RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9409
(472 letters)
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 527 bits (1361), Expect = 0.0
Identities = 200/469 (42%), Positives = 284/469 (60%), Gaps = 24/469 (5%)
Query: 5 NSPIIGIATPPGRGGVGIIRLSGKNLWSIVEIVCKKTKKQLKPRFATYSSFFCKNNNIID 64
N I IATPPGRGG+GIIR+SG + I + + K K KPR A Y +ID
Sbjct: 4 NDTIAAIATPPGRGGIGIIRISGPDALEIAQKLFGK--KLPKPRTAHYGHIRD-PGEVID 60
Query: 65 KGLVIYFKAPHSYTGEDVIELHGHGGPIILHMLLSSCLEIGKSIGLRLAMPGEFTKRAFL 124
+ LV+YF AP+S+TGEDV+E+ HGGP +L+++L L +G RLA PGEFTKRAFL
Sbjct: 61 EVLVLYFPAPNSFTGEDVVEIQCHGGPAVLNLILELLLALG----ARLAEPGEFTKRAFL 116
Query: 125 NNKLDLIQVEAIIDLINASTESAAKSAMISLSGKFSKLINILLDKLINLRTLIEFSFDFP 184
N KLDL Q EAI DLI+A TE+AA+ A+ L G SKLIN L ++L+ L L+E + DFP
Sbjct: 117 NGKLDLTQAEAIADLIDAKTEAAARLALRQLQGALSKLINELREELLELLALVEAAIDFP 176
Query: 185 EENQELILNKNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSL 244
EE+ E L+ +L ++ +L ++ ++ ++R GL VV+ G+PNVGKSSL N+L
Sbjct: 177 EEDIE-FLSDEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSLLNAL 235
Query: 245 VGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERT 304
+G + AIVT IAGTTRD I + I ++ ++ DTAGI + + +EVEKIGIER+
Sbjct: 236 LGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETD-------DEVEKIGIERS 288
Query: 305 WVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYVWNKIDYSGHQKNINYKNNI 364
++ +D+++ V DA + T+ D +I++ + PVI V NK D +G + ++ +N
Sbjct: 289 REAIEEADLVLLVLDAS-EPLTEEDDEILEE-LKDKPVIVVLNKADLTG-EIDLEEENGK 345
Query: 365 ANIYLSASKRIGINLLRNTLLDLIEK-TQTIESSPYLARERHIHSLNEANYYLSCAIKII 423
I +SA GI+ LR + +L + +L RH+ +L A +L A++ +
Sbjct: 346 PVIRISAKTGEGIDELREAIKELAFGGFGGNQEGVFLTNARHLEALERALEHLERALEGL 405
Query: 424 NQSEKNFEKNLELIAEDLRFCHEKLSSIIGKSTTNDLLDNIFSQFCIGK 472
LEL+AEDLR E L I G+ T+ DLLD IFS FCIGK
Sbjct: 406 ESGL-----PLELLAEDLRLALEALGEITGEVTSEDLLDRIFSSFCIGK 449
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 485 bits (1251), Expect = e-170
Identities = 193/467 (41%), Positives = 274/467 (58%), Gaps = 21/467 (4%)
Query: 8 IIGIATPPGRGGVGIIRLSGKNLWSIVEIVCKKTKKQLKPRFATYSSFFCKNNNIIDKGL 67
I IAT PG G +GI+R+SG + I + + K KPR A Y +N IID+ L
Sbjct: 7 IAAIATAPGEGAIGIVRISGPDALEIAQKLFGG-LKLPKPRTAHYGHIKDENGEIIDEVL 65
Query: 68 VIYFKAPHSYTGEDVIELHGHGGPIILHMLLSSCLEIGKSIGLRLAMPGEFTKRAFLNNK 127
V+YFKAP+S+TGEDV+E+ HGGP++++++L L++G RLA PGEF+KRAFLN K
Sbjct: 66 VLYFKAPNSFTGEDVVEIQCHGGPVVVNLILELLLKLG----ARLAEPGEFSKRAFLNGK 121
Query: 128 LDLIQVEAIIDLINASTESAAKSAMISLSGKFSKLINILLDKLINLRTLIEFSFDFPEEN 187
LDL Q EAI DLI+A TE AA+ A+ L G S+LIN L + L+ L +E + DFPEE+
Sbjct: 122 LDLTQAEAIADLIDAKTEQAARIALRQLQGALSQLINELREALLELLAQVEANIDFPEED 181
Query: 188 QELILNKNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGS 247
E L +L ++ +L +++ K+ ++R GL VV+IG+PNVGKSSL N+L+G
Sbjct: 182 IE-ELVLEKIREKLEELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGR 240
Query: 248 DVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERTWVE 307
D AIVT IAGTTRD I + I +N ++ DTAGI + + + VE+IGIER
Sbjct: 241 DRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIRETD-------DVVERIGIERAKKA 293
Query: 308 LKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYVWNKIDYSGHQKN--INYKNNIA 365
++ +D++++V DA D +I+ P P+I V NK D + N A
Sbjct: 294 IEEADLVLFVLDAS-QPLDKEDLALIELLPKKKPIIVVLNKADLVSKIELESEKLANGDA 352
Query: 366 NIYLSASKRIGINLLRNTLLDLIEKTQTIESSPYLARERHIHSLNEANYYLSCAIKIINQ 425
I +SA G++ LR + L K + +L+ RHI L +A +L A++
Sbjct: 353 IISISAKTGEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQLLEQAAEHLEDALQ---- 408
Query: 426 SEKNFEKNLELIAEDLRFCHEKLSSIIGKSTTNDLLDNIFSQFCIGK 472
+ + L+L+AEDLR E L I G+ + DLLD IFS FCIGK
Sbjct: 409 -QLELGQPLDLLAEDLRLAQEALGEITGEFVSEDLLDEIFSNFCIGK 454
>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 = 273 bits (700), Expect = 4e-87
Identities = 160/464 (34%), Positives = 236/464 (50%), Gaps = 25/464 (5%)
Query: 12 ATPPGRGGVGIIRLSGKNLWSIVEIVCKKTKKQLKPRFATYSSFFCKNNNIIDKGLVIYF 71
ATPP + IIRLSG + SI++ + K R Y NN D L+ F
Sbjct: 1 ATPPFNSAIHIIRLSGPDSLSILKKITNKLNTASGMRIQ-YGHIIDSNNKCKDDELLFKF 59
Query: 72 KAPHSYTGEDVIELHGHGGPIILHMLLSSCLEIGKSIGLRLAMPGEFTKRAFLNNKLDLI 131
AP+SYTGEDVIE+ HG +I+ +L CL+ G RLA PGEFT+RAFLN K+DL
Sbjct: 60 VAPNSYTGEDVIEIQCHGSMLIVQEILQLCLKSG----ARLAQPGEFTQRAFLNGKMDLT 115
Query: 132 QVEAIIDLINASTESAAKSAMISLSGKFSKLINILLDKLINLRTLIEFSFDFPEENQELI 191
Q EAI +LI A A+ L+G+ + I + L+ L +E + D+ E++ E
Sbjct: 116 QAEAINELILAPNNKVKDIALNKLAGELDQKIEAIRKSLLQLLAQVEVNIDYEEDDDEQ- 174
Query: 192 LNKNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAI 251
D N+L+ LK I K + +G + ++G PNVGKSSL N+L+ D AI
Sbjct: 175 ----DSLNQLLLSIIAELKDILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAI 230
Query: 252 VTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERTWVELKNS 311
V+ I GTTRD + ++N L K+ DTAG I+++ + VE++GIE+++ +K +
Sbjct: 231 VSDIKGTTRDVVEGDFELNGILIKLLDTAG-------IREHADFVERLGIEKSFKAIKQA 283
Query: 312 DIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYVWNKIDYSGHQKNINYKNNIANIYLSA 371
D++IYV DA D D II P I V NKID + ++ +
Sbjct: 284 DLVIYVLDASQPLTKD-DFLIIDLNKSKKPFILVLNKIDL-KINSLEFFVSSKVLNSSNL 341
Query: 372 S-KRIGINLLRNTLLDLIEKTQTIESSPYLARERHIHSLNEANYYLSCAIKIINQSEKNF 430
S K++ I L + L +K S + + ++ S +A L AI + Q
Sbjct: 342 SAKQLKIKALVD---LLTQKINAFYSKERVELDDYLISSWQAMILLEKAIAQLQQFLSKL 398
Query: 431 EK--NLELIAEDLRFCHEKLSSIIGKSTTNDLLDNIFSQFCIGK 472
++ L+++ LR L + G+ T D+LD IFS FC+GK
Sbjct: 399 DRQLFLDMLVFHLREAINCLGQVTGEVVTEDVLDEIFSNFCLGK 442
>gnl|CDD|204472 pfam10396, TrmE_N, GTP-binding protein TrmE N-terminus. This
family represents the shorter, B, chain of the
homo-dimeric structure which is a guanine
nucleotide-binding protein that binds and hydrolyses
GTP. TrmE is homologous to the tetrahydrofolate-binding
domain of N,N-dimethylglycine oxidase and indeed binds
formyl-tetrahydrofolate. TrmE actively participates in
the formylation reaction of uridine and regulates the
ensuing hydrogenation reaction of a Schiff's base
intermediate. This B chain is the N-terminal portion of
the protein consisting of five beta-strands and three
alpha helices and is necessary for mediating dimer
formation within the protein.
Length = 114
Score = 181 bits (461), Expect = 8e-56
Identities = 62/121 (51%), Positives = 81/121 (66%), Gaps = 7/121 (5%)
Query: 7 PIIGIATPPGRGGVGIIRLSGKNLWSIVEIVCKKTKKQLKPRFATYSSFFCKNNNIIDKG 66
I IATPPGRGG+ IIR+SG + +EI K K KPR A Y + N +ID+
Sbjct: 1 TIAAIATPPGRGGIAIIRISGPDA---LEIAKKLFGKLPKPRTAHYGTIRDPNGEVIDEV 57
Query: 67 LVIYFKAPHSYTGEDVIELHGHGGPIILHMLLSSCLEIGKSIGLRLAMPGEFTKRAFLNN 126
LV+YF AP+S+TGEDV+E+H HGGP ++ +L + L+ +G RLA PGEFT+RAFLN
Sbjct: 58 LVLYFPAPNSFTGEDVVEIHCHGGPAVVQAILQALLK----LGARLAEPGEFTRRAFLNG 113
Query: 127 K 127
K
Sbjct: 114 K 114
>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 = 169 bits (431), Expect = 9e-51
Identities = 66/168 (39%), Positives = 96/168 (57%), Gaps = 9/168 (5%)
Query: 222 RNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAG 281
R G+ VV+ G+PNVGKSSL N+L G D AIV+ IAGTTRD I + I + ++ DTAG
Sbjct: 1 REGIKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAG 60
Query: 282 IPDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIP 341
+++ +E+EKIGIER ++ +D+++ V DA + + D +I+ P P
Sbjct: 61 -------LRETEDEIEKIGIERAREAIEEADLVLLVVDAS-EGLDEEDLEIL-ELPAKKP 111
Query: 342 VIYVWNKIDYSGHQKNINYKNNIANIYLSASKRIGINLLRNTLLDLIE 389
VI V NK D + I+ N I +SA GI+ L+ LL+L
Sbjct: 112 VIVVLNKSDLLSDAEGISELNGKPIIAISAKTGEGIDELKEALLELAG 159
>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 = 101 bits (255), Expect = 4e-26
Identities = 42/125 (33%), Positives = 64/125 (51%), Gaps = 10/125 (8%)
Query: 226 NVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDI 285
V L+G+PNVGKS+L N+L G+ VAIV+ GTTRD I + + DT G+
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVL-GLGRQIILVDTPGL--- 56
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP--MNIPVI 343
I+ G R ++ +D+I+ V DA + T+ D++I++ P+I
Sbjct: 57 ---IEGASEGKGVEGFNRFLEAIREADLILLVVDAS-EGLTEDDEEILEELEKLPKKPII 112
Query: 344 YVWNK 348
V NK
Sbjct: 113 LVLNK 117
>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 = 102 bits (258), Expect = 5e-26
Identities = 59/171 (34%), Positives = 82/171 (47%), Gaps = 24/171 (14%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINS 287
++G+PNVGKS+LFN L G AIV+ G TRD+ + F + DT GI +
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPDDE 60
Query: 288 KIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKN-FPMNIPVIYVW 346
I K I E +I IE +D+I++V D R + T D++I K PVI V
Sbjct: 61 GISKEIREQAEIAIEE-------ADVILFVVDGR-EGLTPADEEIAKYLRKSKKPVILVV 112
Query: 347 NKIDYSGHQKNINYKNNIAN---------IYLSASKRIGINLLRNTLLDLI 388
NKID NI + A I +SA GI L + +L+L+
Sbjct: 113 NKID------NIKEEEEAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELL 157
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 108 bits (271), Expect = 2e-25
Identities = 54/172 (31%), Positives = 88/172 (51%), Gaps = 23/172 (13%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V ++G+PNVGKS+LFN L G +AIV+ G TRD+I + F + DT G+ D
Sbjct: 6 VAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGL-DDG 64
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PMNIPVIYV 345
+ +E++++ E+ + ++ +D+I++V D R + T D++I K PVI V
Sbjct: 65 DE-----DELQELIREQALIAIEEADVILFVVDGR-EGITPADEEIAKILRRSKKPVILV 118
Query: 346 WNKIDYSGHQKNINYKNNIANIY---------LSASKRIGINLLRNTLLDLI 388
NKID N+ + Y +SA GI L + +L+L+
Sbjct: 119 VNKID------NLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLDAVLELL 164
Score = 90.3 bits (225), Expect = 2e-19
Identities = 51/188 (27%), Positives = 91/188 (48%), Gaps = 32/188 (17%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+ + + +IG+PNVGKSSL N+++G + IV+ IAGTTRD I + + + + DTAGI
Sbjct: 177 DPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAGI 236
Query: 283 PDINSKIKKNINE-VEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKI---IKNFPM 338
+ K I E VEK + RT ++ +D+++ V DA + ++ D +I I+
Sbjct: 237 -----RRKGKITESVEKYSVARTLKAIERADVVLLVIDAT-EGISEQDLRIAGLIEE--A 288
Query: 339 NIPVIYVWNKIDYSGHQKNINYKNNIA--------------NIYLSASKRIGINLLRNTL 384
++ V NK D +++ +++SA G+ + L
Sbjct: 289 GRGIVIVVNKWD--LVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGL----DKL 342
Query: 385 LDLIEKTQ 392
+ I++
Sbjct: 343 FEAIKEIY 350
>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 = 104 bits (262), Expect = 2e-24
Identities = 57/174 (32%), Positives = 82/174 (47%), Gaps = 24/174 (13%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V ++G+PNVGKS+LFN L G AIV+ G TRD+ + F + DT GI + +
Sbjct: 2 VAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEEDD 61
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKN-FPMNIPVIYV 345
+ K I E +I IE +D+I++V D R + T D++I K PVI V
Sbjct: 62 DGLDKQIREQAEIAIE-------EADVILFVVDGR-EGLTPEDEEIAKWLRKSGKPVILV 113
Query: 346 WNKIDYSGHQKNINYKNNIANIY---------LSASKRIGINLLRNTLLDLIEK 390
NKID A Y +SA GI L + +L+L+ +
Sbjct: 114 ANKID------GKKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELLPE 161
Score = 103 bits (259), Expect = 7e-24
Identities = 54/186 (29%), Positives = 91/186 (48%), Gaps = 31/186 (16%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+ + +IG+PNVGKS+L N+L+G + IV+ IAGTTRD I + N + + DTAGI
Sbjct: 171 GPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGKKYTLIDTAGI 230
Query: 283 PDINSKIKKNINE-VEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKII----KNFP 337
+ K + E VEK + RT ++ +D+++ V DA + T+ D +I +
Sbjct: 231 -----RRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDAT-EGITEQDLRIAGLALEA-- 282
Query: 338 MNIPVIYVWNKID--YSGHQKNINYKNNIAN----------IYLSASKRIGINLLRNTLL 385
++ V NK D + +K + +++SA G+ + LL
Sbjct: 283 -GKALVIVVNKWDLVKDEKTRE-EFKKELRRKLPFLDFAPIVFISALTGQGV----DKLL 336
Query: 386 DLIEKT 391
D I++
Sbjct: 337 DAIDEV 342
>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 = 103 bits (260), Expect = 3e-24
Identities = 50/173 (28%), Positives = 89/173 (51%), Gaps = 18/173 (10%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKF---LFKITDTAG 281
L++ + G+ N GKSSL N+L G D+AIV+ + GTT D + K +++ + DTAG
Sbjct: 7 LHIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVYKAMELLPLGPVVL--IDTAG 64
Query: 282 IPDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PMNI 340
+ D E+ ++ +E+T L +D+ + V DA +++ ++I+ I
Sbjct: 65 LDD--------EGELGELRVEKTREVLDKTDLALLVVDAGVGP-GEYELELIEELKERKI 115
Query: 341 PVIYVWNKIDYSGHQKN---INYKNNIANIYLSASKRIGINLLRNTLLDLIEK 390
P I V NKID + K + I++SA GI+ L+ +++L+ +
Sbjct: 116 PYIVVINKIDLGEESAELEKLEKKFGLPPIFVSALTGEGIDELKEAIIELLPE 168
>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 = 98.3 bits (246), Expect = 5e-24
Identities = 53/187 (28%), Positives = 88/187 (47%), Gaps = 32/187 (17%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+ + + +IG+PNVGKSSL N+L+G + IV+ IAGTTRD I + + + + DTAGI
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTLIDTAGI 60
Query: 283 PDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKII----KNFPM 338
K K +EK + RT ++ +D+++ V DA + T+ D +I +
Sbjct: 61 ----RKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDAS-EGITEQDLRIAGLILEE--- 112
Query: 339 NIPVIYVWNKIDYSGHQKNINYKNNIAN--------------IYLSASKRIGINLLRNTL 384
+I V NK D +K+ +++SA G+ + L
Sbjct: 113 GKALIIVVNKWD--LVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGV----DKL 166
Query: 385 LDLIEKT 391
D I++
Sbjct: 167 FDAIKEV 173
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 103 bits (260), Expect = 6e-24
Identities = 53/183 (28%), Positives = 91/183 (49%), Gaps = 28/183 (15%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+ + +IG+PNVGKSSL N+L+G + IV+ IAGTTRD I + + + + DTAGI
Sbjct: 172 EPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGI 231
Query: 283 PDINSKIKKNINE-VEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKII----KNFP 337
+ K + E VEK + RT ++ +D+++ V DA + T+ D +I +
Sbjct: 232 -----RRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDAT-EGITEQDLRIAGLALEA-- 283
Query: 338 MNIPVIYVWNKIDYSGHQKNINYKNNIAN----------IYLSASKRIGINLLRNTLLDL 387
++ V NK D + +K + +++SA G+ + LL+
Sbjct: 284 -GRALVIVVNKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGV----DKLLEA 338
Query: 388 IEK 390
I++
Sbjct: 339 IDE 341
Score = 100 bits (253), Expect = 4e-23
Identities = 55/179 (30%), Positives = 84/179 (46%), Gaps = 24/179 (13%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V ++G+PNVGKS+LFN L G AIV G TRD+I + F + DT GI +
Sbjct: 4 VAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPDD 63
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKN-FPMNIPVIYV 345
+K I E ++ IE +D+I++V D R T D++I K N PVI V
Sbjct: 64 DGFEKQIREQAELAIE-------EADVILFVVDGR-AGLTPADEEIAKILRKSNKPVILV 115
Query: 346 WNKIDYSGHQKNINYKNNIANIY---------LSASKRIGINLLRNTLLDLIEKTQTIE 395
NK+D + + + Y +SA GI L + +L+ + + + +
Sbjct: 116 VNKVD------GPDEEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILEELPEEEEED 168
>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 = 95.0 bits (237), Expect = 4e-23
Identities = 43/167 (25%), Positives = 72/167 (43%), Gaps = 18/167 (10%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFL-FKITDTAGIPDIN 286
+ G+PNVGKSSL N+L+G +V IV+ I GTTRD + K ++ + DT G+ +
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDE-- 58
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYVW 346
+ + +E +D+++ V D+ + K + PV+ V
Sbjct: 59 ------EGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGLL-RERGKPVLLVL 111
Query: 347 NKID-YSGHQKNINYKNNIANIYL-------SASKRIGINLLRNTLL 385
NKID ++ + + SA GI+ LR +
Sbjct: 112 NKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIA 158
>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 = 87.1 bits (217), Expect = 4e-20
Identities = 48/174 (27%), Positives = 83/174 (47%), Gaps = 21/174 (12%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKIT--KTIQINKFLFKITDTAGI 282
V +IG+PNVGKS+L N+LVG ++IV+ TTR++I T + +F DT GI
Sbjct: 4 GFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIF--VDTPGI 61
Query: 283 PDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PMNIP 341
K+ + + + W LK+ D++++V DA + + D+ I++ P
Sbjct: 62 HKPKKKLGERMVKA-------AWSALKDVDLVLFVVDAS-EWIGEGDEFILELLKKSKTP 113
Query: 342 VIYVWNKIDYSGHQKNI--------NYKNNIANIYLSASKRIGINLLRNTLLDL 387
VI V NKID ++++ +SA K ++ L +++
Sbjct: 114 VILVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYIVEY 167
>gnl|CDD|204989 pfam12631, GTPase_Cys_C, Catalytic cysteine-containing C-terminus
of GTPase, MnmE. This short C-terminal region contains
the only cysteine present in these proteins. It is
proposed that MnmE is a tRNA-modifying enzyme and that
Cys-451 functions as a catalytic residue in the
modification reaction.
Length = 73
Score = 79.9 bits (198), Expect = 1e-18
Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 395 ESSPYLARERHIHSLNEANYYLSCAIKIINQSEKNFEKNLELIAEDLRFCHEKLSSIIGK 454
L RH +L A L A++ + L+L+AEDLR E L I G+
Sbjct: 4 NEDVLLTNARHREALERALEALERALEALESGL-----PLDLVAEDLRLALEALGEITGE 58
Query: 455 STTNDLLDNIFSQFC 469
+ DLLD IFS FC
Sbjct: 59 VDSEDLLDEIFSNFC 73
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 82.4 bits (205), Expect = 2e-17
Identities = 48/172 (27%), Positives = 83/172 (48%), Gaps = 21/172 (12%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKIT--KTIQINKFLFKITDTAGIPD 284
V ++G+PNVGKS+L N+LVG ++IV+ TTR +I T + +F DT GI
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIF--VDTPGIHK 65
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP-MNIPVI 343
+ + +N+ W LK+ D++++V DA +K D+ I++ + PVI
Sbjct: 66 PKRALNRAMNKA-------AWSSLKDVDLVLFVVDAD-EKIGPGDEFILEKLKKVKTPVI 117
Query: 344 YVWNKIDYSGHQKNI--------NYKNNIANIYLSASKRIGINLLRNTLLDL 387
V NKID ++ + + + +SA K ++ L + +
Sbjct: 118 LVLNKIDLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKY 169
>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 = 79.0 bits (195), Expect = 2e-17
Identities = 47/168 (27%), Positives = 74/168 (44%), Gaps = 17/168 (10%)
Query: 226 NVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN--KFLFKITDTAGIP 283
+V++G PNVGKS+L N L+G+ ++I GTTR+ +T I+ + + F + DTAG
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQE 62
Query: 284 DINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVI 343
D + + ++ L+ DI+I V D + K+II + +P+I
Sbjct: 63 D--------YDAIRRLYYRAVESSLRVFDIVILVLDVE-EILEKQTKEIIHHAESGVPII 113
Query: 344 YVWNKIDYSGH------QKNINYKNNIANIYLSASKRIGINLLRNTLL 385
V NKID N I LSA I+ +
Sbjct: 114 LVGNKIDLRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVE 161
>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 = 76.7 bits (189), Expect = 1e-16
Identities = 44/171 (25%), Positives = 75/171 (43%), Gaps = 22/171 (12%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTR--DKITKTIQINKFLFKITDTAGIPDI 285
V++G+ VGKSSL N+L+G +V V+ + GTTR D K + K + DT G+ +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKN--FPMNIPVI 343
++ E + L+ +D+I+ V D+ + + K +I IP+I
Sbjct: 61 GGLGRE----------ELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPII 110
Query: 344 YVWNKID-YSGHQKNINYKNNIAN-------IYLSASKRIGINLLRNTLLD 386
V NKID + + +SA G++ L L++
Sbjct: 111 LVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 73.8 bits (182), Expect = 2e-14
Identities = 49/171 (28%), Positives = 79/171 (46%), Gaps = 21/171 (12%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKIT--KTIQINKFLFKITDTAGIPD 284
V +IG+PNVGKS+L N+LVG ++IV+ TTR++I T + +F DT GI
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIF--VDTPGIHK 66
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP-MNIPVI 343
+ + +N+ + LK+ D+I++V DA + D+ I++ PVI
Sbjct: 67 PKHALGELMNKAARSA-------LKDVDLILFVVDAD-EGWGPGDEFILEQLKKTKTPVI 118
Query: 344 YVWNKIDYSGHQKNINYKNNIANIYL--------SASKRIGINLLRNTLLD 386
V NKID + + L SA K ++ L + +
Sbjct: 119 LVVNKIDKVKPKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIKE 169
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 74.6 bits (184), Expect = 2e-14
Identities = 25/56 (44%), Positives = 37/56 (66%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
V L+G+PNVGKSSL N L G + ++V +AGTT D + I++ ++ DTAG+
Sbjct: 214 VALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGL 269
Score = 56.9 bits (138), Expect = 1e-08
Identities = 37/126 (29%), Positives = 66/126 (52%), Gaps = 11/126 (8%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAG-IPDI 285
V ++G+PNVGKS+L N ++G A+V + G TRD+++ + N F + DT G PD
Sbjct: 41 VAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGWEPDA 100
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMN-IPVIY 344
++ ++ E ++ + +D +++V DA T D+ + + + PVI
Sbjct: 101 -KGLQASVAEQAEVAMR-------TADAVLFVVDATVGA-TATDEAVARVLRRSGKPVIL 151
Query: 345 VWNKID 350
NK+D
Sbjct: 152 AANKVD 157
>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 = 70.6 bits (174), Expect = 4e-14
Identities = 53/208 (25%), Positives = 100/208 (48%), Gaps = 34/208 (16%)
Query: 199 NELIKIKKKLLKIIQQ--GKKRALIRNGLNVV-LIGQPNVGKSSLFNSLVGSDV------ 249
+ K++K+L K+ +Q ++ R+G+ V L+G N GKS+LFN+L G+DV
Sbjct: 13 ERIAKLRKELEKVKKQRELQRARRKRSGVPTVALVGYTNAGKSTLFNALTGADVLAEDQL 72
Query: 250 -AIVTSIAGTTRDKITKTIQI-NKFLFKITDTAG-IPDINSKIKKNINEVEKIGIERTWV 306
A T D T+ I++ +TDT G I + + E + +E
Sbjct: 73 FA--------TLDPTTRRIKLPGGREVLLTDTVGFI----RDLPHQLVEAFRSTLE---- 116
Query: 307 ELKNSDIIIYVQDA---RYDKHTDFDKKIIKNFPM-NIPVIYVWNKIDY--SGHQKNINY 360
E+ +D++++V DA ++ + ++++K +IP+I V NKID +
Sbjct: 117 EVAEADLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLLDDEELEERLR 176
Query: 361 KNNIANIYLSASKRIGINLLRNTLLDLI 388
+++SA G++LL+ + +L+
Sbjct: 177 AGRPDAVFISAKTGEGLDLLKEAIEELL 204
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 69.2 bits (170), Expect = 2e-12
Identities = 59/249 (23%), Positives = 104/249 (41%), Gaps = 42/249 (16%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V L+G PNVGK++LFN+L G++ V + G T +K ++ +I D G +
Sbjct: 6 VALVGNPNVGKTTLFNALTGANQK-VGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYSLT 64
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP-------MN 339
+ +E EK+ R ++ D+I+ V DA + +N +
Sbjct: 65 A-----YSEDEKVA--RDFLLEGKPDLIVNVVDA---------TNLERNLYLTLQLLELG 108
Query: 340 IPVIYVWNKIDYSGHQ-KNINYKN-----NIANIYLSASKRIGINLLRNTLLDLIEKTQT 393
IP+I N ID + + I+ + + + A + G+ L+ +++L E T
Sbjct: 109 IPMILALNMIDEAKKRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIELAESKTT 168
Query: 394 IESSPY----LARERHIHSLNEANYYLSCAIKIINQSE------KNFEKNLELIAEDLRF 443
Y + + +L+E +L AIK++ E K EK +E + E+L
Sbjct: 169 PREVDYGEEIEEEIKELEALSEDPRWL--AIKLLEDDELVEAVLKEPEKRVEELLEELSE 226
Query: 444 CHEKLSSII 452
L I
Sbjct: 227 EEGHLLLIA 235
>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 = 67.5 bits (166), Expect = 3e-12
Identities = 50/197 (25%), Positives = 93/197 (47%), Gaps = 35/197 (17%)
Query: 203 KIKKKLLKIIQQGK--KRALIRNGLNVV-LIGQPNVGKSSLFNSLVGSDV-------AIV 252
++KK+L K+ +Q + +R R + V L+G N GKS+LFN+L G+DV A
Sbjct: 165 QLKKELEKVEKQRERQRRRRKRADVPTVALVGYTNAGKSTLFNALTGADVYAADQLFA-- 222
Query: 253 TSIAGTTRDKITKTIQI-NKFLFKITDTAG-IPDINSKIKKNINEVEKIGIERTWVELKN 310
T D T+ + + + +TDT G I + + + +E E++
Sbjct: 223 ------TLDPTTRRLDLPDGGEVLLTDTVGFI----RDLPHELVAAFRATLE----EVRE 268
Query: 311 SDIIIYVQDA---RYDKHTDFDKKIIKNFPMN-IPVIYVWNKIDYSGHQKNINYK--NNI 364
+D++++V DA ++ + +K+++ IP + V+NKID + I
Sbjct: 269 ADLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLD-EPRIERLEEGYP 327
Query: 365 ANIYLSASKRIGINLLR 381
+++SA G++LL
Sbjct: 328 EAVFVSAKTGEGLDLLL 344
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 67.7 bits (166), Expect = 3e-12
Identities = 51/204 (25%), Positives = 94/204 (46%), Gaps = 34/204 (16%)
Query: 203 KIKKKLLKIIQQGKKRALIRNGLN------VVLIGQPNVGKSSLFNSLVGSDVAIVTSIA 256
K+K++L + + R R + V L+G N GKS+LFN+L G+DV V
Sbjct: 168 KLKRELENVEKA---REPRRKKRSRSGIPLVALVGYTNAGKSTLFNALTGADVY-VADQL 223
Query: 257 GTTRDKITKTIQI-NKFLFKITDTAGI-----PDINSKIKKNINEVEKIGIERTWVELKN 310
T D T+ I++ + +TDT G + K + EV K
Sbjct: 224 FATLDPTTRRIELGDGRKVLLTDTVGFIRDLPHPLVEAFKSTLEEV------------KE 271
Query: 311 SDIIIYVQDA---RYDKHTDFDKKIIKNFPMN-IPVIYVWNKIDYSGHQKNIN--YKNNI 364
+D++++V DA + + + ++ + IP+I V NKID ++ + + +
Sbjct: 272 ADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELERGSP 331
Query: 365 ANIYLSASKRIGINLLRNTLLDLI 388
+++SA G++LLR +++L+
Sbjct: 332 NPVFISAKTGEGLDLLRERIIELL 355
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 67.9 bits (166), Expect = 4e-12
Identities = 38/126 (30%), Positives = 63/126 (50%), Gaps = 11/126 (8%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI-PDI 285
V ++G+PNVGKS+L N ++G A+V G TRD+++ + FK+ DT G D+
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGWEADV 337
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PMNIPVIY 344
I I +I + +D +++V D + T D++I++ PV+
Sbjct: 338 EG-IDSAIASQAQIAVS-------LADAVVFVVDGQVGL-TSTDERIVRMLRRAGKPVVL 388
Query: 345 VWNKID 350
NKID
Sbjct: 389 AVNKID 394
Score = 67.9 bits (166), Expect = 5e-12
Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 4/94 (4%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V L+G+PNVGKSSL N L + A+V +AGTTRD + + ++I+ + DTAGI
Sbjct: 453 VALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGI---- 508
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDA 320
+ + + E RT ++ S++ +++ DA
Sbjct: 509 KRRQHKLTGAEYYSSLRTQAAIERSELALFLFDA 542
>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 = 61.7 bits (151), Expect = 3e-11
Identities = 45/183 (24%), Positives = 82/183 (44%), Gaps = 30/183 (16%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPD 284
+ + L+G PNVGK++LFN+L G+ V + G T +K T + + +I D G
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQ-HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYS 59
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP------- 337
++ +E EK+ R ++ + D+II V DA + +N
Sbjct: 60 LSP-----YSEEEKVA--RDYLLEEKPDVIINVVDAT---------NLERNLYLTLQLLE 103
Query: 338 MNIPVIYVWNKIDYSGHQK-NINYKN-----NIANIYLSASKRIGINLLRNTLLDLIEKT 391
+ IPV+ N +D + + I+ K + + SA K GI+ L++ ++++ E
Sbjct: 104 LGIPVVVALNMMDEAEKKGIKIDIKKLSELLGVPVVPTSARKGEGIDELKDAIIEVAEGK 163
Query: 392 QTI 394
Sbjct: 164 VPP 166
>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 = 60.2 bits (147), Expect = 7e-11
Identities = 43/175 (24%), Positives = 74/175 (42%), Gaps = 30/175 (17%)
Query: 229 LIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSK 288
L+G PNVGK++LFN+L G+ V + G T +K ++ +I D G +
Sbjct: 2 LVGNPNVGKTTLFNALTGAR-QKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGTYSLTP- 59
Query: 289 IKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP-------MNIP 341
+E EK+ R ++ + D+I+ V DA + +N + +P
Sbjct: 60 ----YSEDEKVA--RDFLLGEEPDLIVNVVDA---------TNLERNLYLTLQLLELGLP 104
Query: 342 VIYVWNKIDYSGHQK-NINYKN-----NIANIYLSASKRIGINLLRNTLLDLIEK 390
V+ N ID + + I+ + + SA K GI+ L + + L E
Sbjct: 105 VVVALNMIDEAEKRGIKIDLDKLSELLGVPVVPTSARKGEGIDELLDAIAKLAES 159
>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 = 57.5 bits (140), Expect = 6e-10
Identities = 33/84 (39%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 199 NELIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGT 258
+L+K KKLLK ++ K + L+ L +++G PNVGKS+L N L G VA V + G
Sbjct: 90 KKLLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAKVGNKPGV 149
Query: 259 TRDKITKTIQINKFLFKITDTAGI 282
TR + + I+I + + DT GI
Sbjct: 150 TRGQ--QWIRIGPNIE-LLDTPGI 170
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 58.9 bits (143), Expect = 1e-09
Identities = 27/82 (32%), Positives = 49/82 (59%), Gaps = 3/82 (3%)
Query: 201 LIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTR 260
++K + I++ KK+ L++ + V ++G PNVGKS+L N L+G VA ++ GTT+
Sbjct: 109 RKALEKLSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTK 168
Query: 261 DKITKTIQINKFLFKITDTAGI 282
I+++ ++ + DT GI
Sbjct: 169 GIQ--WIKLDDGIY-LLDTPGI 187
Score = 30.4 bits (69), Expect = 2.1
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 19/111 (17%)
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYV 345
K K+ + EV LK+ D+++ V DAR T + ++ + P + V
Sbjct: 21 MKKAKRQLKEV-----------LKSVDVVVEVVDARDPLGT-RNPELERIVK-EKPKLLV 67
Query: 346 WNKIDYSGHQKNINYKNNIAN------IYLSASKRIGINLLRNTLLDLIEK 390
NK D + + +K I++SA R G +R L L E+
Sbjct: 68 LNKADLAPKEVTKKWKKYFKKEEGIKPIFVSAKSRQGGKKIRKALEKLSEE 118
>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 = 56.4 bits (137), Expect = 1e-09
Identities = 47/181 (25%), Positives = 72/181 (39%), Gaps = 32/181 (17%)
Query: 226 NVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFK-----ITDTA 280
+V+ G PNVGKSSL N L + V T TK++ + F +K + DT
Sbjct: 2 TLVIAGYPNVGKSSLVNKLTRAKPE-VAPYPFT-----TKSLFVGHFDYKYLRWQVIDTP 55
Query: 281 GIPDINSKIKKNINEVEKIGIERTWVELKN-SDIIIYVQDAR------YDKHTDFDKKII 333
GI D + + N +E I L + +++ D ++ K+I
Sbjct: 56 GILD---RPLEERNTIEMQAI----TALAHLRAAVLFFIDPSETCGYSIEEQLSLFKEIK 108
Query: 334 KNFPMNIPVIYVWNKIDYSG-----HQKNINYKNNIANIYLSASKRIGINLLRNTLLDLI 388
F N PVI V NKID + K I +S G++ L+N +L+
Sbjct: 109 PLF--NKPVIVVLNKIDLLTEEDLSEIEKELEKEGEEVIKISTLTEEGVDELKNKACELL 166
Query: 389 E 389
Sbjct: 167 L 167
>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 = 56.2 bits (136), Expect = 2e-09
Identities = 48/177 (27%), Positives = 74/177 (41%), Gaps = 26/177 (14%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQ-INKFLFKITDTAGIPDIN 286
L+G PNVGKS+L ++L + V I S TT + + + +I D G+ D
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEI-ASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGA 59
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKII---------KNFP 337
S + E+I L SD+I++V DA D D + F
Sbjct: 60 S---EGRGLGEQI-----LAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFL 111
Query: 338 MNIPVIYVWNKIDYSGHQKNI------NYKNNIANIYLSASKRIGINLLRNTLLDLI 388
N P + V NKID + N+ K I + SA R+G++ + T+ L+
Sbjct: 112 KNKPEMIVANKID-MASENNLKRLKLDKLKRGIPVVPTSALTRLGLDRVIRTIRKLL 167
>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 = 59.4 bits (144), Expect = 2e-09
Identities = 43/219 (19%), Positives = 83/219 (37%), Gaps = 40/219 (18%)
Query: 231 GQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSKIK 290
G PNVGKS+LFN+L G++ V + G T +K + +I D GI + +
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTT--- 56
Query: 291 KNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFP-------MNIPVI 343
+ E++ R ++ + D+++ V DA + +N + IP+I
Sbjct: 57 --FSLEEEVA--RDYLLNEKPDLVVNVVDA---------SNLERNLYLTLQLLELGIPMI 103
Query: 344 YVWNKIDYSGHQKNINYKNNIANIYLSASKRIGINLLRNTLLDLIEKTQTIESSPYLARE 403
N +D + + + + + +R+G+ ++ T E +
Sbjct: 104 LALNLVDEA---EKKGIRIDEEKL----EERLGVPVV---------PTSATEGRGIERLK 147
Query: 404 RHIHSLNEANYYLSCAIKIINQSEKNFEKNLELIAEDLR 442
I AI+I+ ++ + E LI
Sbjct: 148 DAIRKAIGLKELKKRAIEIVPEAYQVVEVVEGLIEIIYS 186
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 56.6 bits (136), Expect = 8e-09
Identities = 55/190 (28%), Positives = 89/190 (46%), Gaps = 17/190 (8%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPD 284
++V +IG+PN GKS+L N ++G ++IVT TTR IT I + + DT GI +
Sbjct: 53 VSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFE 112
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PMNIPVI 343
+ EK + W L ++D+++ + D+ D I+ +NI I
Sbjct: 113 PKGSL-------EKAMVRCAWSSLHSADLVLLIIDS-LKSFDDITHNILDKLRSLNIVPI 164
Query: 344 YVWNKID----YSGHQKNINYKNNIANIYLSASKRIGINLLRNTLLDLIEKTQTIESSPY 399
++ NKID Y K +N+ ++ S G N+ + LL+ I T + SP+
Sbjct: 165 FLLNKIDIESKYLNDIKAFLTENHPDSLLFPISALSGKNI--DGLLEYI--TSKAKISPW 220
Query: 400 LARERHIHSL 409
L E I L
Sbjct: 221 LYAEDDITDL 230
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows 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 sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 51.8 bits (125), Expect = 3e-08
Identities = 31/87 (35%), Positives = 43/87 (49%), Gaps = 7/87 (8%)
Query: 190 LILNKNDFFNELIKIK-KKLLKIIQQGKKRALI--RNGLNVVLIGQPNVGKSSLFNSLVG 246
L+LNK D E + + K ++G N + L+G PNVGKSSL N+LVG
Sbjct: 47 LLLNKADLVTEEQRKAWARYFK--KEGIVVLFFSALNEATIGLVGYPNVGKSSLINALVG 104
Query: 247 SDVAIVTSIAGTTRDKITKTIQINKFL 273
S V+S G T K +TI + +
Sbjct: 105 SKKVSVSSTPGKT--KHFQTIFLEPGI 129
>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 = 53.9 bits (130), Expect = 4e-08
Identities = 38/145 (26%), Positives = 72/145 (49%), Gaps = 14/145 (9%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKIT--KTIQINKFLFKITDTAGIPD 284
V ++G+PNVGKS+L N L G ++I + A TTR++I+ T ++ +F DT G
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIF--IDTPGF-- 58
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDA-RYDKHTDFDKKIIKNFPMNIPVI 343
+ K ++N + + D+I++V D+ +++ +F ++N + PV+
Sbjct: 59 --HEKKHSLNRLMMKEARSA---IGGVDLILFVVDSDQWNGDGEFVLTKLQN--LKRPVV 111
Query: 344 YVWNKIDYSGHQKNINYKNNIANIY 368
NK+D K + + A +
Sbjct: 112 LTRNKLDNKFKDKLLPLIDKYAILE 136
>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 = 53.3 bits (129), Expect = 7e-08
Identities = 34/104 (32%), Positives = 56/104 (53%), Gaps = 7/104 (6%)
Query: 183 FPEENQELI---LNKNDFFNELIKIKKKLLK-IIQQGKKRALIRNGLNVVLIGQPNVGKS 238
F E+ + + K ++IK KKLLK ++ K + L+ + +++G PNVGKS
Sbjct: 73 FEEKGIKALAINAKKGKGVKKIIKAAKKLLKEKNEKLKAKGLLNRPIRAMIVGIPNVGKS 132
Query: 239 SLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+L N L G VA V + G T+ + + I+++ L + DT GI
Sbjct: 133 TLINRLAGKKVAKVGNRPGVTKGQ--QWIKLSDGLE-LLDTPGI 173
>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 = 49.4 bits (119), Expect = 4e-07
Identities = 44/188 (23%), Positives = 72/188 (38%), Gaps = 45/188 (23%)
Query: 227 VVLIGQPNVGKSSLFNSLVGS-DVAIVTSIAGTTRDKITKTIQINKFL----FKITDT-- 279
V G+ NVGKSSL N+L +A + G T+ IN F F++ D
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ-------LINFFNVGDKFRLVDLPG 54
Query: 280 ---AGIP-DINSKIKKNINEVEKIGIERTWVELKNSD---IIIYVQDARYDKHTDFDKKI 332
A + ++ K K I E L+N + ++ + DAR+ T D ++
Sbjct: 55 YGYAKVSKEVREKWGKLIEEY-----------LENRENLKGVVLLIDARH-GPTPIDLEM 102
Query: 333 IKNF-PMNIPVIYVWNKIDYSGHQKNINYKNNIAN-----------IYLSASKRIGINLL 380
++ + IP + V K D + I I S+ K GI+ L
Sbjct: 103 LEFLEELGIPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDEL 162
Query: 381 RNTLLDLI 388
R + + +
Sbjct: 163 RALIAEWL 170
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 48.9 bits (117), Expect = 4e-07
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 20/99 (20%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINS 287
L+G+ GKSSL N+L G++VA V TTR Q + D P +
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDL---PGVGE 57
Query: 288 KIKKNINEVEKIGIERTWVE------LKNSDIIIYVQDA 320
+ G E L +D+++++ DA
Sbjct: 58 R-----------GRRDREYEELYRRLLPEADLVLWLLDA 85
>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 = 49.1 bits (118), Expect = 6e-07
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 207 KLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKT 266
KLLK + K I+ + V ++G PNVGKSS+ NSL S V + G T K +
Sbjct: 102 KLLKNYARNKG---IKTSITVGVVGYPNVGKSSVINSLKRSRACNVGATPGVT--KSMQE 156
Query: 267 IQINKFLFKITDTAGI 282
+ ++K + K+ D+ G+
Sbjct: 157 VHLDKHV-KLLDSPGV 171
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 47.9 bits (114), Expect = 5e-06
Identities = 39/183 (21%), Positives = 72/183 (39%), Gaps = 21/183 (11%)
Query: 195 NDFFNELIKIKKKLL-KIIQQGKKRALIRNG-LNVVLIGQPNVGKSSLFNSLVGSDVAIV 252
N+ L+ + L +I++Q + L +NV+L+G GKSSL N+L +V V
Sbjct: 8 NNVLKGLLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEV 67
Query: 253 TSIAGTTRDKITKTIQINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERTWVELKNSD 312
+ + T + + + DT G+ D K ++ L D
Sbjct: 68 SKVGVGTDITTRLRLSYDGENLVLWDTPGLGDGKDKDAEHRQLYRDY--------LPKLD 119
Query: 313 IIIYVQDA-RYDKHTDFDKKI-IKNFPMNIPVIYVWNKID---------YSGHQKNINYK 361
+++++ A TD D + ++ V++V + D +GHQ + K
Sbjct: 120 LVLWLIKADDRALGTDEDFLRDVIILGLDKRVLFVVTQADRAEPGREWDSAGHQPSPAIK 179
Query: 362 NNI 364
I
Sbjct: 180 QFI 182
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 46.5 bits (111), Expect = 7e-06
Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 32/184 (17%)
Query: 227 VVLIGQPNVGKSSLFNSLVGS-DVAIVTSIAGTTRDKITKTIQINKFL----FKITDTAG 281
+ G+ NVGKSSL N+L ++A + G T+ IN F ++ D G
Sbjct: 27 IAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQ-------LINFFEVDDELRLVDLPG 79
Query: 282 IPDINSKIKKNINEVEKIG--IERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNF-PM 338
K EK IE + N ++ + DAR+ D D+++I+ +
Sbjct: 80 Y----GYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHP-PKDLDREMIEFLLEL 134
Query: 339 NIPVIYVWNKIDYSGHQKNINYKNNIAN------------IYLSASKRIGINLLRNTLLD 386
IPVI V K D + N +A + S+ K+ GI+ L+ +L+
Sbjct: 135 GIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILE 194
Query: 387 LIEK 390
+++
Sbjct: 195 WLKE 198
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 45.9 bits (110), Expect = 2e-05
Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 4/85 (4%)
Query: 199 NELIKIKKKLLK-IIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAG 257
+++K KKLLK ++ K + + + ++IG PNVGKS+L N L G +A + G
Sbjct: 95 KKILKAAKKLLKEKNERRKAKGMRPRAIRAMIIGIPNVGKSTLINRLAGKKIAKTGNRPG 154
Query: 258 TTRDKITKTIQINKFLFKITDTAGI 282
T+ + + I++ K L + DT GI
Sbjct: 155 VTKAQ--QWIKLGKGLE-LLDTPGI 176
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 44.2 bits (104), Expect = 5e-05
Identities = 29/138 (21%), Positives = 55/138 (39%), Gaps = 21/138 (15%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRD-KITKTIQINKFLFKITDTAGIPDI 285
+V++G VGK++L N LVG + D T ++ DTAG +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67
Query: 286 NSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDF-----DKKIIKNFPMNI 340
S + + ++ I+ V D+ + +D +++ + P ++
Sbjct: 68 RSLRPE---------------YYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDV 112
Query: 341 PVIYVWNKIDYSGHQKNI 358
P++ V NKID Q +
Sbjct: 113 PILLVGNKIDLFDEQSSS 130
>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 = 43.8 bits (104), Expect = 5e-05
Identities = 30/100 (30%), Positives = 43/100 (43%), Gaps = 26/100 (26%)
Query: 194 KNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSD----- 248
K ELI+ +I + K R +V ++G NVGKS+L N+L+ S+
Sbjct: 107 KGWGVEELIE------EIKKLAKYRG------DVYVVGATNVGKSTLINALLKSNGGKVQ 154
Query: 249 ------VAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
V+ I GTT I + K L+ DT GI
Sbjct: 155 AQALVQRLTVSPIPGTTLGLIKIPLGEGKKLY---DTPGI 191
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 44.6 bits (106), Expect = 7e-05
Identities = 43/173 (24%), Positives = 79/173 (45%), Gaps = 33/173 (19%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFK-----ITDTAG 281
+V+ G PNVGKSSL L + + T TK I + F + DT G
Sbjct: 171 IVVAGYPNVGKSSLVRKLTTAKPEV-APYPFT-----TKGIHVGHFERGYLRIQVIDTPG 224
Query: 282 IPDINSKIKKNINEVEKIGIERTWVELKN-SDIIIYVQDAR----Y--DKHTDFDKKIIK 334
+ D + + NE+E+ I + L++ + +I+++ D Y ++ ++I +
Sbjct: 225 LLD---RPLEERNEIERQAI----LALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKE 277
Query: 335 NFPMNIPVIYVWNKIDYSGHQK------NINYKNNIANIYLSASKRIGINLLR 381
F P++ V NKID + +K ++ + + +SA+K G++ LR
Sbjct: 278 LF--KAPIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLR 328
>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 = 42.9 bits (102), Expect = 8e-05
Identities = 35/137 (25%), Positives = 61/137 (44%), Gaps = 32/137 (23%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFK----ITDTA 280
+ ++G+ + GKS+L N+L+G +V + T + TT IT + ++ + DT
Sbjct: 1 FLLAVVGEFSAGKSTLLNALLGEEV-LPTGVTPTT-AVIT----VLRYGLLKGVVLVDTP 54
Query: 281 GIPDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHT------DFDKKIIK 334
G +NS I+ + E L +D +I+V A +F K+I+K
Sbjct: 55 G---LNSTIEHHTEITESF--------LPRADAVIFVLSAD---QPLTESEREFLKEILK 100
Query: 335 NFPMNIPVIYVWNKIDY 351
+ +V NKID
Sbjct: 101 WS--GKKIFFVLNKIDL 115
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 40.8 bits (96), Expect = 4e-04
Identities = 33/142 (23%), Positives = 53/142 (37%), Gaps = 30/142 (21%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSD-VAIVTSIAGTTRDKITKTIQINKFLFKITDTAG 281
+ +VLIG VGKSSL SLV + V + TI + ++ T
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEI------TIPADVTPERVPTT-- 52
Query: 282 IPDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTD--FDKKIIKNFPM- 338
I D +S+ + N E++ +++I V Y ++ K P+
Sbjct: 53 IVDTSSRPQDRANLAA---------EIRKANVICLV----YSVDRPSTLERIRTKWLPLI 99
Query: 339 -----NIPVIYVWNKIDYSGHQ 355
+P+I V NK D
Sbjct: 100 RRLGVKVPIILVGNKSDLRDGS 121
>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 = 40.4 bits (95), Expect = 4e-04
Identities = 21/56 (37%), Positives = 31/56 (55%)
Query: 205 KKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTR 260
K L+ +++Q K + ++V IG PNVGKSS+ N+L V V I G T+
Sbjct: 83 KGALINLLRQFAKLHSDKKQISVGFIGYPNVGKSSVINTLRSKKVCKVAPIPGETK 138
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 41.9 bits (99), Expect = 5e-04
Identities = 28/99 (28%), Positives = 45/99 (45%), Gaps = 9/99 (9%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDIN 286
V L+G P+VGKS+L N L + V TT + + ++ ++ D GI +
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSE-VADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIEGA 124
Query: 287 SKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKH 325
S + +V + + R N+D+II V D D H
Sbjct: 125 SSGRGRGRQV--LSVAR------NADLIIIVLDVFEDPH 155
Score = 28.4 bits (64), Expect = 8.1
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 340 IPVIYVWNKIDYSGHQKNINYKNNIANIYLSASKRIGINLLRNTLLDLIE 389
P +YV NKID G ++ ++ +SA K I ++ L+ + D++
Sbjct: 240 KPALYVVNKIDLPGLEELERLARKPNSVPISAKKGINLDELKERIWDVLG 289
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 41.1 bits (97), Expect = 6e-04
Identities = 30/129 (23%), Positives = 54/129 (41%), Gaps = 29/129 (22%)
Query: 213 QQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKF 272
+ K + + L ++++G+ VGKSS NS+ G V++ T + ++++
Sbjct: 20 LEAKLKKELDFSLTILVLGKTGVGKSSTINSIFGERKVSVSAFQSET----LRPREVSRT 75
Query: 273 L--FKIT--DTAGIPD-----INSKIKKNINEVEKIGIERTWVELKNS--DIIIYVQDAR 321
+ FK+ DT G+ + +N KI I LK D+++YV R
Sbjct: 76 VDGFKLNIIDTPGLLESQDQRVNRKILSIIKRF-----------LKKKTIDVVLYVD--R 122
Query: 322 YDKHTDFDK 330
D D
Sbjct: 123 LD-MYRVDN 130
>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 = 41.1 bits (97), Expect = 0.001
Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 222 RNGLNVVLIGQPNVGKSSLFNSLVG-----SDVAIVTSIAGTTRDKITKTIQINKFLFKI 276
RN +V ++G NVGKSSL N L+ DV + GTT D I + L+
Sbjct: 152 RNKKDVYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLY-- 209
Query: 277 TDTAGI 282
DT GI
Sbjct: 210 -DTPGI 214
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 39.3 bits (93), Expect = 0.001
Identities = 49/193 (25%), Positives = 77/193 (39%), Gaps = 53/193 (27%)
Query: 227 VVLIGQPNVGKSSLFNSLVGS-DVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDI 285
+ G+ NVGKSSL N+L ++A + G +T IN F ++
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPG-------RTQLINFF-----------EV 68
Query: 286 NSKI-----------KKNINEVEKIG--IE---RTWVELKNSDIIIYVQDARYDKH--TD 327
N K+ K + E EK IE RT LK ++I D+R H +
Sbjct: 69 NDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTRENLKGVVLLI---DSR---HPLKE 122
Query: 328 FDKKIIKNF-PMNIPVIYVWNKID---YSGHQKNIN-----YKNNIANIYL-SASKRIGI 377
D ++I+ IPV+ V K D +K + K + L S+ K+ GI
Sbjct: 123 LDLQMIEWLKEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGI 182
Query: 378 NLLRNTLLDLIEK 390
+ LR + + +
Sbjct: 183 DELRAAIAKWLAE 195
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 40.0 bits (95), Expect = 0.002
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 224 GLNVVLIGQPNVGKSSLFNSLVGSDVAI 251
GL ++G PNVGKS+LFN+L +
Sbjct: 2 GLKCGIVGLPNVGKSTLFNALTKAGAEA 29
>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 = 38.5 bits (90), Expect = 0.002
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 12/62 (19%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKIT------DTA 280
V ++G P VGKSS+ N+L G A + I G TK IQ L +I DT
Sbjct: 102 VGVVGYPKVGKSSIINALKGRHSASTSPIPG--SPGYTKGIQ----LVRIDSKIYLIDTP 155
Query: 281 GI 282
G+
Sbjct: 156 GV 157
Score = 38.1 bits (89), Expect = 0.003
Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 9/94 (9%)
Query: 308 LKNSDIIIYVQDARYDKHTDFDK--KIIKNFPMNIPVIYVWNKIDYSGHQ-----KNINY 360
+K +D+++ V DAR + T K ++ + +I V NK D + K +
Sbjct: 9 IKEADVVLEVVDARDPELTRSRKLERMALE--LGKKLIIVLNKADLVPREVLEKWKEVFE 66
Query: 361 KNNIANIYLSASKRIGINLLRNTLLDLIEKTQTI 394
+ +Y+SA +R+G +LR T+ +L + +
Sbjct: 67 SEGLPVVYVSARERLGTRILRRTIKELAIDGKPV 100
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 39.9 bits (94), Expect = 0.002
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVGSDVAI 251
L + ++G PNVGKS+LFN+L + I
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKAGAEI 29
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 38.9 bits (91), Expect = 0.004
Identities = 49/192 (25%), Positives = 85/192 (44%), Gaps = 28/192 (14%)
Query: 207 KLLKIIQQGKKRALIRNGL-NVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITK 265
++ K +QG+ RA I+ + V L+G N GKS+LFN + + V + T D +
Sbjct: 180 RVEKQREQGR-RARIKADVPTVSLVGYTNAGKSTLFNRITEARVYAADQLFATL-DPTLR 237
Query: 266 TIQINKFLFKI-TDTAG----IP-DINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQD 319
I + + DT G +P D+ + K T E + + ++++V D
Sbjct: 238 RIDVADVGETVLADTVGFIRHLPHDLVAAFKA------------TLQETRQATLLLHVVD 285
Query: 320 A---RYDKHTDFDKKIIKNFPMN-IPVIYVWNKID-YSGHQKNI--NYKNNIANIYLSAS 372
A R ++ + +++ + IP + V NKID + I + +N ++LSA
Sbjct: 286 AADVRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLDDFEPRIDRDEENKPIRVWLSAQ 345
Query: 373 KRIGINLLRNTL 384
GI LL L
Sbjct: 346 TGAGIPLLFQAL 357
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 39.1 bits (92), Expect = 0.004
Identities = 27/66 (40%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 222 RNGLNVVLIGQPNVGKSSLFNSL----VGSDVAIVTS-IAGTTRDKITKTIQINKFLFKI 276
R G +V ++G NVGKS+L N + G I TS GTT DKI + FL+
Sbjct: 158 REGRDVYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLY-- 215
Query: 277 TDTAGI 282
DT GI
Sbjct: 216 -DTPGI 220
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 38.0 bits (89), Expect = 0.008
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 218 RALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSI 255
A + G V L+G VGKS+L N+L+G +V ++
Sbjct: 189 AAWLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGAV 226
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 38.0 bits (89), Expect = 0.010
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 210 KIIQQGKKRALIR---NGLNVVLIGQPNVGKSSLFNSL 244
K + +K+ L+ N L + ++G PNVGKS+ FN+L
Sbjct: 4 KKKMEEEKKVLLGRPGNNLKMGIVGLPNVGKSTTFNAL 41
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 37.3 bits (87), Expect = 0.014
Identities = 31/139 (22%), Positives = 52/139 (37%), Gaps = 27/139 (19%)
Query: 190 LILNKNDFFNELIKIKKKLLKIIQQGKKRALIRNGLN---------------VVLIGQPN 234
++LNK D ++ K+LL+ + L + N VL+GQ
Sbjct: 115 IVLNKIDLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELLAGKITVLLGQSG 174
Query: 235 VGKSSLFNSLVGSDVAIVTSIAGTT-RDKITKTIQINKFLFK----ITDTAGIPDINSKI 289
VGKS+L N+L+ I+ R + T T + F I DT G +
Sbjct: 175 VGKSTLINALLPELNQKTGEISEKLGRGRHT-TTHVELFPLPGGGWIIDTPGF----RSL 229
Query: 290 KKNINEVEKIGIERTWVEL 308
+ +E + + + E
Sbjct: 230 G--LAHLEPEDLVQAFPEF 246
>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 = 35.9 bits (84), Expect = 0.015
Identities = 37/140 (26%), Positives = 54/140 (38%), Gaps = 42/140 (30%)
Query: 227 VVLIGQPNVGKSSLFNSLVGS--DVAIVTSIAGTTRDKITKTIQINKFLFKIT--DTAGI 282
+VLIG VGK+SL V + ++I D +KTI+++ K+ DTA
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGV---DFKSKTIEVDGKKVKLQIWDTA-- 57
Query: 283 PDINSKIKKNINEVEKIGIER----TWVELKNSDIIIYVQDARYD--KHTDFD------K 330
G ER T + + I V YD F+
Sbjct: 58 -----------------GQERFRSITSSYYRGAHGAILV----YDVTNRESFENLDKWLN 96
Query: 331 KIIKNFPMNIPVIYVWNKID 350
++ + P NIP+I V NK D
Sbjct: 97 ELKEYAPPNIPIILVGNKSD 116
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 35.6 bits (83), Expect = 0.017
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 218 RALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAG-------TTR 260
+ L++ VL GQ VGKS+L N+L+ I+ TT
Sbjct: 30 KPLLKGKT-SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTT 78
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ 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. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 36.2 bits (85), Expect = 0.019
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 218 RALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSI 255
R L++ VL+GQ VGKS+L N+L+ V I
Sbjct: 80 RELLKGKT-SVLVGQSGVGKSTLLNALLPELVLATGEI 116
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 37.2 bits (87), Expect = 0.019
Identities = 19/116 (16%), Positives = 47/116 (40%), Gaps = 19/116 (16%)
Query: 181 FDFPEENQELILNK---NDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVVLI------- 230
D+PE ++ELI + + L+K++ + K ++ + +I + LN ++
Sbjct: 790 EDWPEVDEELIDVEAALAARWEALLKLRDPVNKALEAARLEKVIGSSLNAKVVIYTEDSE 849
Query: 231 ----GQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGI 282
+PN+GK + + S V + ++ + + + + + G
Sbjct: 850 LLYKLKPNLGK--VLIT---SAVEVAKALEALAGAEAEELVDGDGVELTVEKAEGE 900
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 36.4 bits (84), Expect = 0.023
Identities = 31/130 (23%), Positives = 64/130 (49%), Gaps = 8/130 (6%)
Query: 205 KKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKIT 264
+ KLL+++ GK + + L ++++G+ VGKSS NS++G +A V++ +
Sbjct: 21 QTKLLELL--GKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMM 78
Query: 265 KTIQINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDK 324
+ F I DT G+ + IN+ + + I + ++ K D+++YV +
Sbjct: 79 VSRTRAGFTLNIIDTPGLIE-----GGYIND-QAVNIIKRFLLGKTIDVLLYVDRLDAYR 132
Query: 325 HTDFDKKIIK 334
D ++I+
Sbjct: 133 VDTLDGQVIR 142
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 36.7 bits (86), Expect = 0.024
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 229 LIGQPNVGKSSLFNSLVGSDVAI 251
L+G+PNVGKS+ FN+ +DV I
Sbjct: 6 LVGKPNVGKSTFFNAATLADVEI 28
>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 = 36.1 bits (84), Expect = 0.029
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 229 LIGQPNVGKSSLFNSLVGSDVAI 251
L+G+PNVGKS+ FN+ +DV I
Sbjct: 3 LVGKPNVGKSTFFNAATLADVEI 25
>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 = 34.7 bits (80), Expect = 0.032
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 202 IKIKKKLLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRD 261
+ KL I + K + + G+ V ++G PNVGKSS N+L+ V SI GTT+
Sbjct: 69 GQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKL 128
Query: 262 KITKTIQINKFLFKITDTAGI 282
+ + +L+ DT GI
Sbjct: 129 QQDVKLDKEIYLY---DTPGI 146
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 35.3 bits (82), Expect = 0.038
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITD------TA 280
+V +G+ NVGKS+L L G V V G TR K + F +TD +
Sbjct: 12 IVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTR----KPNHYDWGDFILTDLPGFGFMS 66
Query: 281 GIPD-INSKIKKNI 293
G+P + KIK I
Sbjct: 67 GVPKEVQEKIKDEI 80
>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 = 34.8 bits (81), Expect = 0.061
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 12/71 (16%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN-----------KFL 273
N++++G+ +GKS+ N+L G+ + + + ITKT++I K
Sbjct: 5 FNIMVVGESGLGKSTFINTLFGTKL-YPSKYPPAPGEHITKTVEIKISKAELEENGVKLK 63
Query: 274 FKITDTAGIPD 284
+ DT G D
Sbjct: 64 LTVIDTPGFGD 74
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 35.5 bits (82), Expect = 0.061
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGS 247
L + LIG PN GK++LFN L G+
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLTGA 26
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. 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 = 180
Score = 34.1 bits (79), Expect = 0.080
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 226 NVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINK--FLFKITDTAG 281
+ ++G +VGKSSL V V S T + +K I + +I DTAG
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGH--FVESYYPTIENTFSKIITYKGQEYHLEIVDTAG 58
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including YchF,
possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis suggest
that YchF may be part of a nucleoprotein complex and may
function as a GTP-dependent translational factor.
Length = 274
Score = 34.4 bits (80), Expect = 0.090
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 230 IGQPNVGKSSLFNSLVGSDVA 250
+G PNVGKS+LFN+L S+
Sbjct: 4 VGLPNVGKSTLFNALTKSNAE 24
>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 = 32.8 bits (75), Expect = 0.095
Identities = 33/131 (25%), Positives = 50/131 (38%), Gaps = 22/131 (16%)
Query: 226 NVVLIGQPNVGKSSLFNSLVG-SDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPD 284
VV+IG GKSSL + LVG I G T T + + L I D G +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 285 INSKIKKNINEVEKIGIERTWVELKNSDIIIYVQD-ARYDKHTDFDKKI-----IKNFPM 338
+ + + +K +D I+ V D + + + I ++
Sbjct: 61 LKFEHI---------------IFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGG 105
Query: 339 NIPVIYVWNKI 349
IPVI V NK+
Sbjct: 106 KIPVILVGNKL 116
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 32.5 bits (75), Expect = 0.25
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN--KFLFKITDTAG 281
++LIG VGKSSL + + D TKTI+++ + +I DTAG
Sbjct: 3 IILIGDSGVGKSSLLSRFT-DGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAG 58
>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 = 32.9 bits (76), Expect = 0.28
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 227 VVLIGQPNVGKSSLFNSLVG--SDVA 250
V L+G P+VGKS+L + L S+VA
Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSEVA 28
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 33.1 bits (76), Expect = 0.30
Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 19/99 (19%)
Query: 216 KKRALIRNG--LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN--- 270
+ R L + G ++++G+ +GK++ N+L G+ + T I + + T++I
Sbjct: 13 RHRKLSKKGIDFTIMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITK 72
Query: 271 --------KFLFKITDTAGIPDI--NSK----IKKNINE 295
+ DT G D NSK I I++
Sbjct: 73 AELEEDGFHLNLTVIDTPGFGDFIDNSKCWEPIVDYIDD 111
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 32.2 bits (74), Expect = 0.30
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTR 260
+ ++G + GKSS+ N+L+G D+ + TTR
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDI-LPRGPGPTTR 33
>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 = 32.0 bits (73), Expect = 0.33
Identities = 33/149 (22%), Positives = 66/149 (44%), Gaps = 28/149 (18%)
Query: 208 LLKIIQQGKKRALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTI 267
LL I+++ K + R + ++L+G N GK+++ L D++ +T G K +
Sbjct: 1 LLSILRKLKPSS--RQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFN----IKNV 54
Query: 268 QINKFLFKITDTAGIPDINSKIKKNINEVEKIGIERTWVE-LKNSDIIIYVQDA----RY 322
Q + F + D G ++ I W +N+D++IYV D+ R+
Sbjct: 55 QADGFKLNVWDIGG--------QRKIRPY--------WRNYFENTDVLIYVIDSADRKRF 98
Query: 323 DK-HTDFDKKIIKNFPMNIPVIYVWNKID 350
++ + + + + +PV+ NK D
Sbjct: 99 EEAGQELVELLEEEKLAGVPVLVFANKQD 127
>gnl|CDD|215483 PLN02893, PLN02893, Cellulose synthase-like protein.
Length = 734
Score = 33.1 bits (76), Expect = 0.37
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 48 RFATYSSFFCKNNNIIDKGLVIYFKA-PHSYTGE 80
+FAT+ FCK N I+++ YF + HS++ E
Sbjct: 159 KFATHWLPFCKKNKIVERCPEAYFSSNSHSWSPE 192
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 32.3 bits (74), Expect = 0.37
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 226 NVVLIGQPNVGKSSLFNSLV-GSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPD 284
V+L+G + GK++LF L G + VTSI + + + K + D G
Sbjct: 2 TVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKK--LTLVDVPGHEK 59
Query: 285 INSKIKKNINEVEK 298
+ K+ + + K
Sbjct: 60 LRDKLLEYLKASLK 73
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 32.2 bits (74), Expect = 0.40
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQI-----NKFLFKITDT 279
L +VL+G+ GKS+ NS++G + + +TKT Q+ + + + DT
Sbjct: 1 LRIVLVGKTGNGKSATGNSILGRKA-FESKLRAQG---VTKTCQLVSRTWDGRIINVIDT 56
Query: 280 AGIPD---INSKIKKNI 293
G+ D N I K I
Sbjct: 57 PGLFDLSVSNDFISKEI 73
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 31.6 bits (72), Expect = 0.58
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSD 248
VVL+G VGKSSL N
Sbjct: 3 VVLLGDSGVGKSSLANIFTAGV 24
>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 = 31.3 bits (72), Expect = 0.58
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 223 NGLNVVLIGQPNVGKSSLFNSLVG 246
+G + G+ NVGKSSL N+L
Sbjct: 17 DGPEIAFAGRSNVGKSSLINALTN 40
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.3 bits (72), Expect = 0.84
Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 16/81 (19%)
Query: 190 LILNKNDFFNELIKIKKKLLKIIQQ------------GKKRALIR---NGLNVVLIGQPN 234
++LNK D ++L + ++ LL + + G+ ++ G VL GQ
Sbjct: 116 IVLNKIDLLDDLEEARE-LLALYRAIGYDVLELSAKEGEGLDELKPLLAGKVTVLAGQSG 174
Query: 235 VGKSSLFNSLVGSDVAIVTSI 255
VGKS+L N+L I
Sbjct: 175 VGKSTLLNALAPDLELKTGEI 195
>gnl|CDD|184316 PRK13771, PRK13771, putative alcohol dehydrogenase; Provisional.
Length = 334
Score = 31.5 bits (72), Expect = 0.90
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 17/93 (18%)
Query: 218 RALIRNGLNVVLIGQPNVGKSSLFNSLVG----SDVAIVTSIAGTTRD-----KITKTIQ 268
R+L G ++ IG NV S ++ +G D+ I+ I+ T RD K+ +
Sbjct: 243 RSL-NMGGKIIQIG--NVDPSPTYSLRLGYIILKDIEIIGHISATKRDVEEALKLVAEGK 299
Query: 269 INKFLFKITDTAGIPDINSKIK--KNINEVEKI 299
I I + +I+ ++ K+ + + KI
Sbjct: 300 IKPV---IGAEVSLSEIDKALEELKDKSRIGKI 329
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 31.9 bits (73), Expect = 0.96
Identities = 37/146 (25%), Positives = 67/146 (45%), Gaps = 25/146 (17%)
Query: 120 KRAFLNNKLDLIQVEAIIDLINASTESAAKSAM--ISLSGKFSKLINILLDKLINL---- 173
+ +L +L I+ E I+ + K + + L + K+I L KL L
Sbjct: 224 REYYLREQLKAIKKELGIEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSS 283
Query: 174 ------RTLIEFSFDFP-----EENQEL-----ILNKNDFFNELIKIKKKLLKIIQQGKK 217
R +++ D P +EN +L IL+++ + L K+K+++L+ + K
Sbjct: 284 SEFTVTRNYLDWLTDLPWGKYSKENLDLKRAKEILDEDHY--GLKKVKERILEYLAVQKL 341
Query: 218 RALIRNGLNVVLIGQPNVGKSSLFNS 243
R ++ G + L+G P VGK+SL S
Sbjct: 342 RGKMK-GPILCLVGPPGVGKTSLGKS 366
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 31.2 bits (71), Expect = 1.0
Identities = 21/58 (36%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFK---ITDTAGI 282
V GQ VGKSSL N+L S V I+ T + F F I DT G
Sbjct: 124 VFAGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGGLIADTPGF 181
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 30.5 bits (70), Expect = 1.1
Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 18/76 (23%)
Query: 331 KIIKNFPMNIPVIYVWNKID-YSGHQKNIN-YKNNIANIYL--------------SASKR 374
K N+P+I NKID G + + KN ++ + L SA
Sbjct: 95 NHAKAA--NVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTG 152
Query: 375 IGINLLRNTLLDLIEK 390
GI+ L +L L E
Sbjct: 153 EGIDDLLEAILLLAEV 168
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.6 bits (70), Expect = 1.6
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 19/81 (23%)
Query: 190 LILNKND--------FFNELIKIKKKL----LKI-IQQG----KKRALIRNGLNVVLIGQ 232
++LNK D F NE + I + + L + G + A + +++ +GQ
Sbjct: 155 IVLNKIDLLDDEGRAFVNEQLDIYRNIGYRVLMVSSHTGEGLEELEAALTGRISIF-VGQ 213
Query: 233 PNVGKSSLFNSLVGSDVAIVT 253
VGKSSL N+L+ + I+
Sbjct: 214 SGVGKSSLINALLP-EAEILV 233
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 30.6 bits (70), Expect = 1.8
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 221 IRNGLNVVLIGQPNVGKSSLFNSLVG 246
+ G + L+G GK+SL N+L+G
Sbjct: 373 LPAGQRIALVGPSGAGKTSLLNALLG 398
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 29.8 bits (68), Expect = 1.9
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN--KFLFKITDTAG 281
+VL+G VGKSSL + I D TKTI+++ +I DTAG
Sbjct: 2 LVLVGDGGVGKSSLLIRFT-QNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAG 57
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 30.0 bits (67), Expect = 2.1
Identities = 19/55 (34%), Positives = 25/55 (45%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAG 281
++LIG VGKSSL S + S V + G T+ + I DTAG
Sbjct: 17 ILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAG 71
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 30.7 bits (69), Expect = 2.2
Identities = 32/109 (29%), Positives = 53/109 (48%), Gaps = 19/109 (17%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIA-GTTR-DKITKTIQINKFLFKITDTAGI 282
LN++++G+ VGKS+ NS+ G + GTT +I +Q K ++ DT G+
Sbjct: 119 LNILVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVK--IRVIDTPGL 176
Query: 283 PDI---NSKIKKNINEVEKIGIERTWVELKNS--DIIIYVQDARYDKHT 326
SK +K ++ V+K +K + DI++YV R D T
Sbjct: 177 KSSASDQSKNEKILSSVKKF--------IKKNPPDIVLYVD--RLDMQT 215
>gnl|CDD|204014 pfam08652, RAI1, RAI1 like PD-(D/E)XK nuclease. RAI1 is homologous
to Caenorhabditis elegans DOM-3 and human DOM3Z and
binds to a nuclear exoribonuclease. It is required for
5.8S rRNA processing. Profile-profile comparison tools
demonstrate this to be a PD-(D/E)XK nuclease, with a
full set of canonical active site signature motifs
characteristic to the PD-(D/E)XK nuclease superfamily.
Length = 69
Score = 27.9 bits (63), Expect = 2.3
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 9/45 (20%)
Query: 305 WVELKNSDIIIYVQDARYDKHTDFDKKIIK----NFPMNIPVIYV 345
+VELK S I + R +F++K++K +F + +P I V
Sbjct: 18 YVELKTSKEIHNPRQVR-----NFERKLLKWWAQSFLVGVPRIVV 57
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerise to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 30.0 bits (68), Expect = 2.4
Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 224 GLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQI 269
++++G+ +GK++L N+L +D+ I +KI KT++I
Sbjct: 4 DFTLMVVGESGLGKTTLINTLFLTDL-IPERGIPGPSEKIKKTVEI 48
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 30.2 bits (69), Expect = 2.5
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 226 NVVLIGQPNVGKSSLFNSL 244
+V L+G PN GKS+L +++
Sbjct: 161 DVGLVGLPNAGKSTLLSAV 179
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. 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 facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. 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. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 29.6 bits (67), Expect = 2.6
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQIN--KFLFKITDTAG 281
L V+++G VGK+SL N V + A D +TK + ++ +I DTAG
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYK-ATIGADFLTKEVTVDDRLVTLQIWDTAG 58
>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 = 29.3 bits (67), Expect = 2.6
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 229 LIGQPNVGKSSLFNSL 244
L+G PN GKS+L +++
Sbjct: 5 LVGLPNAGKSTLLSAI 20
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.8 bits (65), Expect = 2.8
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 221 IRNGLNVVLIGQPNVGKSS----LFNSLVGSDVAIVTSIAGTTRDKITKTI 267
R VL G+ GK++ L L V V + + T + + I
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKI 51
>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 = 29.7 bits (68), Expect = 3.4
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 227 VVLIGQPNVGKSSLFNSL 244
V L+G PN GKS+L +++
Sbjct: 160 VGLVGLPNAGKSTLISAV 177
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 29.9 bits (67), Expect = 4.0
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 158 KFSKLINILLDKLINLRTLIEFSFDFPEENQELILNKNDF--FNELIKI 204
+F KL+N+ K+I+ L+E F F N+ELI F ++E K
Sbjct: 434 EFLKLLNLYSQKIIDKNDLVERLFAFLGSNEELIRWFKAFINYSEPEKE 482
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. 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
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 28.7 bits (65), Expect = 4.6
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 29/70 (41%)
Query: 227 VVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDK-------------ITKTIQINKFL 273
+VLIG VGKS+L + TR++ T+TIQI+
Sbjct: 6 IVLIGDSGVGKSNLLSRF--------------TRNEFNLDSKSTIGVEFATRTIQIDGKT 51
Query: 274 FK--ITDTAG 281
K I DTAG
Sbjct: 52 IKAQIWDTAG 61
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 28.7 bits (65), Expect = 4.7
Identities = 28/147 (19%), Positives = 46/147 (31%), Gaps = 47/147 (31%)
Query: 222 RNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAG 281
RN ++G GKS+L + +G + A
Sbjct: 2 RNVFLCFVLGAKGSGKSALLQAFLGRSFS---------------------------QNAY 34
Query: 282 IPDINSKIKKNINEVEKIGIERTWV----------------ELKNSDIIIYVQDARYDKH 325
P I + +N VE G E+ + EL D+ V D+
Sbjct: 35 SPTIKPRYA--VNTVEVPGQEKYLILREVGEDEEAILLNDAELAACDVACLVYDSSDPNS 92
Query: 326 TDFDKKIIKNFPM--NIPVIYVWNKID 350
+ ++ K + M IP ++V K D
Sbjct: 93 FSYCAEVYKKYFMLGEIPCLFVAAKAD 119
>gnl|CDD|214412 MTH00047, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 194
Score = 28.8 bits (65), Expect = 4.9
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 52 YSSFFCKNNNIIDKGLVIYFKAPHSY--TGEDVI 83
Y SF + +DK L + + P+ T DVI
Sbjct: 103 YDSFMTDDIFGVDKPLRLVYGVPYHLLVTSSDVI 136
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 29.3 bits (66), Expect = 5.2
Identities = 42/186 (22%), Positives = 71/186 (38%), Gaps = 48/186 (25%)
Query: 157 GKFSKLINILLDKLINLRTLIEFSFDFPEENQELILNK----------NDFFNELIK--I 204
G ++++ L L +R+LI + E E IL +F L K I
Sbjct: 118 GVAARVLENLGVDLSKIRSLI---LNLIGEIIEAILGAEQSRSKTPTLEEFGTNLTKEAI 174
Query: 205 KKKLLKIIQQGKK---------RALIRNGLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSI 255
L +I + K+ R N +LIG+P VGK+ AI +
Sbjct: 175 DGNLDPVIGREKEIERVIQILGRRTKNN---PILIGEPGVGKT-----------AIAEGL 220
Query: 256 AGTTRDKITKTIQINKFLFKITDTAGIPDINSKI--KKNINEVEKIGIERTWVELKNSDI 313
A ++ I +K + + DI + K E E+ ++R + E++ ++
Sbjct: 221 AQRIVNRDVPDILEDKLVITL-------DIGLLLAGTKYRGEFEER-LKRIFDEIQENNN 272
Query: 314 IIYVQD 319
II V D
Sbjct: 273 IILVID 278
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.9 bits (66), Expect = 5.6
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 226 NVVLIGQPNVGKSSL 240
+V L+G PNVGKS+L
Sbjct: 160 DVGLVGFPNVGKSTL 174
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
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.
Length = 222
Score = 28.6 bits (65), Expect = 5.7
Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 221 IRNGLNVVLIGQPN-VGKSSLFNSLVG 246
+ G V L+G N GK++L +++G
Sbjct: 23 VPEGEIVALLG-RNGAGKTTLLKTIMG 48
>gnl|CDD|213067 cd11751, GH94N_like_4, Glycoside hydrolase family 94
N-terminal-like domain of uncharacterized function. The
glycoside hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cellobiose
phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase
(EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-),
amongst other members. Their N-terminal domain is
involved in oligomerization and may play a role in
catalysis, but it is separate from the catalytic domain
[an (alpha/alpha)(6) barrel]. The GH64N domain, as
represented by this model, is found near the N-terminus
of GH94 members and related proteins with
uncharacterized specificities.
Length = 223
Score = 28.5 bits (64), Expect = 5.7
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 15/74 (20%)
Query: 312 DIIIYVQ---DARYDKHTDFDKKIIK---NFPMNIPVIYV----WNKIDYSGHQKNINYK 361
+ Y + D+H +F K I+ + +N IY W D G N N+
Sbjct: 87 SVFSYFEWELGGFPDEHREFHKLFIETSFDRELN--GIYARKYLWGFPDEKGRHNNRNWP 144
Query: 362 NNIANIYLSASKRI 375
+ +AS+ +
Sbjct: 145 Y---VAFHAASEPV 155
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 28.3 bits (64), Expect = 5.9
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 221 IRNGLNVVLIGQPNVGKSSLFNSLVG 246
I+ G +++ G GKSSLF +L G
Sbjct: 24 IKPGDRLLITGPSGTGKSSLFRALAG 49
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 28.9 bits (65), Expect = 6.0
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 4/71 (5%)
Query: 170 LINLRTLIEFSFDFPEENQELILN--KNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNV 227
+ + K++ ++LI L ++ +Q K A +GL V
Sbjct: 47 FLPSEAFSMSELTELQALLPQARPYLKSEALDDLIGESPSLQELREQIK--AYAPSGLPV 104
Query: 228 VLIGQPNVGKS 238
++IG+ GK
Sbjct: 105 LIIGETGTGKE 115
>gnl|CDD|184185 PRK13618, psbV, cytochrome c-550; Provisional.
Length = 163
Score = 28.3 bits (63), Expect = 6.3
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 60 NNIIDKGLVIYFKAPHSYTGEDVI-ELH 86
+NI +GLV Y K P +Y GE+ I E+H
Sbjct: 93 DNI--EGLVDYMKNPTTYDGEEEISEIH 118
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. 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 facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. 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. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 28.0 bits (63), Expect = 6.4
Identities = 43/170 (25%), Positives = 66/170 (38%), Gaps = 35/170 (20%)
Query: 225 LNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITD-TAGIP 283
L ++LIG VGKSSL T + ++ TI ++ FK+ T
Sbjct: 1 LKILLIGDSGVGKSSLLLRFT----------DDTFDEDLSSTIGVD---FKVKTVTVD-- 45
Query: 284 DINSKIKKNINEVEKIGIER----TWVELKNSDIIIYVQD-ARYDKHTDFDKKI--IKNF 336
K+K I + G ER T + + +I V D R D + D + + +
Sbjct: 46 --GKKVKLAIWDTA--GQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTY 101
Query: 337 PMNIPVIY--VWNKIDYSGHQ------KNINYKNNIANIYLSASKRIGIN 378
N + V NKID + + K+N+ I SA RIG+
Sbjct: 102 STNPDAVKMLVGNKIDKENREVTREEGQKFARKHNMLFIETSAKTRIGVQ 151
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 28.8 bits (65), Expect = 6.6
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 184 PEENQELILNKNDFFN-ELIKIKKKLL-KIIQQGKKRALIRNGL----NVVLIGQPNVGK 237
+E++E +L DF I++ ++L+ ++I Q +I+ +V++IG P GK
Sbjct: 4 EDEDEEDLLGGLDFETTSDIEVPERLIDQVIGQEHAVEVIKKAAKQRRHVMMIGSPGTGK 63
Query: 238 SSL 240
S L
Sbjct: 64 SML 66
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 28.3 bits (64), Expect = 7.6
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 224 GLNVVLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDK 262
GL +VL G VGKS+L +L+ D + S++ TTR
Sbjct: 4 GLLIVLSGPSGVGKSTLVKALL-EDDKLRFSVSATTRKP 41
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 28.0 bits (63), Expect = 7.6
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 20/72 (27%)
Query: 169 KLINLRTLIEFSFDFPEENQELILNKNDFFNELIKIKKKLLKIIQQGKKRALIRNGLNVV 228
KL +TL +F F + ++L+ + I N++
Sbjct: 12 KLPARKTLEDFDFRAARG-----------------LDRRLIAELAGL---DWIEQAENLL 51
Query: 229 LIGQPNVGKSSL 240
L+G P VGK+ L
Sbjct: 52 LLGPPGVGKTHL 63
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 28.8 bits (65), Expect = 8.1
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 12/89 (13%)
Query: 167 LDKLINLRTLIEFSFDFPEENQ---ELILNKNDFFNELIKIKKKLLKIIQQGKKRAL--- 220
L +L R +E + E ++ +D + I ++ L + + L
Sbjct: 356 LLRLAEFRQALE-AAQMDTEKPARTGRRIDFDDNADHGITLEN--LSLRTPDGQTLLSEL 412
Query: 221 ---IRNGLNVVLIGQPNVGKSSLFNSLVG 246
+R G +++ G+ GK+SL +L G
Sbjct: 413 NFEVRPGERLLITGESGAGKTSLLRALAG 441
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.5 bits (65), Expect = 8.2
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 229 LIGQPNVGKSSLFNSL 244
L+G PN GKS+L +++
Sbjct: 163 LVGLPNAGKSTLISAV 178
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 28.0 bits (63), Expect = 8.7
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 222 RNGLNVVLIGQPNVGKSSLFNSLVGS 247
+ V++ G P +GK+SL +L
Sbjct: 1 TKNIKVLIYGPPGIGKTSLAKTLPPK 26
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 28.2 bits (62), Expect = 8.7
Identities = 25/203 (12%), Positives = 62/203 (30%), Gaps = 8/203 (3%)
Query: 228 VLIGQPNVGKSSLFNSLVGSDVAIVTSIAGTTRDKITKTIQINKFLFKITDTAGIPDINS 287
V+IG GKS+L +L + + + + + +I
Sbjct: 3 VIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKLLPFLLDEN--------EIEI 54
Query: 288 KIKKNINEVEKIGIERTWVELKNSDIIIYVQDARYDKHTDFDKKIIKNFPMNIPVIYVWN 347
++ I E GI + + + I+ Y K + + ++
Sbjct: 55 PLEFEIEEFLIDGIRYRYGFELDKEDILEELLYEYRKGEELLFERERSKESFEKSPEKKR 114
Query: 348 KIDYSGHQKNINYKNNIANIYLSASKRIGINLLRNTLLDLIEKTQTIESSPYLARERHIH 407
++ + + + + L++ + + LL + + + L + +
Sbjct: 115 ELRGLREVLLLLNLSLSSFLLLASLEILLSILLPFSFILGNLRNLRNIELKLLDLVKRLF 174
Query: 408 SLNEANYYLSCAIKIINQSEKNF 430
++ L IK I+ K
Sbjct: 175 LESDLLRLLKLLIKGISDGTKRL 197
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 0.138 0.391
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,121,780
Number of extensions: 2452634
Number of successful extensions: 3328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3226
Number of HSP's successfully gapped: 238
Length of query: 472
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 372
Effective length of database: 6,502,202
Effective search space: 2418819144
Effective search space used: 2418819144
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 (27.1 bits)