RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4669
(139 letters)
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 116 bits (292), Expect = 5e-31
Identities = 43/137 (31%), Positives = 65/137 (47%), Gaps = 39/137 (28%)
Query: 1 MTLKDLAKSMGVDCDHLYEVMMYVDNSVNYDRPSSVIYDFQVIIDIIQKSGMKYMVINPT 60
+T+ +LA+ M V + + ++I+K ++
Sbjct: 182 ITVAELAEKMAV-------------------KAA----------EVIKKLFKLGVMATIN 212
Query: 61 NSVADDS-------NGKDVERRPPAD---PSVLMKRPPVVTIMGHVDHGKTTLLDTLRNT 110
S+ ++ G +V+ + L+ RPPVVTIMGHVDHGKT+LLD +R T
Sbjct: 213 QSLDQETAELLAEEFGHEVKLVSLLEDDDEEDLVPRPPVVTIMGHVDHGKTSLLDAIRKT 272
Query: 111 SVVKSEFGGITQHIGAF 127
+V E GGITQHIGA+
Sbjct: 273 NVAAGEAGGITQHIGAY 289
>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 = 97.5 bits (244), Expect = 8e-27
Identities = 30/40 (75%), Positives = 34/40 (85%)
Query: 88 PVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAF 127
PVVT+MGHVDHGKTTLLD +R T+V E GGITQHIGA+
Sbjct: 1 PVVTVMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAY 40
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 97.6 bits (244), Expect = 1e-24
Identities = 33/42 (78%), Positives = 36/42 (85%)
Query: 86 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAF 127
RPPVVTIMGHVDHGKTTLLD +R T+V E GGITQHIGA+
Sbjct: 4 RPPVVTIMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAY 45
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 92.5 bits (230), Expect = 7e-23
Identities = 33/47 (70%), Positives = 41/47 (87%)
Query: 81 SVLMKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAF 127
+L++RPPVVTIMGHVDHGKT+LLD++R T V + E GGITQHIGA+
Sbjct: 81 DLLVERPPVVTIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAY 127
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 86.8 bits (215), Expect = 7e-21
Identities = 40/104 (38%), Positives = 55/104 (52%), Gaps = 14/104 (13%)
Query: 24 VDNSVNYDRPSSVIYDFQVIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVL 83
V+ ++ S V DF + I +K+ + N N+ A N
Sbjct: 195 VNQIIDISIISQVADDFGINIISEEKNNINEKTSNLDNTSAFTEN--------------S 240
Query: 84 MKRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGAF 127
+ RPP+VTI+GHVDHGKTTLLD +R T + + E GGITQ IGA+
Sbjct: 241 INRPPIVTILGHVDHGKTTLLDKIRKTQIAQKEAGGITQKIGAY 284
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 84.8 bits (211), Expect = 4e-20
Identities = 28/41 (68%), Positives = 33/41 (80%)
Query: 86 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGA 126
R P+V ++GHVDHGKTTLLD +R T+V E GGITQHIGA
Sbjct: 5 RQPIVVVLGHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGA 45
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 74.1 bits (182), Expect = 2e-16
Identities = 28/41 (68%), Positives = 35/41 (85%)
Query: 86 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGITQHIGA 126
R P+V+++GHVDHGKTTLLD +R ++V K E GGITQHIGA
Sbjct: 3 RSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGA 43
>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 = 52.9 bits (128), Expect = 2e-09
Identities = 22/70 (31%), Positives = 28/70 (40%), Gaps = 18/70 (25%)
Query: 85 KRPPVVTIMGHVDHGKTTLLDTLRNTSVVKSE----------------FGGITQHIGA-- 126
KR + I+GHVDHGKTTL D L + S+ GIT I A
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 127 FVGFLYHLAL 136
F + +
Sbjct: 61 FETKKRLINI 70
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 46.8 bits (111), Expect = 7e-07
Identities = 19/26 (73%), Positives = 20/26 (76%)
Query: 101 TTLLDTLRNTSVVKSEFGGITQHIGA 126
TTLLD +R T V K E GGITQHIGA
Sbjct: 475 TTLLDKIRKTRVAKKEAGGITQHIGA 500
Score = 34.9 bits (80), Expect = 0.008
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 86 RPPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFGGIT 121
R P+V ++GHVDHGK L + V+ E G IT
Sbjct: 9 RCPIVAVLGHVDHGKCLLPE----EKVILPEHGLIT 40
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 38.8 bits (91), Expect = 2e-04
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
V ++GHVDHGKTTL +L
Sbjct: 2 VGVIGHVDHGKTTLTGSL 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 = 38.9 bits (91), Expect = 2e-04
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 87 PPVVTIMGHVDHGKTTLLDTLRNTSVVKSEFG-GITQHIGA 126
+ I+G + GK+TLL+ L + +E+ G T++
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVT 41
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 37.2 bits (87), Expect = 8e-04
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
+ I+ HVDHGKTTL+D L
Sbjct: 5 IAIIAHVDHGKTTLVDAL 22
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 37.6 bits (88), Expect = 0.001
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
+ I+ H+D GKTTL + +
Sbjct: 13 IGIVAHIDAGKTTLTERI 30
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 36.4 bits (85), Expect = 0.002
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
+ I+ HVDHGKTTL D+L
Sbjct: 3 ICIIAHVDHGKTTLSDSL 20
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 36.4 bits (85), Expect = 0.003
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
+ I+ HVDHGKTTL+D L
Sbjct: 8 IAIIAHVDHGKTTLVDAL 25
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 36.0 bits (84), Expect = 0.003
Identities = 14/22 (63%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 84 MKRPPVVTI--MGHVDHGKTTL 103
K P V I +GHVDHGKTTL
Sbjct: 4 EKVQPEVNIGMVGHVDHGKTTL 25
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 35.6 bits (83), Expect = 0.005
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 83 LMKRPPVVTIMG---HVDHGKTTLLDTL 107
LMK P + +G H+DHGKTTL D L
Sbjct: 13 LMKNPEQIRNIGIIAHIDHGKTTLSDNL 40
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 35.7 bits (83), Expect = 0.005
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
+ I+ HVDHGKTTL+D L
Sbjct: 4 IAIIAHVDHGKTTLVDAL 21
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 34.1 bits (79), Expect = 0.008
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 94 GHVDHGKTTLLDTL 107
GH+DHGKTTL+ L
Sbjct: 6 GHIDHGKTTLIKAL 19
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 34.6 bits (80), Expect = 0.011
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 94 GHVDHGKTTLLDTL 107
GHVDHGKTTLL +
Sbjct: 7 GHVDHGKTTLLQAI 20
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 34.0 bits (79), Expect = 0.016
Identities = 12/13 (92%), Positives = 12/13 (92%), Gaps = 1/13 (7%)
Query: 91 TIMGHVDHGKTTL 103
TI GHVDHGKTTL
Sbjct: 17 TI-GHVDHGKTTL 28
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 34.1 bits (78), Expect = 0.017
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 89 VVTIMGHVDHGKTTLLDTLRNTS 111
++ GHVDHGKTTLL L +
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIA 24
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 33.8 bits (78), Expect = 0.019
Identities = 13/15 (86%), Positives = 13/15 (86%), Gaps = 1/15 (6%)
Query: 89 VVTIMGHVDHGKTTL 103
V TI GHVDHGKTTL
Sbjct: 15 VGTI-GHVDHGKTTL 28
>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 = 33.1 bits (76), Expect = 0.023
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 90 VTIMGHVDHGKTTL---LDTLRNTSVV----KSEFGGITQHIGAFVGFL 131
V ++GHVD GKT+L L + +T+ +S+ GIT +G F F
Sbjct: 3 VGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLG-FSSFE 50
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 33.3 bits (77), Expect = 0.023
Identities = 12/13 (92%), Positives = 12/13 (92%), Gaps = 1/13 (7%)
Query: 91 TIMGHVDHGKTTL 103
TI GHVDHGKTTL
Sbjct: 7 TI-GHVDHGKTTL 18
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 33.3 bits (77), Expect = 0.027
Identities = 18/31 (58%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 89 VVTIMGHVDHGKTTLLDTLRNTSVVKSEFGG 119
V TI GHVDHGKTTL T T V+ + GG
Sbjct: 15 VGTI-GHVDHGKTTL--TAAITKVLAKKGGG 42
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 33.4 bits (77), Expect = 0.027
Identities = 13/18 (72%), Positives = 14/18 (77%), Gaps = 2/18 (11%)
Query: 88 PVVTI--MGHVDHGKTTL 103
P V I +GHVDHGKTTL
Sbjct: 11 PHVNIGTIGHVDHGKTTL 28
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 32.7 bits (75), Expect = 0.047
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 84 MKRPPVVTI--MGHVDHGKTTLL 104
P + + +GHVD GK+TL+
Sbjct: 2 ASEKPHLNLVFIGHVDAGKSTLV 24
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 32.3 bits (74), Expect = 0.051
Identities = 15/24 (62%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 86 RPPVVTI--MGHVDHGKTTLLDTL 107
R P V I +GHVDHGKTTL L
Sbjct: 1 RQPEVNIGMVGHVDHGKTTLTKAL 24
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 32.2 bits (74), Expect = 0.054
Identities = 12/13 (92%), Positives = 12/13 (92%), Gaps = 1/13 (7%)
Query: 91 TIMGHVDHGKTTL 103
TI GHVDHGKTTL
Sbjct: 17 TI-GHVDHGKTTL 28
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 32.4 bits (74), Expect = 0.068
Identities = 10/18 (55%), Positives = 16/18 (88%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
++++ HVDHGK+TL D+L
Sbjct: 22 MSVIAHVDHGKSTLTDSL 39
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 32.3 bits (74), Expect = 0.071
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 91 TIMGHVDHGKTTLLDTL 107
+++ HVDHGK+TL D+L
Sbjct: 23 SVIAHVDHGKSTLTDSL 39
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 31.7 bits (73), Expect = 0.073
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 92 IMGHVDHGKTTLLDTL 107
I+ H+DHGK+TL D L
Sbjct: 5 IIAHIDHGKSTLADRL 20
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 32.1 bits (73), Expect = 0.077
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
V + GHVDHGK+TL+ L
Sbjct: 120 VGVAGHVDHGKSTLVGVL 137
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 31.5 bits (72), Expect = 0.091
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 94 GHVDHGKTTLLDTLRNTSVV--KSEFG-GITQHIG 125
GHV HGKTTL+ L V K E IT +G
Sbjct: 7 GHVAHGKTTLVKALSGVWTVRHKEELKRNITIKLG 41
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 31.6 bits (72), Expect = 0.11
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 89 VVTIMGHVDHGKTTLLDTLRNT 110
++ GH+DHGKTTLL L
Sbjct: 2 IIGTAGHIDHGKTTLLKALTGG 23
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 31.1 bits (71), Expect = 0.12
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
V I GH+ HGKT+LLD L
Sbjct: 3 VCIAGHLHHGKTSLLDML 20
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 30.8 bits (70), Expect = 0.17
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 88 PVVTI--MGHVDHGKTTLLDTLRNTSVVK 114
P V I +GHVDHGKTTL L +
Sbjct: 9 PEVNIGMVGHVDHGKTTLTKALSGVWTDR 37
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 31.2 bits (70), Expect = 0.18
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 90 VTIMGHVDHGKTTLLDTLRNTS 111
+ I+ HVDHGKTTL+D L S
Sbjct: 8 IAIIAHVDHGKTTLVDKLLQQS 29
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 31.0 bits (70), Expect = 0.19
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 83 LMKRPPVVT---IMGHVDHGKTTLLDTL 107
LM +P + I+ H+DHGKTTL D L
Sbjct: 12 LMWKPKFIRNIGIVAHIDHGKTTLSDNL 39
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 30.6 bits (69), Expect = 0.25
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 46 IIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLM-----KRPPV-VTIMGHVDHG 99
++ S Y + S +R+ P+ M +P V V +GHVDHG
Sbjct: 14 LLPFSSQIYCACRGSAPSTSASISAADDRQSPSPWWRSMATFTRTKPHVNVGTIGHVDHG 73
Query: 100 KTTL 103
KTTL
Sbjct: 74 KTTL 77
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 30.5 bits (69), Expect = 0.26
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 90 VTIMGHVDHGKTTLLDTLRNTSVVKSEFGG 119
+ +GHVDHGKTTL T T+V+ E G
Sbjct: 15 IGTIGHVDHGKTTL--TAAITTVLAKEGGA 42
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 30.3 bits (69), Expect = 0.33
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 90 VTIMGHVDHGKTTLL 104
+ I+ H+D GKTTL
Sbjct: 11 IGILAHIDAGKTTLT 25
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 30.0 bits (68), Expect = 0.35
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 92 IMGHVDHGKTTLLDTL 107
I+ H+DHGK+TL D L
Sbjct: 8 IIAHIDHGKSTLADRL 23
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 30.2 bits (69), Expect = 0.35
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 92 IMGHVDHGKTTLLDTL 107
I+ H+DHGK+TL D L
Sbjct: 14 IIAHIDHGKSTLADRL 29
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 29.9 bits (68), Expect = 0.43
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 90 VTIMGHVDHGKTTL 103
+ ++GHVDHGK+TL
Sbjct: 9 LAVIGHVDHGKSTL 22
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 29.6 bits (68), Expect = 0.45
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 92 IMGHVDHGKTTLLDTL 107
I+ H+DHGK+TL D L
Sbjct: 12 IIAHIDHGKSTLADRL 27
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 29.6 bits (66), Expect = 0.51
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 85 KRPPV-VTIMGHVDHGKTTLLDTL 107
K+P V + +GHVDHGKTTL L
Sbjct: 78 KKPHVNIGTIGHVDHGKTTLTAAL 101
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 29.0 bits (66), Expect = 0.65
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 92 IMGHVDHGKTTL 103
++GHVD GK+TL
Sbjct: 4 VIGHVDAGKSTL 15
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 28.9 bits (65), Expect = 0.88
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 85 KRPPVVTIMGHVDHGKTTLLDTLRNTSV 112
+ VV ++G VD GK+TL L N +
Sbjct: 71 GKVGVVMVVGPVDSGKSTLTTYLANKLL 98
>gnl|CDD|234199 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 230
Score = 28.6 bits (65), Expect = 0.97
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 89 VVTIMGHVDHGKTTLLDTL 107
V ++G GKTTLL TL
Sbjct: 28 VTCVLGRNGVGKTTLLKTL 46
>gnl|CDD|214829 smart00812, Alpha_L_fucos, Alpha-L-fucosidase. O-Glycosyl
hydrolases (EC 3.2.1.-) are a widespread group of
enzymes that hydrolyse the glycosidic bond between two
or more carbohydrates, or between a carbohydrate and a
non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has
led to the definition of 85 different families. This
classification is available on the CAZy
(CArbohydrate-Active EnZymes) web site. Because the fold
of proteins is better conserved than their sequences,
some of the families can be grouped in 'clans'. Family
29 encompasses alpha-L-fucosidases, which is a lysosomal
enzyme responsible for hydrolyzing the alpha-1,6-linked
fucose joined to the reducing-end N-acetylglucosamine of
the carbohydrate moieties of glycoproteins. Deficiency
of alpha-L-fucosidase results in the lysosomal storage
disease fucosidosis.
Length = 384
Score = 28.8 bits (65), Expect = 1.0
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 38 YDFQVIIDIIQKSGMKYMVI 57
+D + D+ +K+G KY+V+
Sbjct: 81 FDPEEWADLFKKAGAKYVVL 100
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.2 bits (63), Expect = 1.6
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 86 RPPVVT-IMGHVDHGKTTLLDTL 107
+P +T +MG GKTTLL+ L
Sbjct: 787 KPGTLTALMGASGAGKTTLLNVL 809
>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 = 27.4 bits (61), Expect = 2.1
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 92 IMGHVDHGKTTLLDTLRNTSV-VKSEFGGITQHI 124
++G GK++LL+ L V S+ G T+
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDP 35
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 27.5 bits (61), Expect = 2.7
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
V +GHVDHGK+T + L
Sbjct: 10 VAFIGHVDHGKSTTVGHL 27
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 27.1 bits (61), Expect = 2.7
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 94 GHVDHGKTTL 103
G VD GK+TL
Sbjct: 6 GSVDDGKSTL 15
>gnl|CDD|165509 PHA03250, PHA03250, UL35; Provisional.
Length = 564
Score = 27.4 bits (61), Expect = 2.8
Identities = 13/45 (28%), Positives = 16/45 (35%), Gaps = 8/45 (17%)
Query: 52 MKYMVINPTNSVADDSNG--------KDVERRPPADPSVLMKRPP 88
M Y+ P D DV RRP S ++RPP
Sbjct: 457 MAYLEATPAPLGTDTEPDGEPEADLFADVSRRPARPSSKDLERPP 501
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 27.3 bits (61), Expect = 2.9
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 90 VTIMGHVDHGKTTLLDTL 107
V ++G+VD GK+TLL L
Sbjct: 2 VAVVGNVDAGKSTLLGVL 19
>gnl|CDD|147203 pfam04914, DltD_C, DltD C-terminal region. DltD is and integral
membrane protein involved in the biosynthesis of
D-alanyl-lipoteichoic acid. This is important in
controlling the net ionic charge in lipoteichoic acid
(LTA). This family is found in bacteria of the
Bacillus/Clostridium group. DltD binds Dcp and ligates
it with D-alanine. DltD does not ligate acyl carrier
protein (ACP) with D-alanine. It also has thioesterase
activity for mischarged D-alanyl-acyl carrier protein
(ACP). DltD is thought to be responsible for
discriminating between Dcp involved in the
D-alanylation of LTA, and ACP involved in fatty acid
biosynthesis. This family consists of the C-terminal
region of DltD.
Length = 130
Score = 26.4 bits (59), Expect = 3.7
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 29 NYDRPSSVIY-DFQVIIDIIQKSGMKYM-VINPTNSVADDSNGKDVERR 75
N S Y D Q+++D K+G + VI P N D G E R
Sbjct: 26 NESYTESPEYNDLQLVLDQFAKAGADVLFVIPPVNGKWYDYTGLSKEMR 74
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 26.7 bits (60), Expect = 3.7
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 92 IMGHVDHGKTTL 103
I+ H+D GKTT
Sbjct: 4 IIAHIDAGKTTT 15
>gnl|CDD|221281 pfam11871, DUF3391, Domain of unknown function (DUF3391). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is typically
between 122 to 139 amino acids in length. This domain
is found associated with pfam01966.
Length = 127
Score = 26.5 bits (59), Expect = 3.7
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 10/88 (11%)
Query: 12 VDCDHLYEVMMYV---DNSVNYDRP----SSVIYDFQVIIDIIQKSGMKYMVINPTNSVA 64
+ L +V MYV D S + P +I + I+ ++KSG+KY+ I+ + S+
Sbjct: 5 IPVSQL-QVGMYVSLLDRSWL-EHPFLRNRFLIKS-EADIERLRKSGVKYVWIDTSKSLD 61
Query: 65 DDSNGKDVERRPPADPSVLMKRPPVVTI 92
VE + V+
Sbjct: 62 VPELKPPVEADAELEAEPPAPVKKKVSF 89
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 26.4 bits (59), Expect = 4.2
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 99 GKTTLLDTL--RNTSVVKSEFG 118
GKTTLL+ L R VV E+G
Sbjct: 11 GKTTLLEALAARGYPVVP-EYG 31
>gnl|CDD|99984 cd03813, GT1_like_3, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria, while some of them are also found in
Archaea and eukaryotes.
Length = 475
Score = 26.8 bits (60), Expect = 4.4
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 68 NGKDVERRPPADPSVLMKRPPVVTIMGHVD 97
NG D ER PA + K PPVV ++G V
Sbjct: 274 NGIDPERFAPARRARPEKEPPVVGLIGRVV 303
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 26.4 bits (59), Expect = 4.9
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 92 IMGHVDHGKTTL 103
I+ HVD GKTTL
Sbjct: 4 ILAHVDAGKTTL 15
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 26.7 bits (59), Expect = 5.0
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 86 RPPVVT-IMGHVDHGKTTLLDTL 107
RP V+T +MG GKTTL+D L
Sbjct: 904 RPGVLTALMGVSGAGKTTLMDVL 926
>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 = 26.3 bits (59), Expect = 5.1
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 42 VIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKT 101
+ I+ + G+K +I + + N K + L+ RP I+G + GK+
Sbjct: 81 LAINAKKGKGVK-KIIKAAKKLLKEKNEKLKAKG-------LLNRPIRAMIVGIPNVGKS 132
Query: 102 TLLDTLRNTSVVKSE 116
TL++ L V K
Sbjct: 133 TLINRLAGKKVAKVG 147
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 26.6 bits (60), Expect = 5.2
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 92 IMGHVDHGKTT 102
IM H+D GKTT
Sbjct: 15 IMAHIDAGKTT 25
>gnl|CDD|112335 pfam03512, Glyco_hydro_52, Glycosyl hydrolase family 52.
Length = 428
Score = 26.4 bits (58), Expect = 5.5
Identities = 9/48 (18%), Positives = 20/48 (41%)
Query: 36 VIYDFQVIIDIIQKSGMKYMVINPTNSVADDSNGKDVERRPPADPSVL 83
++ +F D + + + + +P V D + E + P+VL
Sbjct: 83 IVREFGAATDTWKAGDLTFRIYSPVEGVPDPETADEEELKFALVPAVL 130
>gnl|CDD|234465 TIGR04092, LTA_DltD, D-alanyl-lipoteichoic acid biosynthesis
protein DltD. Members of this protein family are DltD,
part of the DltABCD system widely distributed in the
Firmicutes for D-alanylation of lipoteichoic acids. The
most common form of LTA, as in Staphylococcus aureus,
has a backbone of polyglycerolphosphate.
Length = 383
Score = 26.4 bits (59), Expect = 5.8
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 29 NYDRPSSVIY-DFQVIIDIIQKSGMKYMVIN-PTN 61
N+D S Y DFQ+++DI ++ G+ + + P N
Sbjct: 282 NFDYLKSPEYGDFQLVLDIFKELGIDVLFVIPPVN 316
>gnl|CDD|213199 cd03232, ABCG_PDR_domain2, Second domain of the pleiotropic drug
resistance-like (PDR) subfamily G of ATP-binding
cassette transporters. The pleiotropic drug resistance
(PDR) is a well-described phenomenon occurring in fungi
and shares several similarities with processes in
bacteria and higher eukaryotes. This PDR subfamily
represents domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 192
Score = 26.1 bits (58), Expect = 5.8
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 86 RPPVVT-IMGHVDHGKTTLLDTL---RNTSVVKSE 116
+P +T +MG GKTTLLD L + V+ E
Sbjct: 31 KPGTLTALMGESGAGKTTLLDVLAGRKTAGVITGE 65
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The conserved
ATP-binding motifs common to Rad50 and the ABC
transporter family include the Walker A and Walker B
motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known as
the ABC signature sequence.
Length = 204
Score = 26.0 bits (58), Expect = 5.8
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 75 RPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTLR 108
R + S + P+ I+G GKTT+++ L+
Sbjct: 10 RSFHERSEIEFFSPLTLIVGQNGAGKTTIIEALK 43
>gnl|CDD|213201 cd03234, ABCG_White, White pigment protein homolog of ABCG
transporter subfamily. The White subfamily represents
ABC transporters homologous to the Drosophila white
gene, which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the cells
of red pigments, which are synthesized from guanine, and
brown pigments, which are synthesized from tryptophan.
The pigment precursors are encoded by the white, brown,
and scarlet genes, respectively. Evidence from genetic
and biochemical studies suggest that the White and Brown
proteins function as heterodimers to import guanine,
while the White and Scarlet proteins function to import
tryptophan. However, a recent study also suggests that
White may be involved in the transport of a metabolite,
such as 3-hydroxykynurenine, across intracellular
membranes. Mammalian ABC transporters belonging to the
White subfamily (ABCG1, ABCG5, and ABCG8) have been
shown to be involved in the regulation of
lipid-trafficking mechanisms in macrophages,
hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8),
the human homolog of the Drosophila white gene is
induced in monocyte-derived macrophages during
cholesterol influx mediated by acetylated low-density
lipoprotein. It is possible that human ABCG1 forms
heterodimers with several heterologous partners.
Length = 226
Score = 26.1 bits (58), Expect = 6.5
Identities = 15/49 (30%), Positives = 23/49 (46%)
Query: 59 PTNSVADDSNGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTL 107
P V + + R D S+ ++ V+ I+G GKTTLLD +
Sbjct: 5 PWWDVGLKAKNWNKYARILNDVSLHVESGQVMAILGSSGSGKTTLLDAI 53
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 26.1 bits (58), Expect = 6.6
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 55 MVINPTNSVADDSNGKDVERRPPADPSVLMKRPPVVTI--MGHVDHGKTTLLDTLR--NT 110
++ D + D+++ P P V + R + I +GHV HGK+T++ L T
Sbjct: 1 VIDTDDGLAKQDLSKLDLDKLTPLTPEV-ISRQATINIGTIGHVAHGKSTVVKALSGVKT 59
Query: 111 SVVKSEF-GGITQHIG 125
K E IT +G
Sbjct: 60 VRFKREKVRNITIKLG 75
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 26.2 bits (59), Expect = 6.7
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 93 MGHVDHGKTTLLDTL 107
+GH GKTTL + +
Sbjct: 1 VGHSGAGKTTLTEAI 15
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 25.9 bits (57), Expect = 6.9
Identities = 9/22 (40%), Positives = 9/22 (40%)
Query: 86 RPPVVTIMGHVDHGKTTLLDTL 107
V I G GKTTL L
Sbjct: 14 GMITVLIDGRSGSGKTTLAGAL 35
>gnl|CDD|180717 PRK06833, PRK06833, L-fuculose phosphate aldolase; Provisional.
Length = 214
Score = 25.9 bits (57), Expect = 7.4
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 37 IYDFQVIIDIIQKSGMKYMVINPTNSVADDSNGKDVE 73
I++ + + I SG+ Y I P + V D +GK VE
Sbjct: 32 IFNREQGLMAITPSGIDYFEIKPEDIVIMDLDGKVVE 68
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 26.3 bits (59), Expect = 7.6
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 92 IMGHVDHGKTT 102
IM H+D GKTT
Sbjct: 13 IMAHIDAGKTT 23
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 25.9 bits (57), Expect = 8.1
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 71 DVER-RPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTL 107
D+E+ R D + PP++ ++G+ GKTTLL+ L
Sbjct: 189 DLEQLRAIPDGTTTG-APPLLGVVGYSGTGKTTLLEKL 225
>gnl|CDD|150568 pfam09910, DUF2139, Uncharacterized protein conserved in archaea
(DUF2139). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 339
Score = 25.9 bits (57), Expect = 8.1
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 4/40 (10%)
Query: 56 VINPTNSVADDSNGKDVERRPPADPSVLMK-RPPVVTIMG 94
PT+ + + PSVL+ PP+V I+G
Sbjct: 273 TYRPTDE--LEEIYQRFTNTIVG-PSVLVYIAPPLVKIVG 309
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 25.9 bits (58), Expect = 8.3
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 10/39 (25%)
Query: 1 MTLKDLAKSMGVDCDH----------LYEVMMYVDNSVN 29
+ + DLAK+M D + LYE ++ D SV
Sbjct: 230 VKIVDLAKAMIGDIEIKITGLRPGEKLYEELLIEDESVT 268
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 25.7 bits (57), Expect = 9.1
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 68 NGKDVERRPPADPSVLMKRPPVVTIMGHVDHGKTTLLDTL 107
G +E+R S+ + VT++G GK+TLL+ +
Sbjct: 13 KGTPLEKRALNGLSLEIAEGDFVTVIGSNGAGKSTLLNAI 52
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.137 0.401
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,088,890
Number of extensions: 630455
Number of successful extensions: 814
Number of sequences better than 10.0: 1
Number of HSP's gapped: 813
Number of HSP's successfully gapped: 110
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.5 bits)