RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15351
(352 letters)
>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 = 160 bits (408), Expect = 4e-47
Identities = 89/343 (25%), Positives = 149/343 (43%), Gaps = 74/343 (21%)
Query: 1 MGRGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHE 60
M + ++I++ LK VD+VIEV D+R+P + RN ++ + N +P ++VLNK DL +
Sbjct: 8 MAKARREIKEKLKLVDVVIEVLDARIPLSSRNPMIDEIRGN-KPRLIVLNKADLADPAVT 66
Query: 61 SLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVV 120
+ ++ + + N + KGV+KI+
Sbjct: 67 KQWLKYFEEKGI---KALAINAKKG--KGVKKIIK------------------------- 96
Query: 121 GVPNVGKSSIINALRSSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVG 180
L +K KA +L M+VG+PNVG
Sbjct: 97 ---------AAKKLLKEKNEKLKAKGLLNR-----------------PIRAMIVGIPNVG 130
Query: 181 KSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGISLPRIDNLE 240
KS++IN + K VG + GVT+ +K+S+ + +LDTPGI P+ ++ E
Sbjct: 131 KSTLIN-----RLAGKKVAKVGNRPGVTKG-QQWIKLSDG--LELLDTPGILWPKFEDQE 182
Query: 241 CGMRLAACATLQDHLVGEINIADYILFYLNRTGNYRYVDFFNLDEPSDDIVMLLAKAAIK 300
G++LAA ++D + ++A ++L YL + + LDE +DIV LL A K
Sbjct: 183 VGLKLAATGAIKDEALDLEDVALFLLEYLLEHYPELLKERYKLDELPEDIVELLEAIAKK 242
Query: 301 KKWFKRAFDVSSNSVRMFPDTGEVARIFIEHFRKGSFGSVMLD 343
+ + ++ D A I + FRKG G + L+
Sbjct: 243 RGCLLKGGEL---------DLDRAAEILLNDFRKGKLGRITLE 276
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 148 bits (375), Expect = 4e-42
Identities = 84/344 (24%), Positives = 152/344 (44%), Gaps = 74/344 (21%)
Query: 1 MGRGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHE 60
M + ++I+++LK VD+VIEV D+R+P + N ++ + + N +P +L+LNK DL + +
Sbjct: 11 MAKARREIKENLKLVDVVIEVLDARIPLSSENPMIDKIIGN-KPRLLILNKSDLADPEVT 69
Query: 61 SLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVV 120
E ++ + + N + +GV+KIL + +
Sbjct: 70 KKWIEYFEEQG---IKALAINAKKG--QGVKKILKAAKKLLKEK---------------- 108
Query: 121 GVPNVGKSSIINALRSSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVG 180
N R + + +A+ R M++G+PNVG
Sbjct: 109 -----------NERRKAKGMRPRAI-----------------RA-------MIIGIPNVG 133
Query: 181 KSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGISLPRIDNLE 240
KS++IN L K K G + GVT++ +K+ + + +LDTPGI P++++ E
Sbjct: 134 KSTLINRL----AGK-KIAKTGNRPGVTKA-QQWIKLGKG--LELLDTPGILWPKLEDQE 185
Query: 241 CGMRLAACATLQDHLVGEINIADYILFYLNRTGNYRYVDFFNLDEPSDDIVMLLAKAAIK 300
G++LA ++D + +A + L YL++ R + + LDE +DI+ LL A
Sbjct: 186 VGLKLALTGAIKDEALDLEEVAIFALEYLSKHYPERLKERYKLDELPEDILELLEAIAR- 244
Query: 301 KKWFKRAFDVSSNSVRMFPDTGEVARIFIEHFRKGSFGSVMLDR 344
KR + D + + + FR G G + L+
Sbjct: 245 ----KRGALRKGGEI----DYERASELLLNEFRNGKLGKITLET 280
>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 = 133 bits (338), Expect = 3e-38
Identities = 67/231 (29%), Positives = 98/231 (42%), Gaps = 66/231 (28%)
Query: 1 MGRGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHE 60
M + L+ I++ LK VD+VIEV D+R+P + RN L + + N +P ++VLNK DL +
Sbjct: 6 MAKALRQIKEKLKLVDVVIEVRDARIPLSSRNPDLDKILGN-KPRLIVLNKADLADPAKT 64
Query: 61 SLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVV 120
+ + + V+F N +N KGV+K+L +
Sbjct: 65 KKWLKYFKSQGEP---VLFVNAKNG--KGVKKLLKKAK---------------------- 97
Query: 121 GVPNVGKSSIINALRSSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVG 180
++ K P+ MVVG+PNVG
Sbjct: 98 --------KLLKENEKLKAKGLLPRPL----------------------RAMVVGIPNVG 127
Query: 181 KSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGI 231
KS++IN LR K A VG K GVTR ++I I +LDTPGI
Sbjct: 128 KSTLINRLR----GKKVAK-VGNKPGVTRGQQ-WIRIGPN--IELLDTPGI 170
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 104 bits (261), Expect = 2e-25
Identities = 84/350 (24%), Positives = 138/350 (39%), Gaps = 79/350 (22%)
Query: 1 MGRGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHE 60
M + + +++ LK+VD+V+EV D+R P RN L++ V +P +LVLNK DL +
Sbjct: 21 MKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIV-KEKPKLLVLNKADLAPKEVT 79
Query: 61 SLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVV 120
++ +KE+ + IF + ++ G +KI L+ +S+
Sbjct: 80 KKWKKYFKKEEG--IKPIFVSAKSRQ--GGKKIRKALEKLSEE----------------- 118
Query: 121 GVPNVGKSSIINALRSSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVG 180
I L+ + K K V VVG PNVG
Sbjct: 119 ---------KIKRLKKKGLLKRK-------------------------IRVGVVGYPNVG 144
Query: 181 KSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGISLPRIDNLE 240
KS++IN L K + G T+ + +K+ + IY+LDTPGI P+ D+ E
Sbjct: 145 KSTLINRLLGK-----KVAKTSNRPGTTKG-IQWIKLDDG--IYLLDTPGIIPPKFDDDE 196
Query: 241 -CGMRLAACATLQDHLVGEIN-IADYILFYLNRTGNYR----YVDFFNLDEPSDDIVMLL 294
++LA ++D V + +A+ +L L +Y + + D L
Sbjct: 197 LVLLKLAPKGEIKD-PVLPADEVAERLLGGLLIDEHYGEKLNITRYESNPIHRTDPEEFL 255
Query: 295 AKAAIKKKWFKRAFDVSSNSVRMFPDTGEVARIFIEHFRKGSFGSVMLDR 344
A K+ W PD A ++ R G G L+
Sbjct: 256 ELIAKKRGWLLLKGG--------EPDLERAAETILKDIRNGKLGWFSLEE 297
>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 = 70.3 bits (173), Expect = 1e-14
Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 8/63 (12%)
Query: 169 TTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDT 228
TV VVG PNVGKSS+IN+L K+ +A VG GVT+S M +V + + + +LD+
Sbjct: 117 ITVGVVGYPNVGKSSVINSL-----KRSRACNVGATPGVTKS-MQEVHLDKH--VKLLDS 168
Query: 229 PGI 231
PG+
Sbjct: 169 PGV 171
Score = 63.7 bits (156), Expect = 3e-12
Identities = 45/161 (27%), Positives = 70/161 (43%), Gaps = 43/161 (26%)
Query: 16 DIVIEVHDSRMPFTGRNHLLQQSVQNIRP---MVLVLNKRDLI----------------- 55
D+++EV D+R P R ++++V + P +VLVLNK DL+
Sbjct: 1 DVILEVLDARDPLGCRCPQVERAVLVLGPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFP 60
Query: 56 ----------NSKHESLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMT 105
K+ S +KV+ + + C G +L L++ + N
Sbjct: 61 TVAFKASTQQQKKNLSRKSKKVKASDDLL--------SSSACLGADALLKLLKNYARNKG 112
Query: 106 RYHRTEVYNTTVMVVGVPNVGKSSIINALRSSHMKKGKAVP 146
+T + TV VVG PNVGKSS+IN+L+ S A P
Sbjct: 113 --IKTSI---TVGVVGYPNVGKSSVINSLKRSRACNVGATP 148
>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 = 68.1 bits (167), Expect = 7e-14
Identities = 38/135 (28%), Positives = 69/135 (51%), Gaps = 14/135 (10%)
Query: 5 LKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNI-RPMVLVLNKRDLINSKHESLI 63
+ + + +K D+V+EV D+R P R+ L++ + + +++VLNK DL+ + +
Sbjct: 2 KRLVRRIIKEADVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKADLV-PREV--L 58
Query: 64 EEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVVGVP 123
E+ +S V++ + R G + + T++ ++ + V VVG P
Sbjct: 59 EKWKEVFESEGLPVVYVSARER--LGTRILRRTIKELA--------IDGKPVIVGVVGYP 108
Query: 124 NVGKSSIINALRSSH 138
VGKSSIINAL+ H
Sbjct: 109 KVGKSSIINALKGRH 123
Score = 61.6 bits (150), Expect = 1e-11
Identities = 28/62 (45%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
V VVG P VGKSSIINAL+ H P+ G T+ + V+I K IY++DTP
Sbjct: 101 IVGVVGYPKVGKSSIINALKGRH--SASTSPIPGSPGYTKG-IQLVRIDSK--IYLIDTP 155
Query: 230 GI 231
G+
Sbjct: 156 GV 157
>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 = 61.5 bits (150), Expect = 6e-12
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 14/98 (14%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
V +VG PNVGKS++INAL K V G TR + V + +I ++DTP
Sbjct: 1 RVALVGRPNVGKSTLINAL-----TGAKVAIVSDYPGTTRDPILGVLGLGRQII-LVDTP 54
Query: 230 GISLPRIDNLECGMRLAACATLQDHLVGEINIADYILF 267
G+ + +++ AD IL
Sbjct: 55 GLIEGASEGKGVEGFNRFLEAIRE--------ADLILL 84
Score = 40.7 bits (96), Expect = 1e-04
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
V +VG PNVGKS++INAL
Sbjct: 1 RVALVGRPNVGKSTLINAL 19
Score = 31.9 bits (73), Expect = 0.17
Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 2 GRGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQ--NIRPMVLVLNK 51
G + ++ D+++ V D+ T + + + ++ +P++LVLNK
Sbjct: 66 VEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>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 = 61.2 bits (149), Expect = 1e-11
Identities = 41/139 (29%), Positives = 63/139 (45%), Gaps = 12/139 (8%)
Query: 16 DIVIEVHDSRMPFTGRN-HLLQQSVQNIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHI 74
D+V+EV D+R P + RN + + + +++VLNK DL+ K + K E S +
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLINEKNKKLIMVLNKADLV-PKE---VLRKWVAELSEL 56
Query: 75 SEVIFTNCRNPNCKGVQKILPT-LQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINA 133
N +G+ K+ + + V VVG+PNVGKSS INA
Sbjct: 57 YGTKTFFISATNGQGILKLKAEITKQKLKLKYKKG------IRVGVVGLPNVGKSSFINA 110
Query: 134 LRSSHMKKGKAVPILPTLQ 152
L + K ++P LQ
Sbjct: 111 LLNKFKLKVGSIPGTTKLQ 129
Score = 48.5 bits (116), Expect = 4e-07
Identities = 28/64 (43%), Positives = 35/64 (54%), Gaps = 8/64 (12%)
Query: 168 NTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILD 227
V VVG+PNVGKSS INAL + VG G T+ VK+ ++ IY+ D
Sbjct: 91 GIRVGVVGLPNVGKSSFINAL-----LNKFKLKVGSIPGTTKL-QQDVKLDKE--IYLYD 142
Query: 228 TPGI 231
TPGI
Sbjct: 143 TPGI 146
>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 = 60.4 bits (147), Expect = 4e-11
Identities = 55/222 (24%), Positives = 87/222 (39%), Gaps = 80/222 (36%)
Query: 16 DIVIEVHDSRMPFTGRNHLLQQSVQNIRP---MVLVLNKRDLINSKHESLIEEKVRKEQS 72
D++I+V D+R P R +++ ++ +P ++ VLNK DL+ + ++
Sbjct: 10 DVIIQVLDARDPMGTRCKHVEKYLRKEKPHKHLIFVLNKCDLVPTW-------VTKRWVK 62
Query: 73 HISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIIN 132
+S K PTL ++T GK ++IN
Sbjct: 63 VLS----------------KEYPTLAF-HASITN-----------------PFGKGALIN 88
Query: 133 ALR---SSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALR 189
LR H K + IS V +G PNVGKSS+IN LR
Sbjct: 89 LLRQFAKLHSDK----------KQIS---------------VGFIGYPNVGKSSVINTLR 123
Query: 190 SSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGI 231
S K V P G T+ V + + ++ IY++D PG+
Sbjct: 124 SK-----KVCKVAPIPGETK-VWQYITLMKR--IYLIDCPGV 157
>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 = 53.4 bits (129), Expect = 1e-08
Identities = 34/150 (22%), Positives = 63/150 (42%), Gaps = 31/150 (20%)
Query: 43 RPMVLVLNKRDLIN-SKHESLIEEKVRKE----QSHISEVIFTNCRNPNCKGVQKILPTL 97
+P++LV NK DL+ + +++ V+K I +VI + + GV+++
Sbjct: 61 KPVILVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGW--GVEEL---- 114
Query: 98 QHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINAL--RSSHMKKGKAVPILPTLQHIS 155
+ + Y V VVG NVGKS++INAL + + +A+ T+ I
Sbjct: 115 ------IEEIKKLAKYRGDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIP 168
Query: 156 DNMTRYHRTEVYNTTVMVVGVPNVGKSSII 185
TT+ ++ +P +
Sbjct: 169 ------------GTTLGLIKIPLGEGKKLY 186
Score = 49.2 bits (118), Expect = 4e-07
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 158 MTRYHRTEVYNTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGV------TRSV 211
+ + Y V VVG NVGKS++INAL S+ K +A + + V T +
Sbjct: 115 IEEIKKLAKYRGDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGL 174
Query: 212 MSQVKISEKPLIYILDTPGI 231
+KI + DTPGI
Sbjct: 175 ---IKIPLGEGKKLYDTPGI 191
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 49.5 bits (119), Expect = 8e-07
Identities = 34/97 (35%), Positives = 50/97 (51%), Gaps = 14/97 (14%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
V ++G PNVGKS+++NAL + + K V PK TR+ + + ++ I +DTPG
Sbjct: 9 VAIIGRPNVGKSTLLNAL----VGQ-KISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPG 63
Query: 231 ISLPRIDNLECGMRLAACATLQDHLVGEINIADYILF 267
I P+ L M AA + L+D D ILF
Sbjct: 64 IHKPK-HALGELMNKAARSALKD--------VDLILF 91
Score = 34.5 bits (80), Expect = 0.071
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 6 KDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIR-PMVLVLNKRDLINSKHESLIE 64
K LK+VD+++ V D+ + + + + ++ + P++LV+NK D + K L
Sbjct: 77 KAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKVKPKTVLLKL 136
Query: 65 EKVRKEQSHISEVI 78
K+ E++
Sbjct: 137 IAFLKKLLPFKEIV 150
Score = 30.6 bits (70), Expect = 1.1
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V ++G PNVGKS+++NAL
Sbjct: 9 VAIIGRPNVGKSTLLNAL 26
>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 = 48.0 bits (115), Expect = 9e-07
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQ-VKISEKPLIYILDTPGI 231
+ G PNVGKSS++NAL ++ V P G TR + + ++ + ++DTPG+
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGI-----VSPIPGTTRDPVRKEWELLPLGPVVLIDTPGL 56
Score = 36.5 bits (85), Expect = 0.007
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 2/93 (2%)
Query: 8 IEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHESLIEEKV 67
+ D+V+ V DS + L + +P++LVLNK DL+ E + +
Sbjct: 70 ARQVADRADLVLLVVDSDLTPVEEEAKLGLLRERGKPVLLVLNKIDLVPESEEEELLRER 129
Query: 68 RKEQSHISEVIFTNCRNPNCKGVQKILPTLQHI 100
+ E VI + +G+ ++ + +
Sbjct: 130 KLELLPDLPVIAVSALPG--EGIDELRKKIAEL 160
Score = 33.4 bits (77), Expect = 0.080
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 119 VVGVPNVGKSSIINAL 134
+ G PNVGKSS++NAL
Sbjct: 2 IFGRPNVGKSSLLNAL 17
>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 = 48.0 bits (115), Expect = 3e-06
Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 9/64 (14%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPL---IYILD 227
V VVGV NVGKSS+IN L + + P G T + + E PL + D
Sbjct: 157 VYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTT------LDLIEIPLDDGHSLYD 210
Query: 228 TPGI 231
TPGI
Sbjct: 211 TPGI 214
Score = 47.2 bits (113), Expect = 5e-06
Identities = 30/96 (31%), Positives = 49/96 (51%), Gaps = 18/96 (18%)
Query: 44 PMVLVLNKRDLIN-SKHESLIEEKVRKEQSHIS----EVIFTNCRNPNCKGVQKILPTLQ 98
P++LV NK DL+ S + S I+E ++K + ++I + + N G+ ++L ++
Sbjct: 92 PVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGN--GIDELLDKIK 149
Query: 99 HISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINAL 134
+ V VVGV NVGKSS+IN L
Sbjct: 150 KARNK-----------KDVYVVGVTNVGKSSLINKL 174
>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 = 45.7 bits (109), Expect = 4e-06
Identities = 36/130 (27%), Positives = 55/130 (42%), Gaps = 45/130 (34%)
Query: 16 DIVIEVHDSRMPFTGRNHLLQQSVQNI---RPMVLVLNKRDLINSKHESLIEEKVRKE-- 70
D+V+++ D+R P R L++ V+ + + VL+LNK DL+ E+ RK
Sbjct: 13 DVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKADLV--------TEEQRKAWA 64
Query: 71 ---QSHISEVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGK 127
+ V+F + N T+ +VG PNVGK
Sbjct: 65 RYFKKEGIVVLFFSALNEA-----------------------------TIGLVGYPNVGK 95
Query: 128 SSIINALRSS 137
SS+INAL S
Sbjct: 96 SSLINALVGS 105
Score = 42.6 bits (101), Expect = 4e-05
Identities = 27/66 (40%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 169 TTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDT 228
T+ +VG PNVGKSS+INAL S K V V G T+ + I +P I + D
Sbjct: 83 ATIGLVGYPNVGKSSLINALVGS-----KKVSVSSTPGKTKHFQT---IFLEPGITLCDC 134
Query: 229 PGISLP 234
PG+ P
Sbjct: 135 PGLVFP 140
>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 = 45.9 bits (110), Expect = 9e-06
Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 31/114 (27%)
Query: 40 QNIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQH 99
I P V+VLNK DL++ + +EE + + V+ + + G+ ++ L+
Sbjct: 32 SGIEP-VIVLNKADLVD---DEELEELLEIYEKLGYPVLAVSAKTGE--GLDELRELLK- 84
Query: 100 ISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALR----------SSHMKKGK 143
T ++VG VGKS+++NAL S + +G+
Sbjct: 85 --------------GKTSVLVGQSGVGKSTLLNALLPELVLATGEISEKLGRGR 124
Score = 33.1 bits (77), Expect = 0.11
Identities = 20/86 (23%), Positives = 30/86 (34%), Gaps = 33/86 (38%)
Query: 163 RTEVYNTTVMVVGVPNVGKSSIINALR----------SSHMKKGKAVPVGPKAGVTRSVM 212
R + T ++VG VGKS+++NAL S + +G+ T
Sbjct: 80 RELLKGKTSVLVGQSGVGKSTLLNALLPELVLATGEISEKLGRGRH--------TTTHRE 131
Query: 213 SQVKISEKPLI------YILDTPGIS 232
L I+DTPG
Sbjct: 132 ---------LFPLPGGGLIIDTPGFR 148
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 47.3 bits (113), Expect = 9e-06
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
TV +VG PNVGK+++ NAL ++ K VG GVT + I I+D P
Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQK------VGNWPGVTVEKKEGKLKYKGHEIEIVDLP 58
Query: 230 GI 231
G
Sbjct: 59 GT 60
Score = 37.3 bits (87), Expect = 0.012
Identities = 14/27 (51%), Positives = 20/27 (74%)
Query: 116 TVMVVGVPNVGKSSIINALRSSHMKKG 142
TV +VG PNVGK+++ NAL ++ K G
Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQKVG 31
>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 = 44.3 bits (106), Expect = 1e-05
Identities = 30/98 (30%), Positives = 42/98 (42%), Gaps = 22/98 (22%)
Query: 174 VGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDTPGIS 232
VG PNVGKS++ N L + A+ V GVTR + + + I ++DT GI
Sbjct: 3 VGRPNVGKSTLFNRLT----GRRDAI-VSDTPGVTRDRKYGEAEWGGREFI-LIDTGGIE 56
Query: 233 LPRIDNLECGMR---LAACATLQDHLVGEINIADYILF 267
P + + +R A I AD ILF
Sbjct: 57 -PDDEGISKEIREQAEIA-----------IEEADVILF 82
Score = 29.7 bits (68), Expect = 1.4
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 120 VGVPNVGKSSIINAL 134
VG PNVGKS++ N L
Sbjct: 3 VGRPNVGKSTLFNRL 17
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 44.0 bits (105), Expect = 2e-05
Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMS-QVKISEKPLIYILDTPGI 231
+VG PNVGK+++ NAL + K VG GVT + K+ K I I+D PG
Sbjct: 2 LVGNPNVGKTTLFNALTGARQK------VGNWPGVTVEKKEGEFKLGGKE-IEIVDLPGT 54
Query: 232 -SL 233
SL
Sbjct: 55 YSL 57
Score = 35.9 bits (84), Expect = 0.011
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 119 VVGVPNVGKSSIINALRSSHMKKG 142
+VG PNVGK+++ NAL + K G
Sbjct: 2 LVGNPNVGKTTLFNALTGARQKVG 25
>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 = 44.0 bits (105), Expect = 2e-05
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDTPGI 231
++G PNVGKSS++NAL + + + + V AG TR S+ + + I DT GI
Sbjct: 7 IIGRPNVGKSSLLNAL----LGEERVI-VSDIAGTTRDSIDVPFEYDGQKYTLI-DTAGI 60
Score = 36.3 bits (85), Expect = 0.010
Identities = 21/101 (20%), Positives = 52/101 (51%), Gaps = 11/101 (10%)
Query: 3 RGLKDIEKHLKNVDIVIEVHDSRMPFTGRN-HLLQQSVQNIRPMVLVLNKRDLINSKHES 61
R LK IE+ D+V+ V D+ T ++ + ++ + +++V+NK DL+ ++
Sbjct: 77 RTLKAIER----ADVVLLVLDASEGITEQDLRIAGLILEEGKALIIVVNKWDLVEKDEKT 132
Query: 62 L--IEEKVRKEQSHIS--EVIFTNCRNPNCKGVQKILPTLQ 98
+ E+++R++ + ++F + +GV K+ ++
Sbjct: 133 MKEFEKELRRKLPFLDYAPIVFISALTG--QGVDKLFDAIK 171
Score = 35.1 bits (82), Expect = 0.022
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 119 VVGVPNVGKSSIINAL 134
++G PNVGKSS++NAL
Sbjct: 7 IIGRPNVGKSSLLNAL 22
>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 = 45.5 bits (109), Expect = 3e-05
Identities = 23/113 (20%), Positives = 56/113 (49%), Gaps = 6/113 (5%)
Query: 10 KHLKNVDIVIEVHDSRMPFTGRN-HLLQQSVQNIRPMVLVLNKRDLI-NSKHESLIEEKV 67
K ++ D+V+ V D+ T ++ + +++ + +V+V+NK DL+ + K ++++
Sbjct: 250 KAIERADVVLLVLDATEGITEQDLRIAGLALEAGKALVIVVNKWDLVKDEKTREEFKKEL 309
Query: 68 RKEQSHIS--EVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVM 118
R++ + ++F + +GV K+L + + +N R T N +
Sbjct: 310 RRKLPFLDFAPIVFISALTG--QGVDKLLDAIDEVYENANRRISTSKLNRVLE 360
Score = 43.6 bits (104), Expect = 1e-04
Identities = 33/102 (32%), Positives = 43/102 (42%), Gaps = 22/102 (21%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMS-QVKISEKPLIYILDT 228
V +VG PNVGKS++ N L K A+ V GVTR + + I ++DT
Sbjct: 1 VVAIVGRPNVGKSTLFNRL----TGKRDAI-VSDTPGVTRDRKYGDAEWGGREFI-LIDT 54
Query: 229 PGISLPRIDNLECGMR---LAACATLQDHLVGEINIADYILF 267
GI D L+ +R A I AD ILF
Sbjct: 55 GGIEEDD-DGLDKQIREQAEIA-----------IEEADVILF 84
Score = 42.4 bits (101), Expect = 2e-04
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDTPGI 231
++G PNVGKS+++NAL + + + + V AG TR S+ + + K I DT GI
Sbjct: 177 IIGRPNVGKSTLVNAL----LGEERVI-VSDIAGTTRDSIDIPFERNGKKYTLI-DTAGI 230
Score = 34.7 bits (81), Expect = 0.068
Identities = 10/16 (62%), Positives = 15/16 (93%)
Query: 119 VVGVPNVGKSSIINAL 134
++G PNVGKS+++NAL
Sbjct: 177 IIGRPNVGKSTLVNAL 192
Score = 30.9 bits (71), Expect = 1.1
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
V +VG PNVGKS++ N L
Sbjct: 1 VVAIVGRPNVGKSTLFNRL 19
>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 = 43.6 bits (103), Expect = 3e-05
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPL--IYILDTPG 230
VVG VGKSS++NAL G+ V G TR VK +K + ++DTPG
Sbjct: 2 VVGRGGVGKSSLLNALL-----GGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPG 56
Query: 231 I 231
+
Sbjct: 57 L 57
Score = 35.9 bits (83), Expect = 0.011
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 3/83 (3%)
Query: 5 LKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIR---PMVLVLNKRDLINSKHES 61
+ L+ D+++ V DS + + L + + P++LV NK DL+ +
Sbjct: 66 EELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVE 125
Query: 62 LIEEKVRKEQSHISEVIFTNCRN 84
+ + V + +
Sbjct: 126 ELLRLEELAKILGVPVFEVSAKT 148
Score = 30.5 bits (69), Expect = 0.79
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 119 VVGVPNVGKSSIINAL 134
VVG VGKSS++NAL
Sbjct: 2 VVGRGGVGKSSLLNAL 17
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 45.2 bits (108), Expect = 3e-05
Identities = 24/62 (38%), Positives = 40/62 (64%), Gaps = 7/62 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM-SQVKISEKPLIYILDTP 229
V+++G PNVGKSS++NAL + + +A+ V AG TR V+ + ++ P+ ++DT
Sbjct: 220 VVIIGRPNVGKSSLLNAL----LGRDRAI-VTDIAGTTRDVIEEDINLNGIPVR-LVDTA 273
Query: 230 GI 231
GI
Sbjct: 274 GI 275
Score = 34.5 bits (80), Expect = 0.077
Identities = 12/18 (66%), Positives = 17/18 (94%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V+++G PNVGKSS++NAL
Sbjct: 220 VVIIGRPNVGKSSLLNAL 237
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 45.0 bits (108), Expect = 3e-05
Identities = 22/101 (21%), Positives = 51/101 (50%), Gaps = 5/101 (4%)
Query: 9 EKHLKNVDIVIEVHDSRMPFTGRN-HLLQQSVQNIRPMVLVLNKRDLINSKHESLIEEKV 67
K ++ D+V+ V D+ T ++ + +++ R +V+V+NK DL++ K ++++
Sbjct: 250 LKAIERADVVLLVIDATEGITEQDLRIAGLALEAGRALVIVVNKWDLVDEKTMEEFKKEL 309
Query: 68 RKEQSHIS--EVIFTNCRNPNCKGVQKILPTLQHISDNMTR 106
R+ + ++F + +GV K+L + +N R
Sbjct: 310 RRRLPFLDYAPIVFISALTG--QGVDKLLEAIDEAYENANR 348
Score = 43.9 bits (105), Expect = 8e-05
Identities = 34/102 (33%), Positives = 45/102 (44%), Gaps = 22/102 (21%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM-SQVKISEKPLIYILDT 228
V +VG PNVGKS++ N L K A+ V GVTR + + + + I ++DT
Sbjct: 3 VVAIVGRPNVGKSTLFNRL----TGKRDAI-VADTPGVTRDRIYGEAEWLGREFI-LIDT 56
Query: 229 PGISLPRIDNLECGMR---LAACATLQDHLVGEINIADYILF 267
GI P D E +R A I AD ILF
Sbjct: 57 GGIE-PDDDGFEKQIREQAELA-----------IEEADVILF 86
Score = 42.3 bits (101), Expect = 3e-04
Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDTPGI 231
++G PNVGKSS+INAL + + + + V AG TR S+ + + + I DT GI
Sbjct: 178 IIGRPNVGKSSLINAL----LGEERVI-VSDIAGTTRDSIDTPFERDGQKYTLI-DTAGI 231
Score = 36.2 bits (85), Expect = 0.019
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 119 VVGVPNVGKSSIINAL 134
++G PNVGKSS+INAL
Sbjct: 178 IIGRPNVGKSSLINAL 193
Score = 30.4 bits (70), Expect = 1.3
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
V +VG PNVGKS++ N L
Sbjct: 3 VVAIVGRPNVGKSTLFNRL 21
>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 = 43.2 bits (103), Expect = 4e-05
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
V ++G PNVGKS+++NAL + + K V PK TR+ + + + I +DTPG
Sbjct: 6 VAIIGRPNVGKSTLLNAL----VGQ-KISIVSPKPQTTRNRIRGIYTDDDAQIIFVDTPG 60
Query: 231 ISLPR 235
I P+
Sbjct: 61 IHKPK 65
Score = 34.7 bits (81), Expect = 0.028
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 5 LKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNI-RPMVLVLNKRDLINSK 58
+K LK+VD+V+ V D+ + + + ++ P++LVLNK DL+ K
Sbjct: 73 VKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLNKIDLVKDK 127
Score = 34.4 bits (80), Expect = 0.042
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V ++G PNVGKS+++NAL
Sbjct: 6 VAIIGRPNVGKSTLLNAL 23
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 43.7 bits (104), Expect = 1e-04
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 7/62 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDTP 229
+ ++G PNVGKSS+INA+ + + + + V AG TR S+ + + + ++DT
Sbjct: 181 IAIIGRPNVGKSSLINAI----LGEERVI-VSDIAGTTRDSIDIEFERDGRK-YVLIDTA 234
Query: 230 GI 231
GI
Sbjct: 235 GI 236
Score = 41.8 bits (99), Expect = 3e-04
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR-SVMSQVKISEKPLIYILDT 228
V +VG PNVGKS++ N L + A+ V GVTR + + + I I DT
Sbjct: 5 VVAIVGRPNVGKSTLFNRL----TGRRIAI-VSDTPGVTRDRIYGDAEWLGREFILI-DT 58
Query: 229 PGI 231
G+
Sbjct: 59 GGL 61
Score = 35.6 bits (83), Expect = 0.038
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 117 VMVVGVPNVGKSSIINAL 134
+ ++G PNVGKSS+INA+
Sbjct: 181 IAIIGRPNVGKSSLINAI 198
Score = 34.9 bits (81), Expect = 0.051
Identities = 27/124 (21%), Positives = 56/124 (45%), Gaps = 17/124 (13%)
Query: 3 RGLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNI----RPMVLVLNKRDLINSK 58
R LK IE+ D+V+ V D+ + + I R +V+V+NK DL+
Sbjct: 253 RTLKAIER----ADVVLLVIDATEGIS---EQDLRIAGLIEEAGRGIVIVVNKWDLVEED 305
Query: 59 HESL--IEEKVRKEQSHIS--EVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYN 114
++ ++K+R++ + ++F + +G+ K+ ++ I + TR T + N
Sbjct: 306 EATMEEFKKKLRRKLPFLDFAPIVFISALTG--QGLDKLFEAIKEIYECATRRISTSLLN 363
Query: 115 TTVM 118
+
Sbjct: 364 RVLE 367
Score = 34.9 bits (81), Expect = 0.067
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
V +VG PNVGKS++ N L
Sbjct: 5 VVAIVGRPNVGKSTLFNRL 23
>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 = 42.8 bits (101), Expect = 1e-04
Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 14/105 (13%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
V ++G PNVGKS+++N L K PKA TR+ +S + + I +DTPG
Sbjct: 3 VAILGRPNVGKSTLLNQLH-----GQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPG 57
Query: 231 ISLPRIDNLECGMRLAACATLQDHLVGEINIADYILFYLNRTGNY 275
+ M+ A A +G + D ILF ++
Sbjct: 58 FHEKKHSLNRLMMKEARSA------IGGV---DLILFVVDSDQWN 93
>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 = 40.5 bits (96), Expect = 4e-04
Identities = 24/66 (36%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMS-QVKISEKPLIYILDT 228
T+ +VG PNVGK+++ NAL + VG GVT K I I+D
Sbjct: 2 TIALVGNPNVGKTTLFNALTGARQH------VGNWPGVTVEKKEGTFKYKGYE-IEIVDL 54
Query: 229 PGI-SL 233
PG SL
Sbjct: 55 PGTYSL 60
Score = 35.5 bits (83), Expect = 0.017
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 116 TVMVVGVPNVGKSSIINALRSSHMKKG 142
T+ +VG PNVGK+++ NAL + G
Sbjct: 2 TIALVGNPNVGKTTLFNALTGARQHVG 28
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 41.2 bits (98), Expect = 5e-04
Identities = 34/97 (35%), Positives = 47/97 (48%), Gaps = 14/97 (14%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
V +VG PNVGKS+++NAL K V PK TR + + + I +DTPG
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQ-----KISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPG 62
Query: 231 ISLPRIDNLECGMRLAACATLQDHLVGEINIADYILF 267
I P+ L M AA ++L+D D +LF
Sbjct: 63 IHKPK-RALNRAMNKAAWSSLKD--------VDLVLF 90
Score = 34.6 bits (81), Expect = 0.052
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 12 LKNVDIVIEVHDSRMPFTGRNHLLQQSVQNI-RPMVLVLNKRDLINSKHESLIEEKVRKE 70
LK+VD+V+ V D+ + + + ++ + P++LVLNK DL+ K E L + E
Sbjct: 82 LKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKDKEELLPLLEELSE 141
Query: 71 QSHISEVI 78
+E++
Sbjct: 142 LMDFAEIV 149
Score = 33.1 bits (77), Expect = 0.16
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V +VG PNVGKS+++NAL
Sbjct: 8 VAIVGRPNVGKSTLLNAL 25
>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 = 41.3 bits (97), Expect = 6e-04
Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 175 GVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGI 231
G PNVGKS++ NAL ++ VG GVT + I I+D PGI
Sbjct: 1 GNPNVGKSTLFNALTGANQT------VGNWPGVTVEKKEGKLGFQGEDIEIVDLPGI 51
Score = 32.0 bits (73), Expect = 0.55
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 121 GVPNVGKSSIINALRSSHMKKG 142
G PNVGKS++ NAL ++ G
Sbjct: 1 GNPNVGKSTLFNALTGANQTVG 22
>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 = 40.9 bits (96), Expect = 7e-04
Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 5/61 (8%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
+ +VG PNVGKSS++NAL +K+ +A+ V G TR V+ LI +LDT G
Sbjct: 206 LAIVGSPNVGKSSLLNAL----LKQDRAI-VSDIKGTTRDVVEGDFELNGILIKLLDTAG 260
Query: 231 I 231
I
Sbjct: 261 I 261
Score = 39.8 bits (93), Expect = 0.002
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 4 GLKDIEKHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHESLI 63
G++ K +K D+VI V D+ P T + L+ ++ +P +LVLNK DL + E +
Sbjct: 272 GIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSKKPFILVLNKIDLKINSLEFFV 331
Query: 64 EEKV 67
KV
Sbjct: 332 SSKV 335
Score = 29.8 bits (67), Expect = 2.1
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 117 VMVVGVPNVGKSSIINAL 134
+ +VG PNVGKSS++NAL
Sbjct: 206 LAIVGSPNVGKSSLLNAL 223
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 40.6 bits (96), Expect = 8e-04
Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 18/96 (18%)
Query: 44 PMVLVLNKRDLI--NSKHESLIE---EKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQ 98
P++LV NK DL+ + K + ++ ++ +V+ + + G+ ++L ++
Sbjct: 98 PVLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKG--HGIDELLEAIE 155
Query: 99 HISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINAL 134
R R +VY VVGV NVGKS++IN +
Sbjct: 156 KY-----REGR-DVY-----VVGVTNVGKSTLINRI 180
Score = 36.0 bits (84), Expect = 0.024
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 19/69 (27%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRS-----VMSQVKISEKPL--- 222
V VVGV NVGKS++IN + G K +T S + +++I PL
Sbjct: 163 VYVVGVTNVGKSTLINRIIKEI--------TGEKDVITTSRFPGTTLDKIEI---PLDDG 211
Query: 223 IYILDTPGI 231
++ DTPGI
Sbjct: 212 SFLYDTPGI 220
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 40.1 bits (93), Expect = 0.001
Identities = 42/155 (27%), Positives = 73/155 (47%), Gaps = 20/155 (12%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
+V ++G PN GKS+++N + K V PK TRS+++ + + + + DTP
Sbjct: 54 SVCIIGRPNSGKSTLLNRIIGE-----KLSIVTPKVQTTRSIITGIITLKDTQVILYDTP 108
Query: 230 GISLPRIDNLECGMRLAACATLQDHLVGEINIADYILFYLNRTGNYRYVDFFNLDE-PSD 288
GI P+ +LE M A ++L AD +L ++ ++ + LD+ S
Sbjct: 109 GIFEPK-GSLEKAMVRCAWSSLHS--------ADLVLLIIDSLKSFDDITHNILDKLRSL 159
Query: 289 DIV--MLLAKAAIKKKWFKRAFDVSSNSVRMFPDT 321
+IV LL K I+ K+ D+ + PD+
Sbjct: 160 NIVPIFLLNKIDIESKYLN---DIKAFLTENHPDS 191
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 40.0 bits (94), Expect = 0.002
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRS-VMSQVKISEKPLIYILDTP 229
V +VG PNVGKSS++N L ++V V AG T V S +++ K ++ DT
Sbjct: 214 VALVGKPNVGKSSLLNKLAGEE----RSV-VDDVAGTTVDPVDSLIELGGKTWRFV-DTA 267
Query: 230 GI 231
G+
Sbjct: 268 GL 269
Score = 34.2 bits (79), Expect = 0.11
Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR 209
V VVG PNVGKS+++N + + + +AV V GVTR
Sbjct: 40 VVAVVGRPNVGKSTLVNRI----LGRREAV-VEDVPGVTR 74
Score = 33.0 bits (76), Expect = 0.21
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 116 TVMVVGVPNVGKSSIIN 132
V VVG PNVGKS+++N
Sbjct: 40 VVAVVGRPNVGKSTLVN 56
Score = 31.9 bits (73), Expect = 0.47
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V +VG PNVGKSS++N L
Sbjct: 214 VALVGKPNVGKSSLLNKL 231
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 39.7 bits (94), Expect = 0.002
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 7/59 (11%)
Query: 174 VGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM-SQVKISEKPLIYILDTPGI 231
G PNVGKSS++NAL + + +A+ V AG TR V+ + + PL ++DT GI
Sbjct: 221 AGRPNVGKSSLLNAL----LGEERAI-VTDIAGTTRDVIEEHINLDGIPLR-LIDTAGI 273
Score = 36.6 bits (86), Expect = 0.016
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 91 QKILPTLQHISDNMTR----YHRTEVYNTTVMVV--GVPNVGKSSIINAL 134
+KIL L+ + + + E+ + VV G PNVGKSS++NAL
Sbjct: 186 EKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSLLNAL 235
Score = 33.2 bits (77), Expect = 0.18
Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 10 KHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHESLIE 64
+ ++ D+V+ V D+ P T + + + +++ +P+++VLNK DL
Sbjct: 290 EAIEEADLVLLVLDASEPLTEEDDEILEELKD-KPVIVVLNKADLTGEIDLEEEN 343
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 39.4 bits (93), Expect = 0.002
Identities = 27/114 (23%), Positives = 49/114 (42%), Gaps = 30/114 (26%)
Query: 40 QNIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQH 99
I+P ++VLNK DL++ E E + ++ +V+ + + +G+ ++ P L
Sbjct: 110 NGIKP-IIVLNKIDLLDDLEE--ARELLALYRAIGYDVLELSAKEG--EGLDELKPLLAG 164
Query: 100 ISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALR----------SSHMKKGK 143
TV + G VGKS+++NAL S + +GK
Sbjct: 165 --------------KVTV-LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGK 203
Score = 30.9 bits (71), Expect = 0.84
Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 34/81 (41%)
Query: 168 NTTVMVVGVPNVGKSSIINALR----------SSHMKKGKAVPVGPKAGVTRSVMSQVKI 217
TV + G VGKS+++NAL S + +GK T V
Sbjct: 165 KVTV-LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKH--------TTTHV------ 209
Query: 218 SEKPLI------YILDTPGIS 232
L ++DTPG S
Sbjct: 210 ---ELYDLPGGGLLIDTPGFS 227
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 39.8 bits (93), Expect = 0.002
Identities = 27/62 (43%), Positives = 35/62 (56%), Gaps = 7/62 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRS-VMSQVKISEKPLIYILDTP 229
V +VG PNVGKSS++N L +AV V AG TR V V+I + ++I DT
Sbjct: 453 VALVGRPNVGKSSLLNQLTHEE----RAV-VNDLAGTTRDPVDEIVEIDGEDWLFI-DTA 506
Query: 230 GI 231
GI
Sbjct: 507 GI 508
Score = 32.5 bits (74), Expect = 0.34
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 5/44 (11%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMS 213
V +VG PNVGKS+++N + + + +AV V GVTR +S
Sbjct: 277 VVAIVGRPNVGKSTLVNRI----LGRREAV-VEDTPGVTRDRVS 315
Score = 31.7 bits (72), Expect = 0.59
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V +VG PNVGKSS++N L
Sbjct: 453 VALVGRPNVGKSSLLNQL 470
Score = 31.7 bits (72), Expect = 0.64
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 116 TVMVVGVPNVGKSSIIN 132
V +VG PNVGKS+++N
Sbjct: 277 VVAIVGRPNVGKSTLVN 293
>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 = 37.5 bits (88), Expect = 0.003
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 13/60 (21%)
Query: 174 VGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISE---KPLIYILDTPG 230
G NVGKSS+INAL + K G T+ I+ ++D PG
Sbjct: 5 AGRSNVGKSSLINAL----TNRKKLARTSKTPGRTQ------LINFFNVGDKFRLVDLPG 54
Score = 31.7 bits (73), Expect = 0.32
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 120 VGVPNVGKSSIINAL 134
G NVGKSS+INAL
Sbjct: 5 AGRSNVGKSSLINAL 19
>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 = 37.4 bits (87), Expect = 0.004
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRS-VMSQVKI-SEKPLIYILDT 228
+++VG PNVGKS+++N L K K G TR+ V + ++ + +LDT
Sbjct: 4 IVIVGDPNVGKSTLLNRL-----LGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDT 58
Query: 229 PGI 231
G
Sbjct: 59 AGQ 61
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 37.6 bits (88), Expect = 0.004
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 168 NTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRS 210
++ VG NVGKS+++ L GK V VG + GVTR
Sbjct: 9 KPEIVFVGRSNVGKSTLVREL------TGKKVRVGKRPGVTRK 45
Score = 28.3 bits (64), Expect = 4.0
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 114 NTTVMVVGVPNVGKSSIINALRSSHMKKGK 143
++ VG NVGKS+++ L ++ GK
Sbjct: 9 KPEIVFVGRSNVGKSTLVRELTGKKVRVGK 38
>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 = 37.2 bits (87), Expect = 0.005
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPL--IYILD 227
T+++ G PNVGKSS++N L + K V P T+S+ V + ++D
Sbjct: 2 TLVIAGYPNVGKSSLVNKL--TRAK----PEVAPYPFTTKSL--FVGHFDYKYLRWQVID 53
Query: 228 TPGI 231
TPGI
Sbjct: 54 TPGI 57
Score = 33.7 bits (78), Expect = 0.074
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
T+++ G PNVGKSS++N L
Sbjct: 2 TLVIAGYPNVGKSSLVNKL 20
>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 = 37.4 bits (87), Expect = 0.006
Identities = 38/125 (30%), Positives = 56/125 (44%), Gaps = 40/125 (32%)
Query: 34 LLQQSVQNIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHI-----SEVIFTNCRNPNCK 88
L+ QNI P ++VLNK DL L +E + KEQ I +V+ T+ +N +
Sbjct: 60 LVVAEAQNIEP-IIVLNKIDL-------LDDEDMEKEQLDIYRNIGYQVLMTSSKNQD-- 109
Query: 89 GVQKILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALR----------SSH 138
G+++++ LQ N + G VGKSS+INAL SS
Sbjct: 110 GLKELIEALQ---------------NRISVFAGQSGVGKSSLINALDPSVKQQVNDISSK 154
Query: 139 MKKGK 143
+ GK
Sbjct: 155 LGLGK 159
Score = 30.5 bits (69), Expect = 1.2
Identities = 22/82 (26%), Positives = 29/82 (35%), Gaps = 23/82 (28%)
Query: 169 TTVMVVGVPNVGKSSIINALR----------SSHMKKGKAVPVGPKAGVTRSVMSQVKIS 218
+V G VGKSS+INAL SS + GK +
Sbjct: 122 ISVFA-GQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTH-----VELFHFHGGL- 174
Query: 219 EKPLIYILDTPGISLPRIDNLE 240
I DTPG + + +LE
Sbjct: 175 ------IADTPGFNEFGLWHLE 190
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 37.7 bits (88), Expect = 0.007
Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 21/99 (21%)
Query: 40 QNIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHIS-EVIFTNCRNPNCKGVQKILPTLQ 98
I P V+VLNK DL++ E +++ +E I V+F + +N + G++++ L
Sbjct: 109 GGIEP-VIVLNKIDLLDD--EEAAVKELLREYEDIGYPVLFVSAKNGD--GLEELAELLA 163
Query: 99 HISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALRSS 137
TV++ G VGKS++INAL
Sbjct: 164 G--------------KITVLL-GQSGVGKSTLINALLPE 187
Score = 29.6 bits (67), Expect = 2.5
Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 34/89 (38%)
Query: 168 NTTVMVVGVPNVGKSSIINALR----------SSHMKKGKAVPVGPKAGVTRSVMSQVKI 217
TV++ G VGKS++INAL S + +G+ T V
Sbjct: 165 KITVLL-GQSGVGKSTLINALLPELNQKTGEISEKLGRGRH--------TTTHVE----- 210
Query: 218 SEKPLI------YILDTPGISLPRIDNLE 240
L +I+DTPG + +LE
Sbjct: 211 ----LFPLPGGGWIIDTPGFRSLGLAHLE 235
>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 = 36.8 bits (86), Expect = 0.008
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAV-PVGPKAGVTRSVMSQVKISEKPLIYILDT 228
+ VVG + GKS+++NAL G+ V P G T +V++ ++ + ++DT
Sbjct: 2 LLAVVGEFSAGKSTLLNALL------GEEVLPTGV--TPTTAVITVLRYGLLKGVVLVDT 53
Query: 229 PGI 231
PG+
Sbjct: 54 PGL 56
Score = 31.7 bits (73), Expect = 0.31
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 8 IEKHLKNVDIVIEVHDSRMPFTGRN-HLLQQSVQ-NIRPMVLVLNKRDLINSKHESLIEE 65
E L D VI V + P T L++ ++ + + + VLNK DL++ + + E
Sbjct: 67 TESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLNKIDLLSEEELEEVLE 126
Query: 66 KVRKEQSHISEVIF 79
R+E +
Sbjct: 127 YSREELGVLELGGG 140
Score = 30.6 bits (70), Expect = 0.67
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
+ VVG + GKS+++NAL
Sbjct: 2 LLAVVGEFSAGKSTLLNAL 20
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 36.7 bits (85), Expect = 0.011
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 150 TLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTR 209
+ I + + TE V+++G GKSS+INAL +K+ V V G
Sbjct: 21 LSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGV----GTDI 76
Query: 210 SVMSQVKISEKPLIYILDTPGI 231
+ ++ + L+ + DTPG+
Sbjct: 77 TTRLRLSYDGENLV-LWDTPGL 97
Score = 29.8 bits (67), Expect = 1.9
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 96 TLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPI 147
+ I + + TE V+++G GKSS+INAL +K+ V +
Sbjct: 21 LSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGV 72
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 36.5 bits (85), Expect = 0.015
Identities = 29/106 (27%), Positives = 43/106 (40%), Gaps = 20/106 (18%)
Query: 128 SSIINALRSSHMKKGKAVPILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINA 187
+SII + KA L L I ++ T++V G PNVGKSS++
Sbjct: 138 ASIIKKIDDDLEFLRKARDHLKKLPAIDPDLP----------TIVVAGYPNVGKSSLVRK 187
Query: 188 LRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPL--IYILDTPGI 231
L V P T+ + V E+ I ++DTPG+
Sbjct: 188 L------TTAKPEVAPYPFTTKGI--HVGHFERGYLRIQVIDTPGL 225
Score = 31.5 bits (72), Expect = 0.64
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
T++V G PNVGKSS++ L
Sbjct: 170 TIVVAGYPNVGKSSLVRKL 188
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 36.5 bits (85), Expect = 0.018
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
TV +VG P+VGKS+++N L ++ + V T + + + I +LD P
Sbjct: 65 TVALVGFPSVGKSTLLNKLTNTKSE------VADYPFTTLEPVPGMLEYKGAQIQLLDLP 118
Query: 230 GI 231
GI
Sbjct: 119 GI 120
Score = 33.4 bits (77), Expect = 0.15
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 116 TVMVVGVPNVGKSSIINALRSSH 138
TV +VG P+VGKS+++N L ++
Sbjct: 65 TVALVGFPSVGKSTLLNKLTNTK 87
>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 = 34.8 bits (81), Expect = 0.022
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 7/59 (11%)
Query: 174 VGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM-SQVKISEKPLIYILDTPGI 231
G PNVGKSS++NAL + +A+ V AG TR V+ ++ + P+ ++DT G+
Sbjct: 9 AGKPNVGKSSLLNAL----AGRDRAI-VSDIAGTTRDVIEEEIDLGGIPVR-LIDTAGL 61
Score = 34.0 bits (79), Expect = 0.041
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 120 VGVPNVGKSSIINAL 134
G PNVGKSS++NAL
Sbjct: 9 AGKPNVGKSSLLNAL 23
Score = 27.5 bits (62), Expect = 7.8
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 10 KHLKNVDIVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLINSKHESLIEEK 66
+ ++ D+V+ V D+ + + + +P+++VLNK DL++
Sbjct: 78 EAIEEADLVLLVVDASEGLDEEDLEILELPAK-KPVIVVLNKSDLLSDAEGISELNG 133
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 36.0 bits (84), Expect = 0.022
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 18/94 (19%)
Query: 41 NIRPMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQHI 100
I P ++VLNK DL++ + + + E++ ++ V+ + +G++++ L
Sbjct: 150 GIEP-LIVLNKIDLLDDEGRAFVNEQLDIYRNIGYRVLMVSSHTG--EGLEELEAALT-- 204
Query: 101 SDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINAL 134
R ++ VG VGKSS+INAL
Sbjct: 205 -------GRISIF------VGQSGVGKSSLINAL 225
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 34.5 bits (80), Expect = 0.039
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 7/60 (11%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPG 230
+ G NVGKSS+INAL + G T+ + + ++D PG
Sbjct: 27 IAFAGRSNVGKSSLINALTNQK----NLARTSKTPGRTQLI---NFFEVDDELRLVDLPG 79
Score = 31.4 bits (72), Expect = 0.48
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 117 VMVVGVPNVGKSSIINAL 134
+ G NVGKSS+INAL
Sbjct: 27 IAFAGRSNVGKSSLINAL 44
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 33.6 bits (77), Expect = 0.062
Identities = 13/42 (30%), Positives = 27/42 (64%), Gaps = 3/42 (7%)
Query: 116 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPILPTLQHISDN 157
++V+G+ N GK++IIN L+ S+ ++ I+PT+ ++
Sbjct: 1 NILVLGLDNSGKTTIINQLKPSNA---QSQNIVPTVGFNVES 39
Score = 33.2 bits (76), Expect = 0.085
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVP 200
++V+G+ N GK++IIN L+ S+ + VP
Sbjct: 1 NILVLGLDNSGKTTIINQLKPSNAQSQNIVP 31
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including YchF,
possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis suggest
that YchF may be part of a nucleoprotein complex and may
function as a GTP-dependent translational factor.
Length = 274
Score = 34.4 bits (80), Expect = 0.066
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 120 VGVPNVGKSSIINALRSSH 138
VG+PNVGKS++ NAL S+
Sbjct: 4 VGLPNVGKSTLFNALTKSN 22
Score = 34.4 bits (80), Expect = 0.066
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 174 VGVPNVGKSSIINALRSSH 192
VG+PNVGKS++ NAL S+
Sbjct: 4 VGLPNVGKSTLFNALTKSN 22
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 34.6 bits (80), Expect = 0.070
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 9/81 (11%)
Query: 168 NTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM----SQVKISEKPL- 222
+ T+MVVG +GK++ IN L + + + +A T + ++ ++ E
Sbjct: 23 DFTIMVVGESGLGKTTFINTLFGTSLVDETEI-DDIRAEGTSPTLEIKITKAELEEDGFH 81
Query: 223 --IYILDTPGISLPRIDNLEC 241
+ ++DTPG IDN +C
Sbjct: 82 LNLTVIDTPGFG-DFIDNSKC 101
Score = 31.9 bits (73), Expect = 0.53
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 114 NTTVMVVGVPNVGKSSIINALRSSHMKKGKAV 145
+ T+MVVG +GK++ IN L + + +
Sbjct: 23 DFTIMVVGESGLGKTTFINTLFGTSLVDETEI 54
>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 = 33.1 bits (76), Expect = 0.11
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSV-MSQVKISEKPLIYILDTPGI 231
+VG+PNVGKS++++AL S+ ++ + T + + + I I+D PG+
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVE------IASYPFTTLEPNVGVFEFGDGVDIQIIDLPGL 55
Query: 232 S 232
Sbjct: 56 L 56
Score = 30.1 bits (68), Expect = 0.95
Identities = 11/18 (61%), Positives = 17/18 (94%)
Query: 119 VVGVPNVGKSSIINALRS 136
+VG+PNVGKS++++AL S
Sbjct: 2 LVGLPNVGKSTLLSALTS 19
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 33.1 bits (77), Expect = 0.19
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 120 VGVPNVGKSSIINAL 134
VG+PNVGKS++ NAL
Sbjct: 8 VGLPNVGKSTLFNAL 22
Score = 33.1 bits (77), Expect = 0.19
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 174 VGVPNVGKSSIINAL 188
VG+PNVGKS++ NAL
Sbjct: 8 VGLPNVGKSTLFNAL 22
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 31.8 bits (73), Expect = 0.24
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 34/81 (41%)
Query: 168 NTTVMVVGVPNVGKSSIINALR----------SSHMKKGKAVPVGPKAGVTRSVMSQVKI 217
T+V+ G VGKS+++NAL S + +G+ T V
Sbjct: 36 KTSVLA-GQSGVGKSTLLNALLPELDLRTGEISEKLGRGRH--------TTTHVE----- 81
Query: 218 SEKPLI------YILDTPGIS 232
L ++DTPG
Sbjct: 82 ----LFPLPGGGLLIDTPGFR 98
Score = 30.6 bits (70), Expect = 0.73
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 27/78 (34%)
Query: 76 EVIFTNCRNPNCKGVQKILPTLQHISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINALR 135
EV+ + + +G++++ P L+ T+V+ G VGKS+++NAL
Sbjct: 14 EVLVVSAKTG--EGIEELKPLLKG--------------KTSVLA-GQSGVGKSTLLNALL 56
Query: 136 ----------SSHMKKGK 143
S + +G+
Sbjct: 57 PELDLRTGEISEKLGRGR 74
>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 = 31.2 bits (72), Expect = 0.39
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 120 VGVPNVGKSSIINAL 134
VG+PN GKS++++A+
Sbjct: 6 VGLPNAGKSTLLSAI 20
Score = 31.2 bits (72), Expect = 0.39
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 174 VGVPNVGKSSIINAL 188
VG+PN GKS++++A+
Sbjct: 6 VGLPNAGKSTLLSAI 20
Score = 28.5 bits (65), Expect = 3.0
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 43 RPMVLVLNKRDLINSKHESLIEEKVRKEQSH 73
+P ++VLNK DL++ EK+++
Sbjct: 115 KPRIVVLNKIDLLD---AEERFEKLKELLKE 142
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 31.3 bits (72), Expect = 0.41
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 124 NVGKSSIINAL 134
NVGKSS+INAL
Sbjct: 28 NVGKSSLINAL 38
Score = 31.3 bits (72), Expect = 0.41
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 178 NVGKSSIINAL 188
NVGKSS+INAL
Sbjct: 28 NVGKSSLINAL 38
>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 = 31.7 bits (73), Expect = 0.42
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 24/71 (33%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKG-------KAVPVGPKAGVTRSVMSQ--VKISEK 220
V +VG P+VGKS++++ L ++ + VP VM KI
Sbjct: 2 RVALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVP---------GVMEYKGAKIQ-- 50
Query: 221 PLIYILDTPGI 231
+LD PGI
Sbjct: 51 ----LLDLPGI 57
Score = 31.7 bits (73), Expect = 0.46
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
V +VG P+VGKS++++ L
Sbjct: 2 RVALVGFPSVGKSTLLSKL 20
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 31.4 bits (72), Expect = 0.42
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTP 229
+++VG GKS+ N++ + K GVT++ + + +I ++DTP
Sbjct: 2 RIVLVGKTGNGKSATGNSILGRKAFESK----LRAQGVTKTCQLVSRTWDGRIINVIDTP 57
Query: 230 GI 231
G+
Sbjct: 58 GL 59
>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 = 32.1 bits (73), Expect = 0.46
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 171 VMVVGVPNVGKSSIINALRS-SHMKKGKAVPVGPKAGVTRSVMSQV--KISEKPLIYILD 227
+ V G GKSS INALR H + G A GV + M + P + + D
Sbjct: 38 IAVTGDSGNGKSSFINALRGIGHEEDGSA-----PTGVVETTMKRTPYSHPHFPNVVLWD 92
Query: 228 TPGI 231
PG+
Sbjct: 93 LPGL 96
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 31.8 bits (73), Expect = 0.47
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 119 VVGVPNVGKSSIINAL 134
+VG+PNVGKS+ NAL
Sbjct: 26 IVGLPNVGKSTTFNAL 41
Score = 31.8 bits (73), Expect = 0.47
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 173 VVGVPNVGKSSIINAL 188
+VG+PNVGKS+ NAL
Sbjct: 26 IVGLPNVGKSTTFNAL 41
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 31.2 bits (72), Expect = 0.49
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 124 NVGKSSIINAL 134
NVGKSS+INAL
Sbjct: 34 NVGKSSLINAL 44
Score = 31.2 bits (72), Expect = 0.49
Identities = 10/11 (90%), Positives = 11/11 (100%)
Query: 178 NVGKSSIINAL 188
NVGKSS+INAL
Sbjct: 34 NVGKSSLINAL 44
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 31.1 bits (70), Expect = 0.62
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPK-AGVTRSVMSQVKISEKPLIYILDTP 229
++V+G VGK++++N L +G +G T + + DT
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTI-----EPYRRNIKLQLWDTA 62
Query: 230 G 230
G
Sbjct: 63 G 63
Score = 29.2 bits (65), Expect = 2.5
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 117 VMVVGVPNVGKSSIINALRSSHMKKGKAVPI 147
++V+G VGK++++N L +G I
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTI 38
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 31.4 bits (72), Expect = 0.64
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 119 VVGVPNVGKSSIINAL 134
+VG+PNVGKS++ NAL
Sbjct: 7 IVGLPNVGKSTLFNAL 22
Score = 31.4 bits (72), Expect = 0.64
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 173 VVGVPNVGKSSIINAL 188
+VG+PNVGKS++ NAL
Sbjct: 7 IVGLPNVGKSTLFNAL 22
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.4 bits (72), Expect = 0.73
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 120 VGVPNVGKSSIINAL 134
VG+PN GKS++++A+
Sbjct: 165 VGLPNAGKSTLLSAV 179
Score = 31.4 bits (72), Expect = 0.73
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 174 VGVPNVGKSSIINAL 188
VG+PN GKS++++A+
Sbjct: 165 VGLPNAGKSTLLSAV 179
>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 = 30.0 bits (68), Expect = 0.82
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 179 VGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGI 231
GKSS+ NAL + + VG + TR+ + V + + +LD PG+
Sbjct: 8 AGKSSLCNALFGTEV-----AAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGV 55
>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 = 0.85
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSV---MSQVKISEKPL---I 223
T+MVVG +GK+++IN L + + + +P GP + ++V + V+I E + +
Sbjct: 6 TLMVVGESGLGKTTLINTLFLTDLIPERGIP-GPSEKIKKTVEIKATTVEIEEDGVKLNL 64
Query: 224 YILDTPGISLPRIDNLEC 241
++DTPG IDN C
Sbjct: 65 TVIDTPGFG-DAIDNSNC 81
>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 = 30.9 bits (71), Expect = 0.99
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 119 VVGVPNVGKSSIINAL 134
+ G N GKSS+INAL
Sbjct: 11 IFGRRNAGKSSLINAL 26
Score = 30.9 bits (71), Expect = 0.99
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 173 VVGVPNVGKSSIINAL 188
+ G N GKSS+INAL
Sbjct: 11 IFGRRNAGKSSLINAL 26
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 30.8 bits (71), Expect = 1.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 120 VGVPNVGKSSIINAL 134
VG PNVGKS++++ +
Sbjct: 164 VGFPNVGKSTLLSVV 178
Score = 30.8 bits (71), Expect = 1.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 174 VGVPNVGKSSIINAL 188
VG PNVGKS++++ +
Sbjct: 164 VGFPNVGKSTLLSVV 178
>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 = 30.4 bits (69), Expect = 1.1
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVM--SQVKISEKPLIYILDT 228
+ V G GKSS INALR ++ A P GV + M + + P + + D
Sbjct: 4 IAVTGESGAGKSSFINALRGIGHEEEGAAPT----GVVETTMKRTPYPHPKFPNVTLWDL 59
Query: 229 PGISLP 234
PGI
Sbjct: 60 PGIGST 65
>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 = 30.5 bits (70), Expect = 1.2
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 120 VGVPNVGKSSIINALRSSHMK 140
VG+PN GKS++I+A+ ++ K
Sbjct: 163 VGLPNAGKSTLISAVSAAKPK 183
Score = 30.5 bits (70), Expect = 1.2
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 174 VGVPNVGKSSIINALRSSHMK 194
VG+PN GKS++I+A+ ++ K
Sbjct: 163 VGLPNAGKSTLISAVSAAKPK 183
Score = 30.1 bits (69), Expect = 1.7
Identities = 7/28 (25%), Positives = 19/28 (67%)
Query: 43 RPMVLVLNKRDLINSKHESLIEEKVRKE 70
+P ++VLNK DL++ + + +++++
Sbjct: 274 KPRIVVLNKIDLLDEEELEELLKELKEA 301
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems.
Length = 148
Score = 29.6 bits (67), Expect = 1.3
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 119 VVGVPNVGKSSIINALRSSHMKKGKAVPIL 148
+ GVP GKS++I+AL ++ +GK V +L
Sbjct: 4 ITGVPGAGKSTLIDALITALRARGKRVAVL 33
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPV 201
+ GVP GKS++I+AL ++ +GK V V
Sbjct: 4 ITGVPGAGKSTLIDALITALRARGKRVAV 32
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 29.9 bits (68), Expect = 1.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 116 TVMVVGVPNVGKSSIINALR 135
V+V GVP VGK++++N
Sbjct: 4 VVVVTGVPGVGKTTVLNKAL 23
Score = 29.9 bits (68), Expect = 1.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 170 TVMVVGVPNVGKSSIINALR 189
V+V GVP VGK++++N
Sbjct: 4 VVVVTGVPGVGKTTVLNKAL 23
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 29.6 bits (67), Expect = 1.8
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 150 TLQHISD-NMTRYHRTEVYNT-------TVMVVGVPNVGKSSIINALRSSHMKKGKAVPV 201
Q D + H V T V+VVG P VGKS++I +L + K+ +
Sbjct: 13 QFQRTQDLEEKKLHVPVVDRTPEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDIK 72
Query: 202 GP 203
GP
Sbjct: 73 GP 74
Score = 28.5 bits (64), Expect = 4.3
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 96 TLQHISD-NMTRYHRTEVYNT-------TVMVVGVPNVGKSSIINAL 134
Q D + H V T V+VVG P VGKS++I +L
Sbjct: 13 QFQRTQDLEEKKLHVPVVDRTPEEPPPLVVVVVGPPGVGKSTLIRSL 59
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. 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 = 163
Score = 29.3 bits (66), Expect = 1.8
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 44 PMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIFTNCRNPNCKGVQKILPTLQH 99
P++LV NK DL + + S+ E EQ ++ + V K+ L
Sbjct: 107 PLLLVGNKCDLEDKRQVSVEEAANLAEQWGVN---YVETSAKTRANVDKVFFDLVR 159
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 29.0 bits (66), Expect = 2.2
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 11/74 (14%)
Query: 16 DIVIEV---HDSRMPFTGR--NHLLQQSVQNIRPMVLVLNKRDLINSKHESLIEEKVRKE 70
DI I V D MP T NH +V P+++ +NK D E+V+ E
Sbjct: 74 DIAILVVAADDGVMPQTIEAINHAKAANV----PIIVAINKIDKPYGTEA--DPERVKNE 127
Query: 71 QSHISEVIFTNCRN 84
S + V +
Sbjct: 128 LSELGLVGEEWGGD 141
Score = 29.0 bits (66), Expect = 2.4
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 10/63 (15%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSV-MSQVKISEK-PLIYILD 227
TVM G + GK+++++ +R +++ G+A G+T+ + QV I K P I +D
Sbjct: 4 TVM--GHVDHGKTTLLDKIRKTNVAAGEA------GGITQHIGAYQVPIDVKIPGITFID 55
Query: 228 TPG 230
TPG
Sbjct: 56 TPG 58
>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 = 29.3 bits (67), Expect = 2.3
Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 19/81 (23%)
Query: 13 KNVDIVIEVHDSRMPFTGRNHLLQ-QSVQNI--------RPMVLVLNKRDLINSKHESLI 63
D+++ V D+ P + Q ++V+ + P++LVLNK DL++
Sbjct: 119 AEADLLLHVVDASDP----DREEQIETVEEVLKELGADDIPIILVLNKIDLLDD------ 168
Query: 64 EEKVRKEQSHISEVIFTNCRN 84
EE + ++ + +F + +
Sbjct: 169 EELEERLRAGRPDAVFISAKT 189
Score = 28.2 bits (64), Expect = 5.2
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
TV +VG N GKS++ NAL
Sbjct: 43 TVALVGYTNAGKSTLFNAL 61
Score = 28.2 bits (64), Expect = 5.2
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 170 TVMVVGVPNVGKSSIINAL 188
TV +VG N GKS++ NAL
Sbjct: 43 TVALVGYTNAGKSTLFNAL 61
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 28.9 bits (65), Expect = 3.5
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 44 PMVLVLNKRDLIN-SKHESLIEEKVRKEQSHISEVIFTNC 82
P+++VLNK DLI + + IE+ ++ Q + + +
Sbjct: 122 PLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDS 161
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 29.3 bits (66), Expect = 3.5
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGK--AVPVGPKAGVTRSVMSQVKISEKPLIYILD 227
T+ ++G PN GK+++ N L + + G V V K G + QV + + P Y L
Sbjct: 5 TIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEGQFSTTDHQVTLVDLPGTYSLT 64
Query: 228 T 228
T
Sbjct: 65 T 65
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 28.8 bits (65), Expect = 3.7
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 15/66 (22%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAV-----PVGPKAGVTRSVMSQVKISEKPLIY 224
T++V+G VGKSS IN++ + K + + K++
Sbjct: 33 TILVLGKTGVGKSSTINSI----FGERKVSVSAFQSETLRPREVSRTVDGFKLN------ 82
Query: 225 ILDTPG 230
I+DTPG
Sbjct: 83 IIDTPG 88
Score = 27.7 bits (62), Expect = 8.3
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 116 TVMVVGVPNVGKSSIINAL 134
T++V+G VGKSS IN++
Sbjct: 33 TILVLGKTGVGKSSTINSI 51
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 29.1 bits (65), Expect = 3.8
Identities = 14/92 (15%), Positives = 22/92 (23%), Gaps = 10/92 (10%)
Query: 173 VVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYILDTPGIS 232
++G + N G AV V + G S+ P +Y
Sbjct: 230 IIGPGERPNVVLANDALPGLALAGGAVLVDERGGT----------SKDPDVYAAGDVAEI 279
Query: 233 LPRIDNLECGMRLAACATLQDHLVGEINIADY 264
+ L A A + E
Sbjct: 280 PAAETGKGGRIALWAIAVAAGRIAAENIAGAL 311
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 28.4 bits (64), Expect = 4.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 117 VMVVGVPNVGKSSIINAL 134
+ VVG + GKSS++NAL
Sbjct: 1 IAVVGDQSAGKSSVLNAL 18
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 29.1 bits (66), Expect = 4.2
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 171 VMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSV-MSQVKISEK--PLIYILD 227
V ++G + GK+++++ +R +++ G+A G+T+ + QV + P I +D
Sbjct: 8 VTIMGHVDHGKTTLLDKIRKTNVAAGEA------GGITQHIGAYQVPLDVIKIPGITFID 61
Query: 228 TPG 230
TPG
Sbjct: 62 TPG 64
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 27.9 bits (62), Expect = 4.5
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 117 VMVVGVPNVGKSSIINALRS 136
V++ G GK+S++ L
Sbjct: 27 VLLTGPSGTGKTSLLRELLE 46
Score = 27.9 bits (62), Expect = 4.5
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 171 VMVVGVPNVGKSSIINALRS 190
V++ G GK+S++ L
Sbjct: 27 VLLTGPSGTGKTSLLRELLE 46
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 28.7 bits (64), Expect = 4.7
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 89 GVQKILPTLQ-HISDNMTRYHRTEVYNTTVMVVGVPNVGKSSIINAL 134
G+Q+ P Q + + + + +V + T++V+G VGKSS +N++
Sbjct: 12 GIQQFPPATQTKLLELLGKLKEEDVSSLTILVMGKGGVGKSSTVNSI 58
>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 = 28.7 bits (65), Expect = 4.9
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 44 PMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIFT 80
PMV+ NK D+ + K+R + V+ T
Sbjct: 216 PMVIAANKADIPD---AEENISKLRLKYPDE-IVVPT 248
Score = 27.6 bits (62), Expect = 9.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 119 VVGVPNVGKSSIINAL 134
+VG PNVGKS+ NA
Sbjct: 3 LVGKPNVGKSTFFNAA 18
Score = 27.6 bits (62), Expect = 9.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 173 VVGVPNVGKSSIINAL 188
+VG PNVGKS+ NA
Sbjct: 3 LVGKPNVGKSTFFNAA 18
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.8 bits (65), Expect = 5.0
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 44 PMVLVLNKRDLINSKHESLIEEKVRKEQSHISEVIF 79
P++LVLNK DL+ EE + + + +F
Sbjct: 306 PIILVLNKIDLLED------EEILAELERGSPNPVF 335
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 27.9 bits (63), Expect = 5.0
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 117 VMVVGVPNVGKSSIINALRSSHMKKGKAVPILPT 150
++++G+ GK++I+ L K G+ V +PT
Sbjct: 2 ILMLGLDGAGKTTILYKL-----KLGEVVTTIPT 30
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.4 bits (64), Expect = 5.2
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 121 GVPNVGKSSIINALRSSHMKKGKAVPIL 148
GVP GKS++I AL ++G V +L
Sbjct: 58 GVPGAGKSTLIEALGRELRERGHRVAVL 85
Score = 27.7 bits (62), Expect = 9.8
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 175 GVPNVGKSSIINALRSSHMKKGKAVPV 201
GVP GKS++I AL ++G V V
Sbjct: 58 GVPGAGKSTLIEALGRELRERGHRVAV 84
>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 = 28.8 bits (64), Expect = 6.1
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 166 VYNTTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPLIYI 225
++ ++V+G VGKS+ IN++ A +G T SV + + I +
Sbjct: 116 DFSLNILVLGKSGVGKSATINSIFGEVKFSTDAFGMG-----TTSVQEIEGLVQGVKIRV 170
Query: 226 LDTPGI 231
+DTPG+
Sbjct: 171 IDTPGL 176
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 28.3 bits (64), Expect = 6.2
Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 11/69 (15%)
Query: 170 TVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPKAGVTRSVMSQVKISEKPL------- 222
+MVVG +GKS+ IN L + + K P P +T++V ++KIS+ L
Sbjct: 6 NIMVVGESGLGKSTFINTLFGTKLYPSK-YPPAPGEHITKTV--EIKISKAELEENGVKL 62
Query: 223 -IYILDTPG 230
+ ++DTPG
Sbjct: 63 KLTVIDTPG 71
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 27.7 bits (62), Expect = 6.4
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 117 VMVVGVPNVGKSSIINAL 134
++++G VGKSS+I +L
Sbjct: 5 IVLIGDEGVGKSSLIMSL 22
Score = 27.7 bits (62), Expect = 6.4
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 171 VMVVGVPNVGKSSIINAL 188
++++G VGKSS+I +L
Sbjct: 5 IVLIGDEGVGKSSLIMSL 22
>gnl|CDD|132259 TIGR03215, ac_ald_DH_ac, acetaldehyde dehydrogenase (acetylating).
Members of this protein family are acetaldehyde
dehydrogenase (acetylating), EC 1.2.1.10. This enzyme
oxidizes acetaldehyde, using NAD(+), and attaches
coenzyme A (CoA), yielding acetyl-CoA. It occurs as a
late step in the meta-cleavage pathways of a variety of
compounds, including catechol, biphenyl, toluene,
salicylate, etc.
Length = 285
Score = 28.0 bits (63), Expect = 6.8
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 169 TTVMVVGVPNVGKSSIINALRSSHMKKGKAVPVGPK-AGVTRSVMSQVKISEKPLIYILD 227
V ++G N+G + LRS H++ V + P+ G+ R+ VK S + + +L
Sbjct: 2 VKVAIIGSGNIGTDLMYKLLRSEHLEMVAMVGIDPESDGLARARELGVKTSAEGVDGLLA 61
Query: 228 TPGISL 233
P I +
Sbjct: 62 NPDIDI 67
>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
Length = 448
Score = 28.4 bits (64), Expect = 7.3
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 212 MSQVKISEKPLIYILDTPGIS 232
++ +S+ P IYI DTPGI
Sbjct: 278 IAMGSLSDAP-IYIDDTPGIK 297
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 27.7 bits (63), Expect = 8.4
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 120 VGVPNVGKSSIINAL 134
VG+PN GKS++I+A+
Sbjct: 164 VGLPNAGKSTLISAV 178
Score = 27.7 bits (63), Expect = 8.4
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 174 VGVPNVGKSSIINAL 188
VG+PN GKS++I+A+
Sbjct: 164 VGLPNAGKSTLISAV 178
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. 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.
Length = 201
Score = 27.7 bits (62), Expect = 9.0
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 117 VMVVGVPNVGKSSII 131
V+V+G VGK+SII
Sbjct: 3 VLVIGDLGVGKTSII 17
Score = 27.7 bits (62), Expect = 9.0
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 171 VMVVGVPNVGKSSII 185
V+V+G VGK+SII
Sbjct: 3 VLVIGDLGVGKTSII 17
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.9 bits (63), Expect = 9.1
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 117 VMVVGVPNVGKSSIINAL 134
V +VG P+ GKSS+I+AL
Sbjct: 162 VGLVGFPSAGKSSLISAL 179
Score = 27.9 bits (63), Expect = 9.1
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 171 VMVVGVPNVGKSSIINAL 188
V +VG P+ GKSS+I+AL
Sbjct: 162 VGLVGFPSAGKSSLISAL 179
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 27.9 bits (63), Expect = 9.5
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 121 GVPNVGKSSIINAL 134
GVP VGKS+ I AL
Sbjct: 63 GVPGVGKSTFIEAL 76
Score = 27.9 bits (63), Expect = 9.5
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 175 GVPNVGKSSIINAL 188
GVP VGKS+ I AL
Sbjct: 63 GVPGVGKSTFIEAL 76
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 27.1 bits (61), Expect = 9.7
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 17 IVIEVHDSRMPFTGRNHLLQQSVQNIRPMVLVLNKRDLIN 56
+V++ + MP T R HLL + P+++ +NK D ++
Sbjct: 95 LVVDAVEGVMPQT-REHLLLAKTLGV-PIIVFINKIDRVD 132
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
0.321 0.136 0.392
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,940,131
Number of extensions: 1721449
Number of successful extensions: 2347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2288
Number of HSP's successfully gapped: 271
Length of query: 352
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 254
Effective length of database: 6,590,910
Effective search space: 1674091140
Effective search space used: 1674091140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)