RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780941|ref|YP_003065354.1| GTP-binding protein Era
[Candidatus Liberibacter asiaticus str. psy62]
(311 letters)
>gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 364 bits (937), Expect = e-101
Identities = 126/284 (44%), Positives = 179/284 (63%), Gaps = 3/284 (1%)
Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80
+SG VA+VG N GKSTL+N VG K+SIV+ K QTTR +RGIV+E ++QI+F+DTPGI
Sbjct: 4 KSGFVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGI 63
Query: 81 FNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKI 140
K + ++ M + +WS++K D+V VVD+ ++ +L+++ K + +IL+LNKI
Sbjct: 64 HKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKI 123
Query: 141 DCVKP-ERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSADQIS 199
D VK E LL E ++L+ + +SA KG D++L+ + LP P Y DQI+
Sbjct: 124 DLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYLPEGPPYYPEDQIT 183
Query: 200 DLPMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVERPSQKKIM 259
D P AEI REKL L E+PYS V EK+EE+ G + I IYVER SQK I+
Sbjct: 184 DRPERFLAAEIIREKLLRLLGDELPYSVAVEIEKFEER--GLVRIEATIYVERDSQKGII 241
Query: 260 LGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQKDWGHDPK 303
+GK G +K I EA+K+I ++L + V L L+VKV+K W D K
Sbjct: 242 IGKGGAMLKKIGTEARKDIEKLLGKKVFLELWVKVKKGWRDDEK 285
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 236 bits (604), Expect = 4e-63
Identities = 125/286 (43%), Positives = 180/286 (62%), Gaps = 13/286 (4%)
Query: 19 NSRSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTP 78
N ++ V ++G N+GKSTL+NR +G K+SIVT KVQTTRSI+ GI++ K++Q++ DTP
Sbjct: 49 NQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTP 108
Query: 79 GIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILN 138
GIF K S K M+R +WS++ AD+V L++DS + H++L ++ + I +LN
Sbjct: 109 GIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLN 168
Query: 139 KIDCVKPERLLEQAEIANKLVFIEKT------FMVSATKGHGCDDVLNYLCSTLPLAPWV 192
KID +E + + F+ + F +SA G D +L Y+ S ++PW+
Sbjct: 169 KID-------IESKYLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKAKISPWL 221
Query: 193 YSADQISDLPMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVER 252
Y+ D I+DLPM AEITRE+LFL+L KE+PY V TEKWE+ KD S+ I QVI V R
Sbjct: 222 YAEDDITDLPMRFIAAEITREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSR 281
Query: 253 PSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQKDW 298
S K I+LGKNG IK I +++ ++ PVHL LFVKV++ W
Sbjct: 282 ESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLFLFVKVRELW 327
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein.
Length = 270
Score = 192 bits (491), Expect = 7e-50
Identities = 98/272 (36%), Positives = 150/272 (55%), Gaps = 3/272 (1%)
Query: 23 GCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFN 82
G VA++G N GKSTL+N+ G K+SI + K QTTR+ + GI + SQI+F+DTPG
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHE 60
Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSR-LILILNKID 141
K S ++LM++ + S I D++ VVDS + + + + R ++L NK+D
Sbjct: 61 KKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNG--DGEFVLTKLQNLKRPVVLTRNKLD 118
Query: 142 CVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSADQISDL 201
++LL + L + +SA G + ++ LP P+ Y D ++D
Sbjct: 119 NKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHLPEGPFRYPEDYVTDQ 178
Query: 202 PMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVERPSQKKIMLG 261
P +EI REK+ + +EIP+S V E+ + G + I +I VER SQKKI++G
Sbjct: 179 PDRFKISEIIREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERESQKKIIIG 238
Query: 262 KNGQNIKTISLEAKKEIAEILEQPVHLILFVK 293
KNG IK I + A+K+I E+ + V L LFVK
Sbjct: 239 KNGSMIKAIGIAARKDILELFDCDVFLELFVK 270
>gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 96.7 bits (242), Expect = 6e-21
Identities = 45/158 (28%), Positives = 76/158 (48%), Gaps = 10/158 (6%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
V + G N GKS+L+N +G + +IVT TTR ++ ++ + +DT GI
Sbjct: 218 VVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETD 277
Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144
D K+ I S I+ AD+V LV+D+ L ++L+E+ + +I++LNK D
Sbjct: 278 DEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEILEELKDK--PVIVVLNKADLTG 335
Query: 145 PERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182
L E+ + +SA G G D++ +
Sbjct: 336 EIDLEEEN--------GKPVIRISAKTGEGIDELREAI 365
>gnl|CDD|163343 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability.
Length = 429
Score = 92.9 bits (232), Expect = 1e-19
Identities = 52/163 (31%), Positives = 75/163 (46%), Gaps = 4/163 (2%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
VA+VG N GKSTL NR G + +IV+ TR G + + +DT GI
Sbjct: 2 VAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEEDD 61
Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144
D K + + I+ AD++ VVD L ++ K + K +IL+ NKID K
Sbjct: 62 DGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDGKK 121
Query: 145 PERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLP 187
+ AE L F + +SA G G D+L+ + LP
Sbjct: 122 ED--AVAAEFY-SLGF-GEPIPISAEHGRGIGDLLDAILELLP 160
Score = 84.4 bits (210), Expect = 4e-17
Identities = 50/184 (27%), Positives = 86/184 (46%), Gaps = 11/184 (5%)
Query: 6 ITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIV 65
+ E ++ ++ +A++G N GKSTLVN +G + IV+ TTR +
Sbjct: 156 LELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPF 215
Query: 66 SEKESQIVFLDTPGI---FNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDL 122
+ + +DT GI + K + + I+ AD+V LV+D+ + DL
Sbjct: 216 ERNGKKYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEG--ITEQDL 273
Query: 123 --LKEIAKRSSRLILILNKIDCVKPERLLEQ--AEIANKLVFIE--KTFMVSATKGHGCD 176
I + L++++NK D VK E+ E+ E+ KL F++ +SA G G D
Sbjct: 274 RIAGLILEAGKALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVD 333
Query: 177 DVLN 180
+L+
Sbjct: 334 KLLD 337
>gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 82.8 bits (206), Expect = 1e-16
Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 16/169 (9%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVS--EKESQIVFLDTPGIFN 82
VA+VG N GKSTL NR G + +IV TR + G +E ++ DT GI
Sbjct: 4 VAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILI--DTGGIEP 61
Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIA----KRSSRLILILN 138
D + K + + I+ AD++ VVD + + +EIA K + +IL++N
Sbjct: 62 DDDGFEKQIREQAELAIEEADVILFVVDG----RAGLTPADEEIAKILRKSNKPVILVVN 117
Query: 139 KIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLP 187
K+D P+ + E L + + +SA G G D+L+ + LP
Sbjct: 118 KVD--GPDEEADAYE-FYSLGL-GEPYPISAEHGRGIGDLLDAILEELP 162
Score = 72.4 bits (179), Expect = 2e-13
Identities = 46/164 (28%), Positives = 80/164 (48%), Gaps = 12/164 (7%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI---F 81
+A++G N GKS+L+N +G + IV+ TTR + + +DT GI
Sbjct: 176 IAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGIRRKG 235
Query: 82 NAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELK---VNIHDLLKEIAKRSSRLILILN 138
+ K + + I+ AD+V LV+D+ + + I L E A R+ L++++N
Sbjct: 236 KVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAGLALE-AGRA--LVIVVN 292
Query: 139 KIDCVKPERLLE-QAEIANKLVFIE--KTFMVSATKGHGCDDVL 179
K D V + + E + E+ +L F++ +SA G G D +L
Sbjct: 293 KWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLL 336
>gnl|CDD|161885 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer.
Length = 442
Score = 75.2 bits (185), Expect = 2e-14
Identities = 43/138 (31%), Positives = 65/138 (47%), Gaps = 1/138 (0%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
+A+VG+ N GKS+L+N + +IV+ TTR +V G I LDT GI
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHA 265
Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144
D +L I S+ IK AD+V V+D+ + L + L+ ++ K IL+LNKID
Sbjct: 266 DFVERLGIEKSFKAIKQADLVIYVLDASQPLTKD-DFLIIDLNKSKKPFILVLNKIDLKI 324
Query: 145 PERLLEQAEIANKLVFIE 162
+ +
Sbjct: 325 NSLEFFVSSKVLNSSNLS 342
>gnl|CDD|163162 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like).
Length = 351
Score = 64.8 bits (159), Expect = 3e-11
Identities = 53/168 (31%), Positives = 77/168 (45%), Gaps = 28/168 (16%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ---TTRSIVRGIVSEKESQIVFLDTPG-I 80
VALVG TNAGKSTL N GA V Q T R + +++ DT G I
Sbjct: 192 VALVGYTNAGKSTLFNALTGADVYA---ADQLFATLDPTTRRLDLPDGGEVLLTDTVGFI 248
Query: 81 FNAKDSYHKLM--IRLSWSTI---KHADIVCLVVD-SHRELKVNI---HDLLKEIAKRSS 131
+D H+L+ R +T+ + AD++ VVD S + + I +L+E+
Sbjct: 249 ---RDLPHELVAAFR---ATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDI 302
Query: 132 RLILILNKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVL 179
+L+ NKID + R+ E + VF+ SA G G D +L
Sbjct: 303 PQLLVYNKIDLLDEPRIERLEEGYPEAVFV------SAKTGEGLDLLL 344
>gnl|CDD|161778 TIGR00231, small_GTP, small GTP-binding protein domain. This model
recognizes a large number of small GTP-binding proteins
and related domains in larger proteins. Note that the
alpha chains of heterotrimeric G proteins are larger
proteins in which the NKXD motif is separated from the
GxxxxGK[ST] motif (P-loop) by a long insert and are not
easily detected by this model.
Length = 161
Score = 62.8 bits (153), Expect = 1e-10
Identities = 50/163 (30%), Positives = 75/163 (46%), Gaps = 12/163 (7%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVF--LDTPGIFN 82
+ +VG N GKSTL+NR +G K I +K TTR+ V ++ E F LDT G
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNK-FITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ-E 61
Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEI---AKRSSRLILILNK 139
+ +L R S+++ DIV LV+D ++ + KEI A+ + +IL+ NK
Sbjct: 62 DYRAIRRLYYRAVESSLRVFDIVILVLD----VEEILEKQTKEIIHHAESNVPIILVGNK 117
Query: 140 IDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182
ID + A + KL +SA G D +
Sbjct: 118 IDLRDAKLKTHVAFLFAKLNGEPI-IPLSAETGKNIDSAFKIV 159
>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 59.4 bits (144), Expect = 1e-09
Identities = 45/186 (24%), Positives = 75/186 (40%), Gaps = 21/186 (11%)
Query: 14 DFVQDNSRSGC-VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQI 72
+ ++ VA+VG N GKSTLVNR +G + ++V TR V +
Sbjct: 266 GDEKAGPKAVGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDF 325
Query: 73 VFLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSR 132
+DT G + + + + AD V VVD +V + + I + R
Sbjct: 326 KLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVDG----QVGLTSTDERIVRMLRR 381
Query: 133 ----LILILNKIDCVKPERLLEQAEIANKLVF----IEKTFMVSATKGHGCDDVLNYLCS 184
++L +NKID E + F + + + +SA G G D+L+
Sbjct: 382 AGKPVVLAVNKIDDQASEYDAAE--------FWKLGLGEPYPISAMHGRGVGDLLDEALD 433
Query: 185 TLPLAP 190
+L +A
Sbjct: 434 SLKVAE 439
Score = 52.9 bits (127), Expect = 1e-07
Identities = 42/148 (28%), Positives = 66/148 (44%), Gaps = 24/148 (16%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
VALVG N GKS+L+N+ + ++V TTR V IV +F+DT GI K
Sbjct: 453 VALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGI---K 509
Query: 85 DSYHKLM-------IRLSWSTIKHADIVCLVVD-----SHRELKVNIHDLLKEIAKRSSR 132
HKL +R + + I+ +++ + D S ++LKV +
Sbjct: 510 RRQHKLTGAEYYSSLR-TQAAIERSELALFLFDASQPISEQDLKV-----MSMAVDAGRA 563
Query: 133 LILILNKIDCVKPER--LLEQAEIANKL 158
L+L+ NK D + R LE+ +
Sbjct: 564 LVLVFNKWDLMDEFRRQRLER-LWKTEF 590
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 58.4 bits (142), Expect = 2e-09
Identities = 56/178 (31%), Positives = 81/178 (45%), Gaps = 18/178 (10%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83
VA+VG N GKSTLVNR +G + ++V TR V + +DT G +A
Sbjct: 41 VAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGWEPDA 100
Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAK---RSSR-LILILNK 139
K + + ++ AD V VVD+ V + +A+ RS + +IL NK
Sbjct: 101 KG-LQASVAEQAEVAMRTADAVLFVVDA----TVGATATDEAVARVLRRSGKPVILAANK 155
Query: 140 IDCVKPERLLEQAEIAN--KLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSA 195
+D + E A+ A L E VSA G G D+L+ + + LP P V SA
Sbjct: 156 VDDERGE-----ADAAALWSLGLGEP-HPVSALHGRGVGDLLDAVLAALPEVPRVGSA 207
Score = 49.2 bits (118), Expect = 1e-06
Identities = 40/143 (27%), Positives = 66/143 (46%), Gaps = 12/143 (8%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI---- 80
VALVG N GKS+L+N+ G + S+V TT V ++ F+DT G+
Sbjct: 214 VALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGLRRRV 273
Query: 81 FNAK--DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILN 138
A + Y L + I+ A++ +++D+ + +L + + L+L N
Sbjct: 274 KQASGHEYYASLRTH---AAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRALVLAFN 330
Query: 139 KIDCVKPER--LLEQAEIANKLV 159
K D V +R LE+ EI +L
Sbjct: 331 KWDLVDEDRRYYLER-EIDRELA 352
>gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 54.0 bits (131), Expect = 5e-08
Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 37/183 (20%)
Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIVTHKVQT---TRSIVRGIVSEKESQIVFLDT 77
+A G +N GKS+L+N A+ S +T T+ I E ++ +D
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTS------KTPGRTQLI---NFFEVNDKLRLVDL 77
Query: 78 PGIF-------NAKDSYHKLMIR--LSWSTIKHADIVCLVVDSHRELK---VNIHDLLKE 125
PG + K+ + KL+ + +K V L++DS LK + + + LKE
Sbjct: 78 PG-YGYAKVSKEEKEKWQKLIEEYLRTRENLK---GVVLLIDSRHPLKELDLQMIEWLKE 133
Query: 126 IAKRSSRLILILNKIDCVKP-ERLLEQAEIANKLVFIEKT-FMVSATKGHGCDDVLNYLC 183
++++L K D +K ER + ++ L F + + S+ K G D++ +
Sbjct: 134 YGI---PVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIA 190
Query: 184 STL 186
L
Sbjct: 191 KWL 193
>gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 51.6 bits (125), Expect = 2e-07
Identities = 52/180 (28%), Positives = 73/180 (40%), Gaps = 31/180 (17%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVS-EKESQIVFLDTPG 79
V LVG NAGKSTL++ AK K+ TT G+V + V D PG
Sbjct: 161 VGLVGLPNAGKSTLISAVSAAKP-----KIADYPFTTLHPNLGVVRVDDYKSFVIADIPG 215
Query: 80 IF-NAKDSYHK---LMIRLSWSTIKH---ADIVCLVVDSHRELKV-NIHDLLKEIAKRSS 131
+ A + L R +KH ++ +VD V + + E+ K S
Sbjct: 216 LIEGA----SEGAGLGHRF----LKHIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSP 267
Query: 132 RL-----ILILNKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTL 186
L IL+LNKID + E E+ F++SA G G D++L L L
Sbjct: 268 ELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELL 327
>gnl|CDD|162989 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal.
Length = 329
Score = 50.9 bits (123), Expect = 5e-07
Identities = 55/184 (29%), Positives = 80/184 (43%), Gaps = 45/184 (24%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVSEKESQ-IVFLDTPG 79
V LVG NAGKSTL++ AK K+ TT G+V + + V D PG
Sbjct: 160 VGLVGLPNAGKSTLISAVSAAKP-----KIADYPFTTLVPNLGVVRVDDGRSFVIADIPG 214
Query: 80 -IFNAKDSYHK---LMIRLSWSTIKH---ADIVCLVVDSHRELKVN-IHD---LLKEIAK 128
I A + L R +KH ++ ++D + I D + E+ K
Sbjct: 215 LIEGA----SEGAGLGHRF----LKHIERTRVLLHLIDISPLDGRDPIEDYEIIRNELKK 266
Query: 129 RSSRL-----ILILNKIDCVKPERLLEQAEIANKLVFIEK-----TFMVSATKGHGCDDV 178
S L I++LNKID LL++ E+A L ++K F +SA G G D++
Sbjct: 267 YSPELAEKPRIVVLNKID------LLDEEELAELLKELKKALGKPVFPISALTGEGLDEL 320
Query: 179 LNYL 182
L L
Sbjct: 321 LYAL 324
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 48.2 bits (115), Expect = 3e-06
Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 8/125 (6%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
V+LVG TNAGKSTL NR A+V T +R I + V DT G +
Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVGETVLADTVGFI--R 257
Query: 85 DSYHKLM--IRLSWSTIKHADIVCLVVD-SHRELKVNI---HDLLKEIAKRSSRLILILN 138
H L+ + + + A ++ VVD + ++ NI + +L+EI +L++N
Sbjct: 258 HLPHDLVAAFKATLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMN 317
Query: 139 KIDCV 143
KID +
Sbjct: 318 KIDML 322
>gnl|CDD|163346 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes.
Length = 179
Score = 47.9 bits (115), Expect = 4e-06
Identities = 40/174 (22%), Positives = 69/174 (39%), Gaps = 37/174 (21%)
Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIVTHKVQT---TRSIVRGIVSEKESQIVFLDT 77
+A G +N GKS+L+N A+ S +T T+ I V++ +D
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTS------KTPGRTQLINFFEVND---GFRLVDL 71
Query: 78 PGIFNAK------DSYHKLMIR--LSWSTIKHADIVCLVVDSHRELK---VNIHDLLKEI 126
PG AK + + KL+ +K V L++D LK + + + L+E
Sbjct: 72 PGYGYAKVSKEEKEKWQKLIEEYLEKRENLKG---VVLLMDIRHPLKELDLEMLEWLRE- 127
Query: 127 AKRSSRLILILNKIDCVKP-ERLLEQAEIANKLVFIE---KTFMVSATKGHGCD 176
++++L K D +K E + +I L + S+ K G D
Sbjct: 128 RGIP--VLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSSLKKTGID 179
>gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 46.0 bits (110), Expect = 1e-05
Identities = 48/177 (27%), Positives = 72/177 (40%), Gaps = 29/177 (16%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVSEKESQ-IVFLDTPG 79
V L+G NAGKST + AK KV TT G+V + + V D PG
Sbjct: 162 VGLLGLPNAGKSTFIRAVSAAK-----PKVADYPFTTLVPNLGVVRVDDERSFVVADIPG 216
Query: 80 IFNAKDSYHKLMIRLSWSTIKHAD--------IVCLVVDSHRELKVNIHDLLKEIAKRSS 131
+ L IR +KH + I +D ++ N ++ E+ K S
Sbjct: 217 LIEGASEGAGLGIRF----LKHLERCRVLLHLIDIAPIDGSDPVE-NARIIINELEKYSP 271
Query: 132 RL-----ILILNKIDCVKPERLLEQA-EIANKLVFIEKTFMVSATKGHGCDDVLNYL 182
+L L+ NKID + E E+A I L + +++SA G G ++ L
Sbjct: 272 KLAEKPRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDL 328
>gnl|CDD|163345 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members.
Length = 276
Score = 44.4 bits (106), Expect = 4e-05
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF 81
+VG N GKSTL+NR G KV+ V ++ T+ +S+ + LDTPGI
Sbjct: 121 AMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKLSD---GLELLDTPGIL 174
>gnl|CDD|116265 pfam07650, KH_2, KH domain.
Length = 55
Score = 42.8 bits (102), Expect = 1e-04
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 246 QVIYVERPSQKKIMLGKNGQNIKTISLEAKKEI 278
VI V R SQ I++GK G NIK + E +K
Sbjct: 1 AVIVVIRTSQPGIVIGKGGSNIKKLGKELRKRF 33
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 42.6 bits (101), Expect = 1e-04
Identities = 43/165 (26%), Positives = 62/165 (37%), Gaps = 34/165 (20%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF-NA 83
+ L+G + GK+TL G + K Q I DTPG +
Sbjct: 4 IMLIGRSGCGKTTLTQALNGE--ELKYKKTQAIEFSDNMI-----------DTPGEYLEN 50
Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKV------NIHDLLKEIAKRSSRLILIL 137
+ Y L++ T AD++ LV D+ V ++ K + I I+
Sbjct: 51 RRFYSALIV-----TAADADVIALVQDATEPWSVFPPGFASM--FNKPV-------IGII 96
Query: 138 NKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182
KID K E +E E EK F VSA G D++ YL
Sbjct: 97 TKIDLAKDEANIEMVEEWLNNAGAEKIFEVSAVTNEGIDELFAYL 141
>gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 41.3 bits (98), Expect = 3e-04
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 28 VGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF 81
+G N GKSTL+NR G K++ ++ T++ + + + LDTPGI
Sbjct: 127 IGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGK---GLELLDTPGIL 177
Score = 28.2 bits (64), Expect = 3.0
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 14/55 (25%)
Query: 99 IKHADIVCLVVD------SHRELKVNIHDLLKEIAKRSSRLILILNKIDCVKPER 147
+K D+V V+D S + ++ +I R +LILNK D PE
Sbjct: 22 LKLVDVVIEVLDARIPLSSE-------NPMIDKIIGNKPR-LLILNKSDLADPEV 68
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site.
Length = 142
Score = 40.1 bits (94), Expect = 7e-04
Identities = 33/161 (20%), Positives = 65/161 (40%), Gaps = 22/161 (13%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83
+ +G+ GK+TL G ++ + T+++ E + DTPG
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEI-----LYKKTQAV------EYNDGAI--DTPGEYVEN 49
Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCV 143
+ Y L++ T AD++ LV + K +I ++ KID
Sbjct: 50 RRLYSALIV-----TAADADVIALVQSATDPESRFPPGFASIFVK---PVIGLVTKIDLA 101
Query: 144 KPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCS 184
+ + +E+A+ + E F +S+ G + +++YL S
Sbjct: 102 EADVDIERAKELLETAGAEPIFEISSVDEQGLEALVDYLNS 142
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 39.9 bits (94), Expect = 0.001
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 14/49 (28%)
Query: 4 GEITFFNEHKDFVQDNSRSG------------CVALVGATNAGKSTLVN 40
G + F + F DNSR G VA+VG T AGKSTL+N
Sbjct: 333 GAVEF--DDVSFSYDNSRQGVEDVSFEAKPGQTVAIVGPTGAGKSTLIN 379
>gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 38.0 bits (89), Expect = 0.003
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 24/70 (34%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----------TTRSIVR----GIVSEKES 70
VAL+G++ GKSTLVN +G +V T V+ T R + G++
Sbjct: 198 VALLGSSGVGKSTLVNALLGEEV-QKTGAVREDDSKGRHTTTHRELHPLPSGGLL----- 251
Query: 71 QIVFLDTPGI 80
+DTPG+
Sbjct: 252 ----IDTPGM 257
>gnl|CDD|161878 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum.
Length = 591
Score = 37.4 bits (87), Expect = 0.004
Identities = 37/149 (24%), Positives = 65/149 (43%), Gaps = 4/149 (2%)
Query: 29 GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAKDSYH 88
G N GKSTL N GA V + T G + + I +D PGI++
Sbjct: 1 GNPNVGKSTLFNALTGANQ-TVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL 59
Query: 89 KLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVKPERL 148
+ + + + D+V VVD+ L+ N++ L ++ + +IL LN +D + + +
Sbjct: 60 EEEVARDYLLNEKPDLVVNVVDA-SNLERNLY-LTLQLLELGIPMILALNLVDEAEKKGI 117
Query: 149 LEQAEIANKLVFIEKTFMVSATKGHGCDD 177
E + + + SAT+G G +
Sbjct: 118 RIDEEKLEERLGV-PVVPTSATEGRGIER 145
>gnl|CDD|149505 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1 and Miro-2), are atypical Rho GTPases. They have
a unique domain organisation, with tandem GTP-binding
domains and two EF hand domains (pfam00036), that may
bind calcium. They are also larger than classical small
GTPases. It has been proposed that they are involved in
mitochondrial homeostasis and apoptosis.
Length = 118
Score = 37.4 bits (87), Expect = 0.005
Identities = 25/125 (20%), Positives = 51/125 (40%), Gaps = 16/125 (12%)
Query: 25 VALVGATNAGKSTLVNRFVGA-KVSIVTHKVQTTRSIVRGIVSEKESQIV-FLDTPGIFN 82
V ++G +GKS+L+++ VG + ++Q V + + +++++ D G
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGG--- 58
Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHR----ELKVNIHDLLKEIAKRSSR--LILI 136
+ + +K AD + LV D + L + K + +IL+
Sbjct: 59 -----REELKFEHIIFMKTADAILLVYDLTDRESLNRVSRLIAWLPHLRKLGKKIPVILV 113
Query: 137 LNKID 141
NK D
Sbjct: 114 GNKFD 118
>gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli.
Length = 360
Score = 36.1 bits (84), Expect = 0.014
Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 25 VALVGATNAGKSTLVNR----FVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80
V +VG TN GKS+L+N+ G K I T T + I + + DTPGI
Sbjct: 157 VYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLY--DTPGI 214
Query: 81 FN 82
N
Sbjct: 215 IN 216
Score = 33.0 bits (76), Expect = 0.11
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 123 LKEIAKRSSRLILILNKIDC----VKPERLLE--QAEIANKLVFIEKTFMVSATKGHGCD 176
LK + ++L+ NKID V ++ E + + +VSA KG+G D
Sbjct: 84 LKRFVGGN-PVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGID 142
Query: 177 DVLNYL 182
++L+ +
Sbjct: 143 ELLDKI 148
>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 35.2 bits (82), Expect = 0.023
Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 25 VALVGATNAGKSTLVNR----FVGAKVSIVT-HKVQTTRSIVRGIVSEKESQIVFLDTPG 79
V +VG TN GKSTL+NR G K I T TT + I + S + DTPG
Sbjct: 163 VYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIE-IPLDDGSFLY--DTPG 219
Query: 80 IFNA 83
I +
Sbjct: 220 IIHR 223
Score = 30.6 bits (70), Expect = 0.56
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 134 ILILNKIDC----VKPERLLE--QAEIANKL-VFIEKTFMVSATKGHGCDDVLNYL 182
+L+ NK D VK ++ + E A +L + ++SA KGHG D++L +
Sbjct: 100 LLVGNKADLLPKSVKKNKVKNWLRQE-AKELGLRPVDVVLISAQKGHGIDELLEAI 154
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end;
this model does not correctly align the sequences from
Methanococcus jannaschii and Pyrococcus horikoshii in
this region.
Length = 590
Score = 34.8 bits (80), Expect = 0.029
Identities = 33/140 (23%), Positives = 60/140 (42%), Gaps = 25/140 (17%)
Query: 19 NSRSGCVALVGATNAGKSTLVNRFVGAKVSI-----VTHKVQTTR---SIVRGI------ 64
RS V+++G + GK+TL+++ G+ V+ +T + T ++ GI
Sbjct: 1 KLRSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLK 60
Query: 65 ---VSEKESQIVFLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHD 121
+ K ++F+DTPG H+ L AD+ L+VD + K +
Sbjct: 61 KFKIRLKIPGLLFIDTPG--------HEAFTNLRKRGGALADLAILIVDINEGFKPQTQE 112
Query: 122 LLKEIAKRSSRLILILNKID 141
L + + ++ NKID
Sbjct: 113 ALNILRMYKTPFVVAANKID 132
>gnl|CDD|131816 TIGR02769, nickel_nikE, nickel import ATP-binding protein NikE.
This family represents the NikE subunit of a
multisubunit nickel import ABC transporter complex.
Nickel, once imported, may be used in urease and in
certain classes of hydrogenase and superoxide dismutase.
Length = 265
Score = 34.8 bits (80), Expect = 0.032
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 9/70 (12%)
Query: 24 CVALVGATNAGKSTLVNRFVG------AKVSIVTHKV-QTTRSIVRGIVSEKESQIVFLD 76
V L+G + GKSTL +G VS + Q R R ++ Q+VF D
Sbjct: 39 TVGLLGRSGCGKSTLARLLLGLEKPAQGTVSFRGQDLYQLDRKQRRAF--RRDVQLVFQD 96
Query: 77 TPGIFNAKDS 86
+P N + +
Sbjct: 97 SPSAVNPRMT 106
>gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 34.6 bits (80), Expect = 0.033
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 8 FFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN 40
+FN H V+D G + G T +GK+TL+N
Sbjct: 423 YFNFH---VRDAKVLGHTLIFGPTGSGKTTLLN 452
>gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 34.3 bits (80), Expect = 0.038
Identities = 53/221 (23%), Positives = 87/221 (39%), Gaps = 54/221 (24%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIV-SEKESQIVFLDTPG 79
V LVG N GKSTL++ AK K+ TT G+V ++ V D PG
Sbjct: 161 VGLVGFPNVGKSTLLSVVSNAKP-----KIANYHFTTLVPNLGVVETDDGRSFVMADIPG 215
Query: 80 -IFNAKDSYHK---LMIRLSWSTIKHAD---IVCLVVD----SHRELKVNIHDLLKEIAK 128
I A + L + ++H + ++ V+D R+ + + KE+
Sbjct: 216 LIEGA----SEGVGLGHQF----LRHIERTRVIVHVIDMSGSEGRDPIEDYEKINKELKL 267
Query: 129 RSSRL-----ILILNKIDCVKPERLLEQAEIANKL--VFIEKTFMVSATKGHGCDDVLNY 181
+ RL I++ NK+D L E E + K F +SA G G D++L
Sbjct: 268 YNPRLLERPQIVVANKMD------LPEAEENLEEFKEKLGPKVFPISALTGQGLDELLYA 321
Query: 182 LCSTLPLAPWVYSADQISDLPMFHFTAEITREKLFLHLHKE 222
+ A+ + + P F E E+++ +E
Sbjct: 322 V------------AELLEETPEFPLEEEEVEEEVYYKFEEE 350
>gnl|CDD|161900 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU.
Length = 587
Score = 34.0 bits (78), Expect = 0.054
Identities = 41/170 (24%), Positives = 71/170 (41%), Gaps = 24/170 (14%)
Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSI-VRGIVSEKESQIVFLDTPG 79
R V ++G + GK++L++ KV+ T+ I + +E I FLDTPG
Sbjct: 86 RPPVVTIMGHVDHGKTSLLDSIRKTKVA-QGEAGGITQHIGAYHVENEDGKMITFLDTPG 144
Query: 80 IFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNK 139
H+ + K DIV LVV + + + + + +I+ +NK
Sbjct: 145 --------HEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINK 196
Query: 140 ID--CVKPERLLEQ--------AEIANKLVFIEKTFMVSATKGHGCDDVL 179
ID P+R+ ++ + +F+ VSA G G D++L
Sbjct: 197 IDKPEANPDRVKQELSEYGLVPEDWGGDTIFV----PVSALTGDGIDELL 242
>gnl|CDD|185557 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 33.4 bits (77), Expect = 0.075
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 125 EIAKRSSRLILILNKIDCVKPERLLEQ-AEIANKLVFIEKTFM-------VSATKGHGCD 176
EI K +I++ NKID VK + +Q EI N F++ T +SA + D
Sbjct: 167 EIMKLK-HIIILQNKIDLVKEAQAQDQYEEIRN---FVKGTIADNAPIIPISAQLKYNID 222
Query: 177 DVLNYLCSTLPL 188
VL Y+C+ +P+
Sbjct: 223 VVLEYICTQIPI 234
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes.
Length = 581
Score = 33.3 bits (76), Expect = 0.088
Identities = 36/168 (21%), Positives = 66/168 (39%), Gaps = 19/168 (11%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVS--EKESQIVFLDTPGIFN 82
+A G + GK+TL+ G + + + +I G + ++ F+D PG
Sbjct: 3 IATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPG--- 59
Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSS--RLILILNKI 140
H+ I + + D LVVD+ + + L + I+++ K
Sbjct: 60 -----HEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLA-VLDLLGIPHTIVVITKA 113
Query: 141 DCVKPERL----LEQAEIANKLVFIE--KTFMVSATKGHGCDDVLNYL 182
D V E + + +I N +F++ K F SA G G ++ L
Sbjct: 114 DRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKEL 161
>gnl|CDD|184050 PRK13430, PRK13430, F0F1 ATP synthase subunit delta; Provisional.
Length = 271
Score = 31.8 bits (73), Expect = 0.20
Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 8/56 (14%)
Query: 18 DNSRSGCVALV--GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQ 71
D RS AL K LV R G KVS T +V V ++ S+
Sbjct: 42 DRERSLRRALTDPARPPEAKVELVKRLFGGKVS------PATLEVVSDAVRQRWSR 91
>gnl|CDD|178972 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 32.0 bits (74), Expect = 0.20
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHL-ILFVK 293
+R I+ RP I++GK G I+ + +KE+ ++ +PV + I+ VK
Sbjct: 64 VRVTIHTARPG---IVIGKKGAEIEKL----RKELEKLTGKPVQINIVEVK 107
>gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 592
Score = 32.0 bits (73), Expect = 0.20
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 23 GCVALVGATNAGKSTLVNRFVG 44
G VALVG T +GKSTL + +G
Sbjct: 368 GFVALVGHTGSGKSTLASLLMG 389
>gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 31.7 bits (73), Expect = 0.24
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 25 VALVGATNAGKSTLVNRFVG 44
+ALVG + AGK++L+N +G
Sbjct: 379 IALVGPSGAGKTSLLNALLG 398
>gnl|CDD|183414 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 31.8 bits (73), Expect = 0.25
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80
V LVG +AGKS+L++ AK I + TT G+V +++ D PG+
Sbjct: 162 VGLVGFPSAGKSSLISALSAAKPKIADYPF-TTLVPNLGVVQAGDTRFTVADVPGL 216
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.3 bits (72), Expect = 0.32
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 10/61 (16%)
Query: 27 LVGATNAGKSTLVNRFVG---AKVSIVTHKVQ----TTRSIVRGIVSEKESQIVFLDTPG 79
L G + GKSTL+N K ++ + TT V ++ DTPG
Sbjct: 169 LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTH-VELYDLPGGGLLI--DTPG 225
Query: 80 I 80
Sbjct: 226 F 226
Score = 27.9 bits (63), Expect = 3.6
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 134 ILILNKIDCVKPERLLEQAEIANKLVFIEK----TFMVSATKGHGCDDVLNYL 182
I++LNKID + + L E E+ +SA +G G D++ L
Sbjct: 115 IIVLNKIDLL--DDLEEARELLA---LYRAIGYDVLELSAKEGEGLDELKPLL 162
>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
Unfortunately, the gene symbol nomenclature adopted
based on this operon in B. subtilis assigns cydC to the
third gene in the operon where this gene is actually
homologous to the E. coli cydD gene. We have chosen to
name all homologs in this family in accordance with the
precedence of publication of the E. coli name, CydD.
Length = 529
Score = 31.1 bits (71), Expect = 0.35
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 25 VALVGATNAGKSTLVN 40
VALVG + AGKSTL+N
Sbjct: 351 VALVGPSGAGKSTLLN 366
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 31.0 bits (71), Expect = 0.44
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG 79
+ VG +N GKSTLV G KV V + TR + + D PG
Sbjct: 12 IVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRKPNHYDWGDF----ILTDLPG 61
>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 = 30.8 bits (70), Expect = 0.48
Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 3/22 (13%)
Query: 25 VALVGATNAGKSTLVN---RFV 43
VALVG + +GKSTLVN RF
Sbjct: 361 VALVGRSGSGKSTLVNLIPRFY 382
>gnl|CDD|181948 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 30.5 bits (69), Expect = 0.58
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSI-----VTHKVQTTRSIVRGIVSEKESQIVFLDTPG 79
+ L+G N+GK+TL N+ GA+ + VT + + G S + Q+ +D PG
Sbjct: 6 IGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKE------GQFSTTDHQVTLVDLPG 59
Query: 80 IF 81
+
Sbjct: 60 TY 61
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 30.6 bits (70), Expect = 0.58
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 230 VTEKWEEKKDGSILIRQVIYVE-RPSQKKIMLGKNGQNIKTISLEAKK 276
V +KK+G +V YVE P K I +GKNG+NI+ AK+
Sbjct: 87 VRSVTIKKKNG----DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKR 130
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 30.6 bits (69), Expect = 0.59
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 25 VALVGATNAGKSTLVNRFVGAKV 47
+A+VG AGKST +N VG +V
Sbjct: 72 LAIVGTMKAGKSTTINAIVGTEV 94
>gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 30.1 bits (69), Expect = 0.80
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 11/53 (20%)
Query: 146 ERLLEQAEIANKLVF--IEK---------TFMVSATKGHGCDDVLNYLCSTLP 187
E+ LE E++ + + + K F SA K G +L+ + LP
Sbjct: 210 EKYLEGEELSEEEIKAGLRKATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLP 262
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related.
Length = 585
Score = 29.9 bits (67), Expect = 0.83
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 14/49 (28%)
Query: 4 GEITFFNEHKDFVQDNSRSGC------------VALVGATNAGKSTLVN 40
G + F + +F NS G VA+VG T AGK+TL+N
Sbjct: 333 GAVEFRHITFEFA--NSSQGVFDVSFEAKAGQTVAIVGPTGAGKTTLIN 379
>gnl|CDD|131633 TIGR02584, cas_NE0113, CRISPR-associated protein, NE0113 family.
Members of this minor CRISPR-associated (Cas) protein
family are found in cas gene clusters in Vibrio
vulnificus YJ016, Nitrosomonas europaea ATCC 19718,
Mannheimia succiniciproducens MBEL55E, and
Verrucomicrobium spinosum.
Length = 209
Score = 29.8 bits (67), Expect = 0.84
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEI 281
IR Y R + ++G + EA E+AE+
Sbjct: 162 IRGFYYPPRKGPILEIRTRDGPPAPADTSEAVVELAEL 199
>gnl|CDD|183705 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 30.0 bits (67), Expect = 0.88
Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 10/46 (21%)
Query: 21 RSGCVALVGATNAGKST----LVNRFVGAK----VSIVTHKVQTTR 58
R G +ALVG T AGK+T L RF V++VT T R
Sbjct: 349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVT--TDTQR 392
>gnl|CDD|164820 PHA00520, PHA00520, packaging NTPase P4.
Length = 330
Score = 29.8 bits (67), Expect = 0.95
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 22 SGCVALVGATNAGKSTLVN 40
SG +VG T +GK+ L+N
Sbjct: 124 SGVEVVVGGTGSGKTPLLN 142
>gnl|CDD|162685 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily
of the penicillin binding proteins includes the member
from E. coli designated penicillin-binding protein 1C.
Members have both transglycosylase and transpeptidase
domains and are involved in forming cross-links in the
late stages of peptidoglycan biosynthesis. All members
of this subfamily are presumed to have the same basic
function.
Length = 727
Score = 29.7 bits (67), Expect = 0.97
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 240 GSILIRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILE 283
GS L Q+ + P + + GK Q + I LEA+ EILE
Sbjct: 85 GSTLTMQLARLLDPELSRTLTGKLRQMWRAIQLEARYSKREILE 128
>gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.6 bits (67), Expect = 1.0
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 8/39 (20%)
Query: 21 RSGCVALVGATNAGKST----LVNRFV---GA-KVSIVT 51
R G AL+G T GK+T L R V GA KV+++T
Sbjct: 255 RGGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLT 293
>gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 255
Score = 29.5 bits (67), Expect = 1.1
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 274 AKKEIAEILEQPVHLILFVKVQKDWGHDPK 303
A ++IA+ LE PV LILF V +W DPK
Sbjct: 101 AAQDIAQHLETPVDLILFHAVL-EWVADPK 129
>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
protein; Provisional.
Length = 648
Score = 29.7 bits (67), Expect = 1.1
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 25 VALVGATNAGKSTLVN 40
VA+VGA+ +GKSTL+N
Sbjct: 37 VAIVGASGSGKSTLMN 52
>gnl|CDD|184132 PRK13547, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 272
Score = 29.4 bits (66), Expect = 1.2
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 6 ITFFNEHKDFVQDNS---RSGCV-ALVGATNAGKSTLVNRFVG 44
+ H+ ++D S G V AL+G AGKSTL+ G
Sbjct: 7 LHVARRHRAILRDLSLRIEPGRVTALLGRNGAGKSTLLKALAG 49
>gnl|CDD|148992 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases are
sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and tend
to undergo disruption to form pseudogenes. A unique
feature of all eukaryotic and certain bacterial KAP
NTPases is the presence of two or four transmembrane
helices inserted into the P-loop NTPase domain. These
transmembrane helices anchor KAP NTPases in the membrane
such that the P-loop domain is located on the
intracellular side.
Length = 301
Score = 29.3 bits (66), Expect = 1.2
Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 102 ADIVCLVVDSHRELKVNIHDLLKEIAKR----SSRLILILNKIDCVKPERLLEQAEIANK 157
+ L ++ ++L+ I +L +IA R+++I++ +D +PE +E E
Sbjct: 127 KSLKLLSIEPLKKLQTEIEELRTDIASTLDDLQKRIVVIIDDLDRCEPEEAVELLEAVRL 186
Query: 158 LVFIEKTFMVSAT 170
L + A
Sbjct: 187 LFDFPNVVFILAY 199
>gnl|CDD|182479 PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB;
Provisional.
Length = 290
Score = 29.4 bits (66), Expect = 1.3
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 134 ILILNKIDCVKP------ERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182
+++LNK+D + P E+ + A N + I ++SAT G G D LN+L
Sbjct: 234 LMLLNKVDLL-PYLNFDVEKCIACAREVNPEIEI---ILISATSGEGMDQWLNWL 284
>gnl|CDD|162997 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 29.2 bits (66), Expect = 1.4
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 4 GEITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN------RFVGAKVSIV 50
G+++ F D +S + +A+VG + AGKS + G KV ++
Sbjct: 416 GQLSAF----DPFDSDSTNYNIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVI 464
>gnl|CDD|152038 pfam11602, NTPase_P4, ATPase P4 of dsRNA bacteriophage phi-12. P4
is a packaging motor which is involved in the packaging
of phi-12 genome into preformed capsids using ATP. P4 is
located at the vertices of the icosahedral capsid. ATP
drives RNA translocation through cooperative
conformational changes.
Length = 320
Score = 28.8 bits (64), Expect = 1.7
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 19 NSRSGCVALVGATNAGKSTLVN 40
SG V + G T +GKS +N
Sbjct: 108 GIYSGMVIVTGKTGSGKSEALN 129
>gnl|CDD|172889 PRK14413, PRK14413, membrane protein; Provisional.
Length = 197
Score = 29.0 bits (65), Expect = 1.8
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 29 GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIV 61
G+ N G ST V R VG K+SI+T + + I+
Sbjct: 35 GSGNIG-STNVKRIVGTKISIITQIIDVLKGII 66
>gnl|CDD|179775 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
Length = 207
Score = 28.7 bits (65), Expect = 1.9
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 11/39 (28%)
Query: 245 RQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILE 283
R IY ERP +++G+ G+NI +E+ EILE
Sbjct: 43 RITIYAERPG---MVIGRGGKNI--------RELTEILE 70
>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 = 28.9 bits (65), Expect = 2.0
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 25 VALVGATNAGKSTLVNRFVGA------KVSIVTHKVQTTRSIVRGIVS 66
VA++G + +GKSTL+ G +V++ V + + +R +S
Sbjct: 364 VAILGPSGSGKSTLLMLLTGLLDPLQGEVTLDGVSVSSLQDELRRRIS 411
>gnl|CDD|177488 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 28.7 bits (65), Expect = 2.0
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 6 ITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN---RFVGAKV-SIVTHKVQ 55
I+F KDF++ + C+ + G + GKS +F+ KV S V K
Sbjct: 418 ISFLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKSH 471
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 28.8 bits (65), Expect = 2.0
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 25 VALVGATNAGKSTLVN---RF 42
VALVG + +GKST+ N RF
Sbjct: 372 VALVGRSGSGKSTIANLLTRF 392
>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 = 28.5 bits (63), Expect = 2.2
Identities = 21/126 (16%), Positives = 38/126 (30%), Gaps = 14/126 (11%)
Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80
+ +VG +GK+TL A+ + G +E L
Sbjct: 1 PGEVILIVGPPGSGKTTLARAL--ARELGPPGGGV---IYIDGEDILEEVLDQLLLIIVG 55
Query: 81 FNAKDSYHKLMIRLSWSTIKHADIVCLVVD---------SHRELKVNIHDLLKEIAKRSS 131
+L +RL+ + + L++D L + L + K
Sbjct: 56 GKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115
Query: 132 RLILIL 137
L +IL
Sbjct: 116 NLTVIL 121
>gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 28.6 bits (65), Expect = 2.2
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 25 VALVGATNAGKSTLVN 40
+ LVG N GKST N
Sbjct: 4 IGLVGKPNVGKSTFFN 19
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 28.4 bits (63), Expect = 2.3
Identities = 33/121 (27%), Positives = 50/121 (41%), Gaps = 26/121 (21%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83
+A VGA AGK+TL N G + K Q +G + DTPG F+
Sbjct: 4 IAFVGAVGAGKTTLFNALQGNYT--LARKTQAVEFNDKGDI----------DTPGEYFSH 51
Query: 84 KDSYHKLMIRLSWSTIKHADIVCLV---VDSHRELKVNIHDLLKEIAKRSSRLILILNKI 140
YH L+ +T++ D++ V D L + D+ S R I +++K
Sbjct: 52 PRWYHALI-----TTLQDVDMLIYVHGANDPESRLPAGLLDI-----GVSKRQIAVISKT 101
Query: 141 D 141
D
Sbjct: 102 D 102
>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 28.4 bits (64), Expect = 2.4
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 17 QDNSRSGCVALVGATNAGKSTL 38
+ +R +AL+G AGKSTL
Sbjct: 128 RRAARRRRIALIGLRGAGKSTL 149
>gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein
PhnL. Members of this family are the PhnL protein of
C-P lyase systems for utilization of phosphonates.
These systems resemble phosphonatase-based systems in
having a three component ABC transporter, where
TIGR01097 is the permease, TIGR01098 is the
phosphonates binding protein, and TIGR02315 is the
ATP-binding cassette (ABC) protein. They differ,
however, in having, typically, ten or more additional
genes, many of which are believed to form a
membrane-associated C-P lysase complex. This protein
(PhnL) and the adjacent-encoded PhnK (TIGR02323)
resemble transporter ATP-binding proteins but are
suggested, based on mutatgenesis studies, to be part of
this C-P lyase complex rather than part of a
transporter per se.
Length = 224
Score = 28.5 bits (64), Expect = 2.5
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 24 CVALVGATNAGKSTL 38
CVAL G + AGKSTL
Sbjct: 36 CVALSGPSGAGKSTL 50
>gnl|CDD|184205 PRK13646, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 286
Score = 28.2 bits (63), Expect = 2.8
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 29/100 (29%)
Query: 26 ALVGATNAGKSTLVNRFVG------AKVSI----VTHK-----VQTTRSIVRGIVSEKES 70
A+VG T +GKSTL+ V++ +THK ++ R + + ES
Sbjct: 37 AIVGQTGSGKSTLIQNINALLKPTTGTVTVDDITITHKTKDKYIRPVRKRIGMVFQFPES 96
Query: 71 QIVFLDT--------PGIFN-----AKDSYHKLMIRLSWS 97
Q+ F DT P F K+ H+L++ L +S
Sbjct: 97 QL-FEDTVEREIIFGPKNFKMNLDEVKNYAHRLLMDLGFS 135
>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type.
TIGRFAMs model TIGR01008 describes S3 of the eukaryotic
cytosol and of the archaea.
Length = 211
Score = 28.1 bits (63), Expect = 2.9
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHL-ILFVK 293
IR I+ RP I++GK G I+ + +K++ ++ + V + I VK
Sbjct: 64 IRVTIHTARPG---IVIGKKGSEIEKL----RKDLQKLTGKEVQINIAEVK 107
>gnl|CDD|162700 TIGR02095, glgA, glycogen/starch synthases, ADP-glucose type. This
family consists of glycogen (or starch) synthases that
use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose
(EC 2.4.1.11) as in animals, as the glucose donor. This
enzyme is found in bacteria and plants. Whether the name
given is glycogen synthase or starch synthase depends on
context, and therefore on substrate.
Length = 473
Score = 28.0 bits (63), Expect = 2.9
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 99 IKHADIVCLVVDSH-RELK-----VNIHDLLKEIAKRSSRLILILNKIDC 142
I +AD V V ++ RE+ + +LK RS +L ILN ID
Sbjct: 203 IVYADRVTTVSPTYAREILTPEFGYGLDGVLKA---RSGKLRGILNGIDT 249
>gnl|CDD|182996 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 28.0 bits (63), Expect = 3.3
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 11 EHKDF-VQDNSRSGCVALVGATNAGKSTL 38
++ + ++DN R V LVG AGKSTL
Sbjct: 20 DNAELHIEDNER---VCLVGRNGAGKSTL 45
>gnl|CDD|178665 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 28.1 bits (62), Expect = 3.3
Identities = 38/157 (24%), Positives = 68/157 (43%), Gaps = 27/157 (17%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84
+ L+G + GKS+L+ F+ + V + + I + V K ++ DT G
Sbjct: 17 ILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAG----- 71
Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVD-SHRELKVNIHDLL-KEIAKRSSRL----ILILN 138
+ L+ S ++A + LV D + RE N+ D+ KE+ S+ +L+ N
Sbjct: 72 ---QERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGN 128
Query: 139 KIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGC 175
K+D + ER + + E ++ K HGC
Sbjct: 129 KVD-RESERDVSREE------------GMALAKEHGC 152
>gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 28.0 bits (63), Expect = 3.5
Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 17/72 (23%)
Query: 25 VALVGATNAGKSTLVNR--FVGAKVSIV--THKVQTT-----RSIVRGI--------VSE 67
+ ++ +AGK+TL R F K+ + T + RGI
Sbjct: 11 IGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAATSCDW 70
Query: 68 KESQIVFLDTPG 79
+I +DTPG
Sbjct: 71 DNHRINLIDTPG 82
>gnl|CDD|116538 pfam07928, Vps54, Vps54-like protein. This family contains various
proteins that are homologs of the yeast Vps54 protein,
such as the rat homolog , the human homolog, and the
mouse homolog. In yeast, Vps54 associates with Vps52 and
Vps53 proteins to form a trimolecular complex that is
involved in protein transport between Golgi, endosomal,
and vacuolar compartments. All Vps54 homologs contain a
coiled coil region (not found in the region featured in
this family) and multiple dileucine motifs.
Length = 133
Score = 28.0 bits (63), Expect = 3.6
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 121 DLLKEIAKRSSRLILILNKIDCVKPERLLEQAEIANKLVFI 161
++ +R+ + +LN+ D V+ + Q EI NKLV I
Sbjct: 88 PYIRRHLRRAPKQSSLLNEFDKVRRDYQEHQNEIHNKLVSI 128
>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
This model describes the ATP binding subunit of the
multisubunit cobalt transporter in bacteria and its
equivalents in archaea. The model is restricted to ATP
subunit that is a part of the cobalt transporter, which
belongs to the ABC transporter superfamily (ATP Binding
Cassette). The model excludes ATP binding subunit that
are associated with other transporters belonging to ABC
transporter superfamily. This superfamily includes two
groups, one which catalyze the uptake of small
molecules, including ions from the external milieu and
the other group which is engaged in the efflux of small
molecular weight compounds and ions from within the
cell. Energy derived from the hydrolysis of ATP drive
the both the process of uptake and efflux.
Length = 190
Score = 27.8 bits (62), Expect = 3.6
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 20 SRSGCVALVGATNAGKSTLVNRFVG 44
R +AL+GA AGKSTL+ G
Sbjct: 16 ERGEVLALLGANGAGKSTLLLHLNG 40
>gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein.
This model describes the energy-transducing ATPase
subunit ThiQ of the ThiBPQ thiamine (and thiamine
pyrophosphate) ABC transporter in several
Proteobacteria. This protein is found so far only in
Proteobacteria, and is found in complete genomes only
if the ThiB and ThiP subunits are also found.
Length = 213
Score = 27.9 bits (62), Expect = 3.7
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 25 VALVGATNAGKSTLVNRFVG 44
VA++G + AGKSTL+N G
Sbjct: 27 VAIMGPSGAGKSTLLNLIAG 46
>gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes an multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHPM, Nitrile Hydratase
Propeptide Microcin.
Length = 710
Score = 27.6 bits (62), Expect = 3.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 25 VALVGATNAGKSTL 38
VALVG + +GKST+
Sbjct: 508 VALVGGSGSGKSTI 521
>gnl|CDD|184133 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 27.8 bits (63), Expect = 4.0
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 25 VALVGATNAGKSTL 38
VA++G AGKSTL
Sbjct: 31 VAILGPNGAGKSTL 44
>gnl|CDD|150474 pfam09810, Morph_protein1, Defects in morphology protein 1,
mitochondrial precursor. Members of this family of
proteins are thought to be involved in cellular
morphology, though little else is known about them.
Length = 329
Score = 27.8 bits (62), Expect = 4.0
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 255 QKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQK 296
Q + L K G+ +T +++ +I E LE VH + V+V
Sbjct: 28 QYEYTLTKFGRKERTPAMKRGIKIHEKLELEVHTTVPVEVTT 69
>gnl|CDD|184201 PRK13641, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 27.9 bits (62), Expect = 4.0
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 25 VALVGATNAGKSTLVNRF 42
VALVG T +GKSTL+ F
Sbjct: 36 VALVGHTGSGKSTLMQHF 53
>gnl|CDD|163393 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. eIF-2 functions in the early steps of protein
synthesis by forming a ternary complex with GTP and
initiator tRNA.
Length = 406
Score = 27.7 bits (62), Expect = 4.1
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 133 LILILNKIDCVKPERLLEQ-AEIANKLVFIEKTFM-------VSATKGHGCDDVLNYLCS 184
++++ NKID V E+ LE EI F++ T VSA D +L +
Sbjct: 137 IVIVQNKIDLVSKEKALENYEEIKE---FVKGTVAENAPIIPVSALHNANIDALLEAIEK 193
Query: 185 TLPL 188
+P
Sbjct: 194 FIPT 197
>gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal propeptide
cleavage domain, and an HlyD homolog (TIGR03794). In a
number of genomes, a conserved propeptide sequence with
a classic Gly-Gly motif.
Length = 686
Score = 27.6 bits (62), Expect = 4.1
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 25 VALVGATNAGKSTL 38
VA+VG + +GKSTL
Sbjct: 482 VAIVGPSGSGKSTL 495
>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 = 27.7 bits (62), Expect = 4.4
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 25 VALVGATNAGKSTL 38
VALVG + AGKSTL
Sbjct: 369 VALVGPSGAGKSTL 382
>gnl|CDD|178771 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 27.6 bits (61), Expect = 4.5
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNA 83
VA+VG T GK++L++ +G ++H +T+ ++RG V+ IFNA
Sbjct: 646 VAIVGGTGEGKTSLISAMLGE----LSH-AETSSVVIRGSVAYVPQ------VSWIFNA 693
>gnl|CDD|183321 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 27.6 bits (62), Expect = 4.6
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 83 AKDSYHKLMIRLS----W-STIKHADI 104
A+ S +LMIRL W S IK A +
Sbjct: 421 ARRSRRRLMIRLVKGAYWDSEIKRAQV 447
>gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 27.5 bits (62), Expect = 4.6
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 25 VALVGATNAGKSTL 38
VAL+G T GKSTL
Sbjct: 369 VALLGRTGCGKSTL 382
>gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein.
Length = 617
Score = 27.3 bits (61), Expect = 4.9
Identities = 8/16 (50%), Positives = 15/16 (93%)
Query: 25 VALVGATNAGKSTLVN 40
+A++G++ AGK+TL+N
Sbjct: 54 LAVMGSSGAGKTTLMN 69
>gnl|CDD|151508 pfam11062, DUF2863, Protein of unknown function (DUF2863). This
bacterial family of proteins have no known function.
Length = 398
Score = 27.3 bits (61), Expect = 4.9
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 186 LPLAPWVYSADQISDLPM-FHFTAEITRE 213
L LAP+++S DQ LP TAE+ R+
Sbjct: 140 LALAPFLFSIDQ---LPRSHCETAELARK 165
>gnl|CDD|130815 TIGR01754, flav_RNR, ribonucleotide reductase-associated
flavodoxin, putative. This model represents a family of
proteins found immediately downstream of ribonucleotide
reductase genes in Xyella fastidiosa and some
Gram-positive bacteria. It appears to be a highly
divergent flavodoxin of the short chain type, more like
the flavodoxins of the sulfate-reducing genus
Desulfovibrio than like the NifF flavodoxins associated
with nitrogen fixation.
Length = 140
Score = 27.5 bits (61), Expect = 5.0
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 273 EAKKEIAEILEQPVHLILFVKVQKDWGHDPKC 304
E K IAE+ +P ++ +F + WG D C
Sbjct: 69 EMKDFIAELGYKPSNVAIFGTGETQWGDDLYC 100
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus.
Length = 527
Score = 27.2 bits (60), Expect = 5.5
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 74 FLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRL 133
LDTPG H+ ++ T+ D +V+D+ + ++ L++ R + +
Sbjct: 84 LLDTPG--------HEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDTPI 135
Query: 134 ILILNKID--CVKPERLLEQAE 153
+NK+D P LL++ E
Sbjct: 136 FTFMNKLDRDIRDPLELLDEVE 157
>gnl|CDD|182707 PRK10762, PRK10762, D-ribose transporter ATP binding protein;
Provisional.
Length = 501
Score = 27.3 bits (61), Expect = 5.8
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 20/62 (32%)
Query: 26 ALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNA-K 84
ALVG AGKST++ KV T GI + I++L FN K
Sbjct: 34 ALVGENGAGKSTMM-------------KVLT------GIYTRDAGSILYLGKEVTFNGPK 74
Query: 85 DS 86
S
Sbjct: 75 SS 76
>gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter
subunit; Provisional.
Length = 262
Score = 27.3 bits (60), Expect = 6.0
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 9 FNEHKDF--VQDNSRSG-CVALVGATNAGKSTLV---------NRFVGAKVSIVTHKVQT 56
FN+H+ V N G VAL+G + +GKSTL+ ++ G+ + ++ VQ
Sbjct: 14 FNQHQALHAVDLNIHHGEMVALLGPSGSGKSTLLRHLSGLITGDKSAGSHIELLGRTVQR 73
Query: 57 TRSIVRGI 64
+ R I
Sbjct: 74 EGRLARDI 81
>gnl|CDD|183231 PRK11614, livF, leucine/isoleucine/valine transporter ATP-binding
subunit; Provisional.
Length = 237
Score = 27.2 bits (60), Expect = 6.4
Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 17/87 (19%)
Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIV-----THKVQTTRSIVRGIVSEKESQIVF- 74
V L+GA AGK+TL+ G IV QT + + + E + VF
Sbjct: 34 VTLIGANGAGKTTLLGTLCGDPRATSGRIVFDGKDITDWQTAKIMREAVAIVPEGRRVFS 93
Query: 75 -------LDTPGIFNAKDSYHKLMIRL 94
L G F +D + + + +
Sbjct: 94 RMTVEENLAMGGFFAERDQFQERIKWV 120
>gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion.
Length = 544
Score = 26.9 bits (60), Expect = 6.8
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 25 VALVGATNAGKSTLVNRFVGA 45
+A++G + +GKSTL VG
Sbjct: 347 LAIIGPSGSGKSTLARLIVGI 367
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 27.0 bits (60), Expect = 7.2
Identities = 10/15 (66%), Positives = 14/15 (93%)
Query: 26 ALVGATNAGKSTLVN 40
AL+GA+ AGK+TL+N
Sbjct: 793 ALMGASGAGKTTLLN 807
>gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional.
Length = 445
Score = 26.6 bits (59), Expect = 8.1
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 32 NAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKES 70
A K LV R KV T ++R VS++ S
Sbjct: 230 AAPKIRLVERLFSGKVG------APTLEVLRTAVSQRWS 262
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 26.5 bits (59), Expect = 8.7
Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 31/91 (34%)
Query: 20 SRSGCVALVGATNAGKST----LVNRFV----GAKVSIVT-------------------- 51
+ G +ALVG T GK+T L RFV KV+++T
Sbjct: 192 EQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILG 251
Query: 52 ---HKVQTTRSIVRGIVSEKESQIVFLDTPG 79
+ + + + + ++ ++ +DT G
Sbjct: 252 VPVKVARDPKELRKALDRLRDKDLILIDTAG 282
>gnl|CDD|184134 PRK13549, PRK13549, xylose transporter ATP-binding subunit;
Provisional.
Length = 506
Score = 26.4 bits (59), Expect = 10.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 24 CVALVGATNAGKSTL 38
V+L G AGKSTL
Sbjct: 33 IVSLCGENGAGKSTL 47
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
0.321 0.136 0.401
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,858,433
Number of extensions: 299911
Number of successful extensions: 974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 940
Number of HSP's successfully gapped: 140
Length of query: 311
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 218
Effective length of database: 3,984,929
Effective search space: 868714522
Effective search space used: 868714522
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 (21.9 bits)
S2: 57 (25.7 bits)