RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11837
(192 letters)
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 105 bits (265), Expect = 1e-26
Identities = 41/97 (42%), Positives = 66/97 (68%), Gaps = 4/97 (4%)
Query: 30 ASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIA 85
ASMALKE AG ++LEP M +E+++ E+Y+ ++ DL+RRR I+ +E RG ++++ A
Sbjct: 583 ASMALKEAAKKAGPVILEPIMKVEVVTPEEYMGDVIGDLNRRRGQIQGMEARGGAQIVKA 642
Query: 86 EAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQ 122
PLSE+ GY +R+ + GR+ FSMEF +++V
Sbjct: 643 FVPLSEMFGYATDLRSATQGRATFSMEFDHYEEVPKN 679
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 102 bits (257), Expect = 1e-25
Identities = 46/107 (42%), Positives = 71/107 (66%), Gaps = 7/107 (6%)
Query: 26 IATGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
IA SMA KE A +LLEP M +E+++ E+Y+ ++ DL+ RR I +EDRG +K
Sbjct: 584 IA--GSMAFKEAAKKANPVLLEPIMKVEVVTPEEYMGDVIGDLNSRRGQIEGMEDRGGAK 641
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
VI AE PLSE+ GY +R+++ GR+ +SMEF +++V +N A+ +
Sbjct: 642 VIRAEVPLSEMFGYATDLRSMTQGRATYSMEFDHYEEV-PKNVAEEI 687
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 99.0 bits (248), Expect = 2e-24
Identities = 42/105 (40%), Positives = 62/105 (59%), Gaps = 5/105 (4%)
Query: 28 TGASMALKE----AGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVI 83
A +A +E A +LLEP M +E+ E++V ++ DLS RR I +E RG V+
Sbjct: 563 IAARLAFREALPKAKPVLLEPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGGDVV 622
Query: 84 IAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 128
AE PL+E+ GY +R+L+ GR FSMEF +++V N A+ V
Sbjct: 623 RAEVPLAEMFGYATDLRSLTQGRGSFSMEFSHYEEVPG-NVAEKV 666
Score = 55.5 bits (135), Expect = 2e-09
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 131 ITGFDP-----VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAV 183
I G + V+ AE PL+E+ GY +R+L+ GR FSMEF +++V N A+ V
Sbjct: 610 ILGMESRGGGDVVRAEVPLAEMFGYATDLRSLTQGRGSFSMEFSHYEEVPG-NVAEKV 666
>gnl|CDD|239683 cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the
C-terminal domain of the bacterial translational
elongation factor (EF) EF-G. Included in this group is
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells
harbor 2 protein synthesis systems: one localized in the
cytoplasm, the other in the mitochondria. Most factors
regulating mitochondrial protein synthesis are encoded
by nuclear genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. During the process
of peptide synthesis and tRNA site changes, the ribosome
is moved along the mRNA a distance equal to one codon
with the addition of each amino acid. In bacteria this
translocation step is catalyzed by EF-G_GTP, which is
hydrolyzed to provide the required energy. Thus, this
action releases the uncharged tRNA from the P site and
transfers the newly formed peptidyl-tRNA from the A site
to the P site. Eukaryotic mtEFG1 proteins show
significant homology to bacterial EF-Gs. Mutants in
yeast mtEFG1 have impaired mitochondrial protein
synthesis, respiratory defects and a tendency to lose
mitochondrial DNA. No clear phenotype has been found for
mutants in the yeast homologue of mtEFG2, MEF2.
Length = 78
Score = 87.6 bits (218), Expect = 3e-23
Identities = 34/78 (43%), Positives = 49/78 (62%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGYCQRVRTL 102
EP M +E+ E+Y+ ++ DLS RR I E RG KVI AE PL+E+ GY +R+L
Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKVIKAEVPLAEMFGYSTDLRSL 60
Query: 103 SSGRSHFSMEFLCFKQVS 120
+ GR F+MEF +++V
Sbjct: 61 TQGRGSFTMEFSHYEEVP 78
Score = 51.8 bits (125), Expect = 2e-09
Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 5/50 (10%)
Query: 131 ITGFDP-----VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVS 175
I G + VI AE PL+E+ GY +R+L+ GR F+MEF +++V
Sbjct: 29 ILGTESRGGWKVIKAEVPLAEMFGYSTDLRSLTQGRGSFTMEFSHYEEVP 78
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 94.5 bits (235), Expect = 9e-23
Identities = 45/110 (40%), Positives = 65/110 (59%), Gaps = 5/110 (4%)
Query: 24 MCIATGASMALKEAGC----ILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGS 79
M AS+A KEAG +LLEP M +E+ E+Y+ ++ DLS RR I +E RG+
Sbjct: 577 MAFKLAASLAFKEAGKKANPVLLEPIMKVEVEVPEEYMGDVMGDLSSRRGIIEGMEARGN 636
Query: 80 SKVIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVR 129
+ I AE PLSE+ GY +R+ + GR +SMEFL + +V S + A +
Sbjct: 637 VQKIKAEVPLSEMFGYATDLRSFTQGRGTYSMEFLHYGEVPS-SVANEII 685
Score = 45.2 bits (107), Expect = 7e-06
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVR 184
I AE PLSE+ GY +R+ + GR +SMEFL + +V S + A +
Sbjct: 639 KIKAEVPLSEMFGYATDLRSFTQGRGTYSMEFLHYGEVPS-SVANEII 685
>gnl|CDD|197906 smart00838, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 85
Score = 85.6 bits (213), Expect = 2e-22
Identities = 33/79 (41%), Positives = 53/79 (67%)
Query: 41 LLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGYCQRVR 100
LLEP M +E+ E+Y+ ++ DL+ RR I +E RG ++VI A+ PLSE+ GY +R
Sbjct: 1 LLEPIMKVEVTVPEEYMGDVIGDLNSRRGKIEGMEQRGGAQVIKAKVPLSEMFGYATDLR 60
Query: 101 TLSSGRSHFSMEFLCFKQV 119
+ + GR+ +SMEF +++V
Sbjct: 61 SATQGRATWSMEFSHYEEV 79
Score = 42.1 bits (100), Expect = 8e-06
Identities = 17/38 (44%), Positives = 27/38 (71%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQV 174
VI A+ PLSE+ GY +R+ + GR+ +SMEF +++V
Sbjct: 42 VIKAKVPLSEMFGYATDLRSATQGRATWSMEFSHYEEV 79
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 91.9 bits (229), Expect = 6e-22
Identities = 41/88 (46%), Positives = 57/88 (64%), Gaps = 1/88 (1%)
Query: 33 ALKEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVII-AEAPLSE 91
A ++A +LLEP M LEI ++V +L DLS+RR I E RG +V++ AEAPL+E
Sbjct: 589 AFRKANPVLLEPIMELEITVPTEHVGDVLGDLSQRRGRIEGTEPRGDGEVLVKAEAPLAE 648
Query: 92 LLGYCQRVRTLSSGRSHFSMEFLCFKQV 119
L GY R+R+++ GR F+MEF F V
Sbjct: 649 LFGYATRLRSMTKGRGSFTMEFSHFDPV 676
>gnl|CDD|201388 pfam00679, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 89
Score = 84.2 bits (209), Expect = 1e-21
Identities = 35/84 (41%), Positives = 54/84 (64%), Gaps = 1/84 (1%)
Query: 40 ILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVII-AEAPLSELLGYCQR 98
+LLEP M +EI E+Y+ ++ DL++RR +I +E G +V+I AE PL+EL G+
Sbjct: 1 VLLEPIMKVEITVPEEYLGDVIGDLNQRRGEILDMEPDGGGRVVIEAEVPLAELFGFSTE 60
Query: 99 VRTLSSGRSHFSMEFLCFKQVSSQ 122
+R+L+ GR FSMEF ++ V
Sbjct: 61 LRSLTQGRGSFSMEFSGYEPVPGD 84
>gnl|CDD|238772 cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This
domain includes the carboxyl terminal regions of
elongation factors (EFs) bacterial EF-G, eukaryotic and
archeal EF-2 and eukaryotic mitochondrial mtEFG1s and
mtEFG2s. This group also includes proteins similar to
the ribosomal protection proteins Tet(M) and Tet(O),
BipA, LepA and, spliceosomal proteins: human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and yeast counterpart Snu114p. This domain adopts a
ferredoxin-like fold consisting of an alpha-beta
sandwich with anti-parallel beta-sheets, resembling the
topology of domain III found in the elongation factors
EF-G and eukaryotic EF-2, with which it forms the
C-terminal block. The two domains however are not
superimposable and domain III lacks some of the
characteristics of this domain. EF-2/EF-G in complex
with GTP, promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome. Tet(M) and Tet(O)
mediate Tc resistance. Typical Tcs bind to the ribosome
and inhibit the elongation phase of protein synthesis,
by inhibiting the occupation of site A by
aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release
of tetracycline (Tc) from the ribosome in a
GTP-dependent manner. BipA is a highly conserved
protein with global regulatory properties in Escherichia
coli. Yeast Snu114p is essential for cell viability and
for splicing in vivo. Experiments suggest that GTP
binding and probably GTP hydrolysis is important for the
function of the U5-116 kD/Snu114p. The function of LepA
proteins is unknown.
Length = 79
Score = 79.4 bits (197), Expect = 6e-20
Identities = 34/78 (43%), Positives = 54/78 (69%), Gaps = 1/78 (1%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVII-AEAPLSELLGYCQRVRT 101
EP M +EI E+Y+ ++ DLS+RR +I +E RG+ +V+I AE PL+E+ G+ +R+
Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRS 60
Query: 102 LSSGRSHFSMEFLCFKQV 119
L+ GR+ FSMEF ++ V
Sbjct: 61 LTQGRASFSMEFSHYEPV 78
Score = 44.4 bits (106), Expect = 1e-06
Identities = 18/38 (47%), Positives = 27/38 (71%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQV 174
VI AE PL+E+ G+ +R+L+ GR+ FSMEF ++ V
Sbjct: 41 VIKAELPLAEMFGFATDLRSLTQGRASFSMEFSHYEPV 78
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 86.1 bits (214), Expect = 6e-20
Identities = 42/106 (39%), Positives = 64/106 (60%), Gaps = 7/106 (6%)
Query: 30 ASMALKEAGC----ILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSS--KVI 83
AS+A KEA +LLEP M +EI + E+Y+ ++ DL+ RR I +E R VI
Sbjct: 584 ASLAFKEAMLKAKPVLLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGGLDVI 643
Query: 84 IAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVR 129
AE PL+E+ GY +R+ + GR+ FSMEF +++V S + A+ +
Sbjct: 644 KAEVPLAEMFGYATDLRSATQGRASFSMEFDHYEEVPS-SVAEEII 688
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 65.3 bits (160), Expect = 1e-12
Identities = 31/99 (31%), Positives = 52/99 (52%)
Query: 33 ALKEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSEL 92
A+ A LLEP ++I + Y+ + ++ RR I +E G +I AEAP++E+
Sbjct: 615 AMLTAKPTLLEPIQKVDINVPQDYMGAVTREIQGRRGKILDMEQEGDMAIIEAEAPVAEM 674
Query: 93 LGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNI 131
G+ +R+ + GR+ +S EF F+ V + VR I
Sbjct: 675 FGFAGEIRSATEGRALWSTEFAGFEPVPDSLQLDIVRQI 713
Score = 37.5 bits (88), Expect = 0.002
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNI 186
+I AEAP++E+ G+ +R+ + GR+ +S EF F+ V + VR I
Sbjct: 664 IIEAEAPVAEMFGFAGEIRSATEGRALWSTEFAGFEPVPDSLQLDIVRQI 713
>gnl|CDD|239764 cd04097, mtEFG1_C, mtEFG1_C: C-terminus of mitochondrial Elongation
factor G1 (mtEFG1)-like proteins found in eukaryotes.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. Eukaryotic EF-2 operates in the
cytosolic protein synthesis machinery of eukaryotes,
EF-Gs in protein synthesis in bacteria. Eukaryotic
mtEFG1 proteins show significant homology to bacterial
EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects and
a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 78
Score = 59.6 bits (145), Expect = 2e-12
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGYCQRVRTL 102
EP M +E+ + ++ ++ L++R+ I + + AE PL+++ GY +R++
Sbjct: 1 EPIMKVEVTAPTEFQGNVIGLLNKRKGTIVDTDTGEDEFTLEAEVPLNDMFGYSTELRSM 60
Query: 103 SSGRSHFSMEFL 114
+ G+ FSMEF
Sbjct: 61 TQGKGEFSMEFS 72
Score = 39.6 bits (93), Expect = 6e-05
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFL 169
+ AE PL+++ GY +R+++ G+ FSMEF
Sbjct: 40 TLEAEVPLNDMFGYSTELRSMTQGKGEFSMEFS 72
>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 = 57.2 bits (138), Expect = 7e-10
Identities = 29/110 (26%), Positives = 55/110 (50%)
Query: 22 ILMCIATGASMALKEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSK 81
++ + +G A+ +A +LLEPY + I + + ++ RR I ++ G
Sbjct: 602 VIPAVRSGIFAAMMQAKPVLLEPYQKVFINVPQDMMGAATREIQNRRGQILEMKQEGDMV 661
Query: 82 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNI 131
IIA+AP++E+ G+ +R +SGR +S E F+ V + + V +
Sbjct: 662 TIIAKAPVAEMFGFAGAIRGATSGRCLWSTEHAGFELVPQNLQQEFVMEV 711
Score = 35.3 bits (81), Expect = 0.014
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNI 186
IIA+AP++E+ G+ +R +SGR +S E F+ V + + V +
Sbjct: 662 TIIAKAPVAEMFGFAGAIRGATSGRCLWSTEHAGFELVPQNLQQEFVMEV 711
>gnl|CDD|239682 cd03711, Tet_C, Tet_C: C-terminus of ribosomal protection proteins
Tet(M) and Tet(O). This domain has homology to the C
terminal domains of the elongation factors EF-G and
EF-2. Tet(M) and Tet(O) catalyze the release of
tetracycline (Tc) from the ribosome in a GTP-dependent
manner thereby mediating Tc resistance. Tcs are
broad-spectrum antibiotics. Typical Tcs bind to the
ribosome and inhibit the elongation phase of protein
synthesis, by inhibiting the occupation of site A by
aminoacyl-tRNA.
Length = 78
Score = 46.8 bits (112), Expect = 1e-07
Identities = 13/71 (18%), Positives = 29/71 (40%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGYCQRVRTL 102
EPY+ E+ + + ++DL++ A + +G + P++ Y + +
Sbjct: 1 EPYLRFELEVPQDALGRAMSDLAKMGATFEDPQIKGDEVTLEGTIPVATSQDYQSELPSY 60
Query: 103 SSGRSHFSMEF 113
+ G EF
Sbjct: 61 THGEGVLETEF 71
Score = 27.6 bits (62), Expect = 1.3
Identities = 5/32 (15%), Positives = 11/32 (34%)
Query: 137 VIIAEAPLSELLGYCQRVRTLSSGRSHFSMEF 168
+ P++ Y + + + G EF
Sbjct: 40 TLEGTIPVATSQDYQSELPSYTHGEGVLETEF 71
>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 = 37.3 bits (87), Expect = 0.003
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV-IIAEAPLSE-LLGYCQRVR 100
EPY+ II+ +Y+ I+ +R ++E ++V +I E PL+E + + +++
Sbjct: 400 EPYVKATIITPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLK 459
Query: 101 TLSSGRSHFSMEFLCFK 117
++S G + F E + ++
Sbjct: 460 SISRGYASFDYELIGYR 476
>gnl|CDD|239681 cd03710, BipA_TypA_C, BipA_TypA_C: a C-terminal portion of BipA or
TypA having homology to the C terminal domains of the
elongation factors EF-G and EF-2. A member of the
ribosome binding GTPase superfamily, BipA is widely
distributed in bacteria and plants. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 79
Score = 33.6 bits (78), Expect = 0.008
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV-IIAEAPLSELLGYCQRVRT 101
EP L I E+Y ++ L +R+ ++ +E G+ + + + P L+G+ T
Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLT 60
Query: 102 LSSG 105
+ G
Sbjct: 61 DTRG 64
>gnl|CDD|239763 cd04096, eEF2_snRNP_like_C, eEF2_snRNP_like_C: this family
represents a C-terminal domain of eukaryotic elongation
factor 2 (eEF-2) and a homologous domain of the
spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. Yeast Snu114p is essential
for cell viability and for splicing in vivo. U5-116 kD
binds GTP. Experiments suggest that GTP binding and
probably GTP hydrolysis is important for the function of
the U5-116 kD/Snu114p. In complex with GTP, EF-2
promotes the translocation step of translation. During
translocation the peptidyl-tRNA is moved from the A site
to the P site, the uncharged tRNA from the P site to the
E-site and, the mRNA is shifted one codon relative to
the ribosome.
Length = 80
Score = 33.7 bits (78), Expect = 0.009
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEA--PLSELLGYCQRVR 100
EP +EI E + + + LS+RR + S E + + + +A P+ E G+ +R
Sbjct: 1 EPIYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLR 60
Query: 101 TLSSGRSHFSMEF 113
+ +SG++ + F
Sbjct: 61 SATSGQAFPQLVF 73
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 35.0 bits (81), Expect = 0.017
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 41 LLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDR-GSSKVII-AEAPLSELLGYCQR 98
LLEP ++I + E + GI + L+RRR + E R G+ I A P++E G+
Sbjct: 718 LLEPMFLVDITAPEDAMGGIYSVLNRRRGVVIGEEQRPGTPLSNIKAYLPVAESFGFTAA 777
Query: 99 VRTLSSGRS 107
+R +SG++
Sbjct: 778 LRAATSGQA 786
>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 = 33.0 bits (76), Expect = 0.080
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 35 KEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIA-EAPLSELL 93
KE LEP L I E++V ++ L +R+ ++ +E G+ + + + P L+
Sbjct: 386 KEIDGKKLEPIEELTIDVPEEHVGAVIEKLGKRKGEMVDMEPSGNGRTRLEFKIPSRGLI 445
Query: 94 GYCQRVRTLSSG 105
G+ T + G
Sbjct: 446 GFRTEFLTDTRG 457
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 33.0 bits (76), Expect = 0.086
Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 35 KEAGCILLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV-IIAEAPLSELL 93
KE + EP+ + I E++ ++ L R+ +++ + G +V + P L+
Sbjct: 390 KEIDGVKCEPFEEVTIDVPEEHQGAVIEKLGERKGEMKDMAPDGKGRVRLEFVIPARGLI 449
Query: 94 GYCQRVRTLSSG 105
G+ T++ G
Sbjct: 450 GFRTEFLTMTRG 461
>gnl|CDD|239680 cd03709, lepA_C, lepA_C: This family represents the C-terminal
region of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. LepA is ubiquitous in Bacteria
and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but
is missing from Archaea. LepA exhibits significant
homology to elongation factors (EFs) Tu and G. The
function(s) of the proteins in this family are unknown.
The N-terminal domain of LepA is homologous to a domain
of similar size found in initiation factor 2 (IF2), and
in EF-Tu and EF-G (factors required for translation in
Escherichia coli). Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including S. cerevisiae GUF1)
originated within the bacterial LepA family. LepA has
never been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage.
Length = 80
Score = 30.9 bits (71), Expect = 0.088
Identities = 17/78 (21%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIA-EAPLSEL-LGYCQRVR 100
EP++ II+ +Y+ I+ RR + +E +++V++ E PL+E+ + +++
Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLK 60
Query: 101 TLSSGRSHFSMEFLCFKQ 118
++S G + E + +++
Sbjct: 61 SISKGYASLDYELIGYRE 78
>gnl|CDD|239765 cd04098, eEF2_C_snRNP, eEF2_C_snRNP: This family includes a
C-terminal portion of the spliceosomal human 116kD U5
small nuclear ribonucleoprotein (snRNP) protein (U5-116
kD) and, its yeast counterpart Snu114p. This domain is
homologous to the C-terminal domain of the eukaryotic
translational elongation factor EF-2. Yeast Snu114p is
essential for cell viability and for splicing in vivo.
U5-116 kD binds GTP. Experiments suggest that GTP
binding and probably GTP hydrolysis is important for
the function of the U5-116 kD/Snu114p. In complex
with GTP, EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site, the uncharged tRNA
from the P site to the E-site and, the mRNA is shifted
one codon relative to the ribosome.
Length = 80
Score = 29.5 bits (67), Expect = 0.27
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 7/53 (13%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGY 95
EP +EI V + LSRRR + I PL E+ +
Sbjct: 1 EPIYEVEITCPADAVSAVYEVLSRRRGHV-------IYDTPIPGTPLYEVKAF 46
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 30.8 bits (69), Expect = 0.46
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 43 EPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEA-PLSELLGYCQRVRT 101
EPY + + +EQ+ ++ L R+ D++++ G +V + P L+G+ T
Sbjct: 398 EPYENVTLDVEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMT 457
Query: 102 LSSG 105
++SG
Sbjct: 458 MTSG 461
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 30.5 bits (69), Expect = 0.63
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 41 LLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV--IIAEAPLSELLGYCQR 98
LLEP +EI + EQ + GI + L+++R + R + + I A P+ E G+
Sbjct: 725 LLEPVYLVEIQAPEQALGGIYSVLNQKRGHVFEEMQRPGTPLYNIKAYLPVIESFGFSGT 784
Query: 99 VRTLSSGRS 107
+R +SG++
Sbjct: 785 LRAATSGQA 793
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 29.5 bits (67), Expect = 1.2
Identities = 18/79 (22%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 41 LLEPYMYLEIISDEQYVHGILADLSRRRADIRSVEDRGSSKV-IIAEAPLSEL-LGYCQR 98
+ EPY+ II+ ++Y+ ++ +R +E ++V + E PL+E+ + +
Sbjct: 404 IEEPYVKATIITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPLAEIVFDFFDK 463
Query: 99 VRTLSSGRSHFSMEFLCFK 117
++++S G + F EF+ ++
Sbjct: 464 LKSISKGYASFDYEFIGYR 482
>gnl|CDD|236705 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 27.7 bits (62), Expect = 4.5
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 48 LEIISDEQYVHGILADLSRRRADIRSVEDRGSSKVIIAEAPLSELLGYCQRVR 100
+ S Q + I D RRR + V + +I + L E+L C +VR
Sbjct: 435 RSLASRWQKIDEIPFDFERRRMSV-VVAENTEHHQLICKGALEEILNVCSQVR 486
>gnl|CDD|238434 cd00854, NagA, N-acetylglucosamine-6-phosphate deacetylase, NagA,
catalyzes the hydrolysis of the N-acetyl group of
N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to
glucosamine 6-phosphate and acetate. This is the first
committed step in the biosynthetic pathway to
amino-sugar-nucleotides, which is needed for cell wall
peptidoglycan and teichoic acid biosynthesis.
Deacetylation of N-acetylglucosamine is also important
in lipopolysaccharide synthesis and cell wall recycling.
Length = 374
Score = 27.5 bits (62), Expect = 4.8
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 37 AGCILLEPYMYLEIISDEQYVHGILADLSRR 67
G L + +Y E+I+D +VH L+ R
Sbjct: 229 VGAALSDDDVYAELIADGIHVHPAAVRLAYR 259
>gnl|CDD|224733 COG1820, NagA, N-acetylglucosamine-6-phosphate deacetylase
[Carbohydrate transport and metabolism].
Length = 380
Score = 27.2 bits (61), Expect = 5.6
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 37 AGCILLEPYMYLEIISDEQYVHGILADLSRR 67
G L P +Y EII+D +VH L+ +
Sbjct: 230 VGAALDNPDVYAEIIADGVHVHPAAIRLALK 260
>gnl|CDD|139427 PRK13250, PRK13250, phycoerythrobilin:ferredoxin oxidoreductase;
Provisional.
Length = 248
Score = 26.7 bits (59), Expect = 7.6
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 54 EQYVHGILADLSRRRADI 71
E+Y+HG L DL R+ + +
Sbjct: 230 EEYIHGFLFDLERKLSAV 247
>gnl|CDD|223877 COG0806, RimM, RimM protein, required for 16S rRNA processing
[Translation, ribosomal structure and biogenesis].
Length = 174
Score = 26.4 bits (59), Expect = 9.0
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 128 VRNITGFDPVIIAEAPLSELLGYCQRVR-TLSSGRSHFSMEFLCFKQVSSQNEAQAVRN 185
V++ T F + P L + T+ S R H ++ L FK + +N A+A++
Sbjct: 25 VKSFTDFPESLFDYGPWLLLKPGGEWQELTVESVRKHKNLLILKFKGIDDRNAAEALKG 83
>gnl|CDD|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal
transduction histidine kinase) [Signal transduction
mechanisms].
Length = 750
Score = 26.6 bits (59), Expect = 9.6
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 7/62 (11%)
Query: 131 ITGFDPVIIAEAPLSELLGYCQRVRTLSSGRSHFSMEFLCFKQVSSQNEAQAVRNITGFD 190
I F+P E S L Y ++ +S ++ L Q VR +TGFD
Sbjct: 114 ILEFEPAGTGET-ASFLGFYHLAKLAMNRLQSAANLRDLL------SRTTQEVRRMTGFD 166
Query: 191 PV 192
V
Sbjct: 167 RV 168
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 0.135 0.392
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,573,450
Number of extensions: 877063
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 51
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
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 (22.0 bits)
S2: 56 (25.2 bits)