RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy50
(505 letters)
>gnl|CDD|234125 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)
[Unknown function, General].
Length = 351
Score = 231 bits (593), Expect = 6e-72
Identities = 113/342 (33%), Positives = 174/342 (50%), Gaps = 23/342 (6%)
Query: 111 LAESKALVSSIQGWRVVDSTIISLLSFDKKSFFGKGNLELLKRQVRGDARVTAVFVSVDV 170
L E L + VV + D ++ GKG +E + V +F
Sbjct: 19 LEELAELAETAGA-EVVGTVTQKRSRPDPATYIGKGKVEEIAELVEELEADLVIFD--HE 75
Query: 171 LKLHQQKMLQDLFQVPVFDRYMIVIQIFKAHAKTREARLQIAIAELPYLWTRYRTIEDAT 230
L Q++ L+ V DR +++ IF A+T E +LQ+ +A+L YL R + T
Sbjct: 76 LSPSQERNLEKALGCRVIDRTGLILDIFAQRARTHEGKLQVELAQLKYLLPRL--VGGWT 133
Query: 231 NMNITKG----------FLDSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVA 280
+++ G L++ R ++ ER +LKK L K++ QRE R +++R PTVA
Sbjct: 134 HLSRQGGGIGTRGPGETQLETDRRLIRERIAQLKKELEKVEKQRERQRRRRKRADVPTVA 193
Query: 281 VVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISNIP 340
+VGYTN GK+TL ALT D +QLFATLD TT LP+ +L DT+GFI ++P
Sbjct: 194 LVGYTNAGKSTLFNALTGADVYA-ADQLFATLDPTTRRLDLPDGGEVLLTDTVGFIRDLP 252
Query: 341 TTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGN 400
L+ F+ TLE+ AD+++HVVD S+PD +Q + V++ L+ L E+ L+V N
Sbjct: 253 HELVAAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDI---PQLLVYN 309
Query: 401 KVDAVPPGERVTEEYD----LLISATRGTGLAQLKEKVQDMI 438
K+D + E + +SA G GL L E + + +
Sbjct: 310 KIDLLDEPRIERLEEGYPEAVFVSAKTGEGLDLLLEAIAERL 351
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 226 bits (578), Expect = 6e-69
Identities = 113/341 (33%), Positives = 176/341 (51%), Gaps = 20/341 (5%)
Query: 111 LAESKALVSSIQGWRVVDSTIISLLSFDKKSFFGKGNLELLKRQVRGDARVTAVFVSVDV 170
L E L + G+ VV+ D K++ G G LE + V +F
Sbjct: 22 LEELAELAETA-GYEVVEVVTQKRERPDPKTYIGSGKLEEIAEAVEETGADLVIFD--HE 78
Query: 171 LKLHQQKMLQDLFQVPVFDRYMIVIQIFKAHAKTREARLQIAIAELPYLWTR-YRTIEDA 229
L Q + L+ V V DR +++ IF A++RE +LQ+ +A+L Y R +
Sbjct: 79 LSPSQLRNLEKELGVKVIDRTQLILDIFAQRARSREGKLQVELAQLRYELPRLVGSGSHL 138
Query: 230 TNMNITKGF-------LDSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVV 282
+ + GF L++ R + R KLK+ L ++ RE R K+ R P VA+V
Sbjct: 139 SRLGGGIGFRGPGETQLETDRRRIRRRIAKLKRELENVEKAREPRRKKRSRSGIPLVALV 198
Query: 283 GYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISNIPTT 342
GYTN GK+TL ALT D V +QLFATLD TT L + ++L DT+GFI ++P
Sbjct: 199 GYTNAGKSTLFNALTGADVYV-ADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDLPHP 257
Query: 343 LLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKV 402
L+E FK TLE+ AD+++HVVD S+P+ L++ + V++ L + +E +++V NK+
Sbjct: 258 LVEAFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI---PIILVLNKI 314
Query: 403 DAVPPGERVTEEYDL-----LISATRGTGLAQLKEKVQDMI 438
D + E + E ISA G GL L+E++ +++
Sbjct: 315 DLLEDEEILAELERGSPNPVFISAKTGEGLDLLRERIIELL 355
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 213 bits (544), Expect = 1e-66
Identities = 83/196 (42%), Positives = 120/196 (61%), Gaps = 9/196 (4%)
Query: 248 EREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQ 307
ER KL+K L K+K QRE+ R +++R PTVA+VGYTN GK+TL ALT D L +Q
Sbjct: 13 ERIAKLRKELEKVKKQRELQRARRKRSGVPTVALVGYTNAGKSTLFNALTGADVLA-EDQ 71
Query: 308 LFATLDVTTHEGMLPNRLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVVDVS 367
LFATLD TT LP +L DT+GFI ++P L+E F+ TLE+ AD+++HVVD S
Sbjct: 72 LFATLDPTTRRIKLPGGREVLLTDTVGFIRDLPHQLVEAFRSTLEEVAEADLLLHVVDAS 131
Query: 368 NPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYD-----LLISAT 422
+PD +Q + V+E L+ L ++ +++V NK+D + E + ISA
Sbjct: 132 DPDREEQIETVEEVLKELGADDI---PIILVLNKIDLLDDEELEERLRAGRPDAVFISAK 188
Query: 423 RGTGLAQLKEKVQDMI 438
G GL LKE +++++
Sbjct: 189 TGEGLDLLKEAIEELL 204
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 130 bits (330), Expect = 2e-33
Identities = 97/338 (28%), Positives = 167/338 (49%), Gaps = 29/338 (8%)
Query: 111 LAESKALVSS--IQGWRVVDSTIISLLSFDKKSFFGKGNLELLKRQVRGDARVTAVFVSV 168
L E ++LVSS ++ +V+ + + K F G+G + V+ +F
Sbjct: 27 LQEFESLVSSAGVEALQVITGSRKAPHP---KYFVGEGKAVEIAEAVKATGASVVLFDHA 83
Query: 169 DVLKLHQQKMLQDLFQVPVFDRYMIVIQIFKAHAKTREARLQIAIAELPYLWTRYRTIED 228
L Q++ L+ L + V DR +++ IF A+T E +LQ+ +A+L +L TR +
Sbjct: 84 --LSPAQERNLERLCECRVIDRTGLILDIFAQRARTHEGKLQVELAQLRHLATRL--VRG 139
Query: 229 ATNMNITKGF----------LDSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPT 278
T++ KG L++ R +L R ++ L +++ QRE R + + PT
Sbjct: 140 WTHLERQKGGIGLRGPGETQLETDRRLLRNRIVQILSRLERVEKQREQGRRARIKADVPT 199
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISN 338
V++VGYTN GK+TL +T+ +QLFATLD T + + + DT+GFI +
Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAA-DQLFATLDPTLRRIDVADVGETVLADTVGFIRH 258
Query: 339 IPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVV 398
+P L+ FK TL++ A +++HVVD ++ + + V+ L+ ++ E L+V
Sbjct: 259 LPHDLVAAFKATLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEI---PTLLV 315
Query: 399 GNKVD----AVPPGERVTEEYDLLI--SATRGTGLAQL 430
NK+D P +R E + + SA G G+ L
Sbjct: 316 MNKIDMLDDFEPRIDRDEENKPIRVWLSAQTGAGIPLL 353
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 80.4 bits (199), Expect = 2e-18
Identities = 42/125 (33%), Positives = 58/125 (46%), Gaps = 9/125 (7%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFIS 337
VA+VG N GK+TLI ALT + + T D G+L +I+ VDT G I
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPI--LGVLGLGRQIILVDTPGLIE 58
Query: 338 NIPTTL-LEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVL 396
+E F LE AD+I+ VVD S DE + ELE+ + ++
Sbjct: 59 GASEGKGVEGFNRFLEAIREADLILLVVDASEG-----LTEDDEEILE-ELEKLPKKPII 112
Query: 397 VVGNK 401
+V NK
Sbjct: 113 LVLNK 117
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 70.9 bits (174), Expect = 2e-14
Identities = 39/167 (23%), Positives = 68/167 (40%), Gaps = 20/167 (11%)
Query: 280 AVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHE-GMLPNRLRILYVDTIGFISN 338
VVG GK++L+ AL + + T D + + +++++ VDT G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 339 IPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVV 398
E ++ L AD+I+ VVD ++ + + D L L K +++V
Sbjct: 61 GGLGREELARLLLRG---ADLILLVVDSTDRESEE-----DAKLLILRRLRKEGIPIILV 112
Query: 399 GNKVDAVPPGERVTEEYDLL-----------ISATRGTGLAQLKEKV 434
GNK+D + E +SA G G+ +L EK+
Sbjct: 113 GNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKL 159
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 66.1 bits (162), Expect = 8e-13
Identities = 38/166 (22%), Positives = 65/166 (39%), Gaps = 20/166 (12%)
Query: 280 AVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISNI 339
A+ G N GK++L+ AL + + T D E L ++ +DT G
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 340 PTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVG 399
+ + A AD+++ VVD +E + L E+ +LV+
Sbjct: 61 GLGRER-VEEARQVADRADLVLLVVDSDLTPV-------EEEAKLGLLRERGKPVLLVL- 111
Query: 400 NKVDAVPPGERVTEEYDLL-----------ISATRGTGLAQLKEKV 434
NK+D VP E + +SA G G+ +L++K+
Sbjct: 112 NKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKI 157
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 58.0 bits (141), Expect = 4e-09
Identities = 49/177 (27%), Positives = 72/177 (40%), Gaps = 37/177 (20%)
Query: 276 FPTVAVVGYTNCGKTTLI-------KALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRIL 328
P VA+VG N GK+TL A+ D V R++++ + E +L
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFIL------- 55
Query: 329 YVDTIGFISNIPTTLLEPFKVTLEDAML-ADIIIHVVDVS---NPDYLQQKQHVDETL-Q 383
+DT G L E + A+ AD+I+ VVD P DE + +
Sbjct: 56 -IDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPA--------DEEIAK 106
Query: 384 HLELEEKILEHVLVVGNKVDAVPPGERVTEEYDL------LISATRGTGLAQLKEKV 434
L +K V++V NK+D + E E Y L ISA G G+ L + V
Sbjct: 107 ILRRSKK---PVILVVNKIDNLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLDAV 160
Score = 36.0 bits (84), Expect = 0.038
Identities = 45/178 (25%), Positives = 77/178 (43%), Gaps = 30/178 (16%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLD-VTTHEGMLPNRLRILYVDTIGF-- 335
+A++G N GK++LI A+ ++ ++ + T D + + + + +DT G
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIE--FERDGRKYVLIDTAGIRR 238
Query: 336 ISNIPTTLLEPFKV--TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE 393
I T +E + V TL+ AD+++ V+D + Q D + L E
Sbjct: 239 KGKI-TESVEKYSVARTLKAIERADVVLLVIDATEGISEQ-----DLRIAGLIEEAGR-G 291
Query: 394 HVLVVGNKVDAVPPGERVTEEYD---------------LLISATRGTGLAQLKEKVQD 436
V+VV NK D V E EE+ + ISA G GL +L E +++
Sbjct: 292 IVIVV-NKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKE 348
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 55.6 bits (135), Expect = 6e-09
Identities = 55/187 (29%), Positives = 75/187 (40%), Gaps = 54/187 (28%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDV-----TT---HEGML-PNRLRIL 328
T+A+VG N GKTTL ALT A V T EG I
Sbjct: 2 TIALVGNPNVGKTTLFNALTG-----------ARQHVGNWPGVTVEKKEGTFKYKGYEIE 50
Query: 329 YVDTIGFISNIPTTLLEPFKVT----LEDAMLADIIIHVVDVSNPD---YLQQKQHVDET 381
VD G S P + E KV LE+ D+II+VVD +N + YL T
Sbjct: 51 IVDLPGTYSLSPYSEEE--KVARDYLLEEK--PDVIINVVDATNLERNLYL--------T 98
Query: 382 LQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDLL----------ISATRGTGLAQLK 431
LQ LEL V+V N +D + + + L SA +G G+ +LK
Sbjct: 99 LQLLELGIP----VVVALNMMDEA-EKKGIKIDIKKLSELLGVPVVPTSARKGEGIDELK 153
Query: 432 EKVQDMI 438
+ + ++
Sbjct: 154 DAIIEVA 160
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 54.6 bits (132), Expect = 7e-08
Identities = 56/192 (29%), Positives = 79/192 (41%), Gaps = 38/192 (19%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLP-NRLRILYVDT 332
K TVA+VG N GKTTL ALT + V N + + V EG L I VD
Sbjct: 1 MKKLTVALVGNPNVGKTTLFNALTGANQKVG-N--WPGVTVEKKEGKLKYKGHEIEIVDL 57
Query: 333 IGFISNIPTTLLEPFKVT----LEDAMLADIIIHVVDVSNPD---YLQQKQHVDETLQHL 385
G S + E KV LE D+I++VVD +N + YL TLQ L
Sbjct: 58 PGTYSLTAYSEDE--KVARDFLLEGK--PDLIVNVVDATNLERNLYL--------TLQLL 105
Query: 386 ELEEKILEHVLVVGNKVDAVPPGERVTEEYDLL----------ISATRGTGLAQLKEKVQ 435
EL +++ N +D + + + L A RG GL +LK +
Sbjct: 106 ELGIP----MILALNMID-EAKKRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAII 160
Query: 436 DMILKATGRKNI 447
++ T + +
Sbjct: 161 ELAESKTTPREV 172
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 52.4 bits (127), Expect = 3e-07
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 357 ADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPP--GERVTEE 414
AD+++ V+D S P + + LEE + V+VV NK D E +
Sbjct: 295 ADLVLLVLDASEPLTEEDDE---------ILEELKDKPVIVVLNKADLTGEIDLEEENGK 345
Query: 415 YDLLISATRGTGLAQLKEKVQDMILK 440
+ ISA G G+ +L+E ++++
Sbjct: 346 PVIRISAKTGEGIDELREAIKELAFG 371
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 47.3 bits (114), Expect = 7e-06
Identities = 49/193 (25%), Positives = 76/193 (39%), Gaps = 65/193 (33%)
Query: 279 VAVVGYTNCGKTTLIKALTDDD-SLV-PRNQLFATLDVTTHEGMLPNRLR---------I 327
VA+VG N GK+TL+ AL S+V P+ Q TT +R+R I
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQ-------TTR-----HRIRGIVTEDDAQI 55
Query: 328 LYVDTIGFISNIPTTLLEPFKV-----TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETL 382
++VDT G + P L +L+D D+++ VVD +
Sbjct: 56 IFVDTPGI--HKPKRALNRAMNKAAWSSLKDV---DLVLFVVDADEK--------IGPG- 101
Query: 383 QHLELEEKILEH-------VLVVGNKVDAVPPGERVTEEYDLL-----------ISATRG 424
+E ILE V++V NK+D V E + + L ISA +G
Sbjct: 102 -----DEFILEKLKKVKTPVILVLNKIDLVKDKEELLPLLEELSELMDFAEIVPISALKG 156
Query: 425 TGLAQLKEKVQDM 437
+ +L + +
Sbjct: 157 DNVDELLDVIAKY 169
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 44.8 bits (107), Expect = 1e-05
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 12/92 (13%)
Query: 350 TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGE 409
E AD+++ VVD S ++ +K V+VV NK D + E
Sbjct: 76 AREAIEEADLVLLVVDASEG------LDEEDLEILELPAKK---PVIVVLNKSDLLSDAE 126
Query: 410 RVTEEYD---LLISATRGTGLAQLKEKVQDMI 438
++E + ISA G G+ +LKE + ++
Sbjct: 127 GISELNGKPIIAISAKTGEGIDELKEALLELA 158
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 47.2 bits (113), Expect = 1e-05
Identities = 52/224 (23%), Positives = 99/224 (44%), Gaps = 40/224 (17%)
Query: 244 MVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDDD--- 300
+VL + +KL++ + +L + K ++ V ++G N GK++L+ AL D
Sbjct: 185 LVLEKIREKLEELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGRDRAI 244
Query: 301 -SLVP---RNQLFATLDVTTHEGMLPNRLRILYVDTIG------FISNIPTTLLEPFKVT 350
+ + R+ + +++ G+ +R+ VDT G + I +E K
Sbjct: 245 VTDIAGTTRDVIEEDINL---NGIP---VRL--VDTAGIRETDDVVERIG---IERAKKA 293
Query: 351 LEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGER 410
+E+A D+++ V+D S P + ++ L ++ I+ VV NK D V E
Sbjct: 294 IEEA---DLVLFVLDASQPLDKEDLALIE----LLPKKKPII----VVLNKADLVSKIEL 342
Query: 411 VTEEY-----DLLISATRGTGLAQLKEKVQDMILKATGRKNITM 449
+E+ + ISA G GL L+E ++ + K G +
Sbjct: 343 ESEKLANGDAIISISAKTGEGLDALREAIKQLFGKGLGNQEGLF 386
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 46.0 bits (110), Expect = 2e-05
Identities = 51/182 (28%), Positives = 76/182 (41%), Gaps = 43/182 (23%)
Query: 279 VAVVGYTNCGKTTLIKALTDDD-SLV-PRNQLFATLD-----VTTHEGMLPNRLRILYVD 331
VA++G N GK+TL+ AL S+V P+ Q T + VTT +I++VD
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQ--TTRNRIRGIVTTDNA------QIIFVD 60
Query: 332 TIGFISNIPTTLLEPFKV-----TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLE 386
T G + P L L+D D+I+ VVD DE + LE
Sbjct: 61 TPGI--HKPKHALGELMNKAARSALKD---VDLILFVVDADEG----WGPG-DEFI--LE 108
Query: 387 LEEKILEHVLVVGNKVDAVPPGERV---TEEYDLL--------ISATRGTGLAQLKEKVQ 435
+K V++V NK+D V P + L ISA +G + L E ++
Sbjct: 109 QLKKTKTPVILVVNKIDKVKPKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIK 168
Query: 436 DM 437
+
Sbjct: 169 EY 170
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 44.4 bits (106), Expect = 2e-05
Identities = 51/181 (28%), Positives = 74/181 (40%), Gaps = 48/181 (26%)
Query: 280 AVVGYTNCGKTTLIKALTDDDSLVPRNQL---FATLDVTTHEGMLPNRLRILY-VDTIGF 335
A+VG N GKTTL ALT Q + + V EG + + VD G
Sbjct: 1 ALVGNPNVGKTTLFNALTGA------RQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGT 54
Query: 336 ISNIPTTLLEPFKVT----LEDAMLADIIIHVVDVSNPD---YLQQKQHVDETLQHLELE 388
S P + E KV L + D+I++VVD +N + YL TLQ LEL
Sbjct: 55 YSLTPYSEDE--KVARDFLLGEE--PDLIVNVVDATNLERNLYL--------TLQLLELG 102
Query: 389 EKILEHVLVVGNKVDAVPPGER--VTEEYDLL----------ISATRGTGLAQLKEKVQD 436
V+V N +D E+ + + D L SA +G G+ +L + +
Sbjct: 103 LP----VVVALNMIDEA---EKRGIKIDLDKLSELLGVPVVPTSARKGEGIDELLDAIAK 155
Query: 437 M 437
+
Sbjct: 156 L 156
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 44.4 bits (106), Expect = 3e-05
Identities = 50/187 (26%), Positives = 78/187 (41%), Gaps = 43/187 (22%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKALTDDD----SLVP---RNQLFATLDVTTHEGMLPNRLR 326
K VA++G N GK+TL+ AL S P RN++ + T + +
Sbjct: 1 FKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---RGIYTDDDA-----Q 52
Query: 327 ILYVDTIGFISNIPTTLLEPFKV-----TLEDAMLADIIIHVVDVSNPDYLQQKQHVDET 381
I++VDT G P L V L+D D+++ VVD S DE
Sbjct: 53 IIFVDTPGIHK--PKKKLGERMVKAAWSALKDV---DLVLFVVDASEW-----IGEGDEF 102
Query: 382 LQHLELEEKILEHVLVVGNKVDAVPPGERV---TEEYDLL--------ISATRGTGLAQL 430
+ L L++ +LV+ NK+D V E + E+ L ISA +G + +L
Sbjct: 103 ILEL-LKKSKTPVILVL-NKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDEL 160
Query: 431 KEKVQDM 437
E + +
Sbjct: 161 LEYIVEY 167
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 44.2 bits (104), Expect = 6e-05
Identities = 27/127 (21%), Positives = 49/127 (38%), Gaps = 14/127 (11%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISN 338
+ V+G GKTTL+ L D+ LD +++ DT G
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEE- 66
Query: 339 IPTTLLEPFKVTLEDAML-ADIIIHVVDVSNPDYLQQ-KQHVDETLQHLELEEKILEHVL 396
++ + A+ I+ V D + + + + E L+ L ++ +L
Sbjct: 67 --------YRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDV---PIL 115
Query: 397 VVGNKVD 403
+VGNK+D
Sbjct: 116 LVGNKID 122
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 44.7 bits (107), Expect = 8e-05
Identities = 47/184 (25%), Positives = 69/184 (37%), Gaps = 54/184 (29%)
Query: 277 PTVAVVGYTNCGKTTLI-------KALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILY 329
P VA+VG N GK+TL A+ D V R++++ + E +L
Sbjct: 2 PVVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFIL-------- 53
Query: 330 VDTIGFISNIPTTLLEPFKVTLEDAML---------ADIIIHVVDVSNPDYLQQKQHV-- 378
+DT G EP E + AD+I+ VVD + +
Sbjct: 54 IDTGGI---------EPDDDGFEKQIREQAELAIEEADVILFVVDG--------RAGLTP 96
Query: 379 -DETL-QHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDL------LISATRGTGLAQL 430
DE + + L K V++V NKVD E Y L ISA G G+ L
Sbjct: 97 ADEEIAKILRKSNK---PVILVVNKVDGPDEEADAYEFYSLGLGEPYPISAEHGRGIGDL 153
Query: 431 KEKV 434
+ +
Sbjct: 154 LDAI 157
Score = 30.8 bits (71), Expect = 1.9
Identities = 49/205 (23%), Positives = 83/205 (40%), Gaps = 62/205 (30%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDV--TT---------HEGMLPNRLRI 327
+A++G N GK++LI AL ++ ++ D+ TT +G +
Sbjct: 176 IAIIGRPNVGKSSLINALLGEERVI-------VSDIAGTTRDSIDTPFERDGQ-----KY 223
Query: 328 LYVDTIGFI---SNIPTTLLEPFKV-----TLEDAMLADIIIHVVDVSNPDYLQQKQHVD 379
+DT G I + T +E + V +E A D+++ V+D + +Q D
Sbjct: 224 TLIDTAG-IRRKGKV-TEGVEKYSVIRTLKAIERA---DVVLLVIDATEG-ITEQ----D 273
Query: 380 ETLQHLELEEKILEHVLVVGNKVDAVPPG--ERVTEEYD-----------LLISATRGTG 426
+ L LE V+VV NK D V E +E + ISA G G
Sbjct: 274 LRIAGLALEAG-RALVIVV-NKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQG 331
Query: 427 LAQLKEKVQDMILKATGRKNITMRV 451
+ +K+ + I +A +N R+
Sbjct: 332 V----DKLLEAIDEA--YENANRRI 350
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 42.0 bits (100), Expect = 1e-04
Identities = 43/185 (23%), Positives = 72/185 (38%), Gaps = 54/185 (29%)
Query: 280 AVVGYTNCGKTTLI-------KALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDT 332
A+VG N GK+TL A+ D V R++ + + E +L +DT
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFIL--------IDT 52
Query: 333 IGFISNIPTTLLEPFKVTLEDAML---------ADIIIHVVD----VSNPDYLQQKQHVD 379
G EP + + AD+I+ VVD ++ D +
Sbjct: 53 GGI---------EPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADE-----EIA 98
Query: 380 ETLQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDL------LISATRGTGLAQLKEK 433
+ L+ K + V++V NK+D + E E Y L ISA G G+ L +
Sbjct: 99 KYLR------KSKKPVILVVNKIDNIKEEEEAAEFYSLGFGEPIPISAEHGRGIGDLLDA 152
Query: 434 VQDMI 438
+ +++
Sbjct: 153 ILELL 157
>gnl|CDD|234274 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
[Protein synthesis, Other].
Length = 429
Score = 44.0 bits (105), Expect = 1e-04
Identities = 43/183 (23%), Positives = 65/183 (35%), Gaps = 54/183 (29%)
Query: 278 TVAVVGYTNCGKTTLI-------KALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYV 330
VA+VG N GK+TL A+ D V R D + R + +
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTR-------DRKYGDAEWGGR-EFILI 52
Query: 331 DTIGFISNIPTTLLEPFKVTLEDAML---------ADIIIHVVD----VSNPDYLQQKQH 377
DT G E L+ + AD+I+ VVD ++ D
Sbjct: 53 DTGGI---------EEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDE-----E 98
Query: 378 VDETLQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDL------LISATRGTGLAQLK 431
+ + L+ K + V++V NK+D E Y L ISA G G+ L
Sbjct: 99 IAKWLR------KSGKPVILVANKIDGKKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLL 152
Query: 432 EKV 434
+ +
Sbjct: 153 DAI 155
Score = 33.6 bits (78), Expect = 0.21
Identities = 43/183 (23%), Positives = 75/183 (40%), Gaps = 43/183 (23%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVT----THEGMLPNRLRILYVDTIG 334
+A++G N GK+TL+ AL ++ ++ + T D G + +DT G
Sbjct: 175 IAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNG-----KKYTLIDTAG 229
Query: 335 FI---SNIPTTLLEPFKV--TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEE 389
I + T +E + V TL+ AD+++ V+D + + + E Q L +
Sbjct: 230 -IRRKGKV-TEGVEKYSVLRTLKAIERADVVLLVLDAT--------EGITE--QDLRIAG 277
Query: 390 KILEH---VLVVGNKVDAVPPGERVTEEYDLL--------------ISATRGTGLAQLKE 432
LE +++V NK D V + E L ISA G G+ +L +
Sbjct: 278 LALEAGKALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLD 337
Query: 433 KVQ 435
+
Sbjct: 338 AID 340
>gnl|CDD|232975 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
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 44.0 bits (104), Expect = 1e-04
Identities = 61/185 (32%), Positives = 82/185 (44%), Gaps = 38/185 (20%)
Query: 283 GYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLR-ILYVDTIGFISNIPT 341
G N GK+TL ALT + V + + V EG L + I VD G S
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGN---WPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTF 57
Query: 342 TLLEPFKVTLEDAML---ADIIIHVVDVSNPD---YLQQKQHVDETLQHLELEEKILEHV 395
+L E +V D +L D++++VVD SN + YL TLQ LEL +
Sbjct: 58 SLEE--EVA-RDYLLNEKPDLVVNVVDASNLERNLYL--------TLQLLELGIPM---- 102
Query: 396 LVVGNKVD-AVPPGERVTEEY--DLL------ISATRGTGLAQLKEKVQDMILKATGRKN 446
++ N VD A G R+ EE + L SAT G G+ +LK D I KA G K
Sbjct: 103 ILALNLVDEAEKKGIRIDEEKLEERLGVPVVPTSATEGRGIERLK----DAIRKAIGLKE 158
Query: 447 ITMRV 451
+ R
Sbjct: 159 LKKRA 163
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 41.2 bits (97), Expect = 3e-04
Identities = 33/168 (19%), Positives = 68/168 (40%), Gaps = 14/168 (8%)
Query: 280 AVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISNI 339
+VG N GK+TL+ ALT + + F TL+ + + I +D G +
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEI-ASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGA 59
Query: 340 PTTLLEPFKVTLEDAMLADIIIHVVDVSNPDY---LQQKQHVDETLQHLELEEKILEHVL 396
++ L +D+I+HV+D S L+ ++ ++E + + +
Sbjct: 60 SEGRGLGEQI-LAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEV-SGSFLFLKNKPEM 117
Query: 397 VVGNKVDAV-------PPGERVTEEYDLL-ISATRGTGLAQLKEKVQD 436
+V NK+D +++ ++ SA GL ++ ++
Sbjct: 118 IVANKIDMASENNLKRLKLDKLKRGIPVVPTSALTRLGLDRVIRTIRK 165
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 40.5 bits (96), Expect = 5e-04
Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 18/94 (19%)
Query: 359 IIIHVVDVSNP-DYLQQKQHVDETLQH-LELEEKILEH--VLVVGNKVDAVPPGERVTEE 414
+++HV+D+S D ++ ET+++ LE L +VV NK+D + ER +
Sbjct: 81 VLLHVIDLSGEDDPVEDY----ETIRNELEAYNPGLAEKPRIVVLNKIDLLDAEERFEKL 136
Query: 415 YDLL----------ISATRGTGLAQLKEKVQDMI 438
+LL ISA G GL +L +K+ ++
Sbjct: 137 KELLKELKGKKVFPISALTGEGLDELLKKLAKLL 170
Score = 28.5 bits (65), Expect = 5.0
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
V +VG N GK+TL+ A++
Sbjct: 3 VGLVGLPNAGKSTLLSAIS 21
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 39.9 bits (94), Expect = 9e-04
Identities = 44/202 (21%), Positives = 74/202 (36%), Gaps = 60/202 (29%)
Query: 266 MMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRL 325
++ K + ++G N GKTT++ L + VTT
Sbjct: 4 ILAKLFGWNKEMRILILGLDNAGKTTILYKLKLGEI------------VTT--------- 42
Query: 326 RILYVDTIGFISNIPTTLLEPFKVTLEDA--------------MLADIIIHVVDVSNPDY 371
+ TIGF N+ T + K T+ D D +I VVD ++ D
Sbjct: 43 ----IPTIGF--NVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDR 96
Query: 372 LQQ-KQHVDETLQHLELEEKILEHVLVVGNKVD---AVPPGERVTEEYDLL--------- 418
+++ K+ + L EL + +L++ NK D A+ E + E L
Sbjct: 97 IEEAKEELHALLNEEELADA---PLLILANKQDLPGAMSEAE-IRELLGLHELKDRPWEI 152
Query: 419 --ISATRGTGLAQLKEKVQDMI 438
SA G GL + + + + I
Sbjct: 153 QGCSAVTGEGLDEGLDWLSNYI 174
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 39.6 bits (93), Expect = 0.001
Identities = 38/173 (21%), Positives = 56/173 (32%), Gaps = 36/173 (20%)
Query: 278 TVAVVGYTNCGKTTLIKALTDD--DSLVPRNQLFATLDVTTHE------------GMLPN 323
V V+G+ + GKTTL +L + LD E
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 324 RLRILYVDTIG---FISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDE 380
+ RI ++DT G F L AD + VVD + Q ++H+
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLA-----------QADGALLVVDANEGVEPQTREHL-N 108
Query: 381 TLQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDLLISATRGTGLAQLKEK 433
L ++V NK+D V E E + + G LK K
Sbjct: 109 IALAGGL------PIIVAVNKIDRVGE-EDFDEVLREIKELLKLIGFTFLKGK 154
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 40.7 bits (96), Expect = 0.001
Identities = 41/134 (30%), Positives = 59/134 (44%), Gaps = 26/134 (19%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHE---GMLP-NRLRILYVDTI 333
TVA+VG+ + GK+TL+ LT+ S V A TT E GML +I +D
Sbjct: 65 TVALVGFPSVGKSTLLNKLTNTKSEV------ADYPFTTLEPVPGMLEYKGAQIQLLDLP 118
Query: 334 GFISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE 393
G I + + L A AD+II V+DV H ++ E+ LE
Sbjct: 119 GIIEGASSGRGRG-RQVLSVARNADLIIIVLDVFEDP------------HHRDIIERELE 165
Query: 394 HVLVVGNKVDAVPP 407
VG +++ PP
Sbjct: 166 D---VGIRLNKRPP 176
Score = 31.5 bits (72), Expect = 1.1
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 396 LVVGNKVDAVPPGE--RVTEEYD-LLISATRGTGLAQLKEKVQDM 437
L V NK+D E R+ + + + ISA +G L +LKE++ D+
Sbjct: 243 LYVVNKIDLPGLEELERLARKPNSVPISAKKGINLDELKERIWDV 287
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 39.0 bits (92), Expect = 0.002
Identities = 44/186 (23%), Positives = 78/186 (41%), Gaps = 43/186 (23%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVP------RNQLFATLDVTTHEGMLPNRLRILYVDT 332
VA G +N GK++LI ALT+ L R QL +V ++ R+ VD
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVG-------DKFRL--VDL 52
Query: 333 IGFI-SNIPTTLLEPFKVTLEDAMLAD-----IIIHVVDVSNPDYLQQKQHVDETLQHLE 386
G+ + + + E + +E+ L + ++ ++D + E L+ LE
Sbjct: 53 PGYGYAKVSKEVREKWGKLIEE-YLENRENLKGVVLLIDARHGP----TPIDLEMLEFLE 107
Query: 387 LEEKILEHVLVVGNKVDAVPPGER------VTEEYDL--------LISATRGTGLAQLKE 432
E I L+V K D + E + EE +L L S+ +GTG+ +L+
Sbjct: 108 -ELGI--PFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRA 164
Query: 433 KVQDMI 438
+ + +
Sbjct: 165 LIAEWL 170
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 38.7 bits (91), Expect = 0.002
Identities = 48/199 (24%), Positives = 75/199 (37%), Gaps = 68/199 (34%)
Query: 277 PTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDV-----TT---HEG-MLPNRLRI 327
T+ + GY N GK++L+ LT A +V TT G LR
Sbjct: 1 RTLVIAGYPNVGKSSLVNKLTR-----------AKPEVAPYPFTTKSLFVGHFDYKYLRW 49
Query: 328 LYVDTIGFISNIPTTLLE-PFKVTLED------------AMLADIIIHVVDVSNP-DYLQ 373
+DT G +L+ P LE+ A L ++ +D S Y
Sbjct: 50 QVIDTPG--------ILDRP----LEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSI 97
Query: 374 QKQHVDETLQHLELEEKILEH----VLVVGNKVDAVPP---------GERVTEEYDLLIS 420
++Q L L ++I V+VV NK+D + E+ EE + IS
Sbjct: 98 EEQ--------LSLFKEIKPLFNKPVIVVLNKIDLLTEEDLSEIEKELEKEGEEV-IKIS 148
Query: 421 ATRGTGLAQLKEKVQDMIL 439
G+ +LK K +++L
Sbjct: 149 TLTEEGVDELKNKACELLL 167
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 38.3 bits (90), Expect = 0.005
Identities = 57/224 (25%), Positives = 88/224 (39%), Gaps = 69/224 (30%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNR-LRILYVDTIGFI 336
VA+VG+ + GK+TL+ LT+ S V F TL T G++ + +I +D G I
Sbjct: 2 RVALVGFPSVGKSTLLSKLTNTKSEVA-AYEFTTL--TCVPGVMEYKGAKIQLLDLPGII 58
Query: 337 SNIPTTLLEPFKVTLEDAML--------------ADIIIHVVDVSNPDYLQQKQHVDETL 382
E A AD+I+ V+D + P+
Sbjct: 59 ---------------EGASDGKGRGRQVIAVARTADLILIVLDATKPE------------ 91
Query: 383 QHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDLLISATRGTGLAQLKEKVQDMILKAT 442
E+ E+ LE VG +++ PP + ++ I+ T L +L EK IL+
Sbjct: 92 GQREILERELEG---VGIRLNKKPPNVTIKKKKKGGINITSTVPLTKLDEKTVKAILR-- 146
Query: 443 GRKNITMRVRSGGSEYQWLMKHTAVSNIREDDTSAEHLLLDVVM 486
EY+ H A IRED T + L+DV+
Sbjct: 147 --------------EYKI---HNADVLIREDITVDD--LIDVIE 171
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 38.7 bits (91), Expect = 0.005
Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 20/133 (15%)
Query: 359 IIIHVVDVS---NPDYLQQKQHVDETLQ--HLELEEKILEHVLVVGNKVDAVPPGERVTE 413
+++HV+D+S D ++ Q + L+ +L EK +VV NK+D E + E
Sbjct: 240 VLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPR---IVVLNKIDLPLDEEELEE 296
Query: 414 -----------EYDLLISATRGTGLAQLKEKVQDMILKATG-RKNITMRVRSGGSEYQWL 461
E LISA GL +L + +++ + + E +
Sbjct: 297 LKKALAEALGWEVFYLISALTREGLDELLRALAELLEETKAEAEAAEAEELPVEVEVLYD 356
Query: 462 MKHTAVSNIREDD 474
+H +R+DD
Sbjct: 357 DEHEDFEIVRDDD 369
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 38.1 bits (90), Expect = 0.007
Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 15/95 (15%)
Query: 359 IIIHVVDVSNPDYLQQKQHVDETLQHL--ELEEKILEHVLVVGNKVDAVPPGERVTEEYD 416
+++H+VD+ D ++ + + L+ EL +K ++V NK+D + E +
Sbjct: 239 LLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKP---RILVLNKIDLLDEEEEREKRAA 295
Query: 417 L----------LISATRGTGLAQLKEKVQDMILKA 441
L LISA G GL +L + +++ +A
Sbjct: 296 LELAALGGPVFLISAVTGEGLDELLRALWELLEEA 330
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 37.3 bits (87), Expect = 0.012
Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 11/116 (9%)
Query: 235 TKGFLDSKRMVLMEREQKLKKALNKLKGQR--EMMRNKKQRQKFPTVAVVGYTNCGKTTL 292
KGF D+ R ++ L L E +R +K + + G T GKTT
Sbjct: 103 EKGFFDTVRAQSGTLSDNDEQLLELLDAGDIKEFLRLAIASRK--NIIISGGTGSGKTTF 160
Query: 293 IKALTDDDSLVPRNQLFATLDVTTHEGML--PNRLRILYVDTIGFISNI-PTTLLE 345
+K+L D +P+++ T++ T E L PN + + Y ++ + P LL+
Sbjct: 161 LKSLVD---EIPKDERIITIE-DTREIFLPHPNYVHLFYSKGGQGLAKVTPKDLLQ 212
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.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 [Unknown function, General].
Length = 162
Score = 36.2 bits (84), Expect = 0.014
Identities = 36/173 (20%), Positives = 62/173 (35%), Gaps = 26/173 (15%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLD-VTTHEGMLPNRLRILYVDTIGFIS 337
+ +VG N GK+TL+ L + + + T + VTT + +DT G
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQED 63
Query: 338 NIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEH--- 394
L ++ + DI+I V+DV LE + K + H
Sbjct: 64 YDAIRRLY-YRAVESSLRVFDIVILVLDVEEI---------------LEKQTKEIIHHAE 107
Query: 395 ----VLVVGNKVDAVPPGERVTEEYDLLISATRGTGLAQLKEKVQDMILKATG 443
+++VGNK+D ++ L + G + L + I A
Sbjct: 108 SGVPIILVGNKIDLR--DAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFK 158
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 36.1 bits (84), Expect = 0.018
Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 35/100 (35%)
Query: 360 IIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEH-----VLVVGNKVDAVPPGERVTE- 413
++HVVD+ + L + E V++VGNK+D +P +
Sbjct: 37 VVHVVDIFDFP--------------GSLIPGLAELIGAKPVILVGNKIDLLPKDVKPNRL 82
Query: 414 ---------------EYDLLISATRGTGLAQLKEKVQDMI 438
+ +L+SA +G G+ +L E+++ +
Sbjct: 83 KQWVKKRLKIGGLKIKDVILVSAKKGWGVEELIEEIKKLA 122
Score = 29.9 bits (68), Expect = 2.1
Identities = 16/48 (33%), Positives = 21/48 (43%)
Query: 270 KKQRQKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTH 317
KK + V VVG TN GK+TLI AL + + Q +
Sbjct: 119 KKLAKYRGDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSP 166
>gnl|CDD|219856 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 = 116
Score = 34.7 bits (80), Expect = 0.022
Identities = 28/127 (22%), Positives = 44/127 (34%), Gaps = 17/127 (13%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISN 338
V V+G GK++L+ L + F + L + DT
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGE--------FPPEPLEIQGDTLAVDTLEVDGDTGLLNIW 53
Query: 339 IPTTLLEPFKVTLEDAM-LADIIIHVVDVSNPDYLQQKQHVDET---LQHLELEEKILEH 394
E K M AD I+ V D+++ + L V L +L +
Sbjct: 54 DFGG-REELKFEHIIFMKWADAILLVYDLTDRESL---NEVSRLIAWLPNLRKLGGKIP- 108
Query: 395 VLVVGNK 401
V++VGNK
Sbjct: 109 VILVGNK 115
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 35.7 bits (83), Expect = 0.026
Identities = 48/205 (23%), Positives = 90/205 (43%), Gaps = 48/205 (23%)
Query: 267 MRNKKQ--RQKFPTVAVVGYTNCGKTTLIKALTDDDSLVP------RNQL--FATLDVTT 316
+ KQ P +A G +N GK++LI ALT+ +L R QL F +D
Sbjct: 13 APDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVD--- 69
Query: 317 HEGMLPNRLRILYVDTIGF-ISNIPTTLLEPFKVTLEDAML--ADI--IIHVVDVSNPDY 371
+ LR+ VD G+ + +P + E +K +E+ + A++ ++ ++D +P
Sbjct: 70 ------DELRL--VDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPP- 120
Query: 372 LQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGERVT---------------EEYD 416
+ + E L L + V+VV K D + ER +++
Sbjct: 121 KDLDREMIEFLLELGIP------VIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWV 174
Query: 417 LLISATRGTGLAQLKEKVQDMILKA 441
+L S+ + G+ +LK K+ + + +A
Sbjct: 175 VLFSSLKKKGIDELKAKILEWLKEA 199
>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 [Protein synthesis, Other].
Length = 270
Score = 36.2 bits (84), Expect = 0.029
Identities = 40/183 (21%), Positives = 64/183 (34%), Gaps = 51/183 (27%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLV--PRNQLFATLD-----VTTHEGMLPNRLRILYVD 331
VA++G N GK+TL+ L + P+ Q T + TT +I+++D
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQ--TTRNRISGIHTTGAS------QIIFID 54
Query: 332 TIGFISNIPTTLLEPFKVTLEDAML---------ADIIIHVVDVSNPDYLQQKQHVDETL 382
T GF E K +L M+ D+I+ VVD Q E +
Sbjct: 55 TPGF--------HEK-KHSLNRLMMKEARSAIGGVDLILFVVDS------DQWNGDGEFV 99
Query: 383 QHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDLL----------ISATRGTGLAQLKE 432
K V++ NK+D + + ISA G + L
Sbjct: 100 LTKLQNLKR--PVVLTRNKLDNKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAA 157
Query: 433 KVQ 435
++
Sbjct: 158 FIE 160
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 35.0 bits (81), Expect = 0.034
Identities = 23/104 (22%), Positives = 40/104 (38%), Gaps = 29/104 (27%)
Query: 357 ADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE---HVLVVGNKVDAVPPGERVTE 413
AD+++ VVD +P+ + + +LE LE +++V NK D VP V E
Sbjct: 12 ADVVLEVVDARDPELTRSR----------KLERMALELGKKLIIVLNKADLVP--REVLE 59
Query: 414 EYD----------LLISATRGTGLAQLKEKVQDMILKATGRKNI 447
++ + +SA G L+ I +
Sbjct: 60 KWKEVFESEGLPVVYVSARERLGTRILR----RTIKELAIDGKP 99
Score = 33.4 bits (77), Expect = 0.11
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 264 REMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALT 297
R ++ K V VVGY GK+++I AL
Sbjct: 87 RRTIKELAIDGKPVIVGVVGYPKVGKSSIINALK 120
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 34.3 bits (79), Expect = 0.040
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 277 PTVAVVGYTNCGKTTLIKAL 296
P V VVG + GKTTLI+ L
Sbjct: 1 PIVLVVGPKDSGKTTLIRKL 20
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 34.6 bits (80), Expect = 0.047
Identities = 34/143 (23%), Positives = 54/143 (37%), Gaps = 50/143 (34%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISN 338
+ +VG N GKTTL+ + E +P T+GF N
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQ---------------FSEDTIP---------TVGF--N 35
Query: 339 IPTTLLEPFKVTLEDAMLA----------------DIIIHVVDVSNPDYLQQKQHVDETL 382
+ VT++ L + I++VVD ++ + L+ + L
Sbjct: 36 MRKVTKG--NVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAK---NEL 90
Query: 383 QHLELEEKILEHV--LVVGNKVD 403
L LE+ LE + LV+GNK D
Sbjct: 91 HDL-LEKPSLEGIPLLVLGNKND 112
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 34.4 bits (80), Expect = 0.062
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 251 QKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALT 297
+KL K KL + E ++ K + VVG N GK+TLI L
Sbjct: 90 KKLLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLR 136
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 35.4 bits (82), Expect = 0.066
Identities = 54/190 (28%), Positives = 81/190 (42%), Gaps = 43/190 (22%)
Query: 277 PTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTT---HEGMLPNR-LRILYVDT 332
PT+ V GY N GK++L++ LT V A TT H G LRI +DT
Sbjct: 169 PTIVVAGYPNVGKSSLVRKLTTAKPEV------APYPFTTKGIHVGHFERGYLRIQVIDT 222
Query: 333 IGFISNIPTTLLE-PF--------KVTLEDAMLADIIIHVVDVSNPDY--LQQKQHVDET 381
G LL+ P + L LA +I+ + D S L+++ + E
Sbjct: 223 PG--------LLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLE- 273
Query: 382 LQHLELEEKILEHVLVVGNKVDAVPPGER---------VTEEYDLLISATRGTGLAQLKE 432
E++E ++VV NK+D + E L ISAT+G GL +L+E
Sbjct: 274 ----EIKELFKAPIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLRE 329
Query: 433 KVQDMILKAT 442
+V+ L+
Sbjct: 330 EVRKTALEPL 339
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 35.2 bits (82), Expect = 0.067
Identities = 36/125 (28%), Positives = 43/125 (34%), Gaps = 49/125 (39%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPR-NQLFATLDVTTHEGMLPNRLRILYVDT---- 332
T+ +VG N GK+T A T D V N F T+D PN + YV
Sbjct: 3 TIGLVGKPNVGKSTFFNAATLAD--VEIANYPFTTID--------PNV-GVAYVRVECPC 51
Query: 333 --------------IGFISNIPTTL-----LEP-----------FKVTLEDAMLADIIIH 362
I IP L L P F L+D AD +IH
Sbjct: 52 KELGVKCNPRNGKCIDGTRFIPVELIDVAGLVPGAHEGRGLGNQF---LDDLRQADALIH 108
Query: 363 VVDVS 367
VVD S
Sbjct: 109 VVDAS 113
>gnl|CDD|232980 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 [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 35.2 bits (81), Expect = 0.087
Identities = 45/203 (22%), Positives = 79/203 (38%), Gaps = 19/203 (9%)
Query: 239 LDSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTD 298
DS +L+ +LK LN K + + +A+VG N GK++L+ AL
Sbjct: 174 QDSLNQLLLSIIAELKDILNSYKLE--------KLDDGFKLAIVGSPNVGKSSLLNALLK 225
Query: 299 DDSLVPRNQLFATLDVTTHEGMLP-NRLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLA 357
D + + T DV EG N + I +DT G + + + + A
Sbjct: 226 QDRAIVSDIKGTTRDVV--EGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQA 283
Query: 358 DIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGERVTEEYDL 417
D++I+V+D S P + + + K + ++V NK+D +
Sbjct: 284 DLVIYVLDASQP--------LTKDDFLIIDLNKSKKPFILVLNKIDLKINSLEFFVSSKV 335
Query: 418 LISATRGTGLAQLKEKVQDMILK 440
L S+ ++K V + K
Sbjct: 336 LNSSNLSAKQLKIKALVDLLTQK 358
>gnl|CDD|233986 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 [Protein synthesis, Other].
Length = 329
Score = 34.7 bits (81), Expect = 0.092
Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 17/94 (18%)
Query: 359 IIIHVVDVSNPD----YLQQKQHVDETLQH-LELEEKILEHVLVVGNKVDAVPPGER--- 410
+++H++D+S D + +E ++ EL EK ++V+ NK+D + E
Sbjct: 238 VLLHLIDISPEDGSDPIEDYEIIRNELKKYSPELAEK--PRIVVL-NKIDLLDEEELEEL 294
Query: 411 ---VTEEYD---LLISATRGTGLAQLKEKVQDMI 438
+ E ISA G GL +L + +++
Sbjct: 295 LKELKEALGKPVFPISALTGEGLDELLYALAELL 328
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 33.5 bits (77), Expect = 0.094
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 246 LMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKAL 296
+ LK K + ++ K R V VVG N GK++ I AL
Sbjct: 66 ATNGQGILKLKAEITKQKLKLKYKKGIR-----VGVVGLPNVGKSSFINAL 111
Score = 33.1 bits (76), Expect = 0.11
Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 22/103 (21%)
Query: 358 DIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEH---VLVVGNKVDAVPPG--ERVT 412
D+++ VVD +P + ++E I E +++V NK D VP +
Sbjct: 1 DVVVEVVDARDPLSSRNP----------DIEVLINEKNKKLIMVLNKADLVPKEVLRKWV 50
Query: 413 EEY-------DLLISATRGTGLAQLKEKVQDMILKATGRKNIT 448
E ISAT G G+ +LK ++ LK +K I
Sbjct: 51 AELSELYGTKTFFISATNGQGILKLKAEITKQKLKLKYKKGIR 93
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 34.7 bits (81), Expect = 0.097
Identities = 29/97 (29%), Positives = 46/97 (47%), Gaps = 26/97 (26%)
Query: 359 IIIHVVDVS-----NP--DYLQQKQHVDETLQHLELE---EKILEHV-LVVGNKVDAVPP 407
+I+HV+D+S +P DY E + EL+ ++LE +VV NK+D
Sbjct: 239 VIVHVIDMSGSEGRDPIEDY--------EKINK-ELKLYNPRLLERPQIVVANKMDLPEA 289
Query: 408 GERVTEEYDLL------ISATRGTGLAQLKEKVQDMI 438
E + E + L ISA G GL +L V +++
Sbjct: 290 EENLEEFKEKLGPKVFPISALTGQGLDELLYAVAELL 326
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 33.9 bits (79), Expect = 0.10
Identities = 43/185 (23%), Positives = 83/185 (44%), Gaps = 44/185 (23%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVT----THEGMLPNRLRILYVDTIG 334
+A++G N GK++L+ AL ++ ++ + T D ++G + +DT G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDG-----QKYTLIDTAG 59
Query: 335 FI---SNIPTTLLEPFKV--TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEE 389
I + + E + V TL+ AD+++ V+D S + + E Q L +
Sbjct: 60 -IRKKGKVTEGI-EKYSVLRTLKAIERADVVLLVLDAS--------EGITE--QDLRIAG 107
Query: 390 KILEH---VLVVGNKVDAVPPGERVTEEYD---------------LLISATRGTGLAQLK 431
ILE +++V NK D V E+ +E++ + ISA G G+ +L
Sbjct: 108 LILEEGKALIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLF 167
Query: 432 EKVQD 436
+ +++
Sbjct: 168 DAIKE 172
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 33.9 bits (78), Expect = 0.11
Identities = 40/151 (26%), Positives = 68/151 (45%), Gaps = 34/151 (22%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLV-----PRNQL--------FATLDVTTHEGMLPN-- 323
V ++G+ + GKT+L KAL++ S P++Q F++ +V + + N
Sbjct: 3 VGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEN 62
Query: 324 ----RLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVD 379
+I VD G S I T + A + D+++ VVD Q Q
Sbjct: 63 PQIENYQITLVDCPGHASLIRTIIG--------GAQIIDLMLLVVDAKKG---IQTQ--- 108
Query: 380 ETLQHLELEEKILEHVLVVGNKVDAVPPGER 410
T + L + E + + ++VV NK+D +P ER
Sbjct: 109 -TAECLVIGELLCKPLIVVLNKIDLIPEEER 138
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 34.5 bits (79), Expect = 0.14
Identities = 19/60 (31%), Positives = 29/60 (48%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTI 333
+K PTV VVG + GKT+ L + + LF LD + + P + ++VD I
Sbjct: 97 EKGPTVMVVGGSQNGKTSFCFTLISYALKLGKKPLFTNLDPSQPGNIFPGAISAIHVDAI 156
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 33.9 bits (78), Expect = 0.17
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 251 QKLKKALNKLKGQR-EMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALT 297
+K++KAL KL ++ + ++ K ++ V VVGY N GK+TLI L
Sbjct: 106 KKIRKALEKLSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLL 153
Score = 30.0 bits (68), Expect = 2.8
Identities = 25/113 (22%), Positives = 46/113 (40%), Gaps = 30/113 (26%)
Query: 357 ADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE-HVLVVGNKVDAVPPGERVTEEY 415
D+++ VVD +P ++ ELE + E L+V NK D P VT+++
Sbjct: 35 VDVVVEVVDARDP----------LGTRNPELERIVKEKPKLLVLNKADLAPK--EVTKKW 82
Query: 416 D-----------LLISATRGTGLAQLKEKVQDM------ILKATGRKNITMRV 451
+ +SA G ++++ ++ + LK G +RV
Sbjct: 83 KKYFKKEEGIKPIFVSAKSRQGGKKIRKALEKLSEEKIKRLKKKGLLKRKIRV 135
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 33.9 bits (78), Expect = 0.17
Identities = 50/187 (26%), Positives = 76/187 (40%), Gaps = 43/187 (22%)
Query: 267 MRNKKQRQKFPTVAVVGYTNCGKTTLIKAL----TDDDSL-VPRN--------------- 306
M + K Q + +VG+ + GKTTL KAL TD S + R
Sbjct: 1 MADPKHIQPEVNIGMVGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKC 60
Query: 307 -QLFATLDVTTHE-----GMLPNRLR-ILYVDTIGFISNIPTTLLEPFKVTLEDAMLADI 359
+ + TT G +R + +VD G TL+ L A L D
Sbjct: 61 PECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGH-----ETLM---ATMLSGAALMDG 112
Query: 360 IIHVVDVSNPDYLQQKQHVDETLQHLELEEKI-LEHVLVVGNKVDAVPPGERVTEEYDLL 418
+ V+ + P Q Q T +HL E I ++++++V NK+D V ER E Y+ +
Sbjct: 113 ALLVIAANEP--CPQPQ----TREHLMALEIIGIKNIIIVQNKIDLVSR-ERALENYEQI 165
Query: 419 ISATRGT 425
+GT
Sbjct: 166 KEFVKGT 172
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the form
of molybdenum cofactor (Moco) which is associated with
the metabolism of nitrogen, carbon and sulfur by redox
active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe and
mog. The mob locus contains mobA and mobB genes. MobB
catalyzes the attachment of the guanine dinucleotide to
molybdopterin.
Length = 159
Score = 32.6 bits (75), Expect = 0.19
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 277 PTVAVVGYTNCGKTTLIKALTD 298
+ VGY+ GKTTL++ L
Sbjct: 2 KVIGFVGYSGSGKTTLLEKLIP 23
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 32.3 bits (74), Expect = 0.25
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 358 DIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVP 406
D+II V+D +P + K HV++ L+ +EK +H++ V NK D VP
Sbjct: 10 DVIIQVLDARDPMGTRCK-HVEKYLR----KEKPHKHLIFVLNKCDLVP 53
>gnl|CDD|205348 pfam13167, GTP-bdg_N, GTP-binding GTPase N-terminal. This is the
N-terminal region of GTP-binding HflX-like proteins. The
full-length members bind and interact with the 50S
ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP.
This N-terminal region is necessary for stability of the
whole protein.
Length = 95
Score = 30.9 bits (70), Expect = 0.36
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 137 FDKKSFFGKGNLELLKRQVRGDARVTAVFVSVDVLKLHQQKMLQDLFQVPVFDRYMIVIQ 196
D K + GKG ++ +K + + V V D L Q K L D V + DR ++++
Sbjct: 35 VDNKYYVGKGKIDEIKAFI--EFHDIDVVVVNDELTTAQSKSLNDNLGVKIIDRTQLILE 92
Query: 197 IF 198
IF
Sbjct: 93 IF 94
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 31.8 bits (73), Expect = 0.44
Identities = 54/188 (28%), Positives = 76/188 (40%), Gaps = 65/188 (34%)
Query: 279 VAVVGYTNCGKTTLIKALT--DDDSLVPRNQL--------FATLDVTTHEGMLPNRLRIL 328
+ G+ + GKTTLIKALT + D L P + FA LD LP+ R+
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIETDRL-PEEKKRGITIDLGFAYLD-------LPDGKRLG 53
Query: 329 YVDTIG---FISNIPTTLLEPFKVTLEDAMLA-----DIIIHVVDVSNPDYLQQKQHVDE 380
++D G F+ N MLA D ++ VV ++ + Q
Sbjct: 54 FIDVPGHEKFVKN----------------MLAGAGGIDAVLLVVA-ADEGIMPQ------ 90
Query: 381 TLQHLE-LEEKILEHVLVVGNKVDAVPPG--ERVTEE-------YDL------LISATRG 424
T +HLE LE ++ LVV K D V E V EE L +S+ G
Sbjct: 91 TREHLEILELLGIKKGLVVLTKADLVDEDRLELVEEEILELLAGTFLADAPIFPVSSVTG 150
Query: 425 TGLAQLKE 432
G+ +LK
Sbjct: 151 EGIEELKN 158
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 31.6 bits (72), Expect = 0.49
Identities = 45/193 (23%), Positives = 70/193 (36%), Gaps = 61/193 (31%)
Query: 265 EMMRNKKQRQKFPT-VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPN 323
++R K + + ++G N GKTT++K L +D +H
Sbjct: 3 SILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASED--------------ISHIT---- 44
Query: 324 RLRILYVDTIGFISNIPTTLLEPFKVTLEDA--------------MLADIIIHVVDVSNP 369
T GF NI + FK+ + D D++I+V+D ++
Sbjct: 45 -------PTQGF--NIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADR 95
Query: 370 DYLQQKQHVDETLQHLELEEKILE-HVLVVGNK---VDAVPPGERVTEEYDL-------- 417
++ + L L EEK+ VLV NK + A P E V E +L
Sbjct: 96 KRFEEAG---QELVELLEEEKLAGVPVLVFANKQDLLTAAPAEE-VAEALNLHDIRDRSW 151
Query: 418 ---LISATRGTGL 427
SA G GL
Sbjct: 152 HIQACSAKTGEGL 164
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 32.2 bits (74), Expect = 0.51
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
+A+VG++ GKTTL +AL
Sbjct: 1 NIALVGHSGSGKTTLAEAL 19
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.5 bits (74), Expect = 0.54
Identities = 43/180 (23%), Positives = 70/180 (38%), Gaps = 32/180 (17%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGF-- 335
VA+VG N GK+TL+ + V + T D +++ VDT G+
Sbjct: 277 VVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGT-DFKLVDTGGWEA 335
Query: 336 -ISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQH----VDETL-QHLELEE 389
+ I + + ++ + LAD ++ VVD Q DE + + L
Sbjct: 336 DVEGIDSAIASQAQIAVS---LADAVVFVVDG---------QVGLTSTDERIVRMLRRAG 383
Query: 390 KILEHVLVVGNKVDAVPPGERVTEEYDLL-------ISATRGTGLAQLKEKVQDMILKAT 442
K V++ NK+D E E+ L ISA G G+ L ++ D + A
Sbjct: 384 K---PVVLAVNKIDD-QASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDSLKVAE 439
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 31.7 bits (73), Expect = 0.56
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 279 VAVVGYTNCGKTTLIKAL 296
VA+VG GK++L+ AL
Sbjct: 34 VAIVGPVGSGKSSLLSAL 51
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 32.5 bits (75), Expect = 0.58
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 20/171 (11%)
Query: 277 PTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLD-VTTHEGMLPNRL-RILYVDTIG 334
+ + G N GK++LI ALT D + + T D V +LP L ++ +DT G
Sbjct: 7 LHIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVYKAMELLP--LGPVVLIDTAG 64
Query: 335 FISNIPTTLLE-PFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE 393
L E + T E D+ + VVD + + ++E L+E+ +
Sbjct: 65 LDDE--GELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEE------LKERKIP 116
Query: 394 HVLVVGNKVDAVPPG---ERVTEEYD---LLISATRGTGLAQLKEKVQDMI 438
+++V+ NK+D E++ +++ + +SA G G+ +LKE + +++
Sbjct: 117 YIVVI-NKIDLGEESAELEKLEKKFGLPPIFVSALTGEGIDELKEAIIELL 166
>gnl|CDD|236898 PRK11308, dppF, dipeptide transporter ATP-binding subunit;
Provisional.
Length = 327
Score = 32.2 bits (74), Expect = 0.60
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 278 TVAVVGYTNCGKTTLIKALT 297
T+AVVG + CGK+TL + LT
Sbjct: 43 TLAVVGESGCGKSTLARLLT 62
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 32.1 bits (74), Expect = 0.62
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 6/34 (17%)
Query: 266 MMRNKKQRQKFPTV--AVVGYTNCGKTTLIKALT 297
MM K Q P V +VG+ + GKTTL++ALT
Sbjct: 1 MMWEKVQ----PEVNIGMVGHVDHGKTTLVQALT 30
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 31.5 bits (72), Expect = 0.69
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHE 318
+ V+G+ + GKTTLI+ + +L R AT T HE
Sbjct: 4 IGVIGFKDSGKTTLIEKIL--KNLKERGYRVATAKHTHHE 41
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 31.2 bits (71), Expect = 0.70
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 275 KFPTVAVVGYTNCGKTTLIKAL 296
+ +VGY N GKTTLI+ L
Sbjct: 1 MMKILGIVGYKNSGKTTLIEKL 22
>gnl|CDD|213834 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 [Protein
synthesis, Other].
Length = 360
Score = 31.8 bits (73), Expect = 0.73
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 252 KLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKAL 296
K +++L + + RNKK V VVG TN GK++LI L
Sbjct: 136 KKGNGIDELLDKIKKARNKKD------VYVVGVTNVGKSSLINKL 174
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 31.8 bits (73), Expect = 0.84
Identities = 29/116 (25%), Positives = 41/116 (35%), Gaps = 35/116 (30%)
Query: 277 PTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYV-----D 331
+ +VG N GK+TL ALT + N F T++ PN ++YV D
Sbjct: 3 LKIGIVGLPNVGKSTLFNALTKAGA-EIANYPFCTIE--------PNV-GVVYVPDCRLD 52
Query: 332 TIGFISNI-PTTLLEPFKVT--------------LEDAMLADI-----IIHVVDVS 367
+ I P P + L + L +I IIHVV
Sbjct: 53 ELAEIVKCPPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCF 108
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 31.2 bits (71), Expect = 0.88
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 279 VAVVGYTNCGKTTLIKAL 296
V VVG GK+TLI++L
Sbjct: 42 VVVVGPPGVGKSTLIRSL 59
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 171
Score = 30.4 bits (70), Expect = 1.1
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 278 TVAVVGYTNCGKTTLIKALT 297
VA+VG + GK+TL+K L
Sbjct: 30 KVAIVGPSGSGKSTLLKLLL 49
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 30.6 bits (70), Expect = 1.2
Identities = 37/145 (25%), Positives = 55/145 (37%), Gaps = 27/145 (18%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDD----SLVPRNQLFATLDVTTHEGM-LPNRLRILYVDT 332
+AVVG + GK+TL+ AL ++ + P T V T L + + VDT
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLPTGVTP------TTAVITVLRYGLLKGVVL--VDT 53
Query: 333 IGFISNIP--TTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEK 390
G S I T + E F L AD +I V+ P + E L+ +
Sbjct: 54 PGLNSTIEHHTEITESF---LPR---ADAVIFVLSADQP----LTESEREFLKEILKWSG 103
Query: 391 ILEHVLVVGNKVDAVPPGERVTEEY 415
+ V NK+D + E
Sbjct: 104 K--KIFFVLNKIDLLSEEELEEVLE 126
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 30.7 bits (70), Expect = 1.2
Identities = 38/145 (26%), Positives = 58/145 (40%), Gaps = 43/145 (29%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKALTDD--DSLVPR-----------NQLFATLDVTTHEGM 320
+K + +G N GKTTL+ L DD VP N F T D+ HE
Sbjct: 17 KKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHE-- 74
Query: 321 LPNRLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQ-KQHVD 379
+ R ++ D P D I+ +VD ++P+ Q+ K+ +D
Sbjct: 75 ---QARRVWKDYF------PE---------------VDGIVFLVDAADPERFQESKEELD 110
Query: 380 ETLQHLELEEKILEHVLVVGNKVDA 404
L EL +L++GNK+D
Sbjct: 111 SLLNDEELANV---PILILGNKIDK 132
>gnl|CDD|213833 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 [Protein synthesis, Other].
Length = 276
Score = 30.9 bits (71), Expect = 1.2
Identities = 27/121 (22%), Positives = 44/121 (36%), Gaps = 45/121 (37%)
Query: 356 LADIIIHVVDV------SNPD---YLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVP 406
L D++I V+D NP K L+V NK D
Sbjct: 21 LVDVVIEVLDARIPLSSRNPMIDEIRGNKPR------------------LIVLNKADLAD 62
Query: 407 PGERVTEEYD----------LLISATRGTGLAQLKEKVQDMI------LKATGRKNITMR 450
P VT+++ L I+A +G G+ ++ + + ++ LKA G N +R
Sbjct: 63 P--AVTKQWLKYFEEKGIKALAINAKKGKGVKKIIKAAKKLLKEKNEKLKAKGLLNRPIR 120
Query: 451 V 451
Sbjct: 121 A 121
Score = 30.6 bits (70), Expect = 1.8
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 251 QKLKKALNKLKGQREMMRNKKQRQKFPT-VAVVGYTNCGKTTLIKAL 296
+K+ KA KL ++ K P +VG N GK+TLI L
Sbjct: 92 KKIIKAAKKLLKEKNEKLKAKGLLNRPIRAMIVGIPNVGKSTLINRL 138
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 30.6 bits (70), Expect = 1.2
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
TV VVGY N GK+++I +L
Sbjct: 118 TVGVVGYPNVGKSSVINSL 136
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 30.4 bits (69), Expect = 1.3
Identities = 39/141 (27%), Positives = 56/141 (39%), Gaps = 45/141 (31%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFIS 337
T+ VG N GKTTL+ AL Q V G P +LR
Sbjct: 1 TLLTVGLDNAGKTTLVSAL----------QGEIPKKVAPTVGFTPTKLR----------- 39
Query: 338 NIPTTLLEPFKVTLED----AMLADI----------IIHVVDVSNPDYLQQ-KQHVDETL 382
L+ ++V + D A I ++ VVD S+ D +Q+ K+ + E L
Sbjct: 40 ------LDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELL 93
Query: 383 QHLELEEKILEHVLVVGNKVD 403
QH + K +LV+ NK D
Sbjct: 94 QHPRVSGK---PILVLANKQD 111
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains each composed of six
transmembrane (TM) helices and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 229
Score = 30.7 bits (70), Expect = 1.3
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 278 TVAVVGYTNCGKTTLIKALT 297
TVA+VG T GKTTLI L
Sbjct: 31 TVAIVGPTGAGKTTLINLLM 50
>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 [Protein synthesis, Translation factors].
Length = 581
Score = 31.4 bits (71), Expect = 1.3
Identities = 46/180 (25%), Positives = 74/180 (41%), Gaps = 39/180 (21%)
Query: 279 VAVVGYTNCGKTTLIKALT--DDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIG-- 334
+A G+ + GKTTL+KALT D L + T+D+ LP+ R+ ++D G
Sbjct: 3 IATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDY-RLGFIDVPGHE 61
Query: 335 -FISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILE 393
FISN + D + VVD Q +H+ L+ +
Sbjct: 62 KFISNA-----------IAGGGGIDAALLVVDADEGVMTQTGEHL------AVLDLLGIP 104
Query: 394 HVLVVGNKVDAVPPGE---------RVTEEYDLL-------ISATRGTGLAQLKEKVQDM 437
H +VV K D V E ++ Y L SA G G+ +LK++++++
Sbjct: 105 HTIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNL 164
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 31.0 bits (71), Expect = 1.3
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLD 313
+FP V + G T GKT L++AL N LD
Sbjct: 139 AQFPLVVLGGNTGSGKTELLQAL--------ANAGAQVLD 170
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 30.3 bits (69), Expect = 1.5
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 12/92 (13%)
Query: 321 LPNRLRILYVDTIGFISNIPTTLLEPFKV-TLEDAMLADIIIHVVDVSNPDYLQQKQHVD 379
L RL +L+++T G P + + F L + D ++ VVDV+ +
Sbjct: 80 LKERLDLLFIETTGLAC--PAPVAQTFLSPELRSDLGLDGVVTVVDVA---------ETE 128
Query: 380 ETLQHLELEEKILEHVLVVGNKVDAVPPGERV 411
+ ++I L+V NK D P +
Sbjct: 129 GEDIPEKAPDQIAFADLIVINKTDLAPAVADL 160
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.0 bits (71), Expect = 1.5
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 386 ELEEKILEHVLVVGNKVDAVPPGER------VTEEYD-----LLISATRGTGLAQLKEKV 434
+L EK +V NK+D + E + E LISA G G+ +L +
Sbjct: 272 KLAEK---PRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDL 328
Query: 435 QDMI 438
I
Sbjct: 329 MTFI 332
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 30.9 bits (70), Expect = 1.6
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 277 PTVAVVGYTNCGKTTLIKAL 296
P + VVGY+ GKTTL++ L
Sbjct: 206 PLLGVVGYSGTGKTTLLEKL 225
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 30.6 bits (70), Expect = 1.8
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 16/59 (27%)
Query: 395 VLVVGNKVDAVPPG---ERVTE-------EYDL------LISATRGTGLAQLKEKVQDM 437
VL+VGNK D +P +V E L LISA +G G+ +L E ++
Sbjct: 99 VLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLEAIEKY 157
Score = 29.4 bits (67), Expect = 4.0
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 279 VAVVGYTNCGKTTLIKAL 296
V VVG TN GK+TLI +
Sbjct: 163 VYVVGVTNVGKSTLINRI 180
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 30.6 bits (70), Expect = 1.9
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 274 QKFPTVAVVGYTNCGKTTLIKAL 296
Q FP + + G T GKT L+ AL
Sbjct: 125 QPFPLIVLGGMTGSGKTELLHAL 147
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 29.7 bits (67), Expect = 2.1
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 280 AVVGYTNCGKTTLIKAL 296
+VG N GKTTLI+ L
Sbjct: 3 QIVGPKNSGKTTLIERL 19
>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 [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 29.3 bits (66), Expect = 2.1
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQ 307
+ +G CGKTTL +AL ++ L + Q
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEILYKKTQ 31
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 29.5 bits (67), Expect = 2.1
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
VA+VG GK+TL++A+
Sbjct: 28 VALVGPNGSGKSTLLRAIA 46
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 30.4 bits (69), Expect = 2.3
Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 24/133 (18%)
Query: 257 LNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLI-----KALTDDDSLVPRNQLFA- 310
++ L QR +KK F T+ VVG + GKTT I +L D+ +
Sbjct: 6 ISNLPNQRHRKLSKKGID-F-TIMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTS 63
Query: 311 -TLDVTTHEGMLPN---RLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVVDV 366
TL++ + L L + +DT GF I +++ + I+ +D
Sbjct: 64 PTLEIKITKAELEEDGFHLNLTVIDTPGFGDFI------------DNSKCWEPIVDYIDD 111
Query: 367 SNPDYLQQKQHVD 379
YL ++Q +
Sbjct: 112 QFDQYLDEEQKIK 124
>gnl|CDD|227601 COG5276, COG5276, Uncharacterized conserved protein [Function
unknown].
Length = 370
Score = 30.2 bits (68), Expect = 2.3
Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 13/86 (15%)
Query: 288 GKTTLIKALTDDDSLVPRNQLFATLDVT-THEGMLPNRLRILYVDTIGFISNIPTTLLEP 346
GK + + V + + A LD+T + I N +
Sbjct: 42 GKGVSAVDVRGAYAYVGQGFILAILDITNVSLQTHD--------VLLSVI-NARDLFAD- 91
Query: 347 FKVTLEDAMLADII--IHVVDVSNPD 370
+V+ E +AD + +VD+S PD
Sbjct: 92 VRVSEEYVYVADWSSGLRIVDISTPD 117
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 29.6 bits (67), Expect = 2.7
Identities = 39/163 (23%), Positives = 65/163 (39%), Gaps = 52/163 (31%)
Query: 267 MRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDDD--SLVPRNQLFATLDVTTHEGMLPNR 324
+R KQ+++ + ++G N GKTT++K +D ++ P
Sbjct: 5 LRKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISP-------------------- 44
Query: 325 LRILYVDTIGFISNIPTTLLEPFKVTLEDA--------------MLADIIIHVVDVSNPD 370
T+GF NI T +K+ + D D +I VVD S+
Sbjct: 45 -------TLGF--NIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRA 95
Query: 371 YLQQKQHVDETLQHLELEEKIL-EHVLVVGNKVD---AVPPGE 409
L+ + LQ L +EE++ +L+ NK D A+ P E
Sbjct: 96 RLEDCK---RELQKLLVEERLAGATLLIFANKQDLPGALSPEE 135
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 29.9 bits (68), Expect = 2.8
Identities = 33/123 (26%), Positives = 46/123 (37%), Gaps = 47/123 (38%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYV------DT 332
+ +VG N GK+T A T D + N F T+D PN + YV
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADVEIA-NYPFTTID--------PNV-GVGYVRVECPCKE 50
Query: 333 IGFISN------------IPTTLLE-----P-----------FKVTLEDAMLADIIIHVV 364
+G N +P L++ P F L+D AD++IHVV
Sbjct: 51 LGVSCNPRYGKCIDGKRYVPVELIDVAGLVPGAHEGKGLGNQF---LDDLRDADVLIHVV 107
Query: 365 DVS 367
D S
Sbjct: 108 DAS 110
>gnl|CDD|234041 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 = 530
Score = 30.0 bits (68), Expect = 2.9
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
VA++G + GK+TL+ L
Sbjct: 364 VAILGPSGSGKSTLLATLA 382
>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 = 29.3 bits (65), Expect = 2.9
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 275 KFPTVAVVGYTNCGKTTLIKAL 296
+ +VG GKTTL +AL
Sbjct: 1 PGEVILIVGPPGSGKTTLARAL 22
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 29.6 bits (67), Expect = 3.0
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNR 324
+ + G T GKTTL+ AL +P ++ T++ T E LP+
Sbjct: 27 NILISGGTGSGKTTLLNALLA---FIPPDERIITIE-DTAELQLPHP 69
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 30.0 bits (68), Expect = 3.0
Identities = 43/175 (24%), Positives = 69/175 (39%), Gaps = 43/175 (24%)
Query: 279 VAVVGYTNCGKTTLIKALTD--------------------------DDSLVPRNQLFATL 312
+ +VG+ + GKTTL KALT + + T
Sbjct: 7 IGMVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGPECYTTE 66
Query: 313 DVTTHEGMLPNRLR-ILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDY 371
V + G LR + +VD G + + T L A L D + V+ + P
Sbjct: 67 PVCPNCGSETELLRRVSFVDAPGHETLMATML--------SGAALMDGALLVIAANEP-- 116
Query: 372 LQQKQHVDETLQHLELEEKI-LEHVLVVGNKVDAVPPGERVTEEYDLLISATRGT 425
Q Q T +HL E I ++++++V NK+D V E+ E Y+ + +GT
Sbjct: 117 CPQPQ----TREHLMALEIIGIKNIVIVQNKIDLVSK-EKALENYEEIKEFVKGT 166
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 29.5 bits (67), Expect = 3.1
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 380 ETLQHL-ELEEKILEHVLVVGNKVDAVPPGERVTEEYDLLISATRGT 425
+T +HL LE L+H++++ NK+D V E+ E Y+ + +GT
Sbjct: 118 QTSEHLAALEIMGLKHIIILQNKIDLVKE-EQALENYEQIKEFVKGT 163
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 29.9 bits (68), Expect = 3.2
Identities = 48/178 (26%), Positives = 68/178 (38%), Gaps = 42/178 (23%)
Query: 277 PTVAVVGYTNCGKTTLI-------KALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILY 329
P VAVVG N GK+TL+ +A+ +D V R D +++ R R
Sbjct: 39 PVVAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTR-------DRVSYDAEWNGR-RFTV 90
Query: 330 VDTIGFISNIPTTLLEPFKVTLEDAM-LADIIIHVVD--VSNPDYLQQKQHVDETLQHLE 386
VDT G+ + L E AM AD ++ VVD V DE + +
Sbjct: 91 VDTGGWEPDA-KGLQASVAEQAEVAMRTADAVLFVVDATVGATA-------TDEAVARVL 142
Query: 387 LEEKILEHVLVVGNKVDAVPPGERVTEEYDLL----------ISATRGTGLAQLKEKV 434
V++ NKVD ER + L +SA G G+ L + V
Sbjct: 143 RRSGKP--VILAANKVD----DERGEADAAALWSLGLGEPHPVSALHGRGVGDLLDAV 194
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 29.5 bits (67), Expect = 3.3
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 277 PTVAVVGYTNCGKTTLIKALT 297
P + VG +N GK+TL++ LT
Sbjct: 10 PEIVFVGRSNVGKSTLVRELT 30
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 29.4 bits (66), Expect = 3.4
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 357 ADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHVLVVGNKVDAVPPGE 409
D V V +P+ ++ + + E + LE++E ++VVGNK+D++ +
Sbjct: 71 GDAFALVYSVDDPESFEEVKRLRE--EILEVKEDKFVPIVVVGNKIDSLAERQ 121
>gnl|CDD|183055 PRK11247, ssuB, aliphatic sulfonates transport ATP-binding subunit;
Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 3.5
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 255 KALNKLKGQREMMRNKKQRQKFPT---VAVVGYTNCGKTTLIKAL 296
A++K G+R ++ P VAVVG + CGK+TL++ L
Sbjct: 16 NAVSKRYGERTVLNQLDLH--IPAGQFVAVVGRSGCGKSTLLRLL 58
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 29.8 bits (68), Expect = 3.6
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
VA++G T CGK+TL++ LT
Sbjct: 369 VALLGRTGCGKSTLLQLLT 387
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 29.6 bits (67), Expect = 3.6
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
+A GY+ GKTTLI AL
Sbjct: 8 IAFCGYSGSGKTTLITALV 26
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.5 bits (67), Expect = 3.7
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
V ++G GK+TL+K L
Sbjct: 33 VLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|217835 pfam03999, MAP65_ASE1, Microtubule associated protein (MAP65/ASE1
family).
Length = 619
Score = 29.4 bits (66), Expect = 5.1
Identities = 20/113 (17%), Positives = 46/113 (40%), Gaps = 15/113 (13%)
Query: 188 FDRYMIVIQIFKAHAKTREARLQIAIAELPYLWTRYRT--------IEDATNMNITKGFL 239
D+ +++ A K R ++ ++ LW R + + +AT ++
Sbjct: 209 IDKLDKMLENLAAQKKQRADKIDDLREQIQELWNRLQISDEEQKRFVREATILSQESIKR 268
Query: 240 DSKRMVLME--REQKLKKALNKLKGQ-----REMMRNKKQRQKFPTVAVVGYT 285
+ + +E ++Q LKK + L+ + + +++QR+ F YT
Sbjct: 269 LEEEVERLEALKKQNLKKFIEDLRIEIQELWDLLFYSEEQRKSFTPYYEELYT 321
>gnl|CDD|227254 COG4917, EutP, Ethanolamine utilization protein [Amino acid
transport and metabolism].
Length = 148
Score = 28.3 bits (63), Expect = 5.2
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQ 307
+A VG CGKTTL ++L +D+L + Q
Sbjct: 4 IAFVGQVGCGKTTLFQSLYGNDTLYKKTQ 32
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 29.0 bits (66), Expect = 5.9
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 252 KLKKALNKL-KGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLI 293
K+ KA KL K + E + K R + ++G N GK+TLI
Sbjct: 96 KILKAAKKLLKEKNERRKAKGMRPRAIRAMIIGIPNVGKSTLI 138
>gnl|CDD|223456 COG0379, NadA, Quinolinate synthase [Coenzyme metabolism].
Length = 324
Score = 29.1 bits (66), Expect = 6.0
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 273 RQKFPTVAVVGYTNCGKTTLIKALTD 298
++K P VV Y N + +KA D
Sbjct: 118 KEKHPDAPVVTYVNT--SAEVKAEAD 141
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 29.2 bits (66), Expect = 6.2
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
TVA+VG T GK+TLI L
Sbjct: 363 TVAIVGPTGAGKSTLINLL 381
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain of
nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein NikA,
two integral membrane components (NikB and NikC), and
two ATPase (NikD and NikE). The NikABCDE transporter is
synthesized under anaerobic conditions to meet the
increased demand for nickel resulting from hydrogenase
synthesis. The molecular mechanism of nickel uptake in
many bacteria and most archaea is not known. Many other
members of this ABC family are also involved in the
uptake of dipeptides and oligopeptides. The oligopeptide
transport system (Opp) is a five-component ABC transport
composed of a membrane-anchored substrate binding
proteins (SRP), OppA, two transmembrane proteins, OppB
and OppC, and two ATP-binding domains, OppD and OppF.
Length = 228
Score = 28.6 bits (65), Expect = 6.2
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
T+ +VG + GK+TL +A+
Sbjct: 33 TLGLVGESGSGKSTLARAI 51
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 234
Score = 28.7 bits (65), Expect = 6.3
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 7/28 (25%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPR 305
TVA+VG + GK+TL+ L+PR
Sbjct: 30 TVALVGPSGSGKSTLVN-------LIPR 50
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 28.2 bits (64), Expect = 6.6
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 17/90 (18%)
Query: 357 ADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEHV--LVVGNKVD-----AVPP-- 407
A I V DV+N + + ++D+ L EL+E ++ ++VGNK D V
Sbjct: 73 AHGAILVYDVTNRESFE---NLDKWLN--ELKEYAPPNIPIILVGNKSDLEDERQVSTEE 127
Query: 408 GERVTEEYDLL---ISATRGTGLAQLKEKV 434
++ +E LL SA G + + E +
Sbjct: 128 AQQFAKENGLLFFETSAKTGENVDEAFESL 157
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 220
Score = 28.6 bits (65), Expect = 6.7
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
VA+VG + CGK+TL++ +
Sbjct: 33 VALVGPSGCGKSTLLRIIA 51
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 28.3 bits (64), Expect = 7.3
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
A++G + CGK+TL++ L
Sbjct: 28 ITALIGPSGCGKSTLLRLL 46
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 28.7 bits (65), Expect = 7.3
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 9/67 (13%)
Query: 278 TVAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPN---------RLRIL 328
+ VVG + GK+T I L + +T + + +L++
Sbjct: 6 NIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLKLT 65
Query: 329 YVDTIGF 335
+DT GF
Sbjct: 66 VIDTPGF 72
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 28.4 bits (64), Expect = 7.5
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 249 REQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDDDSL 302
RE ++ + KL + V +VG GKTTL K + +DDS+
Sbjct: 1 REDMIEALIEKL------LEMSDNLG---VVGIVGMGGVGKTTLAKQIYNDDSV 45
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 27.6 bits (61), Expect = 7.6
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 279 VAVVGYTNCGKTTLIKAL 296
+ + G GK+TL K L
Sbjct: 2 ILITGPPGSGKSTLAKKL 19
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 28.0 bits (63), Expect = 7.9
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 322 PNRLRILYVDTIGFISNIPTTLLEPFKVTLEDAMLADIIIHVV----DVSNPDYLQQKQH 377
P + VDT G S +T E ADII+ VV D+S + L +
Sbjct: 98 PLVPGLTLVDTPGLDSVAV----GDQDLTEEYIKPADIILAVVDANHDLSTSEALFLARE 153
Query: 378 VD 379
VD
Sbjct: 154 VD 155
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 28.8 bits (65), Expect = 8.0
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 279 VAVVGYTNCGKTTLIKALT 297
VA++G + GK+TL++ L
Sbjct: 367 VAILGRSGSGKSTLLQLLA 385
>gnl|CDD|184130 PRK13545, tagH, teichoic acids export protein ATP-binding subunit;
Provisional.
Length = 549
Score = 28.7 bits (64), Expect = 8.1
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 331 DTIGFISNIPTTLLEPFKV---TLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLE 386
IG+IS T +EPFK +EDA LAD+ + V + + + +TL LE
Sbjct: 401 GEIGWIS---TKFIEPFKSNNNIIEDAKLADVTALLKRVYGGNMVSAPTYFGKTLNELE 456
>gnl|CDD|237137 PRK12561, PRK12561, NAD(P)H-quinone oxidoreductase subunit 4;
Provisional.
Length = 504
Score = 28.8 bits (65), Expect = 8.2
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 130 TIISLLSFDKKSFFGKGNLELLKRQVRGDARVTAVFVSVDVL 171
T I LLS ++ F+G + L V DA+ +F+++ +L
Sbjct: 403 TPIYLLSMLRRVFYGPRSELLPALAVVEDAKPRELFIALSLL 444
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They export
degradative enzymes by using a type I protein secretion
system and lack an N-terminal signal peptide, but
contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and an
outer membrane protein (OMP). For the HlyA transporter
complex, HlyB (ABC transporter) and HlyD (MFP) reside in
the inner membrane of E. coli. The OMP component is
TolC, which is thought to interact with the MFP to form
a continuous channel across the periplasm from the
cytoplasm to the exterior. HlyB belongs to the family of
ABC transporters, which are ubiquitous, ATP-dependent
transmembrane pumps or channels. The spectrum of
transport substrates ranges from inorganic ions,
nutrients such as amino acids, sugars, or peptides,
hydrophobic drugs, to large polypeptides, such as HlyA.
Length = 173
Score = 28.0 bits (63), Expect = 8.2
Identities = 6/19 (31%), Positives = 14/19 (73%)
Query: 278 TVAVVGYTNCGKTTLIKAL 296
++A++G + GK+TL + +
Sbjct: 30 SLAIIGPSGSGKSTLARLI 48
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.8 bits (65), Expect = 8.4
Identities = 22/136 (16%), Positives = 39/136 (28%), Gaps = 41/136 (30%)
Query: 203 KTREARLQIAIAELPYLWTRYRTIEDATNMNITKGFLDSKRMVLMEREQKLKKALNKLKG 262
+ + RL+ A ++ SK R ++L+K +L
Sbjct: 240 EQKAERLRQEAAAYEKQQKELAKEQEWIRRGKAAA---SKAKKAKSRIKRLEKLEARLAE 296
Query: 263 QREMMRNKKQRQKFPT--------------------------------------VAVVGY 284
+R + K +FP +A+VG
Sbjct: 297 ERPVEEGKPLAFRFPPPGKRLGKLVLEFENVSKGYDGGRLLLKDLSFRIDRGDRIAIVGP 356
Query: 285 TNCGKTTLIKALTDDD 300
GK+TL+K L +
Sbjct: 357 NGAGKSTLLKLLAGEL 372
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 28.8 bits (65), Expect = 8.4
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 279 VAVVGYTNCGKTTLIKALTDD 299
+A++G CGKTTL+K +
Sbjct: 348 IALIGPNGCGKTTLLKLMLGQ 368
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 28.5 bits (63), Expect = 8.7
Identities = 35/135 (25%), Positives = 61/135 (45%), Gaps = 21/135 (15%)
Query: 240 DSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQKFPTVAVVGYTNCGKTTLIKALTDD 299
D++ + RE + +KL E+ K QK +V ++G N GK+TL+ + +
Sbjct: 18 DTEALAAAVREDASTGSTSKLP--LEVKFGKMSNQKTVSVCIIGRPNSGKSTLLNRIIGE 75
Query: 300 DSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFISNIPTTLLEPFKVTLEDAML--- 356
+ ++ T + T L + ILY DT G + EP K +LE AM+
Sbjct: 76 KLSIVTPKVQTTRSIITGIITLKDTQVILY-DTPG--------IFEP-KGSLEKAMVRCA 125
Query: 357 ------ADIIIHVVD 365
AD+++ ++D
Sbjct: 126 WSSLHSADLVLLIID 140
>gnl|CDD|213835 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 [Protein synthesis, Other].
Length = 178
Score = 27.8 bits (63), Expect = 8.7
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 277 PTVAVVGYTNCGKTTLIKALT 297
P +A G +N GK++LI ALT
Sbjct: 19 PEIAFAGRSNVGKSSLINALT 39
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 28.3 bits (64), Expect = 8.8
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 279 VAVVGYTNCGKTTLIKALTD 298
VA++G + CGK+TL++ +
Sbjct: 32 VAILGPSGCGKSTLLRLIAG 51
>gnl|CDD|184584 PRK14238, PRK14238, phosphate transporter ATP-binding protein;
Provisional.
Length = 271
Score = 28.3 bits (63), Expect = 8.9
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 280 AVVGYTNCGKTTLIKALTDDDSLVP 304
A++G + CGK+T IK L LVP
Sbjct: 54 AIIGPSGCGKSTYIKTLNRMVELVP 78
>gnl|CDD|225824 COG3286, COG3286, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 204
Score = 28.2 bits (63), Expect = 9.0
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 9/72 (12%)
Query: 201 HAKTREARLQIA---IAEL--PYLWTRYRTIEDATNMNITKGFL----DSKRMVLMEREQ 251
REAR Q + +L +DA + G L D R ++ +E+
Sbjct: 129 SEVYREARFQPLTRQVRKLVVAVSIVYGLDPDDAAEEAVELGLLEEGEDGLRELIKNKER 188
Query: 252 KLKKALNKLKGQ 263
L+ L LKG+
Sbjct: 189 ALETLLKALKGR 200
>gnl|CDD|213799 TIGR03344, VI_effect_Hcp1, type VI secretion system effector, Hcp1
family. This family includes Hcp1 (hemolysin
coregulated protein 1), an exported, homohexameric
ring-forming virulence protein from Pseudomonas
aeruginosa. Hcp1 lacks a conventional signal sequence
and is instead exported by means of the type VI
secretion system, encoded by a pathogenicity cluster of
a class previously designated IAHP (IcmF-associated
homologous protein). Homologs of Hcp1, in this protein
family, are found in various bacteria of which most but
not all are known pathogens. Pathogens may have many
multiple members of this family, with three to ten in
Erwinia carotovora, Yersinia pestis, uropathogenic
Escherichia coli, and the insect pathogen Photorhabdus
luminescens [Cellular processes, Pathogenesis].
Length = 166
Score = 27.7 bits (62), Expect = 9.2
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 347 FKVTLEDAMLADIIIHVVDVSNPDYLQQKQHV 378
+ + LE A++ DI ++ +P+ Q + V
Sbjct: 110 YTIKLEGALIVDIKPYMPHCLDPNNAQPLEDV 141
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 28.7 bits (64), Expect = 9.2
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 260 LKGQREMMRN---KKQRQKFPTVAVVGYTNCGKTTLIKALTDDDSLVPRNQ 307
+ + M+ N K R + +A+VG GK+T I A+ + L RN+
Sbjct: 51 IAERHAMLNNELRKISRLEM-VLAIVGTMKAGKSTTINAIVGTEVLPNRNR 100
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 28.2 bits (64), Expect = 9.5
Identities = 33/119 (27%), Positives = 51/119 (42%), Gaps = 17/119 (14%)
Query: 279 VAVVGYTNCGKTTLIKALTDDDSLVPRNQLFATLDVTTHEGMLPNRLRILYVDTIGFIS- 337
VA+VG + GK+TL+ L D L D+T + L L IGF+
Sbjct: 34 VAIVGPSGSGKSTLLNLLGGLDKPTSGEVLINGKDLTK---LSEKELAKLRRKKIGFVFQ 90
Query: 338 --NIPTTLLEPFKVTLEDAMLADIIIHVVDVSNPDYLQQKQHVDETLQHLELEEKILEH 394
N LL V LE+ L +I ++K+ +E L+ L LE+++L+
Sbjct: 91 NFN----LLPDLTV-LENVELPLLIAGKSAG------RRKRAAEELLEVLGLEDRLLKK 138
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 28.8 bits (65), Expect = 9.6
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 239 LDSKRMVLMEREQKLKKALNKLKGQREMMRNKKQRQ--KFPTVAVVGYTNCGKTTLIK 294
+ + E + +AL LK R +R P V+G GKTTL++
Sbjct: 76 DAAAEAEIRELRARFNEALALLKRSR----LGGRRYLYDLPWYLVIGPPGSGKTTLLQ 129
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 28.7 bits (65), Expect = 9.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 278 TVAVVGYTNCGKTTLIKALT 297
T+ +VG + GK+TL + L
Sbjct: 319 TLGLVGESGSGKSTLARILA 338
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
0.320 0.134 0.377
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,743,816
Number of extensions: 2556743
Number of successful extensions: 3308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3217
Number of HSP's successfully gapped: 223
Length of query: 505
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 404
Effective length of database: 6,457,848
Effective search space: 2608970592
Effective search space used: 2608970592
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: 61 (27.7 bits)