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
L+E D I +E + + ++L R+LA K YPAI++ KS +R
Sbjct: 303 LLE-SEEEPDPIGDEIRSILDGHIYLSRKLAAKGHYPAIDVLKSVSR 348
Score = 31.5 bits (72), Expect = 1.5
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 510 NHSEA-IMIVMLIDERPEEVTE----MQRSVRGE---VIASTFDEPAL 549
HSEA + ++ LI ER EVTE ++ S R E ++ +T D ++
Sbjct: 173 EHSEADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSV 220
>gnl|CDD|180762 PRK06936, PRK06936, type III secretion system ATPase; Provisional.
Length = 439
Score = 76.7 bits (189), Expect = 8e-15
Identities = 72/277 (25%), Positives = 128/277 (46%), Gaps = 33/277 (11%)
Query: 92 FDNLTPLHPKKLL---------LLERNIESKENITGRIIDLIAPIGKGQRGLLVASPKSG 142
FD P P + R IE+ ++ R+ID + G+GQR + A+ G
Sbjct: 115 FDGGHPPEPAAWYPVYADAPAPMSRRLIETPLSLGVRVIDGLLTCGEGQRMGIFAAAGGG 174
Query: 143 KSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIASTF 191
KS +L + +E + ++ LI ER EV E ++++V ++ +T
Sbjct: 175 KSTLLASL-----IRSAEVDVTVLALIGERGREVREFIESDLGEEGLRKAV---LVVATS 226
Query: 192 DEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLT--GGVD 249
D P+ + + A+ + K V++L+DS+TR ARA + A+G+ T G
Sbjct: 227 DRPSMERAKAGFVATSIAEYFRDQGKRVLLLMDSVTRFARAQREIGLAAGEPPTRRGYPP 286
Query: 250 SNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLA 309
S P+ A ++ + GS+T + T L+E G M + + +E + + + L R+LA
Sbjct: 287 SVFAALPRLMERAGQS--DKGSITALYTVLVE-GDDMTEPVADETRSILDGHIILSRKLA 343
Query: 310 EKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
YPAI++ +S +R ++ + LR+LL
Sbjct: 344 AANHYPAIDVLRSASRVMNQIVSKEHKTWAGRLRELL 380
>gnl|CDD|180526 PRK06315, PRK06315, type III secretion system ATPase; Provisional.
Length = 442
Score = 73.4 bits (180), Expect = 8e-14
Identities = 78/264 (29%), Positives = 126/264 (47%), Gaps = 32/264 (12%)
Query: 97 PLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAIT 155
PLH KL R I S TG R ID + + +GQR + A GKS +L IA
Sbjct: 138 PLHRAKL----RTILS----TGVRCIDGMLTVARGQRIGIFAGAGVGKSSLLGMIAR--- 186
Query: 156 TNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIASTFDEPAYRHVQVAEM 204
N EA + ++ LI ER EV E M+RSV ++ ST D+ + + A +
Sbjct: 187 -NAEEADVNVIALIGERGREVREFIEGDLGEEGMKRSV---IVVSTSDQSSQLRLNAAYV 242
Query: 205 VLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGK--VLTGGVDSNALQRPKRFFGA 262
A+ + K V++++DS+TR ARA V A+G+ G S PK +
Sbjct: 243 GTAIAEYFRDQGKTVVLMMDSVTRFARALREVGLAAGEPPARAGYTPSVFSTLPKLLERS 302
Query: 263 ARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKS 322
+ + G++T T L+ G M++ + +E K + + L LA+ YPAI++ S
Sbjct: 303 GAS--DKGTITAFYTVLV-AGDDMNEPVADEVKSILDGHIVLSNALAQAYHYPAIDVLAS 359
Query: 323 GTRREELLIQDDKLQKIWVLRKLL 346
+R ++ +++ + I R++L
Sbjct: 360 ISRLLTAIVPEEQRRIIGKAREVL 383
>gnl|CDD|236351 PRK08927, fliI, flagellum-specific ATP synthase; Validated.
Length = 442
Score = 73.5 bits (181), Expect = 8e-14
Identities = 65/220 (29%), Positives = 110/220 (50%), Gaps = 22/220 (10%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVM-LIDERPEEVTE 177
R ++ +GQR + A GKS++L +A +++A + V+ LI ER EV E
Sbjct: 147 RALNTFLTCCRGQRMGIFAGSGVGKSVLLSMLAR-----NADADVSVIGLIGERGREVQE 201
Query: 178 ----------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
+ RSV V+ +T DEPA Q A + L A+ + KDV+ L+DS+T
Sbjct: 202 FLQDDLGPEGLARSV---VVVATSDEPALMRRQAAYLTLAIAEYFRDQGKDVLCLMDSVT 258
Query: 228 RLARAYNTVIPASGKVLT--GGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSR 285
R A A + ++G+ T G + + P+ A G++T + T L++ G
Sbjct: 259 RFAMAQREIGLSAGEPPTTKGYTPTVFAELPRLLERAGPGPIGEGTITGLFTVLVD-GDD 317
Query: 286 MDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
++ + + +G + + +ER +AE+ YPAIN+ KS +R
Sbjct: 318 HNEPVADAVRGILDGHIVMERAIAERGRYPAINVLKSVSR 357
Score = 31.9 bits (73), Expect = 0.91
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 19/66 (28%)
Query: 495 GKSIILQHIAHAITTNHSEAIMIVM-LIDERPEEVTE----------MQRSVRGEVIAST 543
GKS++L +A +++A + V+ LI ER EV E + RSV V+ +T
Sbjct: 170 GKSVLLSMLAR-----NADADVSVIGLIGERGREVQEFLQDDLGPEGLARSV---VVVAT 221
Query: 544 FDEPAL 549
DEPAL
Sbjct: 222 SDEPAL 227
>gnl|CDD|213817 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 [Cellular processes,
Chemotaxis and motility].
Length = 411
Score = 72.5 bits (179), Expect = 2e-13
Identities = 79/283 (27%), Positives = 125/283 (44%), Gaps = 45/283 (15%)
Query: 93 DNLTPLHPKKLLLLER---NIESKENI-----TG-RIIDLIAPIGKGQRGLLVASPKSGK 143
D PL + + L N + I G R I+ + +G+GQR + A GK
Sbjct: 91 DGKGPLDAGERVPLYAPPINPLKRAPIDEPLDVGVRAINGLLTVGRGQRMGIFAGSGVGK 150
Query: 144 SIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIASTFD 192
S +L + ++EA +++V LI ER EV E + RSV V+A+T D
Sbjct: 151 STLLGMM-----ARYTEADVVVVGLIGERGREVKEFIEDILGEEGLARSV---VVAATAD 202
Query: 193 EP-------AYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKV-L 244
E A+ +AE ++ KDV++L+DS+TR A A + A G+
Sbjct: 203 ESPLMRLRAAFYATAIAEYFRDQG-------KDVLLLMDSLTRFAMAQREIALAIGEPPA 255
Query: 245 TGGVDSNALQR-PKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVH 303
T G + + P+ A E GS+T T L+E G D I + + + +
Sbjct: 256 TKGYPPSVFAKLPQLVERAGNGEEGKGSITAFYTVLVE-GDDQQDPIADAARAILDGHIV 314
Query: 304 LERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
L R LAE+ YPAI++ S +R ++ + Q ++LL
Sbjct: 315 LSRELAEQGHYPAIDILASISRVMPDVVSPEHRQAARRFKQLL 357
>gnl|CDD|181182 PRK07960, fliI, flagellum-specific ATP synthase; Validated.
Length = 455
Score = 71.4 bits (175), Expect = 4e-13
Identities = 77/264 (29%), Positives = 121/264 (45%), Gaps = 22/264 (8%)
Query: 96 TPLHPKKLLLLERN-IESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAI 154
P +P L+R IE + R I+ + +G+GQR L A GKS++L +A
Sbjct: 145 PPFNP-----LQRTPIEHVLDTGVRAINALLTVGRGQRMGLFAGSGVGKSVLLGMMAR-- 197
Query: 155 TTNHSEAIMIVM-LIDERPEEVTEMQRSVRGE-------VIASTFDEPAYRHVQVAEMVL 206
+++A +IV+ LI ER EV + ++ G VIA+ D +Q A
Sbjct: 198 ---YTQADVIVVGLIGERGREVKDFIENILGAEGRARSVVIAAPADVSPLLRMQGAAYAT 254
Query: 207 EKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGK--VLTGGVDSNALQRPKRFFGAAR 264
A+ + + V++++DS+TR A A + A G+ G S + P A
Sbjct: 255 RIAEDFRDRGQHVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFAKLPALVERAGN 314
Query: 265 NIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGT 324
I GGS+T T L E G D I + + + + L RRLAE YPAI++ S +
Sbjct: 315 GISGGGSITAFYTVLTE-GDDQQDPIADSARAILDGHIVLSRRLAEAGHYPAIDIEASIS 373
Query: 325 RREELLIQDDKLQKIWVLRKLLYS 348
R LI + ++ ++LL S
Sbjct: 374 RAMTALIDEQHYARVRQFKQLLSS 397
>gnl|CDD|214633 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 = 62.2 bits (152), Expect = 2e-12
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQI--RRFNLHTGDFVEGEIRVPKNGERY 69
G ++ GFGF+R D+++ PSQI +L GD VE ++ P+ GE+
Sbjct: 2 GVVKWFNKGFGFIRPDDGG-----KDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKP 56
Query: 70 FALLKIK 76
A +K
Sbjct: 57 EAENVVK 63
Score = 49.5 bits (119), Expect = 5e-08
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 421 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQI--RRFNLHTGILWKGEIRVPKNGERY 478
G ++ GFGF+R D+++ PSQI +L G + ++ P+ GE+
Sbjct: 2 GVVKWFNKGFGFIRPDDGG-----KDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKP 56
Query: 479 FALLKIK 485
A +K
Sbjct: 57 EAENVVK 63
>gnl|CDD|180696 PRK06793, fliI, flagellum-specific ATP synthase; Validated.
Length = 432
Score = 68.9 bits (168), Expect = 3e-12
Identities = 66/240 (27%), Positives = 113/240 (47%), Gaps = 27/240 (11%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 180
ID + IG GQ+ + A GKS +L IA N I ++ L+ ER EV + R
Sbjct: 147 IDSMLTIGIGQKIGIFAGSGVGKSTLLGMIAK----NAKADINVISLVGERGREVKDFIR 202
Query: 181 SVRGE-------VIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAY 233
GE V+ +T DE ++ A++ A+ + +V++++DS+TR A A
Sbjct: 203 KELGEEGMRKSVVVVATSDESHLMQLRAAKLATSIAEYFRDQGNNVLLMMDSVTRFADAR 262
Query: 234 NTV------IPASGK-VLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRM 286
+V +P GK +L L+R + + GS+T I T L++ G +
Sbjct: 263 RSVDIAVKELPIGGKTLLMESYMKKLLERSGK--------TQKGSITGIYTVLVD-GDDL 313
Query: 287 DDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
+ + + +G + + L+R LA YPAI++ S +R E ++ + Q +RK+L
Sbjct: 314 NGPVPDLARGILDGHIVLKRELATLSHYPAISVLDSVSRIMEEIVSPNHWQLANEMRKIL 373
>gnl|CDD|169656 PRK09099, PRK09099, type III secretion system ATPase; Provisional.
Length = 441
Score = 67.9 bits (166), Expect = 4e-12
Identities = 75/252 (29%), Positives = 118/252 (46%), Gaps = 41/252 (16%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEV 175
TG RI+D + +G+GQR + A GKS ++ A + + ++ LI ER EV
Sbjct: 149 TGVRIVDGLMTLGEGQRMGIFAPAGVGKSTLMGMFARGTQCD----VNVIALIGERGREV 204
Query: 176 TE----------MQRSVRGEVIASTFD-------EPAYRHVQVAEMVLEKAKRLVEMKKD 218
E M RSV V+ +T D + AY +AE ++ R
Sbjct: 205 REFIELILGEDGMARSV---VVCATSDRSSIERAKAAYVATAIAEYFRDRGLR------- 254
Query: 219 VIILLDSITRLARAYNTVIPASGKVLT--GGVDSNALQRPKRFFGAARNIEEGGSLTIIA 276
V++++DS+TR ARA + A+G+ G S + P+ A E GS+T +
Sbjct: 255 VLLMMDSLTRFARAQREIGLAAGEPPARRGFPPSVFAELPRLLERAGMG--ETGSITALY 312
Query: 277 TALIE--TGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDD 334
T L E +GS D I EE +G + + L R +A + YPAI++ S +R ++ +
Sbjct: 313 TVLAEDESGS---DPIAEEVRGILDGHMILSREIAARNQYPAIDVLGSLSRVMPQVVPRE 369
Query: 335 KLQKIWVLRKLL 346
+Q LR+LL
Sbjct: 370 HVQAAGRLRQLL 381
>gnl|CDD|181599 PRK08972, fliI, flagellum-specific ATP synthase; Validated.
Length = 444
Score = 65.9 bits (161), Expect = 2e-11
Identities = 74/266 (27%), Positives = 125/266 (46%), Gaps = 27/266 (10%)
Query: 97 PLHPKKLLLLERNIESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITT 156
P++P L R I ++ R I+ + +GKGQR L A GKS++L + T
Sbjct: 133 PINP----LSRRPITEPLDVGVRAINAMLTVGKGQRMGLFAGSGVGKSVLL-----GMMT 183
Query: 157 NHSEA-IMIVMLIDERPEEVTEM----------QRSVRGEVIASTFDEPAYRHVQVAEMV 205
+ A +++V L+ ER EV E RSV V+A+ D ++ E
Sbjct: 184 RGTTADVIVVGLVGERGREVKEFIEEILGEEGRARSV---VVAAPADTSPLMRLKGCETA 240
Query: 206 LEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKV-LTGGVDSNALQRPKRFFGAAR 264
A+ + +V++L+DS+TR A+A + A G+ T G + + A
Sbjct: 241 TTIAEYFRDQGLNVLLLMDSLTRYAQAQREIALAVGEPPATKGYPPSVFAKLPALVERAG 300
Query: 265 NIEEG-GSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSG 323
N G GS+T T L E G + D I + + + + L R LA+ YPAI++ S
Sbjct: 301 NGGPGQGSITAFYTVLTE-GDDLQDPIADASRAILDGHIVLSRELADSGHYPAIDIEASI 359
Query: 324 TRREELLIQDDKLQKIWVLRKLLYSL 349
+R ++I ++ L+ + +++ +YSL
Sbjct: 360 SRVMPMVISEEHLEAMRRVKQ-VYSL 384
>gnl|CDD|235666 PRK06002, fliI, flagellum-specific ATP synthase; Validated.
Length = 450
Score = 61.9 bits (151), Expect = 4e-10
Identities = 62/221 (28%), Positives = 109/221 (49%), Gaps = 20/221 (9%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEV 175
TG R+ID+ P+ GQR + A GKS +L +A A + + + ++ L+ ER EV
Sbjct: 151 TGVRVIDIFTPLCAGQRIGIFAGSGVGKSTLLAMLARA---DAFDTV-VIALVGERGREV 206
Query: 176 TE---------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSI 226
E ++++V + +T DE A+ + ++V++++DS+
Sbjct: 207 REFLEDTLADNLKKAV---AVVATSDESPMMRRLAPLTATAIAEYFRDRGENVLLIVDSV 263
Query: 227 TRLARAYNTVIPASGK--VLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGS 284
TR A A V A+G+ V G S + P+ A E GGS+T I + L++ G
Sbjct: 264 TRFAHAAREVALAAGEPPVARGYPPSVFSELPRLLERAGPGAEGGGSITGIFSVLVD-GD 322
Query: 285 RMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
+D + + +GT + + L+R +AE+ YPA++ S +R
Sbjct: 323 DHNDPVADSIRGTLDGHIVLDRAIAEQGRYPAVDPLASISR 363
>gnl|CDD|181439 PRK08472, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 58.9 bits (143), Expect = 3e-09
Identities = 65/243 (26%), Positives = 108/243 (44%), Gaps = 27/243 (11%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE-MQ 179
ID + GKGQ+ + A GKS ++ I I +V LI ER E+ E ++
Sbjct: 148 IDGLLTCGKGQKLGIFAGSGVGKSTLMG----MIVKGCLAPIKVVALIGERGREIPEFIE 203
Query: 180 RSVRGE-----VIASTFDEP-------AYRHVQVAEMVLEKAKRLVEMKKDVIILLDSIT 227
+++ G+ ++ +T D+ A+ + VAE + DV+ ++DS+T
Sbjct: 204 KNLGGDLENTVIVVATSDDSPLMRKYGAFCAMSVAEYFKNQGL-------DVLFIMDSVT 256
Query: 228 RLARAYNTVIPASGKVLTG-GVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRM 286
R A A + A G+ T G + L + A E GS+T T L+E G M
Sbjct: 257 RFAMAQREIGLALGEPPTSKGYPPSVLSLLPQLMERAGKEEGKGSITAFFTVLVE-GDDM 315
Query: 287 DDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
D I ++ + + + L R L + +YP IN+ S +R +I + ++ L
Sbjct: 316 SDPIADQSRSILDGHIVLSRELTDFGIYPPINILNSASRVMNDIISPEHKLAARKFKR-L 374
Query: 347 YSL 349
YSL
Sbjct: 375 YSL 377
>gnl|CDD|102061 PRK05922, PRK05922, type III secretion system ATPase; Validated.
Length = 434
Score = 54.5 bits (131), Expect = 9e-08
Identities = 41/137 (29%), Positives = 61/137 (44%), Gaps = 17/137 (12%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE- 177
+ ID +GKGQR + + P SGKS +L IA I ++ LI ER EV E
Sbjct: 146 KAIDAFLTLGKGQRIGVFSEPGSGKSSLLSTIA----KGSKSTINVIALIGERGREVREY 201
Query: 178 ---------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITR 228
QR++ +IAS E A V + A+ + V+ ++DS++R
Sbjct: 202 IEQHKEGLAAQRTI---IIASPAHETAPTKVIAGRAAMTIAEYFRDQGHRVLFIMDSLSR 258
Query: 229 LARAYNTVIPASGKVLT 245
A V A G+ L+
Sbjct: 259 WIAALQEVALARGETLS 275
>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 = 47.1 bits (112), Expect = 2e-05
Identities = 60/232 (25%), Positives = 101/232 (43%), Gaps = 42/232 (18%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEM 178
++ID + PIG+GQR L++ ++GK+ I I + + I I +R V ++
Sbjct: 151 KVIDALIPIGRGQRELILGDRQTGKTAIA--IDTILNQKGRNVLCIYCAIGQRASAVAKV 208
Query: 179 QRSVRGE--------VIASTFDEPA------YRHVQVAEMVLEKAKRLVEMKKDVIILLD 224
++R V+ D P Y + E +E+ +DV+I+ D
Sbjct: 209 VANLREHGAMDYTIVVVTEGNDPPGLQYIAPYAATSIGEHFMEQG-------RDVLIVYD 261
Query: 225 SITRLARAYNTVI-----PASGKVLTGG---VDSNALQRPKRFFGAARNIEE--GGSLTI 274
+T+ ARAY + P + G V S L+R + EE GGSLT
Sbjct: 262 DLTQHARAYRELSLLLRRPPGREAFPGDIFYVHSRLLER------STHLNEELGGGSLT- 314
Query: 275 IATALIETGSR-MDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
A +IET ++ + I + +++L L E V PA+++ KS +R
Sbjct: 315 -ALPIIETEAQNISAYIPTNLISITDGQIYLSPTLFELGVLPAVDVGKSVSR 365
>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 = 44.4 bits (105), Expect = 1e-04
Identities = 38/144 (26%), Positives = 70/144 (48%), Gaps = 10/144 (6%)
Query: 98 LHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITT 156
+H L R+ +S+ TG + ID++ P+ +G + L GK+++L + H +
Sbjct: 105 VHQAPPTLTRRSSKSEVFETGIKAIDVLVPLERGGKAGLFGGAGVGKTVLLTEMIHNMVG 164
Query: 157 NHSEAIMIVMLIDERPEEVTEMQRSVR-GEVIAST------FDEPAYRHVQVAEMVLEKA 209
H + + I I ER E E+ R ++ V+ +T +EP +V L A
Sbjct: 165 QH-QGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHTALTMA 223
Query: 210 KRLV-EMKKDVIILLDSITRLARA 232
+ + K+DV++L+D+I R +A
Sbjct: 224 EYFRDDEKQDVLLLIDNIFRFIQA 247
>gnl|CDD|198027 smart00959, 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.
Length = 43
Score = 36.6 bits (86), Expect = 0.001
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 388 DLEVNSVKRLRKQELMFAIFKKKTKIGE 415
+L + + RLRKQEL+FAI K + K G
Sbjct: 16 ELGIENASRLRKQELIFAILKAQAKKGG 43
>gnl|CDD|140212 PTZ00185, PTZ00185, ATPase alpha subunit; Provisional.
Length = 574
Score = 41.2 bits (96), Expect = 0.001
Identities = 61/242 (25%), Positives = 105/242 (43%), Gaps = 47/242 (19%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGK-SIILQHIAHAITTNH-----SEAIMIVMLI 168
+TG + +D + PIG+GQR L+V ++GK SI + I + + N + I I + I
Sbjct: 174 LTGFKAVDTMIPIGRGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSI 233
Query: 169 DERPEEVTEMQRSVRG-------EVIASTFDEPA-------YRHVQVAEMVLEKAKRLVE 214
+R V + R +R V+A+T EPA Y V + E + + +
Sbjct: 234 GQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQYLAPYSGVTMGEYFMNRGRH--- 290
Query: 215 MKKDVIILLDSITRLARAYNTVI-----PASGKVLTGGV---DSNALQRPKRFFGAARNI 266
+ + D +++ A AY + P + G V S L+R
Sbjct: 291 ----CLCVYDDLSKQAVAYRQISLLLRRPPGREAYPGDVFYLHSRLLERAAMLSPG---- 342
Query: 267 EEGGSLTIIATALIETGSRMDDV---IYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSG 323
+ GGS+T A ++ET S +DV I + +++L+ +L PA+N+ S
Sbjct: 343 KGGGSVT--ALPIVETLS--NDVTAYIVTNVISITDGQIYLDTKLFTGGQRPAVNIGLSV 398
Query: 324 TR 325
+R
Sbjct: 399 SR 400
>gnl|CDD|214640 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 = 39.3 bits (91), Expect = 0.001
Identities = 23/150 (15%), Positives = 48/150 (32%), Gaps = 12/150 (8%)
Query: 129 KGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIA 188
G+ L+V P SGK+ + + +A + I I E + + +I
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDG-------EDILEEVLDQLLLII 53
Query: 189 STFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGGV 248
+ + + L A++L K +++LD IT L A +
Sbjct: 54 VGGKKASGSGELRLRLALALARKL----KPDVLILDEITSLLDA-EQEALLLLLEELRLL 108
Query: 249 DSNALQRPKRFFGAARNIEEGGSLTIIATA 278
++ + ++ G +
Sbjct: 109 LLLKSEKNLTVILTTNDEKDLGPALLRRRF 138
>gnl|CDD|233211 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 [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 40.4 bits (95), Expect = 0.002
Identities = 60/232 (25%), Positives = 98/232 (42%), Gaps = 46/232 (19%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 180
ID + PIG+GQR L++ ++GK+ + I I S+ I + I ++ V ++ R
Sbjct: 152 IDAMIPIGRGQRELIIGDRQTGKTAVA--IDTIINQKDSDVYCIYVAIGQKASTVAQVVR 209
Query: 181 SVRGE-------VIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVIILLDSI 226
+ V+A+T + A Y + E + K +I+ D +
Sbjct: 210 KLEEHGAMAYTIVVAATASDSASLQYLAPYTGCTMGEYFRDNG-------KHALIIYDDL 262
Query: 227 TRLARAYNTVI-----PASGKVLTGGV---DSNALQRPKRFFGAARNIEE--GGSLTIIA 276
++ A AY + P + G V S L+R AA+ +E GGSLT A
Sbjct: 263 SKQAVAYRQISLLLRRPPGREAFPGDVFYLHSRLLER------AAKLNDEKGGGSLT--A 314
Query: 277 TALIETGSRMDDV---IYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
+IET + DV I + ++ LE L + PAIN+ S +R
Sbjct: 315 LPIIET--QAGDVSAYIPTNVISITDGQIFLESDLFNSGIRPAINVGLSVSR 364
>gnl|CDD|211621 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 [Energy metabolism,
ATP-proton motive force interconversion].
Length = 461
Score = 40.1 bits (94), Expect = 0.003
Identities = 62/257 (24%), Positives = 105/257 (40%), Gaps = 33/257 (12%)
Query: 93 DNLTPLHPKKLLLLERNIESKENI--------TG-RIIDLIAPIGKGQRGLLVASPKSGK 143
D P+ K+ + R S E TG ++IDL+AP KG + L GK
Sbjct: 97 DEKGPIPAKERWPIHRKAPSFEEQSTKVEILETGIKVIDLLAPYAKGGKIGLFGGAGVGK 156
Query: 144 SIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVR-GEVIAST------FDEPAY 196
++++Q + + I H + + ER E ++ ++ VI T +EP
Sbjct: 157 TVLIQELINNIAKEHG-GYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPG 215
Query: 197 RHVQVAEMVLEKAKRLVEMKK-DVIILLDSITRLARAYNTV------IP-ASGKVLTGGV 248
++VA L A+ + + DV++ +D+I R +A + V +P A G T
Sbjct: 216 ARMRVALTGLTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLAT 275
Query: 249 DSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRL 308
+ LQ +R GS+T + + D F V L R++
Sbjct: 276 EMGELQ--ERITSTK-----TGSITSVQAVYVPADDLTDPAPATTFAHLDATTV-LSRKI 327
Query: 309 AEKRVYPAINLNKSGTR 325
AE +YPA++ S +R
Sbjct: 328 AELGIYPAVDPLDSTSR 344
>gnl|CDD|203875 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 = 35.2 bits (82), Expect = 0.005
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGER 68
G++ GFGFL DDI++ P Q+ + +H GD V I R
Sbjct: 1 GTVRGHKKGFGFLIPDD-----EEDDIFIPPEQM-KKAMH-GDRVLVRITKGDRRGR 50
Score = 28.6 bits (65), Expect = 0.99
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 421 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRR 456
G++ GFGFL DDI++ P Q+++
Sbjct: 1 GTVRGHKKGFGFLIPDD-----EEDDIFIPPEQMKK 31
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 37.3 bits (87), Expect = 0.006
Identities = 27/143 (18%), Positives = 48/143 (33%), Gaps = 36/143 (25%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMI------VMLIDERPEEVTEMQR 180
+ +G LL +P +GKS + +A A+ T V+ +D E
Sbjct: 30 LPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLD------GEDSE 83
Query: 181 SVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPAS 240
+ + + + L E++ ++++D + L A
Sbjct: 84 A------------------GLRRRLRALGEALEEIEGPDLVVIDPLASLLGGDENDNAAV 125
Query: 241 GKVLTGGVDSNALQRPKRFFGAA 263
G +L AL R R GAA
Sbjct: 126 GALL------AALDRLARRTGAA 142
Score = 28.8 bits (65), Expect = 5.4
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 9/55 (16%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMI------VMLID-ERPEEVTEMQRSVR 536
+P +GKS + +A A+ T V+ +D E E ++R +R
Sbjct: 39 AGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDGEDSEA--GLRRRLR 91
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 39.0 bits (91), Expect = 0.007
Identities = 25/150 (16%), Positives = 56/150 (37%), Gaps = 4/150 (2%)
Query: 81 EKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPIGKGQRGLLVASPK 140
E P S+ +L K+ ++ + + + K + L++ +P
Sbjct: 173 EVPLASQRSKRIFDLNTKGEKRFDEEFLLELTQSADDQDALPGLEALEKYAKLLILGAPG 232
Query: 141 SGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPAYRHVQ 200
SGK+ LQ +A + E + I ++ + + E
Sbjct: 233 SGKTTFLQRLALWLAQRTLEPEDVP--IFLLLNAFALARKFEKQLSLIDYLAE-ELFSQG 289
Query: 201 VAEMVLEKAKRLVEMKKDVIILLDSITRLA 230
+A+ ++E + L++ K +++LLD + L
Sbjct: 290 IAKQLIEAHQELLKTGK-LLLLLDGLDELE 318
>gnl|CDD|203652 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 = 34.3 bits (80), Expect = 0.008
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 388 DLEVNSVKRLRKQELMFAIFKKKTKIGE 415
+L + + RLRKQEL+FAI K + + G
Sbjct: 16 ELGIENYSRLRKQELIFAILKAQAEKGG 43
>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic.
Length = 274
Score = 38.0 bits (89), Expect = 0.009
Identities = 58/250 (23%), Positives = 104/250 (41%), Gaps = 49/250 (19%)
Query: 97 PLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAIT 155
P+H + +E++ +++ TG ++IDL+AP KG + L GK++++ + + I
Sbjct: 35 PIHREAPEFVEQSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNIA 94
Query: 156 TNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTF-----------DEPAYRHVQVAEM 204
H + + ER E ++ E+ S +EP +VA
Sbjct: 95 KAHG-GYSVFAGVGERTREGNDLYH----EMKESGVLSKTALVYGQMNEPPGARARVALT 149
Query: 205 VLEKAK--RLVEMKKDVIILLDSITRLARAYNTV------IP-ASGKVLTGGVDSNALQR 255
L A+ R E +DV++ +D+I R +A + V +P A G T + ALQ
Sbjct: 150 GLTMAEYFRDEE-GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGALQ- 207
Query: 256 PKRFFGAARNIEEGGSLTIIATALIETGSRMDDV-------IYEEFKGTGNMEVHLERRL 308
+R + GS+T + + DD+ + T L R +
Sbjct: 208 -ERITSTKK-----GSITSVQAVYVP----ADDLTDPAPATTFAHLDAT----TVLSRAI 253
Query: 309 AEKRVYPAIN 318
AE +YPA++
Sbjct: 254 AELGIYPAVD 263
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 38.4 bits (90), Expect = 0.009
Identities = 32/138 (23%), Positives = 61/138 (44%), Gaps = 36/138 (26%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKS------IILQHIAHAITTNHSEAIMIVMLID 169
TG +++D + PIG+GQR L++ ++GK+ II Q S+ I + + I
Sbjct: 148 TGIKVVDALIPIGRGQRELIIGDRQTGKTAIAIDAIINQK--------DSDVICVYVAIG 199
Query: 170 ERPEEVTEMQRSVRGE--------VIASTFDEPA------YRHVQVAEMVLEKAKRLVEM 215
++ V + ++R V+A D P + +AE ++
Sbjct: 200 QKASAVARVIETLREHGALEYTTVVVAEASDPPGLQYLAPFAGCAIAEYFRDQG------ 253
Query: 216 KKDVIILLDSITRLARAY 233
+D +I+ D +++ A AY
Sbjct: 254 -QDALIVYDDLSKHAAAY 270
>gnl|CDD|235951 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
Length = 507
Score = 38.4 bits (90), Expect = 0.011
Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 5/48 (10%)
Query: 105 LLERNIESKENITGRI-IDLIAPIGKGQRGLLVASPKSGKSIILQHIA 151
L+ +++ TG I IDL+ PIGKGQR L++ ++GK+ HIA
Sbjct: 117 LMTVKTLNEQLYTGIIAIDLLIPIGKGQRELIIGDRQTGKT----HIA 160
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 38.3 bits (90), Expect = 0.011
Identities = 36/132 (27%), Positives = 57/132 (43%), Gaps = 33/132 (25%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIMIVMLI 168
ID + PIG+GQR L++ ++GK+ II Q I AI S +V
Sbjct: 153 IDALIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGSGVKCIYVAIGQKRSTVANVV--- 209
Query: 169 DERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVII 221
EE M ++ V+A++ + A Y +AE + KDV+I
Sbjct: 210 -RTLEEHGAMDYTI---VVAASASDSAPLQYLAPYAGCAMAEYFRDNG-------KDVLI 258
Query: 222 LLDSITRLARAY 233
+ D +++ A AY
Sbjct: 259 VYDDLSKHAVAY 270
>gnl|CDD|238552 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic.
Length = 274
Score = 37.6 bits (88), Expect = 0.011
Identities = 70/250 (28%), Positives = 103/250 (41%), Gaps = 73/250 (29%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIM 163
TG + ID + PIG+GQR L++ ++GK+ II Q I AI S
Sbjct: 55 TGIKAIDAMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGKKVYCIYVAIGQKASTVAQ 114
Query: 164 IVMLIDERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMK 216
+V + EE M+ ++ V+A+T +PA Y + E ++
Sbjct: 115 VV----KTLEEHGAMEYTI---VVAATASDPAPLQYLAPYTGCAMGEYFMDNG------- 160
Query: 217 KDVIILLDSITRLARAYNTVI-----PASGKVLTGGV---DSNALQRPKRFFGAARNIEE 268
K +I+ D +++ A AY + P + G V S L+R AA+ +E
Sbjct: 161 KHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLER------AAKLNDE 214
Query: 269 --GGSLT---IIAT------ALIETG--SRMDDVIYEEFKGTGNMEVHLERRLAEKRVYP 315
GGSLT II T A I T S D I+ LE L K + P
Sbjct: 215 LGGGSLTALPIIETQAGDVSAYIPTNVISITDGQIF------------LETDLFNKGIRP 262
Query: 316 AINLNKSGTR 325
AIN+ S +R
Sbjct: 263 AINVGLSVSR 272
>gnl|CDD|232875 TIGR00211, glyS, glycyl-tRNA synthetase, tetrameric type, beta
subunit. The glycyl-tRNA synthetases differ even among
the eubacteria in oligomeric structure. In Escherichia
coli and most others, it is a heterodimer of two alpha
chains and two beta chains, encoded by tandem genes. The
genes are similar, but fused, in Chlamydia trachomatis.
By contrast, the glycyl-tRNA synthetases of Thermus
thermophilus and of archaea and eukaryotes differ
considerably; they are homodimeric, mutually similar,
and not detected by this model [Protein synthesis, tRNA
aminoacylation].
Length = 691
Score = 36.3 bits (84), Expect = 0.054
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 474 NGERYFALLKIKKVNVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQR 533
+ + Y LK V +A PK K++ILQ I A + L+DE + E
Sbjct: 201 SPDAYPEQLKENHV-IADPKERKAMILQQIETLAAKLGGIADIDEDLLDE-VVSLVEYPT 258
Query: 534 SVRGEVIASTFDEPALSV 551
++ G+ F+E LS+
Sbjct: 259 ALLGK-----FEEEFLSL 271
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 35.9 bits (83), Expect = 0.073
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 26/71 (36%)
Query: 19 DGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFV-------------EGEI-RV-- 62
DG+GFLR +G DD+YLS Q+ + +H GD V E I RV
Sbjct: 94 DGYGFLRVEGRK-----DDLYLSSEQM-KTCIH-GDQVLAQPLGADRKGRREARIVRVLV 146
Query: 63 PKNGE---RYF 70
PK + RYF
Sbjct: 147 PKTSQIVGRYF 157
Score = 34.7 bits (80), Expect = 0.14
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 16/48 (33%)
Query: 409 KKTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRR 456
K T IG R DG+GFLR +G DD+YLS Q++
Sbjct: 86 KGTVIGHR-----------DGYGFLRVEGRK-----DDLYLSSEQMKT 117
>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 35.3 bits (82), Expect = 0.10
Identities = 61/259 (23%), Positives = 102/259 (39%), Gaps = 49/259 (18%)
Query: 93 DNLTPLHPKKLLLLE--RNIESKENI--------TG-RIIDLIAPIGKGQRGLLVASPKS 141
D P+ + R S E + TG ++IDL+AP KG + L
Sbjct: 99 DEKGPIKAEDFEKWPIHRKAPSFEELSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGV 158
Query: 142 GKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVT----EMQRSVRGEVIASTF---DEP 194
GK++++Q + + I H + + ER E EM+ S + A F +EP
Sbjct: 159 GKTVLIQELINNIAKEHG-GYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEP 217
Query: 195 AYRHVQVAEMVLEKAKRLV-EMKKDVIILLDSITRLARAYNTV------IP-ASGKVLTG 246
++VA L A+ E +DV++ +D+I R +A + V +P A G T
Sbjct: 218 PGARMRVALTGLTMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTL 277
Query: 247 GVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDV-------IYEEFKGTGN 299
+ LQ +R GS+T + + DD+ + T
Sbjct: 278 ATEMGQLQ--ERITSTK-----KGSITSVQAVYVP----ADDLTDPAPATTFAHLDAT-- 324
Query: 300 MEVHLERRLAEKRVYPAIN 318
L R++A +YPA++
Sbjct: 325 --TVLSRQIAALGIYPAVD 341
>gnl|CDD|184033 PRK13404, PRK13404, dihydropyrimidinase; Provisional.
Length = 477
Score = 33.9 bits (78), Expect = 0.26
Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 215 MKKDVIILLDSITRLARAYNT---VIPASGK-VLTGGVDSNA---------LQRPKRFFG 261
+ D+ I I L I A+G+ VL GGVDS+ + F+
Sbjct: 20 FQADIGIRGGRIAALGEGLGPGAREIDATGRLVLPGGVDSHCHIDQPSGDGIMMADDFYT 79
Query: 262 AARNIEEGGSLTIIATALIETGSRMDDVI 290
+ GG+ T+I A G + + +
Sbjct: 80 GTVSAAFGGTTTVIPFAAQHRGQSLREAV 108
>gnl|CDD|100011 cd06154, YjgF_YER057c_UK114_like_6, This group of proteins belong
to a large family of YjgF/YER057c/UK114-like proteins
present in bacteria, archaea, and eukaryotes with no
definitive function. The conserved domain is similar in
structure to chorismate mutase but there is no sequence
similarity and no functional connection. Members of this
family have been implicated in isoleucine (Yeo7, Ibm1,
aldR) and purine (YjgF) biosynthesis, as well as
threonine anaerobic degradation (tdcF) and mitochondrial
DNA maintenance (Ibm1). This domain homotrimerizes
forming a distinct intersubunit cavity that may serve as
a small molecule binding site.
Length = 119
Score = 30.6 bits (70), Expect = 0.78
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 245 TGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVI 290
T G D + + P + R L II AL E G+ ++DV+
Sbjct: 28 TTGYDYDGMVMPGDAYEQTRQC-----LEIIEAALAEAGASLEDVV 68
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 32.2 bits (74), Expect = 0.80
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 131 QRGLLV-ASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDER 171
LLV +SGK+ +L+ IA IT +S ++L+D R
Sbjct: 363 SPHLLVFGDSESGKTTLLRAIARGITRRYSPQQARLVLVDYR 404
Score = 30.7 bits (70), Expect = 2.7
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 492 PKSGKSIILQHIAHAITTNHSEAIMIVMLIDER 524
+SGK+ +L+ IA IT +S ++L+D R
Sbjct: 372 SESGKTTLLRAIARGITRRYSPQQARLVLVDYR 404
>gnl|CDD|235248 PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
Length = 586
Score = 31.7 bits (73), Expect = 1.1
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 13/68 (19%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASP---KSGKSIILQHIAHAITTNHSEA-IMIVMLIDE 170
ITG R+ID P+ KG A P SGK++ +A ++A I+I + E
Sbjct: 212 ITGQRVIDTFFPVAKGGTA---AIPGPFGSGKTVTQHQLA-----KWADADIVIYVGCGE 263
Query: 171 RPEEVTEM 178
R E+TE+
Sbjct: 264 RGNEMTEV 271
Score = 29.0 bits (66), Expect = 9.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 304 LERRLAEKRVYPAINLNKS 322
L+ LA++R +PAIN S
Sbjct: 415 LDAELADRRHFPAINWLTS 433
>gnl|CDD|223822 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
ribosomal structure and biogenesis].
Length = 691
Score = 31.8 bits (73), Expect = 1.1
Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 24/107 (22%)
Query: 417 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGE 476
+ GD EV+P + S I ++ RF L GEI + + +
Sbjct: 169 LLGD---EVIPFEILGI---------KSGRI----TRGHRF------LGPGEITID-SAD 205
Query: 477 RYFALLKIKKVNVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDE 523
Y L+ KV +A P+ K+IIL+ I + A + L++E
Sbjct: 206 DYVEKLREGKV-IADPEERKAIILEQIEELASKLGGVADIDEDLLEE 251
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 31.7 bits (73), Expect = 1.1
Identities = 38/170 (22%), Positives = 69/170 (40%), Gaps = 24/170 (14%)
Query: 93 DNLTPLHPKKLLLLERNIESKENITGR---------IIDLIAPIGKGQRGLLVASPKSGK 143
D PL ++ + I +IDL+ PI KG + L GK
Sbjct: 97 DGGPPLPAEERRPIHSTIPPLAEQDTSTEILETGIKVIDLLCPIAKGGKTGLFGGAGVGK 156
Query: 144 SIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE----------MQRSVRGEVIASTFDE 193
++++ + I+ HS + + ER E E + ++V ++ +E
Sbjct: 157 TVLMMELIFNISKQHS-GSSVFAGVGERSREGHELYHEMKESGVLDKTV---MVYGQMNE 212
Query: 194 PAYRHVQVAEMVLEKAKRLV-EMKKDVIILLDSITRLARAYNTVIPASGK 242
P ++V L A+ L E K+DV++ +D+I R +A + V G+
Sbjct: 213 PPGARMRVVLTGLTIAEYLRDEEKEDVLLFIDNIFRFVQAGSEVSGLLGR 262
>gnl|CDD|227281 COG4945, COG4945, Membrane-anchored protein predicted to be
involved in regulation of amylopullulanase [Carbohydrate
transport and metabolism].
Length = 570
Score = 31.8 bits (72), Expect = 1.1
Identities = 12/39 (30%), Positives = 15/39 (38%)
Query: 119 RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTN 157
I IAP G+ L KS S+I+ IT
Sbjct: 193 NIYTYIAPATVGEGTLTQQEAKSNFSVIVYATLVPITLP 231
>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 [Energy metabolism, ATP-proton motive force
interconversion].
Length = 578
Score = 31.6 bits (72), Expect = 1.2
Identities = 39/143 (27%), Positives = 61/143 (42%), Gaps = 41/143 (28%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPE 173
ITG RI+D PI KG + SGK++ +A S+A I++ + ER
Sbjct: 207 ITGQRILDTFFPIAKGGTAAIPGPFGSGKTVTQHQLA-----KWSDADIVVYIGCGERGN 261
Query: 174 EVTE-----------------MQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKA 209
E+T+ M+R+V +IA+T + P Y + +AE
Sbjct: 262 EMTDVLEEFPELKDPKTGKPLMERTV---LIANTSNMPVAAREASIYTGITIAEY----- 313
Query: 210 KRLVEMKKDVIILLDSITRLARA 232
+M DV ++ DS +R A A
Sbjct: 314 --FRDMGYDVALMADSTSRWAEA 334
>gnl|CDD|239156 cd02755, MopB_Thiosulfate-R-like, The MopB_Thiosulfate-R-like CD
contains thiosulfate-, sulfur-, and
polysulfide-reductases, and other related proteins.
Thiosulfate reductase catalyzes the cleavage of
sulfur-sulfur bonds in thiosulfate. Polysulfide
reductase is a membrane-bound enzyme that catalyzes the
reduction of polysulfide using either hydrogen or
formate as the electron donor. Members of the
MopB_Thiosulfate-R-like CD belong to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 454
Score = 31.5 bits (72), Expect = 1.3
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 523 ERPEEVT-----EMQRSVRGEVIASTFD-EPALSVMCKLARAYNTVIPASGKV 569
ER E + + R I +D P ++ +LAR SGK+
Sbjct: 386 ERDEPFSDKGGPAPAVATRQRAIEPLYDTRPGWDILKELARRLGLFGTPSGKI 438
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 30.7 bits (70), Expect = 2.3
Identities = 37/137 (27%), Positives = 62/137 (45%), Gaps = 34/137 (24%)
Query: 117 TGRI-IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIM 163
TG I ID + PIG+GQR L++ ++GK+ I+ Q + AI S
Sbjct: 127 TGLIAIDSMIPIGRGQRELIIGDRQTGKTAVATDTILNQKGQNVICVYVAIGQKASSVAQ 186
Query: 164 IVMLIDERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMK 216
+V + ER M+ ++ V+A T D PA Y +AE + +
Sbjct: 187 VVTTLQER----GAMEYTI---VVAETADSPATLQYLAPYTGAALAEYFMYR-------G 232
Query: 217 KDVIILLDSITRLARAY 233
+ +I+ D +++ A+AY
Sbjct: 233 RHTLIIYDDLSKQAQAY 249
>gnl|CDD|234034 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 [Cellular processes, Sporulation and
germination].
Length = 270
Score = 30.4 bits (69), Expect = 2.6
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 109 NIESKENITGRIIDLIAPIGKGQR---GLLVASPKSGKSIILQHIAHAITTNHSEAIMI- 164
NI G L+ + + R L+++ P+ GK+ +L+ +A ++T S+ + +
Sbjct: 87 NIRIAREKLGAADKLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILSTGISQ-LGLR 145
Query: 165 ---VMLIDERPE 173
V ++DER E
Sbjct: 146 GKKVGIVDERSE 157
>gnl|CDD|238554 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A.
These ATPases couple ATP hydrolysis to the build up of a
H+ gradient, but V-type ATPases do not catalyze the
reverse reaction. The Vacuolar (V-type) ATPase is found
in the membranes of vacuoles, the golgi apparatus and in
other coated vesicles in eukaryotes. Archaea have a
protein which is similar in sequence to V-ATPases, but
functions like an F-ATPase (called A-ATPase). A similar
protein is also found in a few bacteria.
Length = 369
Score = 29.9 bits (68), Expect = 3.8
Identities = 66/314 (21%), Positives = 117/314 (37%), Gaps = 117/314 (37%)
Query: 73 LKIKKVNGEKPELS--------KNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIIDL 123
+ + +G+K E++ + R + + L P P +TG R++D
Sbjct: 105 ILEVEFDGKKEEITMVQKWPVRQPRPVKEKLPPNEPL--------------LTGQRVLDT 150
Query: 124 IAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----- 177
+ P+ KG + GK++I Q ++ +S + I+I + ER E+TE
Sbjct: 151 LFPVVKGGTAAIPGPFGCGKTVIQQSLS-----KYSNSDIVIYVGCGERGNEMTEVLEEF 205
Query: 178 ------------MQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKD 218
M+R+V +IA+T + P Y + +AE +M +
Sbjct: 206 PELTDPVTGEPLMKRTV---LIANTSNMPVAAREASIYTGITIAEY-------FRDMGYN 255
Query: 219 VIILLDSITRLARAYNTV------IPA------------------SGKVLTGGVDSNALQ 254
V ++ DS +R A A + +P +G+V L
Sbjct: 256 VALMADSTSRWAEALREISGRLEEMPGEEGYPAYLGARLASFYERAGRVKC-------LG 308
Query: 255 RPKRFFGAARNIEEGGSLTIIATALIETGSRMDDV------IYEEFKGTGNMEVHLERRL 308
P R GS+TI+ G + V I + F G L+++L
Sbjct: 309 SPGRE----------GSVTIVGAVSPPGGDFSEPVTQATLRIVQVFWG-------LDKKL 351
Query: 309 AEKRVYPAINLNKS 322
A++R +P+IN S
Sbjct: 352 AQRRHFPSINWLIS 365
>gnl|CDD|233703 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
[Transcription, Degradation of RNA].
Length = 709
Score = 29.5 bits (67), Expect = 6.5
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEI--RVPKNGERY 69
G++ DGFGFLR + DDI++ P Q+ +H GD V I +
Sbjct: 71 GTVIAHRDGFGFLRPED----DDEDDIFIPPRQMNG-AMH-GDRVLVRITGKPDGGDRFE 124
Query: 70 FALLKI 75
++KI
Sbjct: 125 ARVIKI 130
>gnl|CDD|216994 pfam02361, CbiQ, Cobalt transport protein. This family consists of
various cobalt transport proteins Most of which are
found in Cobalamin (Vitamin B12) biosynthesis operons.
In Salmonella the cbiN cbiQ (product CbiQ in this
family) and cbiO are likely to form an active cobalt
transport system.
Length = 217
Score = 28.8 bits (65), Expect = 6.7
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 340 WVLRKLLYSLTMTSFTVSLFFIKRTIPVEK--NLLKDACMPLVLAETQTI 387
+LR LL +L +++ +L F+ T P + + L+ +PL LAE +
Sbjct: 95 GLLRGLLLALRISTSLSALLFLALTTPPAELTSGLRRLGVPLELAEILLL 144
>gnl|CDD|235238 PRK04171, PRK04171, ribosome biogenesis protein; Provisional.
Length = 222
Score = 28.7 bits (65), Expect = 7.1
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 51 HTGD----FVEGEIRVPKNGERYFA----LLKIKKV-NGEKPELS-KNRTLFDNLTPLHP 100
HT D +V E R+PKN R+ LLK +V +P L +N++L + L + P
Sbjct: 87 HTRDDKVIYVNPETRLPKNYNRFVGLMEQLLKEGRVPPNGEPLLEIENKSLEELLEEIGP 146
Query: 101 KKLLLLERN 109
+++LL
Sbjct: 147 DRIILLSEK 155
>gnl|CDD|179373 PRK02118, PRK02118, V-type ATP synthase subunit B; Provisional.
Length = 436
Score = 29.2 bits (66), Expect = 7.6
Identities = 30/94 (31%), Positives = 46/94 (48%), Gaps = 12/94 (12%)
Query: 190 TFDEPAYRHVQVAEMVLEKAKRL-VEMKKDVIILLDSITRLARAYNTV------IPASGK 242
T +P + V +M L A++ +E KK V++LL +T A A + IP S +
Sbjct: 203 TASDPPVECLLVPDMALAVAEKFALEGKKKVLVLLTDMTNFADALKEISITMDQIP-SNR 261
Query: 243 VLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIA 276
G + S R+ A + E+GGS+TIIA
Sbjct: 262 GYPGSLYS---DLASRYEKAV-DFEDGGSITIIA 291
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 28.5 bits (64), Expect = 7.7
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 133 GLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSV-RGEVIASTF 191
L+ + SGKS L + ++ HS + + LID + E+ ++ +A
Sbjct: 41 LLIAGATGSGKSTFLNTLILSLAARHSPEEVRLYLIDPKGGELAALEDLPHLLSPVA--- 97
Query: 192 DEPAYRHVQVAEMVLEKAKRLVEMKKDVI 220
+P + +V E +R +K+ +
Sbjct: 98 TDPEDALSALRALVAEMERRYALLKQLGV 126
>gnl|CDD|172450 PRK13940, PRK13940, glutamyl-tRNA reductase; Provisional.
Length = 414
Score = 28.8 bits (64), Expect = 8.8
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 91 LFDNLTPLHPKKLLLLERNIESKENIT 117
LF ++T L PK+++L R IE + IT
Sbjct: 196 LFRHVTALAPKQIMLANRTIEKAQKIT 222
>gnl|CDD|223063 PHA03374, PHA03374, hypothetical protein; Provisional.
Length = 730
Score = 28.9 bits (65), Expect = 9.3
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 335 KLQKIWVLRKLLYSLTMTSFTVSLFF 360
+L +V++K YS+ SFTVS+F+
Sbjct: 442 RLTNNFVIKK--YSVKEPSFTVSVFY 465
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 27.6 bits (62), Expect = 9.9
Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 20/99 (20%)
Query: 134 LLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDE 193
LLV P +GKS + + +A A++ + + D E++ +R++ AS D
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQ--LTRDTTEEDLK-GRRNIDPG-GASWVDG 58
Query: 194 PAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARA 232
P R ++ I +LD I R
Sbjct: 59 PLVR----------------AAREGEIAVLDEINRANPD 81
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.379
Gapped
Lambda K H
0.267 0.0911 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,281,007
Number of extensions: 3227741
Number of successful extensions: 3138
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3033
Number of HSP's successfully gapped: 142
Length of query: 592
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 490
Effective length of database: 6,413,494
Effective search space: 3142612060
Effective search space used: 3142612060
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 (21.8 bits)
S2: 62 (27.3 bits)