RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1007
(445 letters)
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 361 bits (930), Expect = e-122
Identities = 138/338 (40%), Positives = 183/338 (54%), Gaps = 67/338 (19%)
Query: 98 HGKCGVSVIRVSGPDTLNALKSMACYPDQKVSKPRYASLRNIVDPVSEVVLDEGLCLWFP 157
G+ G+ +IR+SGPD L + + +K+ KPR A +I DP V+DE L L+FP
Sbjct: 14 PGRGGIGIIRISGPDALEIAQKLF---GKKLPKPRTAHYGHIRDP--GEVIDEVLVLYFP 68
Query: 158 KPNSFTGEDCCEFQVHGSIAVINAILGALTKLPGLRPAEPGEFSKRAFFNNKLDLTQTEA 217
PNSFTGED E Q HG AV+N IL L L G R AEPGEF+KRAF N KLDLTQ EA
Sbjct: 69 APNSFTGEDVVEIQCHGGPAVLNLILELLLAL-GARLAEPGEFTKRAFLNGKLDLTQAEA 127
Query: 218 LGDLIQAETELQRQKALHQMKGNLKQLYSEWRQLILESLASVEAYIDFSEDEIIEDNILN 277
+ DLI A+TE + AL Q++G L +L +E R+ +LE LA VEA IDF E++
Sbjct: 128 IADLIDAKTEAAARLALRQLQGALSKLINELREELLELLALVEAAIDFPEED-------- 179
Query: 278 TVRSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVICLASVEAYIDFSEDEIIEDNILNTV 337
I+F DE I + +
Sbjct: 180 -------------------------------------------IEFLSDEKILEKLEE-- 194
Query: 338 RSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIP 397
L +E + + + G +R G+K VI G PNVGKSSL+N L ++ +IVT I
Sbjct: 195 ------LIAELEALLASARQ-GEILREGLKVVIAGRPNVGKSSLLNALLGEERAIVTDIA 247
Query: 398 GTTRDVIEKHLDIGGYPVILLDTAGLRTTTSDIIETEG 435
GTTRDVIE+H+++ G P+ L+DTAG+R T D +E G
Sbjct: 248 GTTRDVIEEHINLDGIPLRLIDTAGIRETD-DEVEKIG 284
Score = 80.5 bits (200), Expect = 2e-16
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 5/68 (7%)
Query: 29 TIFALSSGHGKCGVSVIRVSGPDTLNALKSMACYPDQKVPKPRYASLRNIVDPVSKVVLD 88
TI A+++ G+ G+ +IR+SGPD L + + +K+PKPR A +I DP V+D
Sbjct: 6 TIAAIATPPGRGGIGIIRISGPDALEIAQKLF---GKKLPKPRTAHYGHIRDP--GEVID 60
Query: 89 EGLCLWFP 96
E L L+FP
Sbjct: 61 EVLVLYFP 68
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 337 bits (867), Expect = e-112
Identities = 134/338 (39%), Positives = 184/338 (54%), Gaps = 65/338 (19%)
Query: 98 HGKCGVSVIRVSGPDTLNALKSMACYPDQKVSKPRYASLRNIVDPVSEVVLDEGLCLWFP 157
G+ + ++R+SGPD L + + + K+ KPR A +I D E++ DE L L+F
Sbjct: 14 PGEGAIGIVRISGPDALEIAQKL--FGGLKLPKPRTAHYGHIKDENGEII-DEVLVLYFK 70
Query: 158 KPNSFTGEDCCEFQVHGSIAVINAILGALTKLPGLRPAEPGEFSKRAFFNNKLDLTQTEA 217
PNSFTGED E Q HG V+N IL L KL G R AEPGEFSKRAF N KLDLTQ EA
Sbjct: 71 APNSFTGEDVVEIQCHGGPVVVNLILELLLKL-GARLAEPGEFSKRAFLNGKLDLTQAEA 129
Query: 218 LGDLIQAETELQRQKALHQMKGNLKQLYSEWRQLILESLASVEAYIDFSEDEIIEDNILN 277
+ DLI A+TE + AL Q++G L QL +E
Sbjct: 130 IADLIDAKTEQAARIALRQLQGALSQLINEL----------------------------- 160
Query: 278 TVRSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVICLASVEAYIDFSEDEIIEDNILNTV 337
R +++L LA VEA IDF E++I E+ +L +
Sbjct: 161 --REALLEL---------------------------LAQVEANIDFPEEDI-EELVLEKI 190
Query: 338 RSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIP 397
R ++ +L +++ + + K G +R G+K VI+G PNVGKSSL+N L + +IVT I
Sbjct: 191 REKLEELIAELDELLA-TAKQGKILREGLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIA 249
Query: 398 GTTRDVIEKHLDIGGYPVILLDTAGLRTTTSDIIETEG 435
GTTRDVIE+ +++ G PV L+DTAG+R T D++E G
Sbjct: 250 GTTRDVIEEDINLNGIPVRLVDTAGIR-ETDDVVERIG 286
Score = 74.5 bits (184), Expect = 2e-14
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 29 TIFALSSGHGKCGVSVIRVSGPDTLNALKSMACYPDQKVPKPRYASLRNIVDPVSKVVLD 88
TI A+++ G+ + ++R+SGPD L + + + K+PKPR A +I D + ++D
Sbjct: 6 TIAAIATAPGEGAIGIVRISGPDALEIAQKL--FGGLKLPKPRTAHYGHIKD-ENGEIID 62
Query: 89 EGLCLWFP 96
E L L+F
Sbjct: 63 EVLVLYFK 70
>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 = 193 bits (492), Expect = 8e-57
Identities = 105/332 (31%), Positives = 157/332 (47%), Gaps = 68/332 (20%)
Query: 99 GKCGVSVIRVSGPDTLNALKSMACYPDQKVSKPRYASLRNIVDPVSEVVLDEGLCLWFPK 158
+ +IR+SGPD+L+ LK + S R +I+D ++ DE L F
Sbjct: 5 FNSAIHIIRLSGPDSLSILKKIT-NKLNTASGMRIQYG-HIIDSNNKCKDDE-LLFKFVA 61
Query: 159 PNSFTGEDCCEFQVHGSIAVINAILGALTKLPGLRPAEPGEFSKRAFFNNKLDLTQTEAL 218
PNS+TGED E Q HGS+ ++ IL K G R A+PGEF++RAF N K+DLTQ EA+
Sbjct: 62 PNSYTGEDVIEIQCHGSMLIVQEILQLCLKS-GARLAQPGEFTQRAFLNGKMDLTQAEAI 120
Query: 219 GDLIQAETELQRQKALHQMKGNLKQLYSEWRQLILESLASVEAYIDFSEDEIIEDNILNT 278
+LI A + AL+++ G L Q IE
Sbjct: 121 NELILAPNNKVKDIALNKLAGELDQK--------------------------IEA----- 149
Query: 279 VRSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVICLASVEAYIDFSEDEIIEDNILNTVR 338
+R ++QL LA VE ID+ ED D+ +++
Sbjct: 150 IRKSLLQL---------------------------LAQVEVNIDYEED----DDEQDSLN 178
Query: 339 SQVVQLHGSIEKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPG 398
++ + ++ + + ++ G K IVG PNVGKSSL+N L ++ +IV+ I G
Sbjct: 179 QLLLSIIAELKDILN--SYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKG 236
Query: 399 TTRDVIEKHLDIGGYPVILLDTAGLRTTTSDI 430
TTRDV+E ++ G + LLDTAG+R +
Sbjct: 237 TTRDVVEGDFELNGILIKLLDTAGIREHADFV 268
>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 = 157 bits (401), Expect = 3e-47
Identities = 59/112 (52%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 98 HGKCGVSVIRVSGPDTLNALKSMACYPDQKVSKPRYASLRNIVDPVSEVVLDEGLCLWFP 157
G+ G+++IR+SGPD L K + K+ KPR A I DP EV +DE L L+FP
Sbjct: 9 PGRGGIAIIRISGPDALEIAKKLF----GKLPKPRTAHYGTIRDPNGEV-IDEVLVLYFP 63
Query: 158 KPNSFTGEDCCEFQVHGSIAVINAILGALTKLPGLRPAEPGEFSKRAFFNNK 209
PNSFTGED E HG AV+ AIL AL KL G R AEPGEF++RAF N K
Sbjct: 64 APNSFTGEDVVEIHCHGGPAVVQAILQALLKL-GARLAEPGEFTRRAFLNGK 114
Score = 84.0 bits (209), Expect = 1e-19
Identities = 29/68 (42%), Positives = 42/68 (61%), Gaps = 5/68 (7%)
Query: 29 TIFALSSGHGKCGVSVIRVSGPDTLNALKSMACYPDQKVPKPRYASLRNIVDPVSKVVLD 88
TI A+++ G+ G+++IR+SGPD L K + K+PKPR A I DP + V+D
Sbjct: 1 TIAAIATPPGRGGIAIIRISGPDALEIAKKLF----GKLPKPRTAHYGTIRDP-NGEVID 55
Query: 89 EGLCLWFP 96
E L L+FP
Sbjct: 56 EVLVLYFP 63
>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 = 128 bits (325), Expect = 1e-35
Identities = 45/73 (61%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 363 RSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
R GIK VI G+PNVGKSSL+N L + +IV+ I GTTRDVIE+ +D+GG PV L+DTAG
Sbjct: 1 REGIKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAG 60
Query: 423 LRTTTSDIIETEG 435
LR T D IE G
Sbjct: 61 LR-ETEDEIEKIG 72
>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 = 82.5 bits (205), Expect = 2e-18
Identities = 30/61 (49%), Positives = 39/61 (63%)
Query: 364 SGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
IK I+G PNVGKSSL+N L ++ IV+ I GTTRD I+ + G L+DTAG+
Sbjct: 1 DPIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTLIDTAGI 60
Query: 424 R 424
R
Sbjct: 61 R 61
>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 = 78.9 bits (195), Expect = 6e-18
Identities = 31/67 (46%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
+VG PNVGKS+L+N L +++IV+ PGTTRD I L G +IL+DT GL S
Sbjct: 3 ALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVL-GLGRQIILVDTPGLIEGAS 61
Query: 429 DIIETEG 435
+ EG
Sbjct: 62 EGKGVEG 68
>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 = 84.8 bits (211), Expect = 8e-18
Identities = 29/61 (47%), Positives = 39/61 (63%)
Query: 364 SGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
IK I+G PNVGKS+L+N L ++ IV+ I GTTRD I+ + G L+DTAG+
Sbjct: 171 GPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGKKYTLIDTAGI 230
Query: 424 R 424
R
Sbjct: 231 R 231
Score = 73.6 bits (182), Expect = 4e-14
Identities = 28/66 (42%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
IVG PNVGKS+L N L K+ +IV+ PG TRD + GG IL+DT G+
Sbjct: 3 AIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGI-EEDD 61
Query: 429 DIIETE 434
D ++ +
Sbjct: 62 DGLDKQ 67
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 83.6 bits (208), Expect = 2e-17
Identities = 30/60 (50%), Positives = 39/60 (65%)
Query: 365 GIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLR 424
IK I+G PNVGKSSL+N L ++ IV+ I GTTRD I+ + G L+DTAG+R
Sbjct: 173 PIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGIR 232
Score = 78.2 bits (194), Expect = 1e-15
Identities = 29/66 (43%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
IVG PNVGKS+L N L K+ +IV PG TRD I + G IL+DT G+
Sbjct: 5 AIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGI-EPDD 63
Query: 429 DIIETE 434
D E +
Sbjct: 64 DGFEKQ 69
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 83.0 bits (206), Expect = 3e-17
Identities = 29/66 (43%), Positives = 38/66 (57%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
IVG PNVGKS+L N L ++I+IV+ PG TRD I + G IL+DT GL
Sbjct: 7 AIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDGDE 66
Query: 429 DIIETE 434
D ++
Sbjct: 67 DELQEL 72
Score = 80.7 bits (200), Expect = 2e-16
Identities = 29/61 (47%), Positives = 40/61 (65%)
Query: 364 SGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
IK I+G PNVGKSSL+N + ++ IV+ I GTTRD I+ + G +L+DTAG+
Sbjct: 177 DPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAGI 236
Query: 424 R 424
R
Sbjct: 237 R 237
>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 = 77.9 bits (193), Expect = 4e-17
Identities = 28/66 (42%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
IVG PNVGKS+L N L ++ +IV+ PG TRD + GG IL+DT G+
Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGI-EPDD 59
Query: 429 DIIETE 434
+ I E
Sbjct: 60 EGISKE 65
>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 = 72.3 bits (178), Expect = 4e-15
Identities = 31/73 (42%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHL-DIGGYPVILLDTAGLRTTT 427
I G PNVGKSSL+N L + + IV+ IPGTTRD + K + PV+L+DT GL
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGL---- 56
Query: 428 SDIIETEGNLLEK 440
D G +
Sbjct: 57 -DEEGGLGRERVE 68
>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 = 74.5 bits (184), Expect = 2e-14
Identities = 27/56 (48%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGY-PVILLDTAGL 423
I G N GKSSL+N L + I+IV+ +PGTT D + K +++ PV+L+DTAGL
Sbjct: 10 GIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVYKAMELLPLGPVVLIDTAGL 65
>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 = 63.2 bits (154), Expect = 6e-12
Identities = 28/58 (48%), Positives = 37/58 (63%), Gaps = 2/58 (3%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTR--DVIEKHLDIGGYPVILLDTAGLR 424
V+VG VGKSSL+N L ++ V+ +PGTTR DV K LD G ++L+DT GL
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLD 58
>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 = 62.1 bits (152), Expect = 2e-11
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 363 RSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+SG I+G PNVGKS+L+N L ++ISIV+ P TTR+ I +I +DT G
Sbjct: 2 KSG-FVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFVDTPG 60
Query: 423 L 423
+
Sbjct: 61 I 61
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 63.5 bits (155), Expect = 7e-11
Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLR 424
+VG+PNVGKSSL+N L ++ S+V + GTT D ++ +++GG +DTAGLR
Sbjct: 216 LVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGLR 270
Score = 46.9 bits (112), Expect = 1e-05
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+VG PNVGKS+L+N + ++ ++V +PG TRD + + G ++DT G
Sbjct: 43 VVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGG 95
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 61.6 bits (151), Expect = 1e-10
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
IVG PNVGKS+L+N L ++ISIV+ P TTR I + +I +DT G+
Sbjct: 10 IVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGI 63
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 60.7 bits (148), Expect = 3e-10
Identities = 24/54 (44%), Positives = 35/54 (64%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
I+G PNVGKS+L+N L ++ISIV+ P TTR+ I + +I +DT G+
Sbjct: 11 IIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGI 64
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 60.9 bits (148), Expect = 3e-10
Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 363 RSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+ I+ +VG PNVGKS+L+N L K+++ ++ PGTT+ + LD G Y LLDT G
Sbjct: 130 KRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIY---LLDTPG 186
Query: 423 LRTTTSDIIETEG 435
+ D E
Sbjct: 187 IIPPKFDDDELVL 199
>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 = 57.4 bits (139), Expect = 7e-10
Identities = 31/59 (52%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGG--YPVILLDTAG 422
IK VIVG+PNVGKS+L+N L +ISI PGTTR+ + ++ G Y LLDTAG
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 60.6 bits (147), Expect = 8e-10
Identities = 28/67 (41%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 359 GVRIRSGIKSV-IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL 417
G SG++ V +VG PNVGKSSL+N L ++ ++V + GTTRD +++ ++I G +
Sbjct: 443 GFLTPSGLRRVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLF 502
Query: 418 LDTAGLR 424
+DTAG++
Sbjct: 503 IDTAGIK 509
Score = 49.8 bits (119), Expect = 2e-06
Identities = 22/54 (40%), Positives = 32/54 (59%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
IVG PNVGKS+L+N + ++ ++V PG TRD + + G L+DT G
Sbjct: 279 AIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGG 332
>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 = 58.2 bits (141), Expect = 2e-09
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
I+G PNVGKS+L+N L ++ISI + TTR+ I G +I +DT G
Sbjct: 5 ILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGF 58
>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 = 52.1 bits (126), Expect = 4e-08
Identities = 28/116 (24%), Positives = 56/116 (48%), Gaps = 16/116 (13%)
Query: 315 ASVEAYIDFSEDE----IIEDNILNTVRSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVI 370
A + ++ + + + + + ++++ + K E G+ R +++++
Sbjct: 62 AKTKKWLKYFKSQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPR-PLRAMV 120
Query: 371 VGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDV----IEKHLDIGGYPVILLDTAG 422
VG PNVGKS+L+N L K+++ V + PG TR I +++ LLDT G
Sbjct: 121 VGIPNVGKSTLINRLRGKKVAKVGNKPGVTRGQQWIRIGPNIE-------LLDTPG 169
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 50.6 bits (122), Expect = 5e-07
Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 13/78 (16%)
Query: 349 EKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRD----VI 404
EK+ K G+R R+ I+++I+G PNVGKS+L+N L K+I+ + PG T+ +
Sbjct: 107 EKNERRKAK-GMRPRA-IRAMIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKL 164
Query: 405 EKHLDIGGYPVILLDTAG 422
K L+ LLDT G
Sbjct: 165 GKGLE-------LLDTPG 175
>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 = 50.2 bits (121), Expect = 6e-07
Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 13/78 (16%)
Query: 349 EKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDV----I 404
EK+ +L K G+ R I+++IVG PNVGKS+L+N L K+++ V + PG T+ +
Sbjct: 104 EKNEKLKAK-GLLNRP-IRAMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKL 161
Query: 405 EKHLDIGGYPVILLDTAG 422
L+ LLDT G
Sbjct: 162 SDGLE-------LLDTPG 172
>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 = 49.9 bits (120), Expect = 1e-06
Identities = 29/68 (42%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 361 RIRSGIKSVIVGEPNVGKSSLMNFLCQ----KQISIVTS-IPGTTRDVIEKHLDIGGYPV 415
+ R+ +VG NVGKSSL+N L + + I TS PGTT D+IE LD G
Sbjct: 150 KARNKKDVYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHS-- 207
Query: 416 ILLDTAGL 423
L DT G+
Sbjct: 208 -LYDTPGI 214
>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 = 46.4 bits (111), Expect = 4e-06
Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 362 IRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLD 409
I++ I +VG PNVGKSS++N L + + V + PG T+ + E HLD
Sbjct: 113 IKTSITVGVVGYPNVGKSSVINSLKRSRACNVGATPGVTKSMQEVHLD 160
>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 = 46.9 bits (112), Expect = 4e-06
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 14/65 (21%)
Query: 370 IVGEPNVGKSSLMNFLCQK-----------QISIVTSIPGTTRDVIEKHLDIGGYPVILL 418
+VG NVGKS+L+N L + Q V+ IPGTT +I+ L G L
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGK---KLY 186
Query: 419 DTAGL 423
DT G+
Sbjct: 187 DTPGI 191
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 45.8 bits (109), Expect = 3e-05
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
V+ G PNVGKSSL+ L + + P TT+ + H + G + ++DT GL
Sbjct: 172 VVAGYPNVGKSSLVRKLTTAKPEV-APYPFTTKGIHVGHFERGYLRIQVIDTPGL 225
>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 = 43.0 bits (102), Expect = 4e-05
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 11/57 (19%)
Query: 371 VGEPNVGKSSLMNFLCQKQISIVTSIPGTTRD----VIEKHLDIGGYPVILLDTAGL 423
VG PNVGKSSL+N L + V+S PG T+ +E + L D GL
Sbjct: 88 VGYPNVGKSSLINALVGSKKVSVSSTPGKTKHFQTIFLEPGI-------TLCDCPGL 137
>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 = 43.1 bits (102), Expect = 5e-05
Identities = 28/59 (47%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 365 GIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
GI+ +VG PNVGKSS +N L K V SIPGTT+ + LD Y L DT G+
Sbjct: 91 GIRVGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDVKLDKEIY---LYDTPGI 146
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 45.0 bits (107), Expect = 6e-05
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 370 IVGEPNVGKSSLMNFLC---QKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+VG PNVGK++L N L QK V + PG T + E L G+ + ++D G
Sbjct: 8 LVGNPNVGKTTLFNALTGANQK----VGNWPGVTVEKKEGKLKYKGHEIEIVDLPG 59
>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 = 42.8 bits (102), Expect = 7e-05
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 370 IVGEPNVGKSSLMNFLC---QKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+VG PNVGK++L N L QK V + PG T + E +GG + ++D G
Sbjct: 2 LVGNPNVGKTTLFNALTGARQK----VGNWPGVTVEKKEGEFKLGGKEIEIVDLPG 53
>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 = 42.5 bits (101), Expect = 9e-05
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
VI G PNVGKSSL+N L + + V P TT+ + H D ++DT G+
Sbjct: 4 VIAGYPNVGKSSLVNKLTRAKPE-VAPYPFTTKSLFVGHFDYKYLRWQVIDTPGI 57
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 43.9 bits (103), Expect = 1e-04
Identities = 23/54 (42%), Positives = 34/54 (62%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
I+G PN GKS+L+N + +++SIVT TTR +I + + VIL DT G+
Sbjct: 57 IIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGI 110
>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 = 42.4 bits (100), Expect = 1e-04
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIG-GYPVILLDTAGL 423
+VG PNVGKS+L++ L ++ I S P TT + + G G + ++D GL
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEI-ASYPFTTLEPNVGVFEFGDGVDIQIIDLPGL 55
>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 = 41.6 bits (98), Expect = 1e-04
Identities = 18/54 (33%), Positives = 26/54 (48%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
++G+ GKSSL N L +++ V TTR GG ++LLD G
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPG 54
>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 = 41.7 bits (99), Expect = 2e-04
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 366 IKSVIVGEPNVGKSSLMNFLC---QKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
I +VG PNVGK++L N L Q V + PG T + E GY + ++D G
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQH----VGNWPGVTVEKKEGTFKYKGYEIEIVDLPG 56
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 42.9 bits (102), Expect = 2e-04
Identities = 28/60 (46%), Positives = 36/60 (60%), Gaps = 10/60 (16%)
Query: 370 IVGEPNVGKSSLMNFLCQKQIS-----IVTS-IPGTTRDVIEKHLDIGGYPVILLDTAGL 423
+VG NVGKS+L+N + K+I+ I TS PGTT D IE LD G + L DT G+
Sbjct: 165 VVGVTNVGKSTLINRII-KEITGEKDVITTSRFPGTTLDKIEIPLDDGSF---LYDTPGI 220
>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 = 40.2 bits (95), Expect = 6e-04
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 369 VIVGEPNVGKSSLMNFLC-QKQISIVTSIPGTTR 401
G NVGKSSL+N L +K+++ + PG T+
Sbjct: 3 AFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ 36
>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 = 39.2 bits (92), Expect = 0.001
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTR 401
+G PNVGKSS++N L K++ V IPG T+
Sbjct: 107 FIGYPNVGKSSVINTLRSKKVCKVAPIPGETK 138
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 39.6 bits (92), Expect = 0.001
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 366 IKSVIVGEPNVGKSSLMN------FLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLD 419
K V++G+ VGK++L+N F +I P T + +++ + L D
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKL-----QLWD 60
Query: 420 TAG 422
TAG
Sbjct: 61 TAG 63
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 39.8 bits (93), Expect = 0.002
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
++G GKSSL+N L Q ++ V+ + T L G ++L DT GL
Sbjct: 44 LMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGL 97
>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 = 37.1 bits (87), Expect = 0.006
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTT--RDVIEKHLDIGGYPVILL--DTA 421
K V++G+ VGK+SL+ + S +T D K +++ G V L DTA
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYK---STIGVDFKSKTIEVDGKKVKLQIWDTA 57
Query: 422 G 422
G
Sbjct: 58 G 58
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 38.4 bits (90), Expect = 0.007
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 361 RIRSGIKSV-IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIG-GYPVILL 418
R RSGI V +VG N GKS+L N L + + + T D + +++G G V+L
Sbjct: 187 RSRSGIPLVALVGYTNAGKSTLFNALTGADVYVADQLF-ATLDPTTRRIELGDGRKVLLT 245
Query: 419 DTAG 422
DT G
Sbjct: 246 DTVG 249
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. 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.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 36.7 bits (86), Expect = 0.008
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 367 KSVIVGEPNVGKSSL-MNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V++G VGKS+L + F+ + P T D K + + G L LDTAG
Sbjct: 1 KLVVLGAGGVGKSALTIRFV--SGEFVEEYDP-TIEDSYRKQIVVDGETYTLDILDTAG 56
>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 = 36.1 bits (84), Expect = 0.012
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQK---QISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
+ +VG P VGKSS++N L + S + PG T+ + + I + L+DT G
Sbjct: 100 VIVGVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTKG--IQLVRIDSK-IYLIDTPG 156
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 37.2 bits (87), Expect = 0.013
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 361 RIRSGIKSVIVGEPNVGKSSLMNFLCQKQI 390
R + +K IVG PNVGKS+ N LC++Q+
Sbjct: 17 RPGNNLKMGIVGLPNVGKSTTFNALCKQQV 46
>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 = 37.1 bits (87), Expect = 0.014
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 11/68 (16%)
Query: 361 RIRSGIKSV-IVGEPNVGKSSLMNFLCQKQISI-----VTSIPGTTRDVIEKHLDIGGYP 414
R R+ + +V +VG N GKS+L N L + T P TTR + G
Sbjct: 184 RKRADVPTVALVGYTNAGKSTLFNALTGADVYAADQLFATLDP-TTRRLDLP----DGGE 238
Query: 415 VILLDTAG 422
V+L DT G
Sbjct: 239 VLLTDTVG 246
>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 = 37.4 bits (87), Expect = 0.016
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 372 GEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAG 422
G PNVGKS+L N L V + PG T + E L G + ++D G
Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPG 50
>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 = 35.9 bits (84), Expect = 0.017
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 370 IVGEPNVGKSSLMNFLC-QKQISIVTSIPGTTR 401
G NVGKSSL+N L +K+++ + PG T+
Sbjct: 23 FAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ 55
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 35.7 bits (83), Expect = 0.029
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 369 VIVGEPNVGKSSLMNFLC-QKQISIVTSIPGTTR 401
G NVGKSSL+N L QK ++ + PG T+
Sbjct: 28 AFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQ 61
>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 = 35.9 bits (84), Expect = 0.031
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 370 IVGEPNVGKSSLMNFLCQKQI 390
IVG PNVGKS+L N L +
Sbjct: 3 IVGLPNVGKSTLFNALTKSNA 23
>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 = 35.5 bits (83), Expect = 0.032
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 347 SIEKHIELSNKCGVRIRSGIKSV-IVGEPNVGKSSLMNFLC 386
++K EL R RSG+ +V +VG N GKS+L N L
Sbjct: 24 KVKKQRELQRA--RRKRSGVPTVALVGYTNAGKSTLFNALT 62
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 36.0 bits (84), Expect = 0.034
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 365 GIKSVIVGEPNVGKSSLMNFLCQKQISI 392
+K IVG PNVGKS+L N L + I
Sbjct: 2 SLKIGIVGLPNVGKSTLFNALTKAGAEI 29
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 35.8 bits (84), Expect = 0.042
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 365 GIKSVIVGEPNVGKSSLMNFLCQKQI 390
G+K IVG PNVGKS+L N L +
Sbjct: 2 GLKCGIVGLPNVGKSTLFNALTKAGA 27
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 33.4 bits (77), Expect = 0.046
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGT----TRDVIEKHLDIGGY---PVILLDTA 421
+ G P GKS+L +L + + +P +R+ + D GY PV+++D
Sbjct: 2 WLYGPPGCGKSTLAKYLA-RALLKHLGLPKKDSVYSRNPDDDFWD--GYTGQPVVIIDDF 58
Query: 422 GLRTTTSDIIETE 434
G + E E
Sbjct: 59 G-QNPDGPSDEAE 70
>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 = 34.4 bits (80), Expect = 0.047
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V+VG+ VGKSSL+ Q + IP D K +++ G V L DTAG
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFP-EEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAG 57
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 34.7 bits (81), Expect = 0.048
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 369 VIVGEPNVGKSSLMNFLC-QKQISIVTSIPGTTR 401
G NVGKSSL+N L +K ++ + PG T+
Sbjct: 28 AFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ 61
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 35.4 bits (82), Expect = 0.064
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 343 QLHGSIEKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQK-QISIVTSIPGTT 400
QL G ++K++ G RIR I ++VG+P KS L+ ++ + + TS G++
Sbjct: 301 QLFGGVKKNLPD----GTRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSS 355
>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 = 34.3 bits (80), Expect = 0.072
Identities = 38/133 (28%), Positives = 55/133 (41%), Gaps = 30/133 (22%)
Query: 306 SGIKSVICLASVEAYIDFSEDEIIEDNILNTVRSQVVQLHGSIEKHIELSNKCGV---RI 362
SGI+ VI L D +DE +E+ +L + + +S K G +
Sbjct: 32 SGIEPVIVLNK----ADLVDDEELEE-LLEIYEKLGYPV-------LAVSAKTGEGLDEL 79
Query: 363 RSGIK---SVIVGEPNVGKSSLMNFLC----QKQISIVTSIPG----TTRDVIEKHLDIG 411
R +K SV+VG+ VGKS+L+N L I + G TT L G
Sbjct: 80 RELLKGKTSVLVGQSGVGKSTLLNALLPELVLATGEISEKL-GRGRHTTTHRELFPLPGG 138
Query: 412 GYPVILLDTAGLR 424
G ++DT G R
Sbjct: 139 GL---IIDTPGFR 148
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 33.9 bits (78), Expect = 0.078
Identities = 23/58 (39%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V+VG VGKS+L Q VT T D K +I G L LDTAG
Sbjct: 4 KLVVVGGGGVGKSALTIQFIQSY--FVTDYDPTIEDSYTKQCEIDGQWARLDILDTAG 59
>gnl|CDD|238237 cd00405, PRAI, Phosphoribosylanthranilate isomerase (PRAI)
catalyzes the fourth step of the tryptophan
biosynthesis, the conversion of N-(5'-
phosphoribosyl)-anthranilate (PRA) to
1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate
(CdRP). Most PRAIs are monomeric, monofunctional and
thermolabile, but in some thermophile organisms PRAI is
dimeric for reasons of stability and in others it is
fused to other components of the tryptophan biosynthesis
pathway to form multifunctional enzymes.
Length = 203
Score = 34.1 bits (79), Expect = 0.096
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 322 DFSEDEIIEDNILNTVRSQVVQLHG--SIEKHIELSNKCGVRIRSGIKSVIVGEP 374
+ +EI+E I + VVQLHG S E +L + G+ + IK++ V +
Sbjct: 59 NEDLEEILE--IAEELGLDVVQLHGDESPEYCAQLRARLGLPV---IKAIRVKDE 108
Score = 30.6 bits (70), Expect = 1.1
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 264 DFSEDEIIEDNILNTVRSQVVQLHG--SIEKHIELSNKCGVRIRSGIKSV 311
+ +EI+E I + VVQLHG S E +L + G+ + IK++
Sbjct: 59 NEDLEEILE--IAEELGLDVVQLHGDESPEYCAQLRARLGLPV---IKAI 103
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 34.2 bits (79), Expect = 0.11
Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 363 RSGIKSVI-VGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTA 421
+SG +V VG P+VGKS+L+N L + S V P TT + + L+ G + LLD
Sbjct: 60 KSGDATVALVGFPSVGKSTLLNKLTNTK-SEVADYPFTTLEPVPGMLEYKGAQIQLLDLP 118
Query: 422 GL 423
G+
Sbjct: 119 GI 120
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 32.9 bits (76), Expect = 0.14
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V++G VGKS+L Q V T D K ++I G +L LDTAG
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGH--FVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAG 57
>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 = 32.0 bits (73), Expect = 0.15
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTS-IPGTTRDVIEKHLDIGGYPVILLDTAG 422
K V++G+ GKSSL++ L + I G T V +D + + D G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGG 57
>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 = 33.7 bits (78), Expect = 0.16
Identities = 23/77 (29%), Positives = 29/77 (37%), Gaps = 23/77 (29%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISI----VTSI-------------PGTTRDVIEKH---LD 409
+VG+PNVGKS+ N + I T+I P V
Sbjct: 3 LVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYGKC 62
Query: 410 IGGY---PVILLDTAGL 423
I G PV L+D AGL
Sbjct: 63 IDGKRYVPVELIDVAGL 79
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 32.9 bits (76), Expect = 0.16
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V++G VGKS+L Q V T D K ++I G +L LDTAG
Sbjct: 4 KLVVLGGGGVGKSALTIQFVQGH--FVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAG 59
>gnl|CDD|206650 cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal
domain). Guanylate-binding protein (GBP), N-terminal
domain. Guanylate-binding proteins (GBPs) define a group
of proteins that are synthesized after activation of the
cell by interferons. The biochemical properties of GBPs
are clearly different from those of Ras-like and
heterotrimeric GTP-binding proteins. They bind guanine
nucleotides with low affinity (micromolar range), are
stable in their absence and have a high turnover GTPase.
In addition to binding GDP/GTP, they have the unique
ability to bind GMP with equal affinity and hydrolyze
GTP not only to GDP, but also to GMP. Furthermore, two
unique regions around the base and the phosphate-binding
areas, the guanine and the phosphate caps, respectively,
give the nucleotide-binding site a unique appearance not
found in the canonical GTP-binding proteins. The
phosphate cap, which constitutes the region analogous to
switch I, completely shields the phosphate-binding site
from solvent such that a potential GTPase-activating
protein (GAP) cannot approach.
Length = 224
Score = 33.5 bits (77), Expect = 0.17
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 370 IVGEPNVGKSSLMNFLCQKQIS--IVTSIPGTTRDV---IEKHLDIGG--YPVILLDTAG 422
+ G + GKS L+N L ++ + TT+ + + D G + V+LLDT G
Sbjct: 12 VFGSQSSGKSFLLNHLFGTSDGFDVMDTSQQTTKGIWMWSDPFKDTDGKKHAVLLLDTEG 71
Query: 423 L 423
Sbjct: 72 T 72
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. 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 = 162
Score = 32.6 bits (75), Expect = 0.19
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRD-VIEKHLDIGGYPVIL--LDTAG 422
K V++GE VGK+SL+ + + + TT+ +K ++IGG + L DTAG
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKH--ESTTQASFFQKTVNIGGKRIDLAIWDTAG 58
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 33.4 bits (77), Expect = 0.21
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 368 SVIVGEPNVGKSSLMNFLC---QKQISIVTSIPG----TTRDVIEKHLDIGGYPVILLDT 420
+V++G+ VGKS+L+N L ++ ++ G TT V L GG+ ++DT
Sbjct: 167 TVLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGW---IIDT 223
Query: 421 AGLR 424
G R
Sbjct: 224 PGFR 227
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 33.7 bits (78), Expect = 0.21
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 369 VIVGEPNVGKS----SLMNFLCQKQISIVTS 395
VI G P+ GKS SL+ FL K IS V S
Sbjct: 438 VIYGPPDTGKSMFCMSLIKFLKGKVISFVNS 468
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 33.0 bits (76), Expect = 0.21
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVI 416
V VG NVGKS+L+ L K++ V PG TR H D G + +
Sbjct: 13 VFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRKPN--HYDWGDFILT 57
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 33.3 bits (77), Expect = 0.24
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 369 VIVGEPNVGKS----SLMNFLCQKQISIVTS 395
VI G P+ GKS SL+ FL K IS V S
Sbjct: 266 VIYGPPDTGKSMFCMSLIKFLGGKVISFVNS 296
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 33.2 bits (76), Expect = 0.25
Identities = 33/110 (30%), Positives = 47/110 (42%), Gaps = 28/110 (25%)
Query: 206 FNNKLDLTQTEALGDLIQAE--------------TELQRQKALHQMKGNLKQLYSEWRQL 251
F NK D+ E L +L++ E T + R AL ++G+ +EW
Sbjct: 134 FLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALEGD-----AEWEAK 188
Query: 252 ILESLASVEAYIDFSEDEI-------IEDNILNTVRSQVVQLHGSIEKHI 294
ILE + +V+ YI E E IED T R VV G +E+ I
Sbjct: 189 ILELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVT--GRVERGI 236
>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 = 32.5 bits (75), Expect = 0.28
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGL 423
+VG P+VGKS+L++ L + S V + TT + ++ G + LLD G+
Sbjct: 4 ALVGFPSVGKSTLLSKLTNTK-SEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPGI 57
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 32.1 bits (74), Expect = 0.31
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 368 SVIVGEPNVGKSSLMNFLCQKQISIVTSIPG-------TTRDVIEKHLDIGGYPVILLDT 420
SV+ G+ VGKS+L+N L + I TT V L GG L+DT
Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGL---LIDT 94
Query: 421 AGLR 424
G R
Sbjct: 95 PGFR 98
>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 = 32.4 bits (74), Expect = 0.32
Identities = 21/64 (32%), Positives = 25/64 (39%), Gaps = 11/64 (17%)
Query: 368 SVIVGEPNVGKSSLMNFLCQKQISIVTSIPG-------TTRDVIEKHLDIGGYPVILLDT 420
SV G+ VGKSSL+N L V I TT V H G ++ DT
Sbjct: 123 SVFAGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGG----LIADT 178
Query: 421 AGLR 424
G
Sbjct: 179 PGFN 182
>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 = 31.9 bits (73), Expect = 0.36
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTT-RDVIEKHLDIGGYPVIL--LDTAG 422
K +I+G+ VGK+SLMN K+ S T D + K + + V L DTAG
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFS--NQYKATIGADFLTKEVTVDDRLVTLQIWDTAG 58
>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 = 31.1 bits (71), Expect = 0.54
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 366 IKSVIVGEPNVGKSSLM-NFLCQKQISIVTSIPGTTRDVIEKHLDIGG--YPVILLDTAG 422
+K +++G+ VGKSSL+ F ++S G D K + + G + + DTAG
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGV--DFKVKTVTVDGKKVKLAIWDTAG 58
Query: 423 ---LRTTTS 428
RT TS
Sbjct: 59 QERFRTLTS 67
>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 = 31.4 bits (72), Expect = 0.60
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIG---GYPVILLDTAGL 423
+VGE + GKS+L+N L +++ P TT VI L G G V+L+DT GL
Sbjct: 4 AVVGEFSAGKSTLLNALLGEEVLPTGVTP-TT-AVIT-VLRYGLLKG--VVLVDTPGL 56
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 31.7 bits (73), Expect = 0.63
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 343 QLHGSIEKHIELSNKCGVRIRSGIKSVIVGEPNVGKSSLMNFLCQK-QISIVTSIPGTT 400
QL G ++K++ G R+R I ++VG+P KS L+ ++ + ++ TS G++
Sbjct: 39 QLFGGVKKNLP----DGTRLRGDINVLLVGDPGTAKSQLLKYVAKLAPRAVYTSGKGSS 93
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 31.0 bits (70), Expect = 0.96
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQKQI 390
+K +++G+ VGKSSL++ LC+ Q+
Sbjct: 1 VKVLVLGDSGVGKSSLVHLLCKNQV 25
>gnl|CDD|182284 PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase;
Provisional.
Length = 413
Score = 31.2 bits (71), Expect = 0.97
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 116 ALKSMACYPDQKVSKPRYASLRNIVD-PVSEVVLDEGLCLWFPKPNSFTGEDCCEFQVHG 174
AL +M + P Y L IV+ S ++ C N+F+ + E V G
Sbjct: 164 ALAAMEKELSKLQLTPSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSG 223
Query: 175 SIAVINAILGALT 187
+ V N+++ A T
Sbjct: 224 PLKVGNSLVDAFT 236
>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 = 31.1 bits (71), Expect = 0.99
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILL-DTAGLRTTTS 428
+VGE +GK++L+N L + IPG + I+K ++I V + D L T
Sbjct: 9 VVGESGLGKTTLINTLFLTDLIPERGIPGPSEK-IKKTVEIKATTVEIEEDGVKLNLT-- 65
Query: 429 DIIETEG 435
+I+T G
Sbjct: 66 -VIDTPG 71
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 30.6 bits (70), Expect = 1.0
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 366 IKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG- 422
K +++G+ VGKSSL++ + S D K +++ G V L DTAG
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFS-EQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQ 59
Query: 423 --LRTTTS 428
R+ TS
Sbjct: 60 ERFRSITS 67
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 31.1 bits (71), Expect = 1.1
Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 28/108 (25%)
Query: 206 FNNKLDLTQTEALGDLIQAET-ELQ-------------RQKALHQMKGNLKQLYSEWRQL 251
F NK+DL E L +L++ E EL R AL ++G+ +W
Sbjct: 134 FLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGD-----PKWEDA 188
Query: 252 ILESLASVEAYIDFSEDEI-------IEDNILNTVRSQVVQLHGSIEK 292
I+E + +V+ YI E + +ED T R VV G +E+
Sbjct: 189 IMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVT--GRVER 234
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 29.9 bits (68), Expect = 1.7
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIE 405
+VG+ + GKSS++N L + I P TTR +
Sbjct: 2 AVVGDQSAGKSSVLNALLGRDILPRGPGP-TTRRPLV 37
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
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 Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 29.8 bits (68), Expect = 2.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 366 IKSVIVGEPNVGKSSLM 382
IK V+VG+ VGK+ L+
Sbjct: 1 IKIVVVGDGAVGKTCLL 17
>gnl|CDD|218701 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
C-terminus. In the E. coli cytosol, a fraction of the
newly synthesised proteins requires the activity of
molecular chaperones for folding to the native state.
The major chaperones implicated in this folding process
are the ribosome-associated Trigger Factor (TF), and the
DnaK and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the C-terminal region of
the protein.
Length = 162
Score = 29.5 bits (67), Expect = 2.3
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 29/89 (32%)
Query: 207 NNKLDLTQTEALGDLIQAETELQRQKALHQMKGN--------------LKQLYSEWR--- 249
N +++L ++ L++ E + ++ L Q++G ++L E++
Sbjct: 36 NAEIELPES-----LVEEEIDRLLRQFLQQLQGQGLDLEEYLSLSGSSEEELREEFKEEA 90
Query: 250 ------QLILESLASVEAYIDFSEDEIIE 272
LILE +A E I+ +++EI E
Sbjct: 91 EKRVKLGLILEEIAKEEK-IEVTDEEIKE 118
>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 = 2.4
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 370 IVGEPNVGKSSLMNFL 385
+VG PN GKS+L++ +
Sbjct: 5 LVGLPNAGKSTLLSAI 20
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
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. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 29.3 bits (66), Expect = 2.6
Identities = 23/58 (39%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVIL--LDTAG 422
K V+VG VGKS+L L Q V T D K + I G +L LDTAG
Sbjct: 3 KLVVVGAGGVGKSALTIQLIQNH--FVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG 58
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 30.0 bits (68), Expect = 2.7
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 4/76 (5%)
Query: 362 IRSGIKSVI--VGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLD 419
+ GI I VGE +GK++ +N L + T I + L+I L +
Sbjct: 18 SKKGIDFTIMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEE 77
Query: 420 TAGLRTTTSDIIETEG 435
+I+T G
Sbjct: 78 DG--FHLNLTVIDTPG 91
>gnl|CDD|165089 PHA02716, PHA02716, CPXV016; CPX019; EVM010; Provisional.
Length = 764
Score = 30.3 bits (68), Expect = 2.7
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 270 IIEDNILNTVRSQVVQLHGSIEKHIELSNKCGVRIRSGIKSVICLASVEAYIDFSEDEII 329
I++ N +R V+Q S+ I N G + + S IC A Y D D +I
Sbjct: 368 ILDPETDNDIRLDVIQCLISLGADITAVNCLGY---TPLTSYICTAQNYMYYDII-DCLI 423
Query: 330 EDNILNTVRSQVVQ 343
D +LN V+ +++Q
Sbjct: 424 SDKVLNMVKHRILQ 437
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 30.2 bits (69), Expect = 2.7
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 240 NLKQLYSEWRQLILESLASV-----EAYIDFSEDEIIEDNILNTVR 280
+LK+ E+R+ ++E++A V E Y +EI E+ I +R
Sbjct: 201 DLKEKAEEYREKLIEAVAEVDEELMEKY--LEGEEITEEEIKAAIR 244
>gnl|CDD|185102 PRK15180, PRK15180, Vi polysaccharide biosynthesis protein TviD;
Provisional.
Length = 831
Score = 30.1 bits (67), Expect = 2.8
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 210 LDLTQTEALGDLIQAETELQRQKALHQMKGNLKQLYSEWRQLILESLASVE-AYIDFSED 268
L +T+ A GD+I A +L Q L QL R +I L E AY D S+
Sbjct: 294 LSITKQLADGDIIAASQQLFAALRNQQQDPVLIQL----RSVIFSHLGYYEQAYQDISDV 349
Query: 269 EIIEDNILNTVRSQVVQLHG 288
E I +T+R ++ LHG
Sbjct: 350 EKIIGTTDSTLRCRLRSLHG 369
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.1 bits (66), Expect = 2.9
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGG 412
VI G P+ GK++L+ L + +V R+ IE+ L GG
Sbjct: 3 VITGGPSTGKTTLLEALAARGYPVVPEYG---REYIEEQLADGG 43
>gnl|CDD|219624 pfam07894, DUF1669, Protein of unknown function (DUF1669). This
family is composed of sequences derived from
hypothetical eukaryotic proteins of unknown function.
Some members of this family are annotated as being
potential phospholipases but no literature was found to
support this.
Length = 284
Score = 29.5 bits (67), Expect = 3.0
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 239 GNLKQLYSEWRQLILESLAS--VEAYIDF----------SEDEIIEDNILNTVR 280
L+ LYSE ++L LE+L EAY++F SEDEI + IL
Sbjct: 13 AKLEFLYSEEQRLALEALLEGGPEAYLEFLKEEGERDFLSEDEI--EYILAAAE 64
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 29.7 bits (68), Expect = 3.0
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 8/26 (30%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTS 395
+VG PNVGKS+L +S+V++
Sbjct: 163 LVGFPNVGKSTL--------LSVVSN 180
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 30.0 bits (68), Expect = 3.1
Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 21/95 (22%)
Query: 199 EFSKRAFFNNKLDL----TQTEALGDLI---------QAETELQ----RQKAL----HQM 237
++ A +LDL + ++L D + QAET+L+ + K L
Sbjct: 645 AEARTALKQARLDLQRLQNEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLEQQQAF 704
Query: 238 KGNLKQLYSEWRQLILESLASVEAYIDFSEDEIIE 272
LK + E R L VE +D ++
Sbjct: 705 LEALKDDFRELRTERLAKWQVVEGELDNQLAQLSA 739
>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 = 29.4 bits (67), Expect = 3.2
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDI 410
+VGE +GKS+ +N L ++ + P + I K ++I
Sbjct: 9 VVGESGLGKSTFINTLFGTKL-YPSKYPPAPGEHITKTVEI 48
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.4 bits (67), Expect = 3.5
Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 30/74 (40%)
Query: 368 SVIVGEPNVGKSSLMNFLCQKQISIVTSIPGT---TRDVIEK--------------HLDI 410
+V+ G+ VGKS+L+N L P T ++ E L
Sbjct: 167 TVLAGQSGVGKSTLLNAL----------APDLELKTGEISEALGRGKHTTTHVELYDLPG 216
Query: 411 GGYPVILLDTAGLR 424
GG L+DT G
Sbjct: 217 GGL---LIDTPGFS 227
>gnl|CDD|129610 TIGR00519, asnASE_I, L-asparaginase, type I. Two related families
of asparaginase are designated type I and type II
according to the terminology in E. coli, which has both:
L-asparaginase I is a low-affinity enzyme found in the
cytoplasm, while L-asparaginase II is a high-affinity
secreted enzyme synthesized with a cleavable signal
sequence. This model describes L-asparaginases related
to type I of E. coli. Archaeal putative asparaginases
are of this type but contain an extra ~ 80 residues in a
conserved N-terminal region. These archaeal homologs are
included in this model.
Length = 336
Score = 29.4 bits (66), Expect = 4.0
Identities = 12/67 (17%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 374 PNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTSDIIET 433
+ + + L +K ++++ PG + D+I +L GY I+++ GL + ++
Sbjct: 199 RGEDELEVHDRLEEK-VALIKIYPGISPDIIRNYLSK-GYKGIVIEGTGLGHAPQNKLQE 256
Query: 434 EGNLLEK 440
++
Sbjct: 257 LQEASDR 263
>gnl|CDD|238431 cd00851, MTH1175, This uncharacterized conserved protein belongs to
a family of iron-molybdenum cluster-binding proteins
that includes NifX, NifB, and NifY, all of which are
involved in the synthesis of an iron-molybdenum cofactor
(FeMo-co) that binds the active site of the
dinitrogenase enzyme. This domain is a predicted
small-molecule-binding domain (SMBD) with an alpha/beta
fold that is present either as a stand-alone domain
(e.g. NifX and NifY) or fused to another conserved
domain (e.g. NifB) however, its function is still
undetermined.The SCOP database suggests that this domain
is most similar to structures within the ribonuclease H
superfamily. This conserved domain is represented in
two of the three major divisions of life (bacteria and
archaea).
Length = 103
Score = 27.6 bits (62), Expect = 4.9
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 365 GIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHL 408
G+ VIVG +G + +N L I + GT + IE L
Sbjct: 63 GVDVVIVG--GIGPRA-LNKLRNAGIKVYKGAEGTVEEAIEALL 103
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 29.1 bits (66), Expect = 4.9
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 370 IVGEPNVGKSSLMNFL 385
+VG PN GKS+L++ +
Sbjct: 164 LVGLPNAGKSTLLSAV 179
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 28.4 bits (64), Expect = 5.0
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 359 GVRIRSGIKSVIVGEPNVGKSSLMNFLC 386
G+ R G+ +++ G P GKS+L L
Sbjct: 28 GLLPRGGL-TLLAGAPGTGKSTLALDLA 54
>gnl|CDD|233007 TIGR00522, dph5, diphthine synthase. Alternate name: diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase. This protein participates in the
modification of a specific His of elongation factor 2 of
eukarotes and Archaea to diphthamide. The protein was
characterized in Saccharomyces cerevisiae and designated
DPH5 [Protein fate, Protein modification and repair].
Length = 257
Score = 29.0 bits (65), Expect = 5.1
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 363 RSGIKSVIVGEPNV-----GKSSLMNFLCQKQISIV----TSIPGTTRDVIEKHLDIGGY 413
R GI++ I+ ++ G + L + K +IV P T +VI+++ IG +
Sbjct: 101 RKGIETRIIHGASISSAVCGLTGLQLYKFGKTATIVFFTDNYRPQTPYNVIKENRKIGLH 160
Query: 414 PVILLDTAGLRTTTSDIIETEGNLLEKNNQ 443
++LLD I E NLLE+ +
Sbjct: 161 TLVLLDIHPKENRAMTIGEGLENLLEEEEK 190
>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 = 29.2 bits (65), Expect = 5.2
Identities = 16/61 (26%), Positives = 32/61 (52%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGGYPVILLDTAGLRTTTS 428
+++G+ VGKS+ +N + + + T V E + G + ++DT GL+++ S
Sbjct: 122 LVLGKSGVGKSATINSIFGEVKFSTDAFGMGTTSVQEIEGLVQGVKIRVIDTPGLKSSAS 181
Query: 429 D 429
D
Sbjct: 182 D 182
>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 = 28.9 bits (66), Expect = 5.3
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 370 IVGEPNVGKSSLMNFL 385
+VG PN GKS+L++ +
Sbjct: 162 LVGLPNAGKSTLISAV 177
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 29.3 bits (66), Expect = 5.5
Identities = 21/110 (19%), Positives = 36/110 (32%), Gaps = 9/110 (8%)
Query: 195 AEPGEFSKRA-----FFNNKLDLTQTEALGDLIQAETELQRQKALHQMKGNLKQLYSEWR 249
E + + A +L L EL++ + KG L
Sbjct: 275 FERDKIKQLASELEKKLEKELKK-LENKLEKQEDELEELEKAAEELRQKGELLYAN---L 330
Query: 250 QLILESLASVEAYIDFSEDEIIEDNILNTVRSQVVQLHGSIEKHIELSNK 299
QLI E L SV + +EI + + S+ Q + K ++ +
Sbjct: 331 QLIEEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKV 380
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 29.0 bits (66), Expect = 5.5
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 25/78 (32%)
Query: 370 IVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRD-------VIEK--HLDIG--------- 411
+VG+PNVGKS+ N + I + P TT D V + ++G
Sbjct: 6 LVGKPNVGKSTFFNAATLADVEI-ANYPFTTIDPNVGVAYVRVECPCKELGVKCNPRNGK 64
Query: 412 ---GY---PVILLDTAGL 423
G PV L+D AGL
Sbjct: 65 CIDGTRFIPVELIDVAGL 82
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 28.7 bits (65), Expect = 5.9
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 368 SVIVGEPNVGKSSLMNFL 385
S+ VG+ VGKSSL+N L
Sbjct: 208 SIFVGQSGVGKSSLINAL 225
>gnl|CDD|224997 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy
production and conversion].
Length = 260
Score = 28.8 bits (65), Expect = 5.9
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 125 DQKVSKPRYASLRNIVD----PVSEVVLDE 150
D ++++PRY SL I+ PV + L +
Sbjct: 180 DLRINEPRYPSLPGIMAAKKKPVKKWSLAD 209
Score = 28.0 bits (63), Expect = 8.4
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 64 DQKVPKPRYASLRNIVD----PVSKVVLDE 89
D ++ +PRY SL I+ PV K L +
Sbjct: 180 DLRINEPRYPSLPGIMAAKKKPVKKWSLAD 209
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP [Purines, pyrimidines, nucleosides,
and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 28.2 bits (64), Expect = 6.7
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 369 VIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRD 402
VI G GKS+L+ L ++ ++ SI TTR
Sbjct: 4 VISGPSGAGKSTLVKALLEEDPNLKFSISATTRK 37
>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 = 28.0 bits (63), Expect = 6.9
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 367 KSVIVGEPNVGKSSLMNFLCQKQISIVTSIPGTTRDVIEKHLDIGG--YPVILLDTAG 422
K ++G +VGKSSL + V S T + K + G Y + ++DTAG
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGH--FVESYYPTIENTFSKIITYKGQEYHLEIVDTAG 58
>gnl|CDD|235999 PRK07353, PRK07353, F0F1 ATP synthase subunit B'; Validated.
Length = 140
Score = 27.7 bits (62), Expect = 7.7
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 209 KLDLTQTEALGDLIQA--ETELQRQKALHQMKGNLKQLYSEWRQLILESL 256
L Q EA +A E E Q+Q AL Q++ + L + ILE L
Sbjct: 91 ALAEAQAEAQASKEKARREIEQQKQAALAQLEQQVDAL----SRQILEKL 136
>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like. Rab23-like
subfamily. Rab23 is a member of the Rab family of small
GTPases. In mouse, Rab23 has been shown to function as a
negative regulator in the sonic hedgehog (Shh) signaling
pathway. Rab23 mediates the activity of Gli2 and Gli3,
transcription factors that regulate Shh signaling in the
spinal cord, primarily by preventing Gli2 activation in
the absence of Shh ligand. Rab23 also regulates a step
in the cytoplasmic signal transduction pathway that
mediates the effect of Smoothened (one of two integral
membrane proteins that are essential components of the
Shh signaling pathway in vertebrates). In humans, Rab23
is expressed in the retina. Mice contain an isoform that
shares 93% sequence identity with the human Rab23 and an
alternative splicing isoform that is specific to the
brain. This isoform causes the murine open brain
phenotype, indicating it may have a role in the
development of the central nervous system. 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 = 162
Score = 27.8 bits (62), Expect = 7.8
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 366 IKSVIVGEPNVGKSSLMNFLC 386
IK ++VG NVGKSS++
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFV 21
>gnl|CDD|182525 PRK10532, PRK10532, threonine and homoserine efflux system;
Provisional.
Length = 293
Score = 28.5 bits (64), Expect = 7.8
Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 185 ALTKLPG-----LRPAEP--GEFSKRAFFNNKLDLTQTEALGDLIQA 224
ALT+LP L EP S F L L Q ALG +I A
Sbjct: 229 ALTRLPTRTFGTLMSMEPALAAVSGMIFLGETLTLIQWLALGAIIAA 275
>gnl|CDD|193500 cd03879, M28_AAP, M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica
aminopeptidase. Peptidase family M28; Aeromonas
(Vibrio) proteolytica aminopeptidase (AAP; leucine
aminopeptidase from Vibrio proteolyticus; Bacterial
leucyl aminopeptidase; E.C. 3.4.11.10) subfamily. AAP is
a small (32kDa), heat stable leucine aminopeptidase and
is active as a monomer. Similar forms of the enzyme have
been isolated from Escherichia coli and Staphylococcus
thermophilus. Leucine aminopeptidases, in general, play
important roles in many biological processes such as
protein catabolism, hormone degradation, regulation of
migration and cell proliferation, as well as HIV
infection and proliferation. AAP is a broad-specificity
enzyme, utilizing two zinc(II) ions in its active site
to remove N-terminal amino acids, with preference for
large hydrophobic amino acids in the P1 position of the
substrate, Leu being the most efficiently cleaved. It
can accommodate all residues, except Pro, Asp and Glu in
the P1' position.
Length = 285
Score = 28.3 bits (64), Expect = 8.2
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 388 KQISIVTSIPGTTRD----VIEKHLD 409
Q SI+ +IPG+ + V+ HLD
Sbjct: 73 PQPSIIVTIPGSEKSDETVVVGAHLD 98
>gnl|CDD|182405 PRK10357, PRK10357, putative glutathione S-transferase;
Provisional.
Length = 202
Score = 28.1 bits (63), Expect = 8.2
Identities = 32/138 (23%), Positives = 44/138 (31%), Gaps = 62/138 (44%)
Query: 143 VSEVVLDEGLCLWFPKPNSFTGEDCCEFQVHGSIAVINAILGALTKLPGLRPAEPGEFSK 202
V +V +EG C WF P +I + L P + P +P
Sbjct: 49 VPALVTEEGEC-WFDSP------------------IIAEYIELLNVAPAMLPRDPLA--- 86
Query: 203 RAFFNNKLDLTQTEALGDLI-----------------QAETELQRQKALHQMKGNLKQLY 245
L + Q EAL D I Q+E EL RQ
Sbjct: 87 ------ALRVRQLEALADGIMDAALVSVREQARPAAQQSEDELLRQ-------------- 126
Query: 246 SEWRQLILESLASVEAYI 263
R+ I SL ++E Y+
Sbjct: 127 ---REKINRSLDALEGYL 141
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 28.2 bits (64), Expect = 8.2
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 240 NLKQLYSEWRQLILESLASV-----EAYIDFSEDEIIEDNILNTVR 280
+L + E R+ ++E+LA V E Y++ +EI E+ I +R
Sbjct: 191 DLLEEAEEAREELIETLAEVDDELMEKYLE--GEEITEEEIKAAIR 234
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.1 bits (64), Expect = 8.3
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 376 VGKSSLMNFLCQKQISIVTSIPGTTR 401
GKS+L+ L ++ ++ S+ TTR
Sbjct: 16 AGKSTLVKALLERDPNLQLSVSATTR 41
>gnl|CDD|218006 pfam04286, DUF445, Protein of unknown function (DUF445). Predicted
to be a membrane protein.
Length = 366
Score = 28.4 bits (64), Expect = 9.2
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 238 KGNLKQLYSEWRQLILESLASVEAYIDFSEDEIIEDNILNTVRSQVVQL----HGSIEKH 293
+L S RQ I E LA + + +ED + D + + ++ H I +
Sbjct: 259 LDDLADPDSLLRQRISELLAELGERL--AEDPALRDKLNRWLEDAAERILERYHLEIGQL 316
Query: 294 IE 295
I
Sbjct: 317 IS 318
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 28.0 bits (63), Expect = 9.6
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 362 IRSGIKSVIVGEPNVGKSSLMNFLCQKQISIVTSIPG---------TTRDVIEKHLDIGG 412
+ G ++G VGKS+L+N L +++ ++ T R++ L GG
Sbjct: 192 LSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHTTTHRELHP--LPSGG 249
Query: 413 YPVILLDTAGLR 424
+L+DT G+R
Sbjct: 250 ---LLIDTPGMR 258
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 28.2 bits (63), Expect = 9.8
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 368 SVIVGEPNVGKSSLMNFLC 386
++I+G GK+ LMNFLC
Sbjct: 449 TLIIGPTGAGKTVLMNFLC 467
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.3 bits (64), Expect = 9.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 361 RIRSGIKSVIVGEPNVGKSSLMNFL 385
+ +G + +VG GK+SL+N L
Sbjct: 372 TLPAGQRIALVGPSGAGKTSLLNAL 396
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
0.318 0.135 0.390
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: 22,020,078
Number of extensions: 2138950
Number of successful extensions: 2499
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2452
Number of HSP's successfully gapped: 166
Length of query: 445
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 345
Effective length of database: 6,502,202
Effective search space: 2243259690
Effective search space used: 2243259690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.1 bits)