RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026538
(237 letters)
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 186 bits (474), Expect = 1e-59
Identities = 70/146 (47%), Positives = 96/146 (65%)
Query: 69 NIFRNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT 128
+F + EF +A P D PEIAFAGRSNVGKSS++NALT + + RTS PG T
Sbjct: 1 KLFIHNAEFVTSAPKLEQLPPDDGPEIAFAGRSNVGKSSLINALTNRKNLARTSKTPGRT 60
Query: 129 QTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGV 188
Q INFF++ KL LVDLPGYG+A +E K+ W++L++EY+ TR +LK V LLID++ +
Sbjct: 61 QLINFFEVNDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTRENLKGVVLLIDSRHPL 120
Query: 189 KPRDHELISLMERSQTKYQVVLTKTD 214
K D ++I ++ +VLTK D
Sbjct: 121 KELDLQMIEWLKEYGIPVLIVLTKAD 146
>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 = 181 bits (462), Expect = 4e-58
Identities = 66/139 (47%), Positives = 94/139 (67%)
Query: 94 EIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYA 153
E+AFAGRSNVGKSS++NALT + + RTS PG TQ INFF +G K LVDLPGYG+A
Sbjct: 1 EVAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKV 60
Query: 154 KEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKT 213
+EV++ W +L++EY+ R +LK V LLID + G P D E++ +E + +VLTK
Sbjct: 61 SKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKA 120
Query: 214 DTVFPIDVARRAMQIEEVI 232
D + ++A+ +I+E +
Sbjct: 121 DKLKKSELAKVLKKIKEEL 139
>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 = 176 bits (449), Expect = 4e-56
Identities = 66/139 (47%), Positives = 88/139 (63%)
Query: 76 EFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFK 135
EF +A P D PEIAFAGRSNVGKSS++NALT + + RTS PG TQ INFF+
Sbjct: 2 EFVKSAVKLKQLPPDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFE 61
Query: 136 LGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL 195
+ LVDLPGYG+A +E K+ W++L++EY+ R +LK V LL+D + +K D E+
Sbjct: 62 VNDGFRLVDLPGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEM 121
Query: 196 ISLMERSQTKYQVVLTKTD 214
I + +VLTK D
Sbjct: 122 IEWLRERGIPVLIVLTKAD 140
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 172 bits (439), Expect = 2e-54
Identities = 73/164 (44%), Positives = 103/164 (62%)
Query: 69 NIFRNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT 128
+ +K +F +A +P DLPEIAFAGRSNVGKSS++NALT Q + RTS PG T
Sbjct: 1 KLNYHKAKFITSAPDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRT 60
Query: 129 QTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGV 188
Q INFF++ +L LVDLPGYG+A +EVK+ W++L++EY+ R +LK V LLID +
Sbjct: 61 QLINFFEVDDELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPP 120
Query: 189 KPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEEVI 232
K D E+I + VVLTK D + + ++ ++ E +
Sbjct: 121 KDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEEL 164
>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 = 86.6 bits (215), Expect = 8e-22
Identities = 35/122 (28%), Positives = 56/122 (45%), Gaps = 8/122 (6%)
Query: 94 EIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ--TINFFKLGTKLCLVDLPGYGFA 151
+A GR NVGKS+++NALT V SD PG T+ + LG ++ LVD PG
Sbjct: 1 RVALVGRPNVGKSTLINALTGA-KVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLI-- 57
Query: 152 YAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELIS-LMERSQTKYQVVL 210
+ + E ++ + L++D G+ D E++ L + + +VL
Sbjct: 58 --EGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVL 115
Query: 211 TK 212
K
Sbjct: 116 NK 117
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 71.9 bits (177), Expect = 2e-15
Identities = 31/78 (39%), Positives = 49/78 (62%), Gaps = 4/78 (5%)
Query: 93 PEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF-A 151
PEI F GRSNVGKS+++ LT + VR +PG+T+ N + G + L DLPG+GF +
Sbjct: 10 PEIVFVGRSNVGKSTLVRELTGKK--VRVGKRPGVTRKPNHYDWGDFI-LTDLPGFGFMS 66
Query: 152 YAKEEVKDAWEELVKEYV 169
+EV++ ++ + Y+
Sbjct: 67 GVPKEVQEKIKDEIVRYI 84
>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 = 59.6 bits (145), Expect = 3e-11
Identities = 38/126 (30%), Positives = 54/126 (42%), Gaps = 18/126 (14%)
Query: 96 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTIN----FFKLGTKLCLVDLPGY--G 149
A GR NVGKSS+LNAL Q V S PG T+ + L+D PG
Sbjct: 1 AIFGRPNVGKSSLLNALLGQN-VGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEE 59
Query: 150 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL-ISLMERSQTKYQV 208
+E V++A + R L V L++D+ + P + E + L+ +
Sbjct: 60 GGLGRERVEEARQVA------DRADL--VLLVVDS--DLTPVEEEAKLGLLRERGKPVLL 109
Query: 209 VLTKTD 214
VL K D
Sbjct: 110 VLNKID 115
>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 = 57.1 bits (138), Expect = 2e-10
Identities = 35/146 (23%), Positives = 53/146 (36%), Gaps = 16/146 (10%)
Query: 96 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGT-----KLCLVDLPGYGF 150
GR VGKSS+LNAL V SD PG T+ + + KL LVD PG
Sbjct: 1 VVVGRGGVGKSSLLNALLGGE-VGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGL-- 57
Query: 151 AYAKEEVKDAWEELVKEYVSTRVSLKRVCLLID-TKWGVKPR-DHELISLMERSQTKYQV 208
+E E + + L + L++D T + ++ + + +
Sbjct: 58 ----DEFGGLGREELARLLLRGADL--ILLVVDSTDRESEEDAKLLILRRLRKEGIPIIL 111
Query: 209 VLTKTDTVFPIDVARRAMQIEEVIFY 234
V K D + +V E
Sbjct: 112 VGNKIDLLEEREVEELLRLEELAKIL 137
>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 = 53.9 bits (130), Expect = 2e-09
Identities = 36/140 (25%), Positives = 53/140 (37%), Gaps = 14/140 (10%)
Query: 96 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTK---LCLVDLPGYGFAY 152
G++ GKSS+ NAL V D+ T+ + T L L+DLPG G
Sbjct: 1 GLMGKTGAGKSSLCNALFGT-EVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERG 59
Query: 153 AKEEVKDAW-EELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISL-MERSQTKYQVVL 210
+D EEL + + V L+D DH+ L + VL
Sbjct: 60 ----RRDREYEELYRRLLPE---ADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVL 112
Query: 211 TKTDTVFPIDVARRAMQIEE 230
+ D V + AR ++E
Sbjct: 113 NQVDPVLAV-SARTGWGLDE 131
>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 = 1e-08
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 102 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
NVGKS+++N L + V + +KPG+T+ + ++G + L+D PG
Sbjct: 125 NVGKSTLINRLRGK-KVAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 53.2 bits (128), Expect = 2e-08
Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 99 GRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF 150
G NVGKS+++N L + V +TS++PG T+ I + KL + L+D PG
Sbjct: 139 GYPNVGKSTLINRLLGK-KVAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIP 189
>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 = 50.9 bits (123), Expect = 4e-08
Identities = 39/131 (29%), Positives = 61/131 (46%), Gaps = 21/131 (16%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLG------TKLCLVDLPGY 148
+A GR NVGKS++LNAL Q + S KP T+ G ++ VD PG
Sbjct: 6 VAIIGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRNRI---RGIYTDDDAQIIFVDTPGI 61
Query: 149 GFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTK 205
+ ++ E +VK S +LK V ++D + D ++ L+++S+T
Sbjct: 62 ---HKPKKKLG--ERMVKAAWS---ALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTP 113
Query: 206 YQVVLTKTDTV 216
+VL K D V
Sbjct: 114 VILVLNKIDLV 124
>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 = 52.5 bits (127), Expect = 5e-08
Identities = 42/147 (28%), Positives = 61/147 (41%), Gaps = 23/147 (15%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT-----QTINFFKLGTKLCLVDLPGYG 149
I GR N GKSS++NALT Q + SD PG T + + LG + L+D G
Sbjct: 9 IGIFGRRNAGKSSLINALTGQ-DIAIVSDVPGTTTDPVYKAMELLPLGPVV-LIDTAG-- 64
Query: 150 FAYAKEEVKDAWE--ELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQT 204
+ D E EL E TR L + L++D G + ELI ++ +
Sbjct: 65 -------LDDEGELGELRVE--KTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKI 115
Query: 205 KYQVVLTKTDTVFPIDVARRAMQIEEV 231
Y VV+ K D + + +
Sbjct: 116 PYIVVINKIDLGEESAELEKLEKKFGL 142
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 52.2 bits (126), Expect = 6e-08
Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 20/132 (15%)
Query: 92 LPEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLTQTINFFK---LGTKLCLVDL 145
P +A GR NVGKS++ N LT + R SD PG+T+ + LG + L+D
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLTGR----RIAIVSDTPGVTRDRIYGDAEWLGREFILIDT 58
Query: 146 PGYGFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERS 202
G + +D +EL++E ++++ + ++D + G+ P D E+ ++ RS
Sbjct: 59 GGL-----DDGDEDELQELIRE--QALIAIEEADVILFVVDGREGITPADEEIAKILRRS 111
Query: 203 QTKYQVVLTKTD 214
+ +V+ K D
Sbjct: 112 KKPVILVVNKID 123
Score = 39.5 bits (93), Expect = 8e-04
Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 4/53 (7%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVD 144
IA GR NVGKSS++NA+ + V+ SD G T+ I F + G K L+D
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVI-VSDIAGTTRDSIDIEFERDGRKYVLID 232
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 26/64 (40%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 87 FPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT---QTINFFKLGTKLCLV 143
F A + I G NVGKSS++NAL V S PG T QTI L + L
Sbjct: 77 FSALNEATIGLVGYPNVGKSSLINALVGS-KKVSVSSTPGKTKHFQTIF---LEPGITLC 132
Query: 144 DLPG 147
D PG
Sbjct: 133 DCPG 136
>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 = 49.0 bits (118), Expect = 2e-07
Identities = 31/125 (24%), Positives = 57/125 (45%), Gaps = 21/125 (16%)
Query: 99 GRSNVGKSSMLNALTRQWGVVR---TSDKPGLT---QTINFFKLGTKLCLVDLPGYGFAY 152
GR NVGKS++ N LT + R SD PG+T + G + L+D G
Sbjct: 4 GRPNVGKSTLFNRLTGR----RDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGI---- 55
Query: 153 AKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQVV 209
E + + ++E ++++ + ++D + G+ P D E+ + +S+ +V
Sbjct: 56 --EPDDEGISKEIRE--QAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILV 111
Query: 210 LTKTD 214
+ K D
Sbjct: 112 VNKID 116
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 49.7 bits (120), Expect = 4e-07
Identities = 35/134 (26%), Positives = 63/134 (47%), Gaps = 25/134 (18%)
Query: 92 LPEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLT-----QTINFFKLGTKLCLV 143
P +A GR NVGKS++ N LT + R +D PG+T + LG + L+
Sbjct: 1 KPVVAIVGRPNVGKSTLFNRLTGK----RDAIVADTPGVTRDRIYGEAEW--LGREFILI 54
Query: 144 DLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLME 200
D G E D +E+ ++E ++++ + ++D + G+ P D E+ ++
Sbjct: 55 DTGGI------EPDDDGFEKQIRE--QAELAIEEADVILFVVDGRAGLTPADEEIAKILR 106
Query: 201 RSQTKYQVVLTKTD 214
+S +V+ K D
Sbjct: 107 KSNKPVILVVNKVD 120
Score = 44.3 bits (106), Expect = 3e-05
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 82 KVSSSFPAPDLPE-------IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TI 131
+ P + + IA GR NVGKSS++NAL + V+ SD G T+
Sbjct: 156 AILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVI-VSDIAGTTRDSIDT 214
Query: 132 NFFKLGTKLCLVD 144
F + G K L+D
Sbjct: 215 PFERDGQKYTLID 227
>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 = 47.8 bits (114), Expect = 4e-07
Identities = 32/132 (24%), Positives = 52/132 (39%), Gaps = 21/132 (15%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTIN--FFKLG---TKLCLVDLPGYG 149
I G NVGKS++LN L + T KPG T+ + K L+D G
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISI-TEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG-- 60
Query: 150 FAYAKEEVKDAWEELVKEYVSTRVSLKRVC----LLIDTKWGVKPRDHELISLMERSQTK 205
++ ++ + + Y S RV L++D + ++ + E+I E S
Sbjct: 61 --------QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE-SGVP 111
Query: 206 YQVVLTKTDTVF 217
+V K D
Sbjct: 112 IILVGNKIDLRD 123
>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 = 47.8 bits (115), Expect = 5e-07
Identities = 41/149 (27%), Positives = 68/149 (45%), Gaps = 14/149 (9%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVDLPGYGFA 151
IA GR NVGKSS+LNAL + V+ SD G T+ + F G K L+D G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVI-VSDIAGTTRDSIDVPFEYDGQKYTLIDTAG---I 60
Query: 152 YAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQV 208
K +V + E+ + T +++R V L++D G+ +D + L+ +
Sbjct: 61 RKKGKVTEGIEKYS--VLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALII 118
Query: 209 VLTKTDTVFPIDVARRAM--QIEEVIFYL 235
V+ K D V + + ++ + +L
Sbjct: 119 VVNKWDLVEKDEKTMKEFEKELRRKLPFL 147
>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 = 49.4 bits (119), Expect = 5e-07
Identities = 34/131 (25%), Positives = 59/131 (45%), Gaps = 25/131 (19%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLT-----QTINFFKLGTKLCLVDLP 146
+A GR NVGKS++ N LT + R SD PG+T + G + L+D
Sbjct: 2 VAIVGRPNVGKSTLFNRLTGK----RDAIVSDTPGVTRDRKYGDAEW--GGREFILIDTG 55
Query: 147 GYGFAYAKEEVKDAWEELVKEYVSTRVSLK---RVCLLIDTKWGVKPRDHELISLMERSQ 203
G EE D ++ ++E ++++ + ++D + G+ P D E+ + +S
Sbjct: 56 GI------EEDDDGLDKQIRE--QAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSG 107
Query: 204 TKYQVVLTKTD 214
+V K D
Sbjct: 108 KPVILVANKID 118
Score = 47.8 bits (115), Expect = 2e-06
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 12/74 (16%)
Query: 82 KVSSSFPAPDLPE--------IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---T 130
+ P + E IA GR NVGKS+++NAL + V+ SD G T+
Sbjct: 154 AILELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVI-VSDIAGTTRDSID 212
Query: 131 INFFKLGTKLCLVD 144
I F + G K L+D
Sbjct: 213 IPFERNGKKYTLID 226
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 46.5 bits (111), Expect = 2e-06
Identities = 29/155 (18%), Positives = 54/155 (34%), Gaps = 30/155 (19%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVV--------RTSD------KPGLTQTINFFKLGTKL 140
+ G + GK+++ +L Q G + D + G+T +
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 141 C---LVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELIS 197
+D PG+ E+ KE V L++D GV+P+ E ++
Sbjct: 62 RRINFIDTPGH-------------EDFSKETVRGLAQADGALLVVDANEGVEPQTREHLN 108
Query: 198 LMERSQTKYQVVLTKTDTVFPIDVARRAMQIEEVI 232
+ V + K D V D +I+E++
Sbjct: 109 IALAGGLPIIVAVNKIDRVGEEDFDEVLREIKELL 143
>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 = 46.1 bits (110), Expect = 2e-06
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 97 FAGRSNVGKSSMLNALTRQWGVVR----------TSDKPGLTQTINFFKLGTKLCLVDLP 146
G +NVGKS+++NAL + G S PG T + LG L D P
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTP 189
Query: 147 GY 148
G
Sbjct: 190 GI 191
>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 = 45.0 bits (107), Expect = 4e-06
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTS---DKPGLTQTINFFKLGTKLCLVDLPG 147
+ G VGKSS++NAL + TS PG T+ I ++ +K+ L+D PG
Sbjct: 102 VGVVGYPKVGKSSIINALKGR-HSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
>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 = 45.2 bits (108), Expect = 6e-06
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 11/70 (15%)
Query: 95 IAFAGRSNVGKSSMLNALT--RQWGVVRTSDKPGLTQTIN--FFKL-GTKLCLVDLPG-Y 148
IA G NVGK+++ NALT RQ + PG+T FK G ++ +VDLPG Y
Sbjct: 3 IALVGNPNVGKTTLFNALTGARQ----HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTY 58
Query: 149 GF-AYAKEEV 157
Y++EE
Sbjct: 59 SLSPYSEEEK 68
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 45.7 bits (109), Expect = 1e-05
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 93 PEIAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLT---QTINFFKLGTKLCLVDLPG- 147
+A G NVGK+++ NALT G + + PG+T + G ++ +VDLPG
Sbjct: 4 LTVALVGNPNVGKTTLFNALT---GANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGT 60
Query: 148 YGFAYAKEEVKDAWEELVKE 167
Y E+ K A + L++
Sbjct: 61 YSLTAYSEDEKVARDFLLEG 80
>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 = 44.9 bits (107), Expect = 1e-05
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 97 FAGRSNVGKSSMLNALTRQWG----VVRTSDKPGLTQTINFFKLGTKLCLVDLPGY 148
G +NVGKSS++N L +Q V+ TS PG T + L L D PG
Sbjct: 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGI 214
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 43.9 bits (105), Expect = 2e-05
Identities = 34/146 (23%), Positives = 53/146 (36%), Gaps = 43/146 (29%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-------------GLTQTINFFKLGTKLC 141
+A GR NVGKS++LNAL Q + S KP Q I
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRHRIRGIVTEDDAQII---------- 56
Query: 142 LVDLPGYGFA-------YAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHE 194
VD PG + + ++ V L V ++D + P D
Sbjct: 57 FVDTPGI-HKPKRALNRAMNKAAWSSLKD---------VDL--VLFVVDADEKIGPGDEF 104
Query: 195 LISLMERSQTKYQVVLTKTDTVFPID 220
++ +++ +T +VL K D V +
Sbjct: 105 ILEKLKKVKTPVILVLNKIDLVKDKE 130
>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 = 42.5 bits (101), Expect = 7e-05
Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 102 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
NVGKS+++N L + V + ++PG+T+ + KL L L+D PG
Sbjct: 128 NVGKSTLINRLAGK-KVAKVGNRPGVTKGQQWIKLSDGLELLDTPG 172
>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 = 41.3 bits (98), Expect = 7e-05
Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 11/68 (16%)
Query: 96 AFAGRSNVGKSSMLNALT--RQWGVVRTSDKPGLT--QTINFFKLGTKLC-LVDLPG-YG 149
A G NVGK+++ NALT RQ + + PG+T + FKLG K +VDLPG Y
Sbjct: 1 ALVGNPNVGKTTLFNALTGARQ----KVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGTYS 56
Query: 150 F-AYAKEE 156
Y+++E
Sbjct: 57 LTPYSEDE 64
>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 = 41.8 bits (99), Expect = 8e-05
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 95 IAFAGRSNVGKSSMLNALTRQ----WGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
+A G + GKS++LNAL + GV T+ T+ + L + LVD PG
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVI----TVLRYGLLKGVVLVDTPG 55
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 41.4 bits (98), Expect = 9e-05
Identities = 40/149 (26%), Positives = 67/149 (44%), Gaps = 26/149 (17%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-GLTQTINF----FKLGTKLCLVDLPGYG 149
I AG + GK++++ ALT +K G+T + F G +L +D+PG+
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGH- 60
Query: 150 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKP--RDH-ELISLMERSQTKY 206
E+ VK ++ + V L++ G+ P R+H E++ L+ +
Sbjct: 61 ------------EKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKG-- 106
Query: 207 QVVLTKTDTVFPIDVARRAMQIEEVIFYL 235
VVLTK D V D R + EE++ L
Sbjct: 107 LVVLTKADLV---DEDRLELVEEEILELL 132
>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 = 40.6 bits (96), Expect = 2e-04
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 102 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGY 148
NVGKSS++N+L R PG+T+++ L + L+D PG
Sbjct: 126 NVGKSSVINSLKRS-RACNVGATPGVTKSMQEVHLDKHVKLLDSPGV 171
>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 = 41.7 bits (98), Expect = 2e-04
Identities = 38/126 (30%), Positives = 59/126 (46%), Gaps = 16/126 (12%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTI---NFFKLGTKLCLVDLPGYGFA 151
+A G NVGKSS+LNAL +Q + SD G T+ + +F G + L+D G
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAI-VSDIKGTTRDVVEGDFELNGILIKLLDTAGI--- 261
Query: 152 YAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQV 208
E D E L E + ++K+ V ++D + D LI + +S+ + +
Sbjct: 262 ---REHADFVERLGIE--KSFKAIKQADLVIYVLDASQPLTKDD-FLIIDLNKSKKPFIL 315
Query: 209 VLTKTD 214
VL K D
Sbjct: 316 VLNKID 321
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 41.4 bits (98), Expect = 2e-04
Identities = 39/150 (26%), Positives = 67/150 (44%), Gaps = 20/150 (13%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT----QTINFFKLGTKLCLVDLPGYGF 150
+A GR NVGKS++LNAL Q + S KP T + I ++ VD PG
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRNRIRGIVTTD-NAQIIFVDTPGI-- 64
Query: 151 AYAKEEVKDAWEE-LVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVV 209
+ K A E + K S + + ++D G P D ++ +++++T +V
Sbjct: 65 ----HKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILV 120
Query: 210 LTKTDTVFP-------IDVARRAMQIEEVI 232
+ K D V P I ++ + +E++
Sbjct: 121 VNKIDKVKPKTVLLKLIAFLKKLLPFKEIV 150
>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 = 39.3 bits (92), Expect = 4e-04
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
+ G NVGKSS +NAL ++ ++ PG T+ KL ++ L D PG
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFK-LKVGSIPGTTKLQQDVKLDKEIYLYDTPG 145
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 40.2 bits (95), Expect = 5e-04
Identities = 39/155 (25%), Positives = 59/155 (38%), Gaps = 32/155 (20%)
Query: 95 IAFAGRSNVGKSSMLNALTRQ-WGVVRTSDKPGLTQTI--NFFKLGTKLC-LVDLPGY-- 148
+ GR NVGKSS+LNAL + +V +D G T+ + L LVD G
Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIV--TDIAGTTRDVIEEDINLNGIPVRLVDTAGIRE 277
Query: 149 --------GFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLME 200
G AK+ +++A V ++D + D LI L
Sbjct: 278 TDDVVERIGIERAKKAIEEA---------------DLVLFVLDASQPLDKEDLALIEL-L 321
Query: 201 RSQTKYQVVLTKTDTVFPIDVARRAMQIEEVIFYL 235
+ VVL K D V I++ + + I +
Sbjct: 322 PKKKPIIVVLNKADLVSKIELESEKLANGDAIISI 356
>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 = 39.3 bits (92), Expect = 5e-04
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 96 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINF----FKLGTKLCLVDLPG 147
G NVGKS++L+ALT V + P T N F G + ++DLPG
Sbjct: 1 GLVGLPNVGKSTLLSALTS--AKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPG 54
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 40.2 bits (94), Expect = 7e-04
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 52 LDNIPFSTSSERERIEENIFRNKLEFFAAAKVSSSFPAPD-LPEIAFAGRSNVGKSSMLN 110
L P+ S+ R ++ L+ A+ +S F P L +A GR NVGKSS+LN
Sbjct: 410 LGE-PYPISAMHGRGVGDLLDEALDSLKVAEKTSGFLTPSGLRRVALVGRPNVGKSSLLN 468
Query: 111 ALTRQ 115
LT +
Sbjct: 469 QLTHE 473
Score = 34.4 bits (79), Expect = 0.045
Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 13/125 (10%)
Query: 95 IAFAGRSNVGKSSMLNA-LTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVDLPGYGF 150
+A GR NVGKS+++N L R+ VV D PG+T+ + + GT LVD G+
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVE--DTPGVTRDRVSYDAEWAGTDFKLVDTGGW-- 333
Query: 151 AYAKEEVKDAWEELVKEYVSTRVSLKR-VCLLIDTKWGVKPRDHELISLMERSQTKYQVV 209
+ +V+ + + VSL V ++D + G+ D ++ ++ R+ +
Sbjct: 334 ---EADVEGIDSAIASQ-AQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLA 389
Query: 210 LTKTD 214
+ K D
Sbjct: 390 VNKID 394
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 39.4 bits (93), Expect = 8e-04
Identities = 19/46 (41%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 102 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
NVGKS+++N L + + +T ++PG+T+ + KLG L L+D PG
Sbjct: 131 NVGKSTLINRLAGK-KIAKTGNRPGVTKAQQWIKLGKGLELLDTPG 175
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 37.9 bits (89), Expect = 0.001
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 95 IAFAGRSNVGKSSMLNALT---RQW-GVVRTSDKPG--LTQTINFFKLGTKLCLVDLPG- 147
AG+S VGKS++LNAL G + G T + F L L+D PG
Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLIDTPGF 97
Query: 148 --YGFAY-AKEEVKDAWEELVK 166
G + EE+ + + E +
Sbjct: 98 RELGLWHLDPEELAEYFPEFRE 119
>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 = 37.7 bits (88), Expect = 0.002
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
+ F G NVGKSS++N L R V + + PG T+ + L ++ L+D PG
Sbjct: 105 VGFIGYPNVGKSSVINTL-RSKKVCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 38.6 bits (91), Expect = 0.002
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 95 IAFAGRSNVGKSSMLNALTRQ 115
+ AGR NVGKSS+LNAL +
Sbjct: 218 VVIAGRPNVGKSSLLNALLGE 238
>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 = 37.5 bits (88), Expect = 0.002
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 95 IAFAGRSNVGKSSMLNALTRQ 115
+ AG+ NVGKSS+LNAL +
Sbjct: 6 VVIAGKPNVGKSSLLNALAGR 26
>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 = 37.8 bits (88), Expect = 0.003
Identities = 29/132 (21%), Positives = 54/132 (40%), Gaps = 14/132 (10%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT----QTINFFKLGTKLCLVDLPGYGF 150
+A GR NVGKS++LN L Q + TS K T I +++ +D PG+
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQ-KISITSPKAQTTRNRISGI-HTTGASQIIFIDTPGF-- 58
Query: 151 AYAKEEVKDAWEELVKEYVSTRVSLKRVCLLID-TKWGVKPRDHELISLMERSQTKYQVV 209
E+ ++KE S + + ++D +W +++ ++ + +
Sbjct: 59 ---HEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQW--NGDGEFVLTKLQNLKRPVVLT 113
Query: 210 LTKTDTVFPIDV 221
K D F +
Sbjct: 114 RNKLDNKFKDKL 125
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 37.7 bits (88), Expect = 0.003
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 96 AFAGRSNVGKSSMLNAL----TRQWGVVRTSDKPG--LTQTINFFKLGTKLCLVDLPGY- 148
G+S VGKS+++NAL ++ G + G T + F L ++D PG+
Sbjct: 168 VLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDTPGFR 227
Query: 149 --GFAYA-KEEVKDAWEEL 164
G A+ E++ A+ E
Sbjct: 228 SLGLAHLEPEDLVQAFPEF 246
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 37.1 bits (86), Expect = 0.005
Identities = 28/92 (30%), Positives = 35/92 (38%), Gaps = 10/92 (10%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKL---GTKLCLVDLPGYGFA 151
+ G + GKSS++NAL Q V S T +L G L L D PG G
Sbjct: 42 VLLMGATGAGKSSLINALF-QGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGLG-- 98
Query: 152 YAKEEVKDAWEELVKEYVSTRVSLKRVCLLID 183
+ KD E + Y L V LI
Sbjct: 99 ----DGKDKDAEHRQLYRDYLPKLDLVLWLIK 126
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 37.2 bits (86), Expect = 0.006
Identities = 32/147 (21%), Positives = 65/147 (44%), Gaps = 26/147 (17%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-----GLTQTINFFKL---GTKLCLVDLP 146
IA AG + GK+++L ALT + P G+T + F +L +D+P
Sbjct: 3 IATAGHVDHGKTTLLKALTG----IAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVP 58
Query: 147 GYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKY 206
G+ E+ + ++ + L++D GV + E +++++ +
Sbjct: 59 GH-------------EKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPH 105
Query: 207 Q-VVLTKTDTVFPIDVARRAMQIEEVI 232
VV+TK D V ++ R M +++++
Sbjct: 106 TIVVITKADRVNEEEIKRTEMFMKQIL 132
>gnl|CDD|130988 TIGR01933, hflK, HflK protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully
described.//Regulation of FtsH by HflKC appears to be
negative (PMID:8947034,PMID:96367) [SS 8/27/03].
Length = 261
Score = 36.2 bits (84), Expect = 0.009
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 98 AGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEV 157
A R +G S+M + LT +R K L + I+ + LG + V+ A EEV
Sbjct: 95 ALRGVIGDSTMDDILTEGRSQIREDTKERLNEIIDNYDLGITVTDVNFQS---ARPPEEV 151
Query: 158 KDAWEELVK 166
K+A+++++
Sbjct: 152 KEAFDDVII 160
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 35.7 bits (83), Expect = 0.013
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 75 LEFFAAAKVS-SSFPA--PDLPEIAFAGRSNVGKSSMLNALTR 114
LEF A+ PA PDLP I AG NVGKSS++ LT
Sbjct: 148 LEFLRKARDHLKKLPAIDPDLPTIVVAGYPNVGKSSLVRKLTT 190
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 35.3 bits (82), Expect = 0.023
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 79 AAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLN-ALTRQWGVVRTSDKPGLT 128
A++ ++ P LP +A GR NVGKS+++N L R+ VV D PG+T
Sbjct: 26 DLAELEAAEGGP-LPVVAVVGRPNVGKSTLVNRILGRREAVVE--DVPGVT 73
Score = 34.9 bits (81), Expect = 0.032
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 82 KVSSSFPAPDLP-EIAFAGRSNVGKSSMLNALTRQWGVV 119
+V A P +A G+ NVGKSS+LN L + V
Sbjct: 200 EVPRVGSASGGPRRVALVGKPNVGKSSLLNKLAGEERSV 238
>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 = 35.1 bits (81), Expect = 0.027
Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 99 GRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTK---LCLVDLPG-YGF-AYA 153
G NVGKS++ NALT + PG+T KLG + + +VDLPG Y ++
Sbjct: 1 GNPNVGKSTLFNALTG--ANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFS 58
Query: 154 KEE 156
EE
Sbjct: 59 LEE 61
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 34.8 bits (81), Expect = 0.027
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 97 FAGRSNVGKSSMLNAL 112
F G+S VGKSS++NAL
Sbjct: 210 FVGQSGVGKSSLINAL 225
>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 = 33.6 bits (78), Expect = 0.045
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALTR 114
+P +A G +N GKS++ NALT
Sbjct: 40 GVPTVALVGYTNAGKSTLFNALTG 63
>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 = 33.9 bits (79), Expect = 0.045
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 95 IAFAGRSNVGKSSMLNALT---RQW-GVVRTSDKPGL--TQTINFFKLGTKLCLVDLPG- 147
G+S VGKS++LNAL G + G T F L ++D PG
Sbjct: 88 SVLVGQSGVGKSTLLNALLPELVLATGEISEKLGRGRHTTTHRELFPLPGGGLIIDTPGF 147
Query: 148 --YGFAY-AKEEVKDAWEELVK 166
G + EE+ + + E +
Sbjct: 148 RELGLLHIDPEELAEYFPEFEE 169
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 33.3 bits (77), Expect = 0.098
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 95 IAFAGRSNVGKSSMLNALTRQW----GVVRTSDKP 125
+A GR+ GKS++L LTR W G + + +P
Sbjct: 369 VALLGRTGCGKSTLLQLLTRAWDPQQGEILLNGQP 403
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 32.7 bits (75), Expect = 0.10
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 93 PEIAFAGRSNVGKSSMLNAL-TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYG 149
P + G S+ GK+++ L T + TS +P + + G KL LVD+PG+
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHE 58
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 32.4 bits (74), Expect = 0.11
Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 16/95 (16%)
Query: 93 PEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLTQTINFFKLGTKLCLVDLPGYG 149
P + AG + GK+S+ LT G V+ TS +P K G L+D PG+
Sbjct: 4 PAVIIAGLCDSGKTSLFTLLTT--GTVKKTVTSQEPSAAYKYMLHK-GFSFTLIDFPGH- 59
Query: 150 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDT 184
VK + + E + SL+ + ++D+
Sbjct: 60 -------VKLRQK--LLETIKDSSSLRGIVFVVDS 85
>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 = 32.6 bits (75), Expect = 0.13
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 95 IAFAGRSNVGKSSMLNALT 113
I G+ NVGKS+ NA T
Sbjct: 1 IGLVGKPNVGKSTFFNAAT 19
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 32.5 bits (75), Expect = 0.16
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 93 PEIAFAGRSNVGKSSMLNALTR 114
+I G NVGKS++ NALT+
Sbjct: 3 LKIGIVGLPNVGKSTLFNALTK 24
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 32.5 bits (74), Expect = 0.18
Identities = 23/65 (35%), Positives = 29/65 (44%), Gaps = 13/65 (20%)
Query: 94 EIAFAGRSNVGKSSMLNAL---------TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVD 144
+IA G S GKSS +NAL + GVV T+ K +F + L D
Sbjct: 37 KIAVTGDSGNGKSSFINALRGIGHEEDGSAPTGVVETTMKRTPYSHPHF----PNVVLWD 92
Query: 145 LPGYG 149
LPG G
Sbjct: 93 LPGLG 97
>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 = 32.1 bits (74), Expect = 0.24
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALTR 114
D+P +A G +N GKS++ NALT
Sbjct: 188 DVPTVALVGYTNAGKSTLFNALTG 211
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.7 bits (73), Expect = 0.26
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 97 FAGRSNVGKSSMLNAL 112
AG+S VGKS++LNAL
Sbjct: 169 LAGQSGVGKSTLLNAL 184
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 31.6 bits (72), Expect = 0.29
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 97 FAGRSNVGKSSMLNAL 112
FAG+S VGKSS++NAL
Sbjct: 125 FAGQSGVGKSSLINAL 140
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.5 bits (72), Expect = 0.32
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALT 113
+P +A G +N GKS++ NALT
Sbjct: 191 GIPLVALVGYTNAGKSTLFNALT 213
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 31.6 bits (72), Expect = 0.34
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 95 IAFAGRSNVGKSSMLNALT--RQ----WGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 147
I G N GK+++ N LT RQ W V K G F ++ LVDLPG
Sbjct: 6 IGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEG-----QFSTTDHQVTLVDLPG 59
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 31.4 bits (72), Expect = 0.35
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 95 IAFAGRSNVGKSSMLNALTRQ----WGVVRTSDKPG--LTQTINFFKLGTKLCLVDLPG 147
+A G S VGKS+++NAL + G VR D G T L + L+D PG
Sbjct: 198 VALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHTTTHRELHPLPSGGLLIDTPG 256
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 31.5 bits (72), Expect = 0.36
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLTQTINFFKL---GTKLCLVDLPG--Y 148
+A G +VGKS++LN LT +D P T L G ++ L+DLPG
Sbjct: 66 VALVGFPSVGKSTLLNKLT---NTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE 122
Query: 149 GFAYAK 154
G + +
Sbjct: 123 GASSGR 128
>gnl|CDD|178633 PLN03084, PLN03084, alpha/beta hydrolase fold protein; Provisional.
Length = 383
Score = 31.4 bits (71), Expect = 0.36
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 145 LPGYGFAYAKEEVKDAWEELVKEYVSTRVSL 175
PGYGF Y +E + E L+ E S +VSL
Sbjct: 171 QPGYGFNYTLDEYVSSLESLIDELKSDKVSL 201
>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 = 31.0 bits (71), Expect = 0.40
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLTQTINFFKL---GTKLCLVDLPG 147
+A G +VGKS++L+ LT + T T + G K+ L+DLPG
Sbjct: 3 VALVGFPSVGKSTLLSKLT---NTKSEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPG 56
>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 = 30.6 bits (70), Expect = 0.46
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 98 AGRSNVGKSSMLNALTR 114
AG NVGKSS++N LTR
Sbjct: 6 AGYPNVGKSSLVNKLTR 22
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 31.2 bits (71), Expect = 0.56
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 98 AGRSNVGKSSMLNALTR 114
GR+ GKSSMLNAL R
Sbjct: 1271 VGRTGAGKSSMLNALFR 1287
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 30.4 bits (69), Expect = 0.78
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 94 EIAFAGRSNVGKSSMLNALTRQ 115
EIAF G S GK++++ AL R+
Sbjct: 7 EIAFCGYSGSGKTTLITALVRR 28
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 30.2 bits (69), Expect = 0.86
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 94 EIAFAGRSNVGKSSMLNALT 113
I G+ NVGKS+ NA T
Sbjct: 3 TIGLVGKPNVGKSTFFNAAT 22
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of CydCD,
subfamily C. The CYD subfamily implicated in cytochrome
bd biogenesis. The CydC and CydD proteins are important
for the formation of cytochrome bd terminal oxidase of
E. coli and it has been proposed that they were
necessary for biosynthesis of the cytochrome bd quinol
oxidase and for periplasmic c-type cytochromes. CydCD
were proposed to determine a heterooligomeric complex
important for heme export into the periplasm or to be
involved in the maintenance of the proper redox state of
the periplasmic space. In Bacillus subtilis, the absence
of CydCD does not affect the presence of halo-cytochrome
c in the membrane and this observation suggests that
CydCD proteins are not involved in the export of heme in
this organism.
Length = 178
Score = 29.6 bits (67), Expect = 0.89
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 95 IAFAGRSNVGKSSMLNALTRQW 116
IA GRS GKS++L LT
Sbjct: 31 IALLGRSGSGKSTLLQLLTGDL 52
>gnl|CDD|206690 cd04104, p47_IIGP_like, p47 GTPase family includes IGTP, TGTP/Mg21,
IRG-47, GTPI, LRG-47, and IIGP1. The p47 GTPase family
consists of several highly homologous proteins,
including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and
IIGP1. They are found in higher eukaryotes where they
play a role in immune resistance against intracellular
pathogens. p47 proteins exist at low resting levels in
mouse cells, but are strongly induced by Type II
interferon (IFN-gamma). ITGP is critical for resistance
to Toxoplasma gondii infection and in involved in
inhibition of Coxsackievirus-B3-induced apoptosis. TGTP
was shown to limit vesicular stomatitis virus (VSV)
infection of fibroblasts in vitro. IRG-47 is involved in
resistance to T. gondii infection. LRG-47 has been
implicated in resistance to T. gondii, Listeria
monocytogenes, Leishmania, and mycobacterial infections.
IIGP1 has been shown to localize to the ER and to the
Golgi membranes in IFN-induced cells and inflamed
tissues. In macrophages, IIGP1 interacts with hook3, a
microtubule binding protein that participates in the
organization of the cis-Golgi compartment.
Length = 197
Score = 29.6 bits (67), Expect = 0.99
Identities = 23/65 (35%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 94 EIAFAGRSNVGKSSMLNAL---------TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVD 144
IA G S GKSS +NAL GVV T+ K F + L D
Sbjct: 3 NIAVTGESGAGKSSFINALRGIGHEEEGAAPTGVVETTMKRTPYPHPKF----PNVTLWD 58
Query: 145 LPGYG 149
LPG G
Sbjct: 59 LPGIG 63
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. 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
interferon-induced Mx proteins that inhibit a wide range
of viruses by blocking an early stage of the replication
cycle. Dynamin oligomerizes into helical structures
around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 29.9 bits (68), Expect = 1.0
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALT 113
DLP+I G + GKSS+L AL
Sbjct: 2 DLPQIVVVGDQSSGKSSVLEALV 24
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 29.6 bits (66), Expect = 1.0
Identities = 41/153 (26%), Positives = 62/153 (40%), Gaps = 31/153 (20%)
Query: 92 LPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFA 151
+ IAF G GK+++ NAL + + R TQ + F G +D PG F+
Sbjct: 1 MKRIAFVGAVGAGKTTLFNALQGNYTLARK------TQAVEFNDKGD----IDTPGEYFS 50
Query: 152 YAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQV-VL 210
+ + W Y + +L+ V +LI P L++ +K Q+ V+
Sbjct: 51 HPR------W------YHALITTLQDVDMLIYVHGANDPESRLPAGLLDIGVSKRQIAVI 98
Query: 211 TKTDTVFP-IDVAR-----RAMQIEEVIFYLCG 237
+KTD P DVA EE IF L
Sbjct: 99 SKTD--MPDADVAATRKLLLETGFEEPIFELNS 129
>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 = 28.9 bits (66), Expect = 1.5
Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 28/61 (45%)
Query: 102 NVGKSSMLNALTR---------------QWGVVRTSDKPGLTQTINFFKLGTKLCLVDLP 146
N GKS++L+A++ GVVR D + D+P
Sbjct: 10 NAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFV-------------IADIP 56
Query: 147 G 147
G
Sbjct: 57 G 57
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.2 bits (65), Expect = 1.5
Identities = 16/73 (21%), Positives = 22/73 (30%), Gaps = 11/73 (15%)
Query: 95 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINF----FKLGTKLCLVDLPGYGF 150
I G VGK+++LN L ++ KL L D G
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDE-FPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQ-- 64
Query: 151 AYAKEEVKDAWEE 163
EE + E
Sbjct: 65 ----EEYRSLRPE 73
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 29.4 bits (67), Expect = 1.6
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 99 GRSNVGKSSMLNALTRQWG----VVRTSDKPGLT 128
G +NVGKS+++N + ++ V+ TS PG T
Sbjct: 167 GVTNVGKSTLINRIIKEITGEKDVITTSRFPGTT 200
>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 = 29.3 bits (67), Expect = 1.6
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 102 NVGKSSMLNALTR 114
NVGKS++ NALT+
Sbjct: 8 NVGKSTLFNALTK 20
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 29.4 bits (66), Expect = 1.6
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 98 AGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEV 157
A R +GK +M LT V+R+ + L +TI + +G L V+ A EEV
Sbjct: 191 ALRGVIGKYTMDRILTEGRTVIRSDTQRELEETIRPYDMGITLLDVNFQA---ARPPEEV 247
Query: 158 KDAWEELV 165
K A+++ +
Sbjct: 248 KAAFDDAI 255
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 29.6 bits (66), Expect = 1.8
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 86 SFPAPDLPEIAFAGRSNVGKSSMLNALTR 114
SF ++ GR+ GKSSMLNAL R
Sbjct: 1256 SFFVSPSEKVGVVGRTGAGKSSMLNALFR 1284
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 29.2 bits (66), Expect = 2.1
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 9/72 (12%)
Query: 48 LSAPLDNIPFSTSSERERIEENIFR-NKLEF------FAAAKVSSSFPAPDLPEIAFAGR 100
L +P+ +E L F A + ++ + A L A G
Sbjct: 298 LESPVATPGSGEKAEVANEPPIEISLENLSFRYPDGKPALSDLNLTIKAGQL--TALVGA 355
Query: 101 SNVGKSSMLNAL 112
S GKS++LN L
Sbjct: 356 SGAGKSTLLNLL 367
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 29.2 bits (66), Expect = 2.1
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 95 IAFAGRSNVGKSSMLNALTRQW----GVVRTSDKP 125
+A GRS GKS++L L W G + +
Sbjct: 367 VAILGRSGSGKSTLLQLLAGAWDPQQGSITLNGVE 401
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 28.9 bits (66), Expect = 2.2
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 102 NVGKSSMLNALTR 114
NVGKS++ NALT+
Sbjct: 12 NVGKSTLFNALTK 24
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the form
of molybdenum cofactor (Moco) which is associated with
the metabolism of nitrogen, carbon and sulfur by redox
active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe and
mog. The mob locus contains mobA and mobB genes. MobB
catalyzes the attachment of the guanine dinucleotide to
molybdopterin.
Length = 159
Score = 28.0 bits (63), Expect = 2.8
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 93 PEIAFAGRSNVGKSSMLNALTRQ 115
I F G S GK+++L L
Sbjct: 2 KVIGFVGYSGSGKTTLLEKLIPA 24
>gnl|CDD|152022 pfam11586, DUF3242, Protein of unknown function (DUF3242). This
protein from Thermotoga maritima is a hypothetical ORFan
protein, TM1622, whose structure has been determined.
The protein is composed of seven beta strands and three
alpha helices.
Length = 127
Score = 27.9 bits (62), Expect = 2.9
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 143 VDLPGYGFAYAKEEVKDAWEELVKEY 168
+ P Y F Y EE K W+++ K
Sbjct: 44 ENGPFYVFKYKDEEAKKIWKKINKRA 69
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.7 bits (65), Expect = 3.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 86 SFPAPDLPEIAFAGRSNVGKSSMLNAL 112
+F P IA G S GK+S+LNAL
Sbjct: 370 NFTLPAGQRIALVGPSGAGKTSLLNAL 396
>gnl|CDD|233405 TIGR01418, PEP_synth, phosphoenolpyruvate synthase. Also called
pyruvate,water dikinase and PEP synthase. The member
from Methanococcus jannaschii contains a large intein.
This enzyme generates phosphoenolpyruvate (PEP) from
pyruvate, hydrolyzing ATP to AMP and releasing inorganic
phosphate in the process. The enzyme shows extensive
homology to other enzymes that use PEP as substrate or
product. This enzyme may provide PEP for
gluconeogenesis, for PTS-type carbohydrate transport
systems, or for other processes [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 782
Score = 28.5 bits (64), Expect = 3.3
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 83 VSSSFPAPDLPEIAFAGRS----NV-GKSSMLNALTRQWG 117
V SS A DLP+ +FAG+ NV G+ +L + + W
Sbjct: 120 VRSSATAEDLPDASFAGQQETYLNVTGEEEVLEHVKKCWA 159
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 28.4 bits (64), Expect = 3.3
Identities = 31/109 (28%), Positives = 45/109 (41%), Gaps = 26/109 (23%)
Query: 10 NAQFR----AIQPSPSILSFVEDNLLGRRRPIELRRAGYNIELSAPLDNIPFSTSSERER 65
NAQF+ A Q +IL ++ G+R + RA +IE N+ F+ +
Sbjct: 305 NAQFQRGMAACQTLFAILDLEQEKDEGKR---VIERAKGDIEF----RNVTFTYPGKEVP 357
Query: 66 IEENIFRNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTR 114
NI +F P +A GRS GKS++ N LTR
Sbjct: 358 ALRNI---------------NFKIPAGKTVALVGRSGSGKSTIANLLTR 391
>gnl|CDD|143438 cd07120, ALDH_PsfA-ACA09737, Pseudomonas putida aldehyde
dehydrogenase PsfA (ACA09737)-like. Included in this CD
is the aldehyde dehydrogenase (PsfA, locus ACA09737) of
Pseudomonas putida involved in furoic acid metabolism.
Transcription of psfA was induced in response to
2-furoic acid, furfuryl alcohol, and furfural.
Length = 455
Score = 28.5 bits (64), Expect = 3.6
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 69 NIFRNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNA 111
N+F AA V+S PD+ I+F G + G++ M A
Sbjct: 179 NLFTESGSEGAAHLVAS----PDVDVISFTGSTATGRAIMAAA 217
>gnl|CDD|237737 PRK14507, PRK14507, putative bifunctional
4-alpha-glucanotransferase/malto-oligosyltrehalose
synthase; Provisional.
Length = 1693
Score = 28.5 bits (64), Expect = 3.6
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 11 AQFRAIQPSPSILSFVEDNLLGRRRPIELRRA 42
A+ R+ P S+ FV D LLGR
Sbjct: 1249 AKRRSRLPDRSVHDFVRDVLLGRIDLGGAGHP 1280
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 28.4 bits (64), Expect = 3.8
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 90 PDLPEIAFAGRSNVGKSSMLNALTRQ 115
P+LP + G GK++ + AL R+
Sbjct: 34 PNLPHLLVQGPPGSGKTAAVRALARE 59
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 27.6 bits (62), Expect = 4.8
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 95 IAFAGRSNVGKSSMLNAL 112
IA G + GKSS+LNAL
Sbjct: 1 IAVVGDQSAGKSSVLNAL 18
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 27.8 bits (62), Expect = 5.5
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALT 113
D+P ++ G +N GKS++ N +T
Sbjct: 196 DVPTVSLVGYTNAGKSTLFNRIT 218
>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 = 27.5 bits (62), Expect = 5.8
Identities = 38/170 (22%), Positives = 62/170 (36%), Gaps = 43/170 (25%)
Query: 98 AGRSNVGKSSMLNAL------TRQWGVVRTSDKPGLTQTI--------NFFKLGTKLCLV 143
G S +GKS+ +N L ++ + N KL KL ++
Sbjct: 10 VGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKL--KLTVI 67
Query: 144 DLPGYGFAYAKEEVKDAWEELVK-------EYVSTRVSLKRVCLLIDTK----------- 185
D PG+G D W+ +V Y+ + R + DT+
Sbjct: 68 DTPGFGDNINNS---DCWKPIVDYIDDQFESYLREESRINRNRRIPDTRVHCCLYFIPPT 124
Query: 186 -WGVKPRDHELISLMERSQTKYQV--VLTKTDTVFPIDVARRAMQIEEVI 232
G+KP D I M++ K + V+ K DT+ P ++ +I E I
Sbjct: 125 GHGLKPLD---IEFMKKLSKKVNIIPVIAKADTLTPEELTEFKKRIMEDI 171
>gnl|CDD|226469 COG3960, COG3960, Glyoxylate carboligase [General function
prediction only].
Length = 592
Score = 27.9 bits (62), Expect = 6.0
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 186 WGVKPRDHELISLMERSQTKYQ---VVLTKTDTVFPI 219
WG P DH L++ M QT ++ L +D VF I
Sbjct: 241 WGCIPDDHPLMAGMVGLQTSHRYGNATLLASDMVFGI 277
>gnl|CDD|236726 PRK10618, PRK10618, phosphotransfer intermediate protein in
two-component regulatory system with RcsBC; Provisional.
Length = 894
Score = 28.0 bits (63), Expect = 6.1
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 36 PIELRRAGYNIELSAPLDNIPFS 58
+ + G IE+SA L++ P
Sbjct: 262 SVSISFNGSWIEISAALNSTPLK 284
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 27.6 bits (62), Expect = 6.6
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 99 GRSNVGKSSMLNALTRQ 115
G NVGKS+ NAL +Q
Sbjct: 28 GLPNVGKSTTFNALCKQ 44
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 27.3 bits (61), Expect = 6.8
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 97 FAGRSNVGKSSMLNALT 113
AG S VGKSS++N L
Sbjct: 177 VAGPSGVGKSSLINRLI 193
>gnl|CDD|239161 cd02760, MopB_Phenylacetyl-CoA-OR, The MopB_Phenylacetyl-CoA-OR CD
contains the phenylacetyl-CoA:acceptor oxidoreductase,
large subunit (PadB2), and other related proteins. The
phenylacetyl-CoA:acceptor oxidoreductase has been
characterized as a membrane-bound molybdenum-iron-sulfur
enzyme involved in anaerobic metabolism of phenylalanine
in the denitrifying bacterium Thauera aromatica. Members
of this CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 760
Score = 27.6 bits (61), Expect = 7.3
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 86 SFPAPDLPEIAFAGRSNVGKS 106
F P LP++ F R+N S
Sbjct: 507 KFELPTLPDVWFNYRTNPAIS 527
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 27.2 bits (60), Expect = 7.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 91 DLPEIAFAGRSNVGKSSMLNALT 113
DLP+IA G + GKSS+L
Sbjct: 25 DLPQIAVVGGQSAGKSSVLENFV 47
>gnl|CDD|234321 TIGR03708, poly_P_AMP_trns, polyphosphate:AMP phosphotransferase.
Members of this protein family contain a domain
duplication. The characterized member from Acinetobacter
johnsonii is polyphosphate:AMP phosphotransferase (PAP),
which can transfer the terminal phosphate from poly(P)
to AMP, yielding ADP. In the opposite direction, this
enzyme can synthesize poly(P). Each domain of this
protein family is homologous to polyphosphate kinase, an
enzyme that can run in the forward direction to extend a
polyphosphate chain with a new terminal phosphate from
ATP, or in reverse to make ATP (or GTP) from ADP (or
GDP) [Central intermediary metabolism, Phosphorus
compounds].
Length = 493
Score = 27.3 bits (61), Expect = 7.7
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 161 WEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDT 215
W L K+ R LK++ +T+W V P D + + + +R + + +L T T
Sbjct: 150 WLHLSKKQQKER--LKKLEKDPETRWRVTPEDWKQLKVYDRYRKLAERMLRYTST 202
>gnl|CDD|218872 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function. The C-terminal
half of this family contains a P-loop motif.
Length = 284
Score = 27.2 bits (61), Expect = 8.0
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 83 VSSSFPAPDLPEIA-------FAGRSNVGKSSMLNALTRQWG 117
VS++ AP L + F G S+ GK++ L WG
Sbjct: 175 VSAALAAPLLKLLGAEGGGFHFVGDSSTGKTTALKLAASVWG 216
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 27.2 bits (61), Expect = 8.3
Identities = 17/59 (28%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 68 ENIFRNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSM---LNALTRQWGVVRTSD 123
E +F L F F I AG VGKS+ L AL +W D
Sbjct: 64 ERLFAELLRFLGTNNQQRPFI------IGIAGSVAVGKSTTARILQALLSRWPESPKVD 116
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 26.7 bits (60), Expect = 8.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 95 IAFAGRSNVGKSSMLNALTR 114
+ GR+ GKSS+L AL R
Sbjct: 33 VGIVGRTGSGKSSLLLALFR 52
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They belong
to the subfamily C of the ATP-binding cassette (ABC)
superfamily of transport proteins. The ABCC subfamily
contains transporters with a diverse functional spectrum
that includes ion transport, cell surface receptor, and
toxin secretion activities. The MRP-like family, similar
to all ABC proteins, have a common four-domain core
structure constituted by two membrane-spanning domains,
each composed of six transmembrane (TM) helices, and two
nucleotide-binding domains (NBD). ABC transporters are a
subset of nucleotide hydrolases that contain a signature
motif, Q-loop, and H-loop/switch region, in addition to,
the Walker A motif/P-loop and Walker B motif commonly
found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 171
Score = 26.6 bits (60), Expect = 9.5
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 95 IAFAGRSNVGKSSMLNALTR 114
+A G S GKS++L L R
Sbjct: 31 VAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|212675 cd10233, HSPA1-2_6-8-like_NBD, Nucleotide-binding domain of
HSPA1-A, -B, -L, HSPA-2, -6, -7, -8, and similar
proteins. This subfamily includes human HSPA1A (70-kDa
heat shock protein 1A, also known as HSP72; HSPA1;
HSP70I; HSPA1B; HSP70-1; HSP70-1A), HSPA1B (70-kDa heat
shock protein 1B, also known as HSPA1A; HSP70-2;
HSP70-1B), and HSPA1L (70-kDa heat shock protein 1-like,
also known as HSP70T; hum70t; HSP70-1L; HSP70-HOM). The
genes for these three HSPA1 proteins map in close
proximity on the major histocompatibility complex (MHC)
class III region on chromosome 6, 6p21.3. This subfamily
also includes human HSPA8 (heat shock 70kDa protein 8,
also known as LAP1; HSC54; HSC70; HSC71; HSP71; HSP73;
NIP71; HSPA10; the HSPA8 gene maps to 11q24.1), human
HSPA2 (70-kDa heat shock protein 2, also known as
HSP70-2; HSP70-3, the HSPA2 gene maps to 14q24.1), human
HSPA6 (also known as heat shock 70kDa protein 6
(HSP70B') gi 94717614, the HSPA6 gene maps to 1q23.3),
human HSPA7 (heat shock 70kDa protein 7 , also known as
HSP70B; the HSPA7 gene maps to 1q23.3) and Saccharmoyces
cerevisiae Stress-Seventy subfamily B/Ssb1p. This
subfamily belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs).
Associations of polymorphisms within the MHC-III HSP70
gene locus with longevity, systemic lupus erythematosus,
Meniere's disease, noise-induced hearing loss,
high-altitude pulmonary edema, and coronary heart
disease, have been found. HSPA2 is involved in cancer
cell survival, is required for maturation of male
gametophytes, and is linked to male infertility. The
induction of HSPA6 is a biomarker of cellular stress.
HSPA8 participates in the folding and trafficking of
client proteins to different subcellular compartments,
and in the signal transduction and apoptosis process; it
has been shown to protect cardiomyocytes against
oxidative stress partly through an interaction with
alpha-enolase. S. cerevisiae Ssb1p, is part of the
ribosome-associated complex (RAC), it acts as a
chaperone for nascent polypeptides, and is important for
translation fidelity; Ssb1p is also a [PSI+]
prion-curing factor.
Length = 376
Score = 26.9 bits (60), Expect = 9.6
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 45 NIELSAPLDNIPFSTSSERERIEE---NIFRNKLE 76
+IE+ + + I F TS R R EE ++FR LE
Sbjct: 276 SIEIDSLFEGIDFYTSITRARFEELCADLFRGTLE 310
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.389
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,106,676
Number of extensions: 1141935
Number of successful extensions: 1415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1379
Number of HSP's successfully gapped: 133
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.0 bits)