RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15712
(358 letters)
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 389 bits (1001), Expect = e-135
Identities = 127/282 (45%), Positives = 186/282 (65%), Gaps = 1/282 (0%)
Query: 73 MYNFKKIAVVPTAKEFVDIMLSKTQRKTPTVIH-KQYKISRIRSFYMRKIKYTQSNFHER 131
M FKKI VPTA E +D + +R TV K KI + R F +R++K + +R
Sbjct: 2 MNPFKKIPTVPTADELIDKAFRRAERAESTVRPDKGPKIVKAREFEIRRVKTASNIVRDR 61
Query: 132 LSQIIQEFPKLDNIHPFYADLMNILYDKDHYKLGLGQLNQARHLIDNVAKDYLRLMKYAD 191
L +I++ FP LD++HPFY +L+++L D DH K+ L ++ A +I+ +A++Y+RL+K A
Sbjct: 62 LDKIVERFPSLDDLHPFYRELIDVLVDIDHLKISLSAVSWASKIIEKLAREYIRLLKAAK 121
Query: 192 SLYRCKQLKKAALGRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGK 251
QL++ A GR+A+I+K+ +LE+L + R HL +LP+IDP TI++ G+PNVGK
Sbjct: 122 DPKEANQLRRQAFGRVASIIKKIDDDLEFLRKARDHLKKLPAIDPDLPTIVVAGYPNVGK 181
Query: 252 SSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSLEDRNIIEMQAV 311
SS + K+T A +V PY FTTK ++VGH + YLR QVIDTPG+LD LE+RN IE QA+
Sbjct: 182 SSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLEERNEIERQAI 241
Query: 312 TALAHLRAAVLYFIDISEQCGHSIQEQIGLFKSIRPLFNNKV 353
AL HL +L+ D SE CG+S++EQI L + I+ LF +
Sbjct: 242 LALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKELFKAPI 283
>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 = 244 bits (626), Expect = 3e-81
Identities = 84/112 (75%), Positives = 98/112 (87%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDH 298
RT++I G+PNVGKSS +NK+TRA +V PY FTTKSL+VGH DYKYLRWQVIDTPGILD
Sbjct: 1 RTLVIAGYPNVGKSSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGILDR 60
Query: 299 SLEDRNIIEMQAVTALAHLRAAVLYFIDISEQCGHSIQEQIGLFKSIRPLFN 350
LE+RN IEMQA+TALAHLRAAVL+FID SE CG+SI+EQ+ LFK I+PLFN
Sbjct: 61 PLEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSIEEQLSLFKEIKPLFN 112
>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 = 108 bits (271), Expect = 2e-28
Identities = 36/106 (33%), Positives = 58/106 (54%), Gaps = 4/106 (3%)
Query: 242 IICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYK-YLRWQVIDTPGILDHSL 300
+ G PNVGKS+ L+ +T A V++ Y FTT VG ++ + Q+ID PG+LD +
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGAS 60
Query: 301 EDRNIIEMQAVTALAHLRAAVLYFIDISEQCGH-SIQEQIGLFKSI 345
E R + E + A + +L+ ID SE C +++Q L + +
Sbjct: 61 EGRGLGE--QILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEV 104
>gnl|CDD|115510 pfam06858, NOG1, Nucleolar GTP-binding protein 1 (NOG1). This
family represents a conserved region of approximately 60
residues in length within nucleolar GTP-binding protein
1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown
to be essential for cell viability, suggesting that NOG1
may play an important role in nucleolar functions.
Family members include eukaryotic, bacterial and
archaeal proteins.
Length = 58
Score = 86.9 bits (216), Expect = 8e-22
Identities = 33/48 (68%), Positives = 40/48 (83%)
Query: 305 IIEMQAVTALAHLRAAVLYFIDISEQCGHSIQEQIGLFKSIRPLFNNK 352
IE QA+TALAHLRAAVL+ D SEQCG+S++EQ+ LFK I+PLF NK
Sbjct: 1 NIEKQAITALAHLRAAVLFVFDPSEQCGYSLEEQLHLFKEIKPLFKNK 48
>gnl|CDD|191952 pfam08155, NOGCT, NOGCT (NUC087) domain. This C terminal domain
is found in the NOG subfamily of nucleolar GTP-binding
proteins.
Length = 55
Score = 82.3 bits (204), Expect = 4e-20
Identities = 31/55 (56%), Positives = 41/55 (74%), Gaps = 3/55 (5%)
Query: 17 KRKLERHIEEE--MQDDYVLDLKKNYDL-PDEYKYDVIPEFMEGVNIADYIDPDI 68
+RKLER +EEE Y +DL+KNY L +E+KYD+IPE + G N+AD+IDPDI
Sbjct: 1 RRKLERDLEEENGGAGVYSVDLRKNYILANEEWKYDIIPEILNGKNVADFIDPDI 55
>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 = 72.3 bits (178), Expect = 9e-16
Identities = 30/101 (29%), Positives = 50/101 (49%), Gaps = 6/101 (5%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDH 298
+ + G PNVGKS+ +N +T A V V Y TT+ +G + ++DTPG+++
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGR-QIILVDTPGLIEG 59
Query: 299 SLEDRNIIEMQAVTALAHLRAA--VLYFIDISEQCGHSIQE 337
+ E + +E L +R A +L +D SE +E
Sbjct: 60 ASEGK-GVEG-FNRFLEAIREADLILLVVDASEGLTEDDEE 98
>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 = 61.4 bits (150), Expect = 6e-11
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILD 297
+ + GFP+VGKS+ L+K+T +V Y FTT + G +YK + Q++D PGI++
Sbjct: 2 RVALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPGIIE 59
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 59.6 bits (145), Expect = 6e-10
Identities = 26/65 (40%), Positives = 39/65 (60%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHS 299
T+ + GFP+VGKS+ LNK+T +V Y FTT G +YK + Q++D PGI++ +
Sbjct: 65 TVALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIEGA 124
Query: 300 LEDRN 304
R
Sbjct: 125 SSGRG 129
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 56.7 bits (138), Expect = 1e-09
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 11/89 (12%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVG--HTDYKYLRWQVIDTPGILDHSLED 302
G PN GKS+ L+ I+ A + Y FTT +G D + + D PG+++ + E
Sbjct: 7 GLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDD-GRSFVIADIPGLIEGASEG 65
Query: 303 RNI-IEMQAVTALAHL-RAAVL-YFIDIS 328
+ + L H+ R VL + ID+S
Sbjct: 66 KGLGHRF-----LRHIERTRVLLHVIDLS 89
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 53.7 bits (130), Expect = 5e-08
Identities = 30/100 (30%), Positives = 45/100 (45%), Gaps = 11/100 (11%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTK--SLYVGHTDYKYLRWQVIDTPGILDHSLED 302
G PN GKS+ L+ ++ A + Y FTT +L V D + V D PG+++ + E
Sbjct: 166 GLPNAGKSTLLSAVSAAKPKIADYPFTTLVPNLGVVRVDG-GESFVVADIPGLIEGASEG 224
Query: 303 RNI-IEMQAVTALAHL-RAAVLYF-IDISEQCGHSIQEQI 339
+ + L H+ R VL ID+S G E
Sbjct: 225 VGLGLRF-----LRHIERTRVLLHVIDLSPIDGRDPIEDY 259
>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 = 49.7 bits (120), Expect = 8e-07
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVI-DTPGI 295
G PN GKS+ ++ ++ A + Y FTT +G R VI D PG+
Sbjct: 164 GLPNAGKSTLISAVSAAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGL 215
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 50.4 bits (121), Expect = 9e-07
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILD-- 297
T+ + G PNVGK++ N +T A+ V + T G YK +++D PG
Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYSLT 64
Query: 298 -HSLEDR 303
+S +++
Sbjct: 65 AYSEDEK 71
>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 = 46.5 bits (111), Expect = 3e-06
Identities = 22/62 (35%), Positives = 28/62 (45%), Gaps = 16/62 (25%)
Query: 245 GFPNVGKSSFLNKITRADV-DVQPYAFTTKSLYVGHTDYKYLRWQV--------IDTPGI 295
G PNVGKSS LN + +V V P TT D W++ IDTPG+
Sbjct: 4 GRPNVGKSSLLNALLGQNVGIVSPIPGTT-------RDPVRKEWELLPLGPVVLIDTPGL 56
Query: 296 LD 297
+
Sbjct: 57 DE 58
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 48.1 bits (116), Expect = 3e-06
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 11/57 (19%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLY-----VGHTDYKYLRWQVI-DTPGI 295
G PN GKS+ ++ ++ A + Y FTT L+ V DYK VI D PG+
Sbjct: 165 GLPNAGKSTLISAVSAAKPKIADYPFTT--LHPNLGVVRVDDYKSF---VIADIPGL 216
>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 = 46.4 bits (111), Expect = 4e-06
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 217 NLEYLEQVRQHLSRLPSIDPFTRTI--IICGFPNVGKSSFLNKIT-RADVDVQPYAFTTK 273
L+ +++ + +L + R + ++ G PNVGKS+ +N++ + V T+
Sbjct: 92 LLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLRGKKVAKVGNKPGVTR 151
Query: 274 SLYVGHTDYKYLRWQVIDTPGIL 296
+++DTPGIL
Sbjct: 152 GQQWIRIGPN---IELLDTPGIL 171
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 47.4 bits (113), Expect = 5e-06
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 234 IDPFTRTIIICGFPNVGKSSFLNKIT-RADVDVQPYAFTTKSL-YVGHTDYKYLRWQVID 291
+ + + G+PNVGKS+ +N++ + TTK + ++ D YL +D
Sbjct: 128 LLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYL----LD 183
Query: 292 TPGILDHSLEDR 303
TPGI+ +D
Sbjct: 184 TPGIIPPKFDDD 195
>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 = 47.2 bits (113), Expect = 6e-06
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
I + G PNVGKS+F N T ADV++ Y FTT
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADVEIANYPFTT 32
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 47.2 bits (113), Expect = 7e-06
Identities = 31/93 (33%), Positives = 40/93 (43%), Gaps = 19/93 (20%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVI-DTPGILDHSLEDR 303
G PN GKS+F+ ++ A V Y FTT +G R V+ D PG
Sbjct: 166 GLPNAGKSTFIRAVSAAKPKVADYPFTTLVPNLGVVRVDDERSFVVADIPG--------- 216
Query: 304 NIIEMQAVTA------LAHL-RAAVLYF-IDIS 328
+IE + A L HL R VL IDI+
Sbjct: 217 -LIEGASEGAGLGIRFLKHLERCRVLLHLIDIA 248
>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 = 45.1 bits (108), Expect = 8e-06
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSLE 301
G PNVGK++ N +T A V + T G +++D PG +SL
Sbjct: 4 GNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGT--YSLT 58
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 47.1 bits (113), Expect = 8e-06
Identities = 19/33 (57%), Positives = 23/33 (69%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
TI + G PNVGKS+F N T ADV++ Y FTT
Sbjct: 3 TIGLVGKPNVGKSTFFNAATLADVEIANYPFTT 35
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 46.8 bits (112), Expect = 9e-06
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
I I G PNVGKS+ N +T+A ++ Y F T
Sbjct: 4 KIGIVGLPNVGKSTLFNALTKAGAEIANYPFCT 36
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 45.2 bits (108), Expect = 1e-05
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
TI + G PNVGK++ N +T A V + T G YK +++D PG
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGT 57
>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 = 45.1 bits (108), Expect = 1e-05
Identities = 34/101 (33%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 238 TRTIIICGFPNVGKSSFLNKITRAD-VDVQPYAFTTK-SLYVGHTDYKYLRWQVIDTPGI 295
I I G PNVGKSS LN + + V V A TT+ S+ V +Y ++ +IDT GI
Sbjct: 2 PIKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDV-PFEYDGQKYTLIDTAGI 60
Query: 296 LDHSLEDRNIIEMQAVTALAHLRAA--VLYFID----ISEQ 330
I + + L + A VL +D I+EQ
Sbjct: 61 RKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQ 101
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 45.9 bits (110), Expect = 2e-05
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVI-DTPGI 295
GFPNVGKS+ L+ ++ A + Y FTT +G + R V+ D PG+
Sbjct: 165 GFPNVGKSTLLSVVSNAKPKIANYHFTTLVPNLGVVETDDGRSFVMADIPGL 216
>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 = 23/91 (25%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 243 ICGFPNVGKSSFLNKITRADV-DVQPYAFTTKS--LYVGHTDYKYLRWQVIDTPGILD-H 298
+ G VGKSS LN + +V +V TT+ +YV D ++ ++DTPG+ +
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG 61
Query: 299 SLEDRNIIEMQAVTALAHLRAAVLYFIDISE 329
L + + A +L +D ++
Sbjct: 62 GLGREELARLLLRGA-----DLILLVVDSTD 87
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 45.3 bits (108), Expect = 3e-05
Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 237 FTRTIIICGFPNVGKSSFLNKITR---ADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTP 293
T + I G PNVGKS+ N++T A V P T +Y G ++ + +IDT
Sbjct: 2 STPVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTP-GVTRDRIY-GDAEWLGREFILIDTG 59
Query: 294 GILDHSLEDRNIIEMQAVTALAHLRA-AVLYFIDISEQ 330
G LD ED ++ +A A +L+ +D E
Sbjct: 60 G-LDDGDEDELQELIREQALIAIEEADVILFVVDGREG 96
Score = 39.1 bits (92), Expect = 0.002
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 241 IIICGFPNVGKSSFLNKITRAD-VDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
I I G PNVGKSS +N I + V V A TT+ + ++ +IDT GI
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAGI 236
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 43.2 bits (103), Expect = 1e-04
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 23/82 (28%)
Query: 234 IDPFTRTIIICGFPNVGKSSFLNKITR---ADVDVQPYAFTTKSLYVGHTDYKYLRW--- 287
R +II G PNVGKS+ +N++ A +P G T K +W
Sbjct: 118 RPRAIRAMII-GIPNVGKSTLINRLAGKKIAKTGNRP----------GVT--KAQQWIKL 164
Query: 288 ----QVIDTPGILDHSLEDRNI 305
+++DTPGIL LED+ +
Sbjct: 165 GKGLELLDTPGILWPKLEDQEV 186
>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 = 43.6 bits (104), Expect = 1e-04
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 221 LEQVRQHLS-RLPSIDPFTRTIIIC--GFPNVGKSSFLNKITRAD-VDVQPYAFTTK-SL 275
L+ + + L + I I G PNVGKS+ +N + + V V A TT+ S+
Sbjct: 152 LDAILELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSI 211
Query: 276 YVGHTDYKYLRWQVIDTPGI 295
+ + ++ +IDT GI
Sbjct: 212 DI-PFERNGKKYTLIDTAGI 230
Score = 40.9 bits (97), Expect = 8e-04
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 240 TIIICGFPNVGKSSFLNKITRA-DVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
+ I G PNVGKS+ N++T D V T+ G ++ + +IDT GI
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGI 57
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 43.3 bits (103), Expect = 1e-04
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 8/93 (8%)
Query: 241 IIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHS 299
++I G PNVGKSS LN + D V A TT+ + + + +++DT GI +
Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIRETD 279
Query: 300 LEDRNIIEMQAVT-ALAHLRAA--VLYFIDISE 329
+++E + A + A VL+ +D S+
Sbjct: 280 ----DVVERIGIERAKKAIEEADLVLFVLDASQ 308
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 42.5 bits (101), Expect = 2e-04
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 241 IIICGFPNVGKSSFLNK-ITRADVDVQPYAFTTKSLYVGHTDYKYLRW-------QVIDT 292
+I G PNVGKS+ +N+ + V TK +W +++DT
Sbjct: 121 AMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKG----------QQWIKLSDGLELLDT 170
Query: 293 PGILDHSLEDRNI 305
PGIL ED+ +
Sbjct: 171 PGILWPKFEDQEV 183
>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 = 42.8 bits (101), Expect = 2e-04
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSLED 302
G PNVGKS+ N +T A+ V + T G ++ +++D PGI +SL
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGI--YSLTT 56
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 42.6 bits (101), Expect = 2e-04
Identities = 24/64 (37%), Positives = 31/64 (48%), Gaps = 13/64 (20%)
Query: 239 RTIIICGFPNVGKSSFLNKITRAD-VDVQPYAFTTK----SLYV--GHTDYKYLRWQVID 291
R + + G PNVGKSS LNK+ + V A TT SL G T W+ +D
Sbjct: 212 RRVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKT------WRFVD 265
Query: 292 TPGI 295
T G+
Sbjct: 266 TAGL 269
Score = 29.2 bits (66), Expect = 3.8
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 240 TIIICGFPNVGKSSFLNKI 258
+ + G PNVGKS+ +N+I
Sbjct: 40 VVAVVGRPNVGKSTLVNRI 58
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 40.0 bits (95), Expect = 0.001
Identities = 31/99 (31%), Positives = 41/99 (41%), Gaps = 27/99 (27%)
Query: 240 TIIICGFPNVGKSSFLNKITR---ADVDVQPYAFTTKSLYVGHT-DYKY-------LRWQ 288
+ I G PNVGKS+ N++T A V P G T D Y +
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAIVADTP----------GVTRDRIYGEAEWLGREFI 52
Query: 289 VIDTPGIL--DHSLEDRNIIEMQAVTALAHLRAAVLYFI 325
+IDT GI D E + I QA A+ A V+ F+
Sbjct: 53 LIDTGGIEPDDDGFEKQ--IREQAELAIEE--ADVILFV 87
Score = 39.6 bits (94), Expect = 0.002
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 221 LEQVRQHLSRLPSIDPFTRTIIIC--GFPNVGKSSFLNKITRAD-VDVQPYAFTTK-SLY 276
L+ + + L D I I G PNVGKSS +N + + V V A TT+ S+
Sbjct: 154 LDAILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSID 213
Query: 277 VGHTDYKYLRWQVIDTPGI 295
+ ++ +IDT GI
Sbjct: 214 T-PFERDGQKYTLIDTAGI 231
>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 = 38.7 bits (91), Expect = 0.001
Identities = 21/57 (36%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 240 TIIICGFPNVGKSSFLNKITRADV-DVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
T+ + G+PNVGKSS +N + R+ +V TKS+ H D K+++ ++D+PG+
Sbjct: 118 TVGVVGYPNVGKSSVINSLKRSRACNVGATPGVTKSMQEVHLD-KHVK--LLDSPGV 171
>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 = 39.4 bits (93), Expect = 0.002
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 243 ICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
I G PNVGKS+ N +T+++ + Y F T
Sbjct: 3 IVGLPNVGKSTLFNALTKSNAEAANYPFCT 32
>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 = 38.2 bits (90), Expect = 0.002
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDH 298
++I G PNVGKSS LN + D V A TT+ + D + ++IDT G+ +
Sbjct: 5 KVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGLRET 64
Query: 299 SLEDRNIIEMQAVT-ALAHLRAA--VLYFIDISEQ 330
+ IE + A + A VL +D SE
Sbjct: 65 E----DEIEKIGIERAREAIEEADLVLLVVDASEG 95
>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 = 37.8 bits (89), Expect = 0.002
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 243 ICGFPNVGKSSFLNKITR---ADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
I G PNVGKS+ N++T A V T+ G ++ + +IDT GI
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVS--DTPGVTRDRKYGEAEWGGREFILIDTGGI 55
>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 = 38.5 bits (90), Expect = 0.003
Identities = 35/121 (28%), Positives = 55/121 (45%), Gaps = 14/121 (11%)
Query: 241 IIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVG-HTDYKYLRWQVI--DTPGIL 296
+ I G PNVGKS+ LN++ + P A TT++ G HT Q+I DTPG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGAS---QIIFIDTPGFH 59
Query: 297 D--HSLEDRNIIEMQAVTALAHLRAAVLYFIDISEQCGHS--IQEQIGLFKSIRPLFNNK 352
+ HSL N + M+ + +L+ +D + G + ++ K L NK
Sbjct: 60 EKKHSL---NRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRPVVLTRNK 116
Query: 353 V 353
+
Sbjct: 117 L 117
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 38.9 bits (92), Expect = 0.003
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 243 ICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
I G PNVGKS+ N +T+A + Y F T
Sbjct: 7 IVGLPNVGKSTLFNALTKAGAEAANYPFCT 36
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 36.6 bits (85), Expect = 0.008
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 241 IIICGFPNVGKSSFLNKITRADV-DVQPYAFTTKSLYVGHTDY--KYLRWQVIDTPGILD 297
I+I G PNVGKS+ LN++ + + TT++ + K ++ ++DT G
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ-- 61
Query: 298 HSLEDRNIIE---MQAVTALAHLRAAVLYFIDISE 329
ED + I +AV + + V+ +D+ E
Sbjct: 62 ---EDYDAIRRLYYRAVESSLRVFDIVILVLDVEE 93
>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 = 36.3 bits (85), Expect = 0.010
Identities = 35/103 (33%), Positives = 47/103 (45%), Gaps = 20/103 (19%)
Query: 244 CGF------PNVGKSSFLNKITRADVD-VQPYAFTTKSLYVG-HTDYKYLRWQVI--DTP 293
GF PNVGKS+ LN + + V P TT++ G +TD Q+I DTP
Sbjct: 3 SGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDA---QIIFVDTP 59
Query: 294 GILDHSLEDRNIIEM--QAVTALAHLRA-AVLYFIDISEQCGH 333
GI H + + M A +AL VL+ +D SE G
Sbjct: 60 GI--HKPKKKLGERMVKAAWSALKD--VDLVLFVVDASEWIGE 98
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 36.8 bits (86), Expect = 0.011
Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 241 IIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVG-HTDYKYLRWQVI--DTPGI 295
+ I G PNVGKS+ LN + + V P TT++ G T Q+I DTPGI
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNA---QIIFVDTPGI 64
>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 = 36.3 bits (85), Expect = 0.011
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 15/72 (20%)
Query: 206 RMATIMKRQASNLEYLEQVRQHL-----SRLPSIDPFTRTIIICGFPNVGKSSFLNKITR 260
R+A + K LE+V++ R S P T+ + G+ N GKS+ N +T
Sbjct: 14 RIAKLRKE-------LEKVKKQRELQRARRKRSGVP---TVALVGYTNAGKSTLFNALTG 63
Query: 261 ADVDVQPYAFTT 272
ADV + F T
Sbjct: 64 ADVLAEDQLFAT 75
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 37.0 bits (85), Expect = 0.011
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 238 TRTIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVIDTPGIL 296
T ++ I G PN GKS+ LN+I + V P TT+S+ G K + + DTPGI
Sbjct: 52 TVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIF 111
Query: 297 D 297
+
Sbjct: 112 E 112
>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 = 35.4 bits (82), Expect = 0.015
Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 217 NLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSL 275
L+ ++ + +L ++ G PNVGKSSF+N + V TTK
Sbjct: 72 ILKLKAEITKQKLKLKYKKGIRVGVV--GLPNVGKSSFINALLNKFKLKVGSIPGTTKLQ 129
Query: 276 YVGHTDYKY-LRWQVIDTPGI 295
D K + DTPGI
Sbjct: 130 ----QDVKLDKEIYLYDTPGI 146
>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 = 36.4 bits (85), Expect = 0.018
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 15/69 (21%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHT---------DYKYLRWQV 289
+ + + G NVGKSS +NK+ + + + T S + G T D L
Sbjct: 155 KDVYVVGVTNVGKSSLINKLLKQNNGDKDVI--TTSPFPGTTLDLIEIPLDDGHSL---- 208
Query: 290 IDTPGILDH 298
DTPGI++
Sbjct: 209 YDTPGIINS 217
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 36.7 bits (85), Expect = 0.018
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 15/65 (23%)
Query: 239 RTIIICGFPNVGKSSFLNKIT---RADVDVQPYAFTTKS-----LYVGHTDYKYLRWQVI 290
R + + G PNVGKSS LN++T RA V+ A TT+ + + D W I
Sbjct: 451 RRVALVGRPNVGKSSLLNQLTHEERAVVN--DLAGTTRDPVDEIVEIDGED-----WLFI 503
Query: 291 DTPGI 295
DT GI
Sbjct: 504 DTAGI 508
Score = 30.5 bits (69), Expect = 1.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 240 TIIICGFPNVGKSSFLNKI 258
+ I G PNVGKS+ +N+I
Sbjct: 277 VVAIVGRPNVGKSTLVNRI 295
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 36.4 bits (85), Expect = 0.020
Identities = 28/133 (21%), Positives = 48/133 (36%), Gaps = 51/133 (38%)
Query: 197 KQLKKAALGRMATIMKRQASN----------------------LEYLEQVRQHLSRLPSI 234
K +KK ++ ++++A LE +E+ R+
Sbjct: 111 KSVKK---NKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLEAIEKYREG------- 160
Query: 235 DPFTRTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHT---------DYKYL 285
R + + G NVGKS+ +N+I + + T S + G T D +L
Sbjct: 161 ----RDVYVVGVTNVGKSTLINRIIKEITGEK--DVITTSRFPGTTLDKIEIPLDDGSFL 214
Query: 286 RWQVIDTPGILDH 298
DTPGI+
Sbjct: 215 ----YDTPGIIHR 223
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 35.9 bits (83), Expect = 0.026
Identities = 34/112 (30%), Positives = 52/112 (46%), Gaps = 6/112 (5%)
Query: 241 IIICGFPNVGKSSFLNKITRAD-VDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHS 299
+ I G PNVGKSS LN + + D V TT+ + G + + +++DT GI +H+
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHA 265
Query: 300 --LEDRNIIEMQAVTALAHLRAAVLYFIDISEQCGHSIQEQIGLFKSIRPLF 349
+E I + A L V+Y +D S+ I L KS +P
Sbjct: 266 DFVERLGIEKSFKAIKQADL---VIYVLDASQPLTKDDFLIIDLNKSKKPFI 314
>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 = 34.1 bits (79), Expect = 0.035
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 240 TIIICGFPNVGKSSFLNKI 258
TI + G+PNVGKSS +N +
Sbjct: 84 TIGLVGYPNVGKSSLINAL 102
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.6 bits (79), Expect = 0.044
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 238 TRTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVG---HTDYKYLRWQVIDTPG 294
I++ G VGK++ LN++ + Y T +L + ++ Q+ DT G
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEG-YPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63
Query: 295 ILD 297
+
Sbjct: 64 QEE 66
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 35.1 bits (82), Expect = 0.045
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDH 298
++I G PNVGKSS LN + + V A TT+ + H + + ++IDT GI +
Sbjct: 217 KVVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRET 276
Query: 299 SLEDRNIIEMQAVT-ALAHLRAA--VLYFIDISE 329
+ +E + + + A VL +D SE
Sbjct: 277 D----DEVEKIGIERSREAIEEADLVLLVLDASE 306
>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 = 34.9 bits (80), Expect = 0.060
Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 9/105 (8%)
Query: 204 LGRMATIMKRQASNLEYLEQVRQHLSRLPSI--DP--FTRTIIICGFPNVGKSSFLNKI- 258
L R+ + RQ L+ + +L + DP F+ I++ G VGKS+ +N I
Sbjct: 80 LYRLGLLAGRQGGGAFSLDAAKAMAEQLEAEGQDPLDFSLNILVLGKSGVGKSATINSIF 139
Query: 259 --TRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSLE 301
+ D T+ G +R VIDTPG+ + +
Sbjct: 140 GEVKFSTDAFGMGTTSVQEIEGLVQGVKIR--VIDTPGLKSSASD 182
>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 = 34.8 bits (81), Expect = 0.062
Identities = 29/101 (28%), Positives = 36/101 (35%), Gaps = 33/101 (32%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTD--YKYLRWQ------VI 290
I I G N GKSS +N +T D+ V TT TD YK + +I
Sbjct: 8 HIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTT-------TDPVYKAMELLPLGPVVLI 60
Query: 291 DTPGILDHSLEDRNIIEMQAVTALAHLRA----AVLYFIDI 327
DT G+ D L LR VL D+
Sbjct: 61 DTAGLDD-------------EGELGELRVEKTREVLDKTDL 88
>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 = 34.2 bits (79), Expect = 0.075
Identities = 29/108 (26%), Positives = 45/108 (41%), Gaps = 14/108 (12%)
Query: 205 GRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKITRADVD 264
G Q E ++++ L F+ TI++ G VGKSS +N I
Sbjct: 5 GFQFFPDATQTKLHELEAKLKKELD-------FSLTILVLGKTGVGKSSTINSIFGERK- 56
Query: 265 VQPYAF---TTKSLYVGHTDYKYLRWQVIDTPGILDHSLE--DRNIIE 307
V AF T + V T + +IDTPG+L+ + +R I+
Sbjct: 57 VSVSAFQSETLRPREVSRT-VDGFKLNIIDTPGLLESQDQRVNRKILS 103
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 34.5 bits (80), Expect = 0.082
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 245 GFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGI 295
GFP+ GKSS ++ ++ A + Y FTT +G R+ V D PG+
Sbjct: 166 GFPSAGKSSLISALSAAKPKIADYPFTTLVPNLGVVQAGDTRFTVADVPGL 216
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 34.3 bits (79), Expect = 0.091
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 16/74 (21%)
Query: 201 KAALGRMATIMKRQASNLEYLEQVRQHLSR--LPSIDPFTRTIIICGFPNVGKSSFLNKI 258
L R+ + K++ EQ R+ + +P T+ + G+ N GKS+ N+I
Sbjct: 172 VQILSRLERVEKQR-------EQGRRARIKADVP-------TVSLVGYTNAGKSTLFNRI 217
Query: 259 TRADVDVQPYAFTT 272
T A V F T
Sbjct: 218 TEARVYAADQLFAT 231
>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 = 33.1 bits (76), Expect = 0.099
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 223 QVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKIT-RADVDVQP----YAFTTKSLYV 277
+R+ + L +ID + + G+P VGKSS +N + R P +T V
Sbjct: 85 ILRRTIKEL-AIDGKPVIVGVVGYPKVGKSSIINALKGRHSASTSPIPGSPGYTKGIQLV 143
Query: 278 GHTDYKYLRWQVIDTPGI 295
YL IDTPG+
Sbjct: 144 RIDSKIYL----IDTPGV 157
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 32.6 bits (75), Expect = 0.11
Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSL 300
++ G GK++ L ++ R + + SL K L +++ L L
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSL----GTPKDLLRKIL---RALGLPL 59
Query: 301 EDRNIIEM-QAVTALAHLRAAVLYFID 326
E+ +A+ R L ID
Sbjct: 60 SGGTTAELLEAILDALKRRGRPLLIID 86
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 33.6 bits (78), Expect = 0.14
Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 23/76 (30%)
Query: 206 RMATIMKRQASNLEYLEQVRQHLSR---------LPSIDPFTRTIIICGFPNVGKSSFLN 256
R+A + K LE+V + R +P T+ + G+ N GKS+ N
Sbjct: 162 RIAQLKKE-------LEKVEKQRERQRRRRKRADVP-------TVALVGYTNAGKSTLFN 207
Query: 257 KITRADVDVQPYAFTT 272
+T ADV F T
Sbjct: 208 ALTGADVYAADQLFAT 223
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 32.4 bits (75), Expect = 0.15
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYA-----FTTKSLYVGHTDYKYLRWQVIDTPG 294
I++ G VGK+S L + + F +K++ V K Q+ DT G
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKL---QIWDTAG 58
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 32.7 bits (75), Expect = 0.16
Identities = 25/77 (32%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 221 LEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKITRADV-DVQPYAFTTKS-LYVG 278
L Q + S I ++ G+PNVGKSS +N + V V P TK Y+
Sbjct: 90 LRQFAKLHSDKKQI-----SVGFIGYPNVGKSSVINTLRSKKVCKVAPIPGETKVWQYIT 144
Query: 279 HTDYKYLRWQVIDTPGI 295
YL ID PG+
Sbjct: 145 LMKRIYL----IDCPGV 157
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 33.4 bits (77), Expect = 0.17
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 206 RMATIMKRQASNLEYLEQVRQHL--SRLPSIDPFTRTIIICGFPNVGKSSFLNKITRADV 263
R+A + + LE +E+ R+ R S P + + G+ N GKS+ N +T ADV
Sbjct: 165 RIAKLKRE----LENVEKAREPRRKKRSRSGIP---LVALVGYTNAGKSTLFNALTGADV 217
Query: 264 DVQPYAFTT 272
V F T
Sbjct: 218 YVADQLFAT 226
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 33.4 bits (77), Expect = 0.17
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 229 SRLPSI-DPFTRTIIICGFPNVGKSSFLNKI 258
S SI D R I+ G P GKS+ + KI
Sbjct: 20 SLYDSIIDGANRIFILKGGPGTGKSTLMKKI 50
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 32.3 bits (75), Expect = 0.28
Identities = 23/62 (37%), Positives = 29/62 (46%), Gaps = 13/62 (20%)
Query: 244 CGF------PNVGKSSFLNKITRADVD-VQPYAFTTKSLYVG-HTDYKYLRWQVI--DTP 293
GF PNVGKS+ LN + + V P TT+ G T+ Q+I DTP
Sbjct: 5 SGFVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDA---QIIFVDTP 61
Query: 294 GI 295
GI
Sbjct: 62 GI 63
>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 = 31.9 bits (73), Expect = 0.36
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 9/66 (13%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGH---TDYKYLRWQ------V 289
+ + G NVGKS+ +N + +++ + L V T ++ +
Sbjct: 126 GDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKL 185
Query: 290 IDTPGI 295
DTPGI
Sbjct: 186 YDTPGI 191
>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 = 31.3 bits (72), Expect = 0.40
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 241 IIICGFPNVGKSSFLNKITR 260
+ G NVGKSS +N +T
Sbjct: 2 VAFAGRSNVGKSSLINALTN 21
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 32.3 bits (73), Expect = 0.52
Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 10/97 (10%)
Query: 141 KLDNIHPFYADLMNILYDKDHYKLGLGQLNQARHLIDNVAKDYLRLMKYADSLYRCKQLK 200
L P +L + +L + + AR +++ + + R
Sbjct: 377 GLGGAAP--ESAEELLELNNAARLTVDEYPAAREALESAGQRNVE------DRTRAVDEF 428
Query: 201 KAALGRMATIMKRQASNLEY-LEQVRQHLSRLPSIDP 236
KAA ++++ K SN+EY L QVR++L + + P
Sbjct: 429 KAADQELSSLSKGS-SNIEYRLLQVRENLCQDLGVSP 464
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 31.0 bits (71), Expect = 0.53
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 19/77 (24%)
Query: 240 TIIICGFPNVGKSSFLNKITRADV---DVQPYAFTTKSLYVGHTDYKYLRWQV------I 290
+ + G + GKS+ LN + +V V P TT + V LR+ + +
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLPTGVTP---TTAVITV-------LRYGLLKGVVLV 51
Query: 291 DTPGILDHSLEDRNIIE 307
DTPG+ I E
Sbjct: 52 DTPGLNSTIEHHTEITE 68
>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 = 31.4 bits (72), Expect = 0.63
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 237 FTRTIIICGFPNVGKSSFLN-----KITRADVDVQPYAFTTKSLYVGHTDYK------YL 285
F I++ G +GKS+F+N K+ + P TK++ + + + L
Sbjct: 3 FQFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKL 62
Query: 286 RWQVIDTPGILDH 298
+ VIDTPG D+
Sbjct: 63 KLTVIDTPGFGDN 75
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 31.5 bits (72), Expect = 0.68
Identities = 25/106 (23%), Positives = 38/106 (35%), Gaps = 30/106 (28%)
Query: 239 RTIIICGFPNVGKSSFLNKIT-RADVDVQPYAFTTKSLYVG-HTD-----YKYLR-WQVI 290
+ ++ G VGKS+ +N + + ++ L G HT + +I
Sbjct: 165 KITVLLGQSGVGKSTLINALLPELNQKTGE---ISEKLGRGRHTTTHVELFPLPGGGWII 221
Query: 291 DTPGILDHSLEDRNIIEMQAVTALAHLRAA--VLYFIDI---SEQC 331
DTPG SL LAHL V F + + QC
Sbjct: 222 DTPGF--RSLG------------LAHLEPEDLVQAFPEFAELARQC 253
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 30.2 bits (69), Expect = 0.80
Identities = 29/132 (21%), Positives = 45/132 (34%), Gaps = 42/132 (31%)
Query: 215 ASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKIT-RADVDVQPYA---- 269
A E +E+++ L +T ++ G VGKS+ LN + D+ +
Sbjct: 20 AKTGEGIEELKPLLK--------GKTSVLAGQSGVGKSTLLNALLPELDLRTGEISEKLG 71
Query: 270 ----FTTKS-LYVGHTDYKYLRWQVIDTPGILDHSLEDRNIIEMQAVTALAHLRAAVL-- 322
TT L+ +IDTPG + L HL L
Sbjct: 72 RGRHTTTHVELF--PLPGG---GLLIDTPGF--------RELG------LWHLDPEELAE 112
Query: 323 YFIDI---SEQC 331
YF + + QC
Sbjct: 113 YFPEFRELAGQC 124
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 31.1 bits (71), Expect = 0.86
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 243 ICGFPNVGKSSFLNKITRADVDVQPYAFTT 272
I G PNVGKS+ N + + V + + F T
Sbjct: 26 IVGLPNVGKSTTFNALCKQQVPAENFPFCT 55
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 29.7 bits (67), Expect = 0.88
Identities = 16/108 (14%), Positives = 36/108 (33%), Gaps = 6/108 (5%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILDHSL 300
+++ G GKSS L+++ + G T DT +
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFP------PEPLEIQGDTLAVDTLEVDGDTGLLNIWDF 55
Query: 301 EDRNIIEMQAVTALAHLRAAVLYFIDISEQCGHSIQEQIGLFKSIRPL 348
R ++ + + + A +L + + + + I ++R L
Sbjct: 56 GGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKL 103
>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 449
Score = 31.1 bits (70), Expect = 1.1
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 184 LRLMKYADSLYRCKQLK---KAALGRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRT 240
L LM C + +A R+ MKR S E+L+ V++ + +P + T
Sbjct: 251 LSLMAKNPRF--CPNIHLPLQAGNTRVLEEMKRSYSKEEFLDVVKEIRNIVPDVG--ITT 306
Query: 241 IIICGFPNVGKSSFLNKI 258
II GFPN + F + +
Sbjct: 307 DIIVGFPNETEEEFEDTL 324
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 29.7 bits (68), Expect = 1.6
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 248 NVGKSSFLNKIT 259
NVGKSS +N +T
Sbjct: 34 NVGKSSLINALT 45
>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 = 29.1 bits (66), Expect = 1.9
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 241 IIICGFPNVGKSSFLNKITRADVD-VQPYAFTTKSLYVGHTDYKYLRWQVID 291
I++ G GK++ L K+ +V P T V +YK +++ V D
Sbjct: 2 ILMLGLDGAGKTTILYKLKLGEVVTTIP----TIGFNVETVEYKNVKFTVWD 49
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 29.1 bits (66), Expect = 2.4
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDV 265
I+ G NVGKS+ + ++T V V
Sbjct: 11 EIVFVGRSNVGKSTLVRELTGKKVRV 36
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 29.2 bits (66), Expect = 2.5
Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 239 RTIIICGFPNVGKSSFLNK-ITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPGILD 297
T+++ G + GK++ K T + K + ++D PG
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVT-SIEPNVASFYSNSSKGKKLTLVDVPG--- 56
Query: 298 HSLEDRNIIEMQAVTALAHLRAAVLYFIDISEQ 330
H ++ ++ + L A+++ +D +
Sbjct: 57 H---EKLRDKL--LEYLKASLKAIVFVVDSATF 84
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 29.0 bits (65), Expect = 2.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 240 TIIICGFPNVGKSSF 254
I +CG P VGK+SF
Sbjct: 2 QIFLCGLPTVGKTSF 16
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 29.6 bits (67), Expect = 2.6
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 119 RKIKYTQSNFHERLSQIIQEFPKLDNIHPFYADLMNILY 157
KIK +QS++ E ++ +E K++ + L+++L
Sbjct: 135 EKIKASQSDYKELYEKLKEELKKINFNEESFNSLLSLLE 173
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 28.7 bits (65), Expect = 3.0
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 240 TIIICGFPNVGKSSFLNKITRADVDVQPYA 269
++ GF GK++ L + + + A
Sbjct: 2 VTVLTGFLGSGKTTLLEHLLEKNREGLKIA 31
>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 = 29.0 bits (66), Expect = 3.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 248 NVGKSSFLNKITR 260
NVGKSS +N +T
Sbjct: 28 NVGKSSLINALTN 40
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 29.6 bits (67), Expect = 3.4
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 14/72 (19%)
Query: 2 EEAALLKKAERERGVKR----------KLERHIEEEMQDD-YVLDLKKNYDLPDEYKYDV 50
EEA LKK E ER ++R + + + DD + D N+ L + +
Sbjct: 266 EEAERLKKLEAER-LRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEE 324
Query: 51 IPEFMEGVNIAD 62
E +GV+ D
Sbjct: 325 EEE--DGVDDED 334
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 28.7 bits (65), Expect = 3.5
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 241 IIICGFPNVGKSSFLNKITR 260
I G NVGKSS +N +T
Sbjct: 27 IAFAGRSNVGKSSLINALTN 46
>gnl|CDD|223694 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
ribosomal structure and biogenesis].
Length = 437
Score = 29.1 bits (66), Expect = 3.7
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 206 RMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFP 247
R+ MKR + EYLE + + + P D T II GFP
Sbjct: 268 RILKRMKRGYTVEEYLEIIEKLRAARP--DIAISTDIIVGFP 307
>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 = 28.8 bits (65), Expect = 3.7
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 11/69 (15%)
Query: 237 FTRTIIICGFPNVGKSSFLN-----KITRADVDVQPYAFTTKSLYVGHT------DYKYL 285
F T+++ G +GK++ +N + P K++ + T D L
Sbjct: 3 FDFTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKL 62
Query: 286 RWQVIDTPG 294
VIDTPG
Sbjct: 63 NLTVIDTPG 71
>gnl|CDD|215851 pfam00310, GATase_2, Glutamine amidotransferases class-II.
Length = 223
Score = 28.8 bits (65), Expect = 3.9
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 102 TVIHKQYKISRIRSFYMRKIKYTQSN--FHERLSQIIQEFPKLDNIHPFYAD 151
VI K+ + S + FY++ ++ + H R S FP +N HPF +
Sbjct: 62 FVIRKRGEKSIVAEFYLQDERFKSALAIVHTRFST--NGFPSWENAHPFRRE 111
>gnl|CDD|235338 PRK05082, PRK05082, N-acetylmannosamine kinase; Provisional.
Length = 291
Score = 28.7 bits (65), Expect = 4.6
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 220 YLEQVRQHLSRLPSI 234
YLE V+ +L++ P+I
Sbjct: 249 YLELVQAYLAQEPAI 263
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 28.4 bits (63), Expect = 4.9
Identities = 34/147 (23%), Positives = 60/147 (40%), Gaps = 58/147 (39%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYA-----FTTKSLYVGHTDYKYLRWQVIDTPG- 294
I++ G VGKS+ L++ TR + ++ + F T++L V + K ++ Q+ DT G
Sbjct: 15 IVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQV---EGKTVKAQIWDTAGQ 71
Query: 295 --------------------------------------ILDHSLEDRNIIEMQA--VTAL 314
+ DH+ D NI+ M A + L
Sbjct: 72 ERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHA--DSNIVIMMAGNKSDL 129
Query: 315 AHLRAAVLYFIDISEQCGHSIQEQIGL 341
HLR+ ++E+ G ++ E+ GL
Sbjct: 130 NHLRS-------VAEEDGQALAEKEGL 149
>gnl|CDD|240312 PTZ00202, PTZ00202, tuzin; Provisional.
Length = 550
Score = 29.0 bits (65), Expect = 5.2
Identities = 27/108 (25%), Positives = 40/108 (37%), Gaps = 21/108 (19%)
Query: 195 RCKQLKKAALGRMATIMKRQASNLEYLEQVRQHLSR----------LPSIDPF-TRTIII 243
R QLK A + R ++ +RQ +SR L +D R ++
Sbjct: 232 RSYQLKVAVSTLTQPLNPRPSTLQSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVF 291
Query: 244 CGFPNVGKSSFLNKITRAD------VDVQPYAFT----TKSLYVGHTD 281
GF GKSS R + VDV+ T K+L V + +
Sbjct: 292 TGFRGCGKSSLCRSAVRKEGMPAVFVDVRGTEDTLRSVVKALGVPNVE 339
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.4 bits (61), Expect = 5.4
Identities = 10/51 (19%), Positives = 19/51 (37%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVID 291
I+I G P GK++ ++ DV L + + + +D
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLD 51
>gnl|CDD|236154 PRK08119, PRK08119, flagellar motor switch protein; Validated.
Length = 382
Score = 28.7 bits (65), Expect = 5.4
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 59 NIADYIDPDIFK-MPMYNFKKIAVVPTAKEFVDIMLSKTQRKTPTV 103
I + ID +I + +P V AKE V I+L + + + V
Sbjct: 198 KIGELIDSEIMQLLP---------VDFAKELVAILLGEEEEEEEEV 234
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 28.3 bits (64), Expect = 5.5
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 14/67 (20%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFTTKSLYVGHT---DYKYLRWQ-----VI 290
I++ G GKS+ N I F +K G T W VI
Sbjct: 1 LRIVLVGKTGNGKSATGNSILGRKA------FESKLRAQGVTKTCQLVSRTWDGRIINVI 54
Query: 291 DTPGILD 297
DTPG+ D
Sbjct: 55 DTPGLFD 61
>gnl|CDD|222707 pfam14357, DUF4404, Domain of unknown function (DUF4404). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 90 amino acids in length.
There are two completely conserved residues (P and G)
that may be functionally important.
Length = 85
Score = 26.8 bits (60), Expect = 5.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 219 EYLEQVRQHLSRLPSIDPFTR 239
E LEQ+ + L + S+D TR
Sbjct: 4 ELLEQLHEELEQTDSLDEETR 24
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like
subfamily of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Neisseria
meningitides Nape and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity; for example, Neisseria meningitides Nape and
NExo. Nape, found in this subfamily, is the dominant AP
endonuclease. It exhibits strong AP endonuclease
activity, and also exhibits 3'-5'exonuclease and
3'-deoxyribose phosphodiesterase activities.
Length = 253
Score = 28.0 bits (63), Expect = 6.4
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 17/57 (29%)
Query: 213 RQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGF--------------PNVGKSSFL 255
RQ + + +L+ +HL L R I+CG N S FL
Sbjct: 118 RQEAKMAFLDAFLEHLKELRRKR---REFIVCGDFNIAHTEIDIKNWKANQKNSGFL 171
>gnl|CDD|184632 PRK14336, PRK14336, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 418
Score = 28.3 bits (63), Expect = 6.8
Identities = 29/114 (25%), Positives = 51/114 (44%), Gaps = 13/114 (11%)
Query: 147 PFYADLMNILYDKDHYKLGLGQLNQARHLIDNVAKDYLRLMKYADSLYR-CKQLK---KA 202
P ADL++ L+D GL ++ R L + +L+ L + C+ L +A
Sbjct: 191 PCLADLLSALHDIP----GLLRI---RFLTSHPKDISQKLIDAMAHLPKVCRSLSLPVQA 243
Query: 203 ALGRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLN 256
+ M+R +N +Y E V + + +P I +T +I GFP+ + F
Sbjct: 244 GDDTILAAMRRGYTNQQYRELVERLKTAMPDIS--LQTDLIVGFPSETEEQFNQ 295
>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 = 28.1 bits (63), Expect = 7.0
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 211 MKRQASNLEYLEQVRQHL---SRLPSIDPFTRTIIICGFPNVGKSSFLNKITR 260
RQ + LE+ + H+ R P P +++ G P VGKS+ + + +
Sbjct: 10 AARQFQRTQDLEEKKLHVPVVDRTPEEPPPL-VVVVVGPPGVGKSTLIRSLIK 61
>gnl|CDD|184624 PRK14327, PRK14327, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 509
Score = 28.1 bits (63), Expect = 7.8
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 210 IMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPN 248
IM R+ + YLE VR+ +P++ T T II GFPN
Sbjct: 339 IMARKYTRESYLELVRKIKEAIPNV-ALT-TDIIVGFPN 375
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 27.6 bits (62), Expect = 7.9
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 239 RTIIICGFPNVGKSSFLNKITRADVDVQPYAFT-----TKSLYVGHTDYKYLRWQVIDTP 293
R I + G +VGKSS + V+ Y T +K + +Y +++DT
Sbjct: 2 RKIAVLGSRSVGKSSLTVQFVEGHF-VESYYPTIENTFSKIITYKGQEYHL---EIVDTA 57
Query: 294 G 294
G
Sbjct: 58 G 58
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 28.1 bits (63), Expect = 8.0
Identities = 25/119 (21%), Positives = 40/119 (33%), Gaps = 29/119 (24%)
Query: 124 TQSNFHERLSQIIQEFPKL-------DNIHPFYADLMNILYDKDHYKLGL--GQLNQARH 174
TQ ER ++++ PKL I A++ L +L Q
Sbjct: 321 TQEELEERDKELLESLPKLALPAEHVKEIAAELAEIDKPATTDSEIPHRLSGSELTQLEV 380
Query: 175 LIDNVAKDYLRLMKYADSLYRCKQLKKAALGRMATIMKRQASNLEYLEQVRQHLSRLPS 233
LI V ++ Q K+ L +K E L +V + +S +PS
Sbjct: 381 LIQQVKRE--------------LQDAKSQL------LKELRELEEELAEVDKKISTIPS 419
>gnl|CDD|205495 pfam13315, DUF4085, Protein of unknown function (DUF4085). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 101 and 269 amino
acids in length.
Length = 208
Score = 27.5 bits (61), Expect = 8.4
Identities = 23/123 (18%), Positives = 44/123 (35%), Gaps = 3/123 (2%)
Query: 143 DNIHPFYADLMNILYDKDHYKLGLGQLNQARHLIDNVAKDYLRLMKYADSLYRCKQLKKA 202
+ I DL+ L H + G LN + + + K L D R +QL +
Sbjct: 46 EEIEEIKEDLLKFLPSSIHPYVHDGTLNS-EYPSEKLKKLVLEWS--QDYEKRFEQLDQE 102
Query: 203 ALGRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICGFPNVGKSSFLNKITRAD 262
+I K+ ++++ L H S + I+ ++ G S +K+
Sbjct: 103 YNEHFTSIAKKLPAHVKQLHNYSLHDSVILVIERRDEGTLVIVLDCSGGFSEFDKLIITF 162
Query: 263 VDV 265
+
Sbjct: 163 AGI 165
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.0 bits (60), Expect = 8.5
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 16/60 (26%)
Query: 239 RTIIICGFPNVGKSSF----LNKITRADVDVQPYAFTTKSLYVGHTDYKYLRWQVIDTPG 294
+++ G + GK++ LN + R V K L G + ID PG
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVV----KHLDHGQGE--------IDKPG 48
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 27.1 bits (61), Expect = 8.6
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
Query: 241 IIICGFPNVGKSSFLNKITRADVDVQPYA-----FTTKSLYVGHTDYKYLRWQVIDTPG 294
I++ G VGKS+ L++ TR + ++ + F T+++ + D K ++ Q+ DT G
Sbjct: 6 IVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQI---DGKTIKAQIWDTAG 61
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 27.7 bits (62), Expect = 8.8
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 187 MKYADSLY-RCKQLKKAALGRMATIMKRQASNLEYLEQVRQHLSRLPSIDPFTRTIIICG 245
D L R + AL R T++ ++ ++ R+ L L I I G
Sbjct: 1 EATVDELIERLLAGDRRALARAITLV--ESRRPDHRALARELLRALYPRTGNAHVIGITG 58
Query: 246 FPNVGKSSFLNKITR 260
P GKS+ + + R
Sbjct: 59 VPGAGKSTLIEALGR 73
>gnl|CDD|143493 cd06819, PLPDE_III_LS_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Low Specificity D-Threonine
Aldolase. Low specificity D-threonine aldolase (Low
specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene
from Arthrobacter sp. strain DK-38, is the prototype of
this subfamily. Low specificity D-TAs are fold type III
PLP-dependent enzymes that catalyze the interconversion
between D-threonine/D-allo-threonine and glycine plus
acetaldehyde. Both PLP and divalent cations (eg. Mn2+)
are required for catalytic activity. Members of this
subfamily show similarity to bacterial alanine racemase
(AR), which contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
AR exists as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Based on its similarity to AR, it is possible
that low specificity D-TAs also form dimers in solution.
Experimental data show that the monomeric form of low
specificity D-TAs exhibit full catalytic activity.
Length = 358
Score = 28.0 bits (63), Expect = 9.1
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 290 IDTPG-ILDHSLEDRNIIEMQAVTALAHLR 318
IDTP +LD +RNI M A +R
Sbjct: 5 IDTPALVLDLDALERNIKRMAAFAKAHGVR 34
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 27.4 bits (61), Expect = 9.1
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 228 LSRLPSIDPFTRT---IIICGFPNVGKSSFLNKITRADV-DVQPYA-FTTKSLYVGHTDY 282
LS L + P +R I++ G N GK++ L ++ D+ + P F K+ V +
Sbjct: 2 LSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKN--VQADGF 59
Query: 283 KYLRWQV 289
K W +
Sbjct: 60 KLNVWDI 66
>gnl|CDD|192726 pfam11232, Med25, Mediator complex subunit 25 PTOV activation and
synapsin 2. Mediator is a large complex of up to 33
proteins that is conserved from plants to fungi to
humans - the number and representation of individual
subunits varying with species. It is arranged into four
different sections, a core, a head, a tail and a
kinase-active part, and the number of subunits within
each of these is what varies with species. Overall,
Mediator regulates the transcriptional activity of RNA
polymerase II but it would appear that each of the four
different sections has a slightly different function.
The overall function of the full-length Med25 is
efficiently to coordinate the transcriptional activation
of RAR/RXR (retinoic acid receptor/retinoic X receptor)
in higher eukaryotic cells. Human Med25 consists of
several domains with different binding properties, the
N-terminal, VWA domain, an SD1 - synapsin 1 - domain
from residues 229-381, a PTOV(B) or ACID domain from
395-545, an SD2 domain from residues 564-645 and a
C-terminal NR box-containing domain (646-650) from
646-747. This family is the combined PTOV and SD2
domains. the PTOV domain being the domain through which
Med25 co-operates with the histone acetyltransferase
CBP, but the function of the SD2 domain is unclear.
Length = 151
Score = 27.0 bits (60), Expect = 9.7
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 111 SRIRSFYMRKIKYTQSNFHERLSQIIQE 138
S + ++ I QSNF R+ ++IQ
Sbjct: 120 SSKKKAFLGLIPNDQSNFVNRIREVIQN 147
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
0.323 0.139 0.402
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,973,644
Number of extensions: 1897027
Number of successful extensions: 2200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2162
Number of HSP's successfully gapped: 147
Length of query: 358
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 260
Effective length of database: 6,590,910
Effective search space: 1713636600
Effective search space used: 1713636600
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: 60 (27.3 bits)