RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5461
(221 letters)
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 130 bits (329), Expect = 5e-35
Identities = 53/128 (41%), Positives = 76/128 (59%), Gaps = 12/128 (9%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------AMFQHFGDS--LCARA 105
VPVLCGS++KN GVQ L+DA+VD LPSP + P + A+ + D L A
Sbjct: 253 VPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALV 312
Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
FK++ D G +TF R+YSG K G + N + E++ RLLL ++ +EV+E+ G+
Sbjct: 313 FKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGD 372
Query: 166 IAAVTGLK 173
I A+ GLK
Sbjct: 373 IVALVGLK 380
Score = 58.4 bits (142), Expect = 4e-10
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 12/67 (17%)
Query: 1 MDAIVDILPSPTERPAL----------AMFQHFGDS--LCARAFKVVHDKHRGAVTFFRI 48
+DA+VD LPSP + P + A+ + D L A FK++ D G +TF R+
Sbjct: 270 LDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRV 329
Query: 49 YSGAFKK 55
YSG K
Sbjct: 330 YSGTLKS 336
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 124 bits (315), Expect = 5e-33
Identities = 53/128 (41%), Positives = 74/128 (57%), Gaps = 12/128 (9%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS------------LCARA 105
VPVLCGS++KN GVQ L+DA+VD LPSP + PA+ G+ A A
Sbjct: 255 VPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALA 314
Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
FK++ D G +TFFR+YSG + G N + E+I R+L A+ +E+ E++ G+
Sbjct: 315 FKIMTDPFVGKLTFFRVYSGVLESGSYVLNSTKGKKERIGRILQMHANKREEIKEVRAGD 374
Query: 166 IAAVTGLK 173
IAA GLK
Sbjct: 375 IAAAVGLK 382
Score = 54.4 bits (132), Expect = 9e-09
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 12/66 (18%)
Query: 2 DAIVDILPSPTERPALAMFQHFGDS------------LCARAFKVVHDKHRGAVTFFRIY 49
DA+VD LPSP + PA+ G+ A AFK++ D G +TFFR+Y
Sbjct: 273 DAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIMTDPFVGKLTFFRVY 332
Query: 50 SGAFKK 55
SG +
Sbjct: 333 SGVLES 338
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 123 bits (311), Expect = 2e-32
Identities = 49/126 (38%), Positives = 65/126 (51%), Gaps = 9/126 (7%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------LCARAFKV 108
VPV CGS+ KN GVQ+L+DA+VD LPSP E P + + L A FK
Sbjct: 237 VPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKT 296
Query: 109 VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA 168
+ D G ++ R+YSG KKG YN + E++ RL +EV+E G+I A
Sbjct: 297 MDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVA 356
Query: 169 VTGLKR 174
V LK
Sbjct: 357 VAKLKD 362
Score = 60.9 bits (149), Expect = 6e-11
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 1 MDAIVDILPSPTERPALAMFQHFGDS---------LCARAFKVVHDKHRGAVTFFRIYSG 51
+DA+VD LPSP E P + + L A FK + D G ++ R+YSG
Sbjct: 254 LDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSG 313
Query: 52 AFKKNH 57
KK
Sbjct: 314 TLKKGD 319
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 121 bits (305), Expect = 1e-31
Identities = 53/129 (41%), Positives = 72/129 (55%), Gaps = 15/129 (11%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS-------------LCAR 104
PVLCGS++KN GVQ L+DA+VD LPSP + PA + D+ A
Sbjct: 253 FPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPA--IKGINPDTEEEIERPASDDEPFAAL 310
Query: 105 AFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG 164
AFK++ D G +TFFR+YSG + G N + E+I RLL A+ +E+ E+ G
Sbjct: 311 AFKIMTDPFVGRLTFFRVYSGVLESGSYVLNTTKGKKERIGRLLQMHANKREEIKEVYAG 370
Query: 165 NIAAVTGLK 173
+IAA GLK
Sbjct: 371 DIAAAVGLK 379
Score = 50.6 bits (122), Expect = 2e-07
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 15/68 (22%)
Query: 1 MDAIVDILPSPTERPALAMFQHFGDS-------------LCARAFKVVHDKHRGAVTFFR 47
+DA+VD LPSP + PA + D+ A AFK++ D G +TFFR
Sbjct: 270 LDAVVDYLPSPLDVPA--IKGINPDTEEEIERPASDDEPFAALAFKIMTDPFVGRLTFFR 327
Query: 48 IYSGAFKK 55
+YSG +
Sbjct: 328 VYSGVLES 335
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 118 bits (298), Expect = 8e-31
Identities = 51/139 (36%), Positives = 74/139 (53%), Gaps = 11/139 (7%)
Query: 52 AFKKNH-VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------- 100
+ H VPVL GS+ KNIG++ L+DA+VD LPSP E P + G
Sbjct: 246 GTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKP 305
Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
L A FKV +D + G +T+ R+YSG + G + YN + E++ RL + + +EV+
Sbjct: 306 LLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDR 365
Query: 161 IQCGNIAAVTGLKRERGKD 179
+ G+I AV GLK D
Sbjct: 366 AKAGDIVAVAGLKELETGD 384
Score = 53.0 bits (128), Expect = 3e-08
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 2 DAIVDILPSPTERPALAMFQHFGDS----------LCARAFKVVHDKHRGAVTFFRIYSG 51
DA+VD LPSP E P + G L A FKV +D + G +T+ R+YSG
Sbjct: 271 DAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSG 330
Query: 52 AFKKN 56
+
Sbjct: 331 TLRAG 335
>gnl|CDD|239759 cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial
Elongation factor G2 (mtEFG2)-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. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG1s are not present in this group.
Length = 83
Score = 100 bits (252), Expect = 7e-28
Identities = 38/73 (52%), Positives = 49/73 (67%)
Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
LCA AFKVVHD RG +TF R+YSG K+G YN + + E+I+RLL AD Y+E+
Sbjct: 1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPS 60
Query: 161 IQCGNIAAVTGLK 173
+ GNI +TGLK
Sbjct: 61 LSAGNIGVITGLK 73
Score = 54.9 bits (133), Expect = 2e-10
Identities = 19/32 (59%), Positives = 22/32 (68%)
Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV 58
LCA AFKVVHD RG +TF R+YSG K+
Sbjct: 1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSA 32
>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 = 107 bits (269), Expect = 6e-27
Identities = 52/127 (40%), Positives = 74/127 (58%), Gaps = 11/127 (8%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA---------MFQHFGDSL--CARAF 106
PVLCGS++KN GVQ L+DA+VD LPSPT+ PA+ + + D A AF
Sbjct: 254 FPVLCGSAFKNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAF 313
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
KV D G +TF R+YSG K G N ++ E++ RL+ A++ +E+ E++ G+I
Sbjct: 314 KVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDI 373
Query: 167 AAVTGLK 173
A GLK
Sbjct: 374 CAAIGLK 380
Score = 48.3 bits (115), Expect = 1e-06
Identities = 31/84 (36%), Positives = 39/84 (46%), Gaps = 18/84 (21%)
Query: 1 MDAIVDILPSPTERPALA---------MFQHFGDSL--CARAFKVVHDKHRGAVTFFRIY 49
+DA+VD LPSPT+ PA+ + + D A AFKV D G +TF R+Y
Sbjct: 271 LDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVY 330
Query: 50 SGAFKKNHVPVLCGSSYKNIGVQK 73
SG K GS KN K
Sbjct: 331 SGVLKS-------GSYVKNSRKNK 347
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. 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 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. mtEFG1 and mtEFG2 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 = 83
Score = 92.2 bits (230), Expect = 1e-24
Identities = 29/73 (39%), Positives = 38/73 (52%)
Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
A FK +HD G ++F R+YSG K G YN + E++ RLL +EV E
Sbjct: 1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEE 60
Query: 161 IQCGNIAAVTGLK 173
G+I AV GLK
Sbjct: 61 AGAGDIGAVAGLK 73
Score = 50.9 bits (123), Expect = 7e-09
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNH 57
A FK +HD G ++F R+YSG K
Sbjct: 1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGS 31
>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 = 63.7 bits (156), Expect = 3e-12
Identities = 21/28 (75%), Positives = 25/28 (89%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSP 85
VPVLCGS++KN GVQ L+DA+VD LPSP
Sbjct: 243 VPVLCGSAFKNKGVQPLLDAVVDYLPSP 270
>gnl|CDD|239758 cd04091, mtEFG1_II_like, 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 = 81
Score = 55.4 bits (134), Expect = 2e-10
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
AFK+ + G +T+ RIY G KKG YN+ + ++ RL+ +++ +EV E
Sbjct: 1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEE 59
Query: 161 IQCGNIAAVTGLK 173
G+I A+ G+
Sbjct: 60 AGAGDICAIFGID 72
Score = 31.1 bits (71), Expect = 0.093
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLM 75
AFK+ + G +T+ RIY G KK + + K + V +L+
Sbjct: 1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDT-IYNVRTGKKVRVPRLV 47
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 52.7 bits (127), Expect = 1e-09
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEV 158
L A FKV DK RG V R+ SG KKG K ++ L + EV
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK----GEV 56
Query: 159 NEIQCGNIAAVTGLKRE 175
+E G+I + ++
Sbjct: 57 DEAVAGDIVGIVLKDKD 73
Score = 35.0 bits (81), Expect = 0.003
Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNI 69
L A FKV DK RG V R+ SG KK V G +
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDK-VRVGPGGGGV 42
>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 = 51.4 bits (123), Expect = 9e-08
Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
K+V DKH G V R+YSG + G + Y + +I ++ + + EV+EI GNI
Sbjct: 296 KIVVDKHAGEVAVGRLYSGTIRPGMEVYIVDRKAKARIQQVGVYMGPERVEVDEIPAGNI 355
Query: 167 AAVTGLK 173
AV GLK
Sbjct: 356 VAVIGLK 362
Score = 30.6 bits (69), Expect = 0.67
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 33 KVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN 68
K+V DKH G V R+YSG + + K
Sbjct: 296 KIVVDKHAGEVAVGRLYSGTIRPGMEVYIVDRKAKA 331
>gnl|CDD|239661 cd03690, Tet_II, Tet_II: This subfamily represents domain II of
ribosomal protection proteins Tet(M) and Tet(O). This
domain has homology to domain II 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 = 85
Score = 47.2 bits (113), Expect = 2e-07
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
L FK+ D + + R+YSG + + ++ ++ +IT L + +
Sbjct: 1 ESELSGTVFKIERDDKGERLAYLRLYSGTLRL-RDSVRVNREEKIKITELRVFNNGEVVT 59
Query: 158 VNEIQCGNIAAVTGLK 173
+ + G+IA +TGLK
Sbjct: 60 ADTVTAGDIAILTGLK 75
Score = 30.3 bits (69), Expect = 0.17
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 24 GDSLCARAFKVVHDKHRGAVTFFRIYSG 51
L FK+ D + + R+YSG
Sbjct: 1 ESELSGTVFKIERDDKGERLAYLRLYSG 28
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2
found eukaryotes and archaea and, the C-terminal portion
of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. 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. This translocation step is
catalyzed by EF-2_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.
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.
Length = 93
Score = 46.8 bits (112), Expect = 3e-07
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 107 KVVHDK-HRGAVTFFRIYSGAFKKGQKFY----NIHLDQSE-----QITRLLLAEADDYK 156
K+V G + F R++SG +KGQK N + E I RL L +
Sbjct: 7 KMVPTPDKGGFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYRE 66
Query: 157 EVNEIQCGNIAAVTGLK 173
V+E+ GNI + GL
Sbjct: 67 PVDEVPAGNIVLIVGLD 83
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 49.9 bits (120), Expect = 3e-07
Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 4/112 (3%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSPTERPA-LAMFQHFGDSLCARAFKV---VHDKHR 114
PV GS+ N GV +DA+VD PSP R A + D FK+ + KHR
Sbjct: 252 PVFFGSALGNFGVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHR 311
Query: 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
+ F R+ SG F++G K ++ + +++ L A D + V E G+I
Sbjct: 312 DRIAFMRVCSGKFERGMKVTHVRTGKDVKLSDALTFMAQDRETVEEAYAGDI 363
Score = 29.5 bits (67), Expect = 1.3
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 1 MDAIVDILPSPTERPA-LAMFQHFGDSLCARAFKV---VHDKHRGAVTFFRIYSGAFKK- 55
+DA+VD PSP R A + D FK+ + KHR + F R+ SG F++
Sbjct: 268 LDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSGKFERG 327
Query: 56 ---NHV 58
HV
Sbjct: 328 MKVTHV 333
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 48.7 bits (116), Expect = 7e-07
Identities = 34/119 (28%), Positives = 50/119 (42%), Gaps = 18/119 (15%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSPTER--------PALAMFQHFGDSLCARAFKV-- 108
PV G++ N GV +D ++ P P R P F F FK+
Sbjct: 251 PVFFGTALGNFGVDHFLDGLLQWAPKPEARQSDTRTVEPTEEKFSGF-------VFKIQA 303
Query: 109 -VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
+ KHR V F R+ SG ++KG K ++ + I+ L A D + V E G+I
Sbjct: 304 NMDPKHRDRVAFMRVVSGKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDI 362
>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 = 48.5 bits (116), Expect = 8e-07
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 60 VLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTF 119
+ S+ IG++++++AIV +P P P L A F +D +RG V
Sbjct: 157 AILASAKTGIGIEEILEAIVKRVPPPKGDP--------DAPLKALIFDSHYDNYRGVVAL 208
Query: 120 FRIYSGAFKKGQKFYNIHLDQSEQITRL 147
R++ G K G K + + ++ +
Sbjct: 209 VRVFEGTIKPGDKIRFMSTGKEYEVDEV 236
Score = 34.6 bits (80), Expect = 0.030
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 8/56 (14%)
Query: 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN 56
++AIV +P P P L A F +D +RG V R++ G K
Sbjct: 172 LEAIVKRVPPPKGDP--------DAPLKALIFDSHYDNYRGVVALVRVFEGTIKPG 219
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 48.7 bits (117), Expect = 9e-07
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
++ D H G V R++SG +KGQ+ Y + + ++ ++ + + +EV EI GNI
Sbjct: 297 DIIVDPHAGEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNI 356
Query: 167 AAVTGLKRER 176
AAVTGLK R
Sbjct: 357 AAVTGLKDAR 366
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 44.5 bits (106), Expect = 9e-07
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 115 GAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
G V R+ SG KKG K + ++T L + D + V G I A GL
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 173 K 173
K
Sbjct: 61 K 61
Score = 25.3 bits (56), Expect = 8.6
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 41 GAVTFFRIYSGAFKKN 56
G V R+ SG KK
Sbjct: 1 GTVATGRVESGTLKKG 16
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 48.2 bits (116), Expect = 1e-06
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA-MFQHFGDSLCARAFKV---VHDKHR 114
PV GS+ N GVQ+ +DA V+ P+P R + + FK+ + KHR
Sbjct: 250 PVFFGSALNNFGVQEFLDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHR 309
Query: 115 GAVTFFRIYSGAFKKGQK 132
+ F R+ SG F+KG K
Sbjct: 310 DRIAFVRVCSGKFEKGMK 327
Score = 29.7 bits (68), Expect = 1.2
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 1 MDAIVDILPSPTERPALA-MFQHFGDSLCARAFKV---VHDKHRGAVTFFRIYSGAFKK- 55
+DA V+ P+P R + + FK+ + KHR + F R+ SG F+K
Sbjct: 266 LDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHRDRIAFVRVCSGKFEKG 325
Query: 56 ---NHV 58
HV
Sbjct: 326 MKVRHV 331
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 47.9 bits (115), Expect = 1e-06
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVT 118
VL S+ IG++ +++AIV+ +P P P L A F +D + G V
Sbjct: 163 AVLV-SAKTGIGIEDVLEAIVEKIPPPKGDP--------DAPLKALIFDSWYDNYLGVVV 213
Query: 119 FFRIYSGAFKKGQKFYNIHLDQSEQITRL 147
RI+ G KKG K + + ++ +
Sbjct: 214 LVRIFDGTLKKGDKIRMMSTGKEYEVDEV 242
Score = 33.7 bits (78), Expect = 0.058
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN 56
++AIV+ +P P P L A F +D + G V RI+ G KK
Sbjct: 178 LEAIVEKIPPPKGDP--------DAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKG 225
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
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 only bacterial members.
Length = 268
Score = 46.8 bits (112), Expect = 2e-06
Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSP 85
VPV GS+ IGV++L+DA+V++ PSP
Sbjct: 241 VPVFFGSALTGIGVRRLLDALVELAPSP 268
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 47.0 bits (113), Expect = 3e-06
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 16/68 (23%)
Query: 69 IGVQKLMDAIVDILPSPT---ERPALAM-FQHFGDSLCARAFKVVHDKHRGAVTFFRIYS 124
IG++++++AIV+ +P P + P A+ F DS +D +RG V R+
Sbjct: 170 IGIEEVLEAIVERIPPPKGDPDAPLKALIF----DS--------WYDNYRGVVVLVRVVD 217
Query: 125 GAFKKGQK 132
G KKG K
Sbjct: 218 GTLKKGDK 225
Score = 33.5 bits (78), Expect = 0.068
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 16/60 (26%)
Query: 1 MDAIVDILPSPT---ERPALAM-FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN 56
++AIV+ +P P + P A+ F DS +D +RG V R+ G KK
Sbjct: 176 LEAIVERIPPPKGDPDAPLKALIF----DS--------WYDNYRGVVVLVRVVDGTLKKG 223
>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 = 42.5 bits (101), Expect = 4e-05
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 52 AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84
F VPV+ GS+ G+ +L++A+ LPS
Sbjct: 152 GFGGETVPVVPGSALTGEGIDELLEALDLYLPS 184
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. 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 = 86
Score = 38.6 bits (91), Expect = 2e-04
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 121 RIYSGAFKKGQKFYNIHLDQSEQ---ITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
RI+ G K GQ+ + D + IT+L E EV E + G+I A+ G+
Sbjct: 21 RIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAIAGI 75
>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal
domain:eEF2_C_snRNP: This family includes 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
domain II 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 = 94
Score = 37.2 bits (87), Expect = 7e-04
Identities = 26/65 (40%), Positives = 29/65 (44%), Gaps = 11/65 (16%)
Query: 118 TFFRIYSGAFKKGQKFY----NIHLD-----QSEQITRLLLAEADDYK-EVNEIQCGNIA 167
F RIYSG KKGQK N LD I RL + YK EVNE GN
Sbjct: 19 AFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGG-RYKIEVNEAPAGNWV 77
Query: 168 AVTGL 172
+ G+
Sbjct: 78 LIKGI 82
>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 = 40.0 bits (94), Expect = 7e-04
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 11/102 (10%)
Query: 74 LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF 133
L DAIV +P+P Q + +D++ G + R++ G KKGQ+
Sbjct: 182 LFDAIVRHVPAPKGDLD-EPLQ-------MLVTNLDYDEYLGRIAIGRVHRGTVKKGQQV 233
Query: 134 YNIHLDQSEQ---ITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
+ D + + I++LL E + E++E G+I AV GL
Sbjct: 234 ALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDIVAVAGL 275
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 39.1 bits (92), Expect = 0.001
Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 11/102 (10%)
Query: 74 LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF 133
L + I+D +P+P Q L ++ G + RI+ G K Q+
Sbjct: 186 LFETILDHVPAPKGDLD-EPLQMQVTQLDYNSY-------VGRIGIGRIFRGTVKPNQQV 237
Query: 134 YNIHLDQSE---QITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
I D + +IT+LL + E+ E + G+I A+ GL
Sbjct: 238 ALIKSDGTTENGRITKLLGFLGLERIEIEEAEAGDIVAIAGL 279
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 38.0 bits (89), Expect = 0.002
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSP 85
PV GS+ N GVQ+L+DA V + P+P
Sbjct: 242 PVFFGSALNNFGVQELLDAFVKLAPAP 268
>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 = 35.0 bits (81), Expect = 0.015
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSP 85
VP++ S+ G+++L+DAIV+ LP P
Sbjct: 156 VPIIPISALTGEGIEELLDAIVEHLPPP 183
>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 = 34.5 bits (80), Expect = 0.024
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 59 PVLCGSSYKNIGVQKLMDAIVDILPSP 85
PV GS+ K IG+ +L++ I ++ P+
Sbjct: 211 PVYHGSALKGIGIDELLEGITNLFPTS 237
>gnl|CDD|239670 cd03699, lepA_II, lepA_II: This subfamily represents the domain II
of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. The N-terminal domain of LepA
shares regions of homology to translation factors. In
terms of interaction with the ribosome, EF-G, EF-Tu and
IF2 have all been demonstrated to interact at
overlapping sites on the ribosome. Chemical protection
studies demonstrate that they all include the
universally conserved alpha-sarcin loop as part of their
binding site. These data indicate that LepA may bind to
this location on the ribosome as well. 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 = 86
Score = 32.4 bits (75), Expect = 0.027
Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 110 HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRL--LLAEADDYKEVNEIQCGNIA 167
+D +RG + R++ G KKG K + + ++ + E +E+ G +
Sbjct: 10 YDPYRGVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVGIFRPEM---TPTDELSAGQVG 66
Query: 168 AV-TGLK 173
+ G+K
Sbjct: 67 YIIAGIK 73
Score = 26.6 bits (60), Expect = 3.5
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 36 HDKHRGAVTFFRIYSGAFKKN 56
+D +RG + R++ G KK
Sbjct: 10 YDPYRGVIALVRVFDGTLKKG 30
>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 = 29.0 bits (66), Expect = 1.3
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL 91
VPV+ S+ K G+ +L DAI+++ L
Sbjct: 136 VPVVPTSARKGEGIDELKDAIIEVAEGKVPPAPL 169
>gnl|CDD|227365 COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of
the PI-3 kinase family [Signal transduction mechanisms /
Cell division and chromosome partitioning / Chromatin
structure and dynamics / DNA replication, recombination,
and repair / Intracellular trafficking and secretion].
Length = 2105
Score = 29.4 bits (66), Expect = 1.6
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 141 SEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARW-- 198
SE +RLL D+ + +E++C + V+ L + D+ IP S + S R
Sbjct: 796 SENASRLLPPLMDNLSKSHELRCVSEDDVSALLIQLLTDRVICFIPVINSSLGDSRRIFL 855
Query: 199 -TLNLEVGASS 208
L + S
Sbjct: 856 SLLAQLLDDSL 866
>gnl|CDD|227770 COG5483, COG5483, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 29.1 bits (65), Expect = 1.6
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 15/77 (19%)
Query: 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84
D+L +R +V+H + RG T H C + N +Q +D +VD+ +
Sbjct: 132 DTLKSRGLRVLHIQERGLFT-----------EHYETRCIDLFLNPLIQNSIDVLVDVRKN 180
Query: 85 PTERPALAMFQHFGDSL 101
P F +SL
Sbjct: 181 PFSMK----FDFTKNSL 193
>gnl|CDD|239660 cd03689, RF3_II, RF3_II: this subfamily represents the domain II of
bacterial Release Factor 3 (RF3). Termination of protein
synthesis by the ribosome requires two release factor
(RF) classes. The class II RF3 is a GTPase that removes
class I RFs (RF1 or RF2) from the ribosome after release
of the nascent polypeptide. RF3 in the GDP state binds
to the ribosomal class I RF complex, followed by an
exchange of GDP for GTP and release of the class I RF.
Sequence comparison of class II release factors with
elongation factors shows that prokaryotic RF3 is more
similar to EF-G whereas eukaryotic eRF3 is more similar
to eEF1A, implying that their precise function may
differ.
Length = 85
Score = 27.6 bits (62), Expect = 1.8
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 112 KHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
HR + F R+ SG F++G K ++ L + +++ A D + V+E G+I
Sbjct: 13 AHRDRIAFVRVCSGKFERGMKVKHVRLGKEVRLSNPQQFFAQDRETVDEAYPGDI 67
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 28.6 bits (64), Expect = 2.6
Identities = 39/154 (25%), Positives = 66/154 (42%), Gaps = 28/154 (18%)
Query: 53 FKKNHVPVLCGSSY-------KNIG---VQKLMDAIVDILPSP---TERPALAMFQHFGD 99
F + +P++ GS+ IG + KLMDA+ + +P P ++P L +
Sbjct: 212 FPGDEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYIPEPVRVLDKPFLMPIE---- 267
Query: 100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVN 159
V + RG V R+ G K G++ + L + + K ++
Sbjct: 268 -------DVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMFKKILD 320
Query: 160 EIQCG-NIAA-VTGLKRERGKDKRTRVIPKPTSV 191
+ Q G N+ + GLKRE +R +VI KP S+
Sbjct: 321 QGQAGDNVGLLLRGLKRE--DVQRGQVICKPGSI 352
>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 = 28.2 bits (63), Expect = 3.4
Identities = 38/153 (24%), Positives = 71/153 (46%), Gaps = 30/153 (19%)
Query: 53 FKKNHVPVLCGSSYKNI--------GVQKLMDAIVDILPSP---TERPALAMFQHFGDSL 101
F + P++ GS+ K + + +LMDA+ + +P+P T++P L +
Sbjct: 163 FPGDDTPIIRGSALKALEGDAEWEAKILELMDAVDEYIPTPERETDKPFLMPIE------ 216
Query: 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDY-KEVNE 160
V RG V R+ G K G++ + L + + T + + + KE++E
Sbjct: 217 -----DVFSITGRGTVVTGRVERGIVKVGEEVEIVGLKDTRKTT---VTGVEMFRKELDE 268
Query: 161 IQCG-NIAA-VTGLKRERGKDKRTRVIPKPTSV 191
+ G N+ + G+KRE + +R V+ KP S+
Sbjct: 269 GRAGDNVGLLLRGIKRE--EIERGMVLAKPGSI 299
>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 = 27.4 bits (62), Expect = 3.6
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 58 VPVLCGSSYKNIGVQKLMDAIVDILPS 84
VPV+ S+ K G+ +L+DAI + S
Sbjct: 133 VPVVPTSARKGEGIDELLDAIAKLAES 159
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 27.7 bits (63), Expect = 4.4
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 52 AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82
PV S+ G+ +L+ A+ ++L
Sbjct: 297 ELAALGGPVFLISAVTGEGLDELLRALWELL 327
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 27.4 bits (62), Expect = 4.9
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 52 AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82
A K V+ SS K G+ +L AI L
Sbjct: 163 ALKFGDDEVILFSSLKKQGIDELRAAIAKWL 193
>gnl|CDD|129586 TIGR00495, crvDNA_42K, 42K curved DNA binding protein. Proteins
identified by This model have been identified in a
number of species as a nuclear (but not nucleolar)
protein with a cell cycle dependence. Various names
given to members of this family have included cell cycle
protein p38-2G4, DNA-binding protein GBP16, and
proliferation-associated protein 1. This protein is
closely related to methionine aminopeptidase, a
cobolt-binding protein [Unknown function, General].
Length = 389
Score = 27.5 bits (61), Expect = 6.3
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 157 EVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKR 216
E NE+ +I TG + + D+RT + + S T L++ AS S+ +R
Sbjct: 220 EENEVYAVDILVSTGEGKAKDADQRTTIYKRDPSK-------TYGLKMKASRAFFSEIER 272
Query: 217 R 217
R
Sbjct: 273 R 273
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
0.324 0.137 0.408
Gapped
Lambda K H
0.267 0.0666 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,315,317
Number of extensions: 1061406
Number of successful extensions: 1064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1034
Number of HSP's successfully gapped: 68
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 57 (25.9 bits)