MULTISPECIES: peptide chain release factor 3 [Stenotrophomonas]
Protein Classification
peptide chain release factor 3( domain architecture ID 11479193)
peptide chain release factor 3, RF3, is a GTP-binding protein that promotes rapid dissociation of release factors RF1 and RF2 from the ribosome during translation termination
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| prfC | PRK00741 | peptide chain release factor 3; Provisional |
2-526 | 0e+00 | ||||||||
peptide chain release factor 3; Provisional : Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 1087.09 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||
| prfC | PRK00741 | peptide chain release factor 3; Provisional |
2-526 | 0e+00 | ||||||||
peptide chain release factor 3; Provisional Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 1087.09 E-value: 0e+00
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| PrfC | COG4108 | Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Peptide ... |
2-526 | 0e+00 | ||||||||
Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Peptide chain release factor RF-3 is part of the Pathway/BioSystem: Translation factors Pssm-ID: 443284 [Multi-domain] Cd Length: 528 Bit Score: 1075.08 E-value: 0e+00
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| prfC | TIGR00503 | peptide chain release factor 3; This translation releasing factor, RF-3 (prfC) was originally ... |
1-526 | 0e+00 | ||||||||
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] Pssm-ID: 129594 [Multi-domain] Cd Length: 527 Bit Score: 799.12 E-value: 0e+00
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| RF3 | cd04169 | Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; ... |
10-277 | 0e+00 | ||||||||
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. Pssm-ID: 206732 [Multi-domain] Cd Length: 268 Bit Score: 515.99 E-value: 0e+00
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| RF3_C | pfam16658 | Class II release factor RF3, C-terminal domain; |
385-512 | 2.44e-69 | ||||||||
Class II release factor RF3, C-terminal domain; Pssm-ID: 465221 [Multi-domain] Cd Length: 129 Bit Score: 218.46 E-value: 2.44e-69
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| Name | Accession | Description | Interval | E-value | ||||||||
| prfC | PRK00741 | peptide chain release factor 3; Provisional |
2-526 | 0e+00 | ||||||||
peptide chain release factor 3; Provisional Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 1087.09 E-value: 0e+00
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| PrfC | COG4108 | Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Peptide ... |
2-526 | 0e+00 | ||||||||
Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Peptide chain release factor RF-3 is part of the Pathway/BioSystem: Translation factors Pssm-ID: 443284 [Multi-domain] Cd Length: 528 Bit Score: 1075.08 E-value: 0e+00
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| prfC | TIGR00503 | peptide chain release factor 3; This translation releasing factor, RF-3 (prfC) was originally ... |
1-526 | 0e+00 | ||||||||
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] Pssm-ID: 129594 [Multi-domain] Cd Length: 527 Bit Score: 799.12 E-value: 0e+00
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| RF3 | cd04169 | Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; ... |
10-277 | 0e+00 | ||||||||
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. Pssm-ID: 206732 [Multi-domain] Cd Length: 268 Bit Score: 515.99 E-value: 0e+00
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| FusA | COG0480 | Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
1-466 | 1.77e-87 | ||||||||
Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-G, a GTPase is part of the Pathway/BioSystem: Translation factors Pssm-ID: 440248 [Multi-domain] Cd Length: 693 Bit Score: 283.86 E-value: 1.77e-87
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| PRK12740 | PRK12740 | elongation factor G-like protein EF-G2; |
17-466 | 9.85e-86 | ||||||||
elongation factor G-like protein EF-G2; Pssm-ID: 237186 [Multi-domain] Cd Length: 668 Bit Score: 278.55 E-value: 9.85e-86
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| PRK13351 | PRK13351 | elongation factor G-like protein; |
12-466 | 2.56e-72 | ||||||||
elongation factor G-like protein; Pssm-ID: 237358 [Multi-domain] Cd Length: 687 Bit Score: 243.32 E-value: 2.56e-72
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| RF3_C | pfam16658 | Class II release factor RF3, C-terminal domain; |
385-512 | 2.44e-69 | ||||||||
Class II release factor RF3, C-terminal domain; Pssm-ID: 465221 [Multi-domain] Cd Length: 129 Bit Score: 218.46 E-value: 2.44e-69
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| EF-G_bact | cd04170 | Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ... |
13-277 | 4.39e-59 | ||||||||
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. Pssm-ID: 206733 [Multi-domain] Cd Length: 268 Bit Score: 196.66 E-value: 4.39e-59
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| EF-G | TIGR00484 | translation elongation factor EF-G; After peptide bond formation, this elongation factor of ... |
10-459 | 2.07e-55 | ||||||||
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] Pssm-ID: 129575 [Multi-domain] Cd Length: 689 Bit Score: 197.72 E-value: 2.07e-55
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
10-276 | 2.02e-54 | ||||||||
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. Pssm-ID: 425418 [Multi-domain] Cd Length: 187 Bit Score: 181.57 E-value: 2.02e-54
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| EF-G | cd01886 | Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling ... |
16-277 | 9.94e-54 | ||||||||
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. Pssm-ID: 206673 [Multi-domain] Cd Length: 270 Bit Score: 182.69 E-value: 9.94e-54
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| RF3_II | cd03689 | Domain II of bacterial Release Factor 3; This subfamily represents domain II of bacterial ... |
294-380 | 1.79e-51 | ||||||||
Domain II of bacterial Release Factor 3; This subfamily represents 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. Pssm-ID: 293890 [Multi-domain] Cd Length: 87 Bit Score: 170.15 E-value: 1.79e-51
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| GTP_translation_factor | cd00881 | GTP translation factor family primarily contains translation initiation, elongation and ... |
13-277 | 7.12e-46 | ||||||||
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. Pssm-ID: 206647 [Multi-domain] Cd Length: 183 Bit Score: 159.00 E-value: 7.12e-46
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| TetM_like | cd04168 | Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline ... |
16-268 | 1.17e-38 | ||||||||
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. Pssm-ID: 206731 [Multi-domain] Cd Length: 237 Bit Score: 141.22 E-value: 1.17e-38
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| RF3_III | cd16259 | Domain III of bacterial Release Factor 3 (RF3); The class II RF3 is a member of one of two ... |
393-462 | 1.58e-32 | ||||||||
Domain III of bacterial Release Factor 3 (RF3); The class II RF3 is a member of one of two release factor (RF) classes required for the termination of protein synthesis by the ribosome. 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. Pssm-ID: 293916 [Multi-domain] Cd Length: 70 Bit Score: 118.90 E-value: 1.58e-32
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| LepA | cd01890 | LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ... |
12-164 | 1.47e-29 | ||||||||
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. Pssm-ID: 206677 [Multi-domain] Cd Length: 179 Bit Score: 114.55 E-value: 1.47e-29
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| TypA_BipA | cd01891 | Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ... |
12-156 | 1.02e-27 | ||||||||
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. Pssm-ID: 206678 [Multi-domain] Cd Length: 194 Bit Score: 109.99 E-value: 1.02e-27
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| TypA_BipA | TIGR01394 | GTP-binding protein TypA/BipA; This bacterial (and Arabidopsis) protein, termed TypA or BipA, ... |
12-384 | 2.47e-24 | ||||||||
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] Pssm-ID: 273597 [Multi-domain] Cd Length: 594 Bit Score: 107.00 E-value: 2.47e-24
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| aEF-2 | TIGR00490 | translation elongation factor aEF-2; This model represents archaeal elongation factor 2, a ... |
1-466 | 1.07e-22 | ||||||||
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] Pssm-ID: 129581 [Multi-domain] Cd Length: 720 Bit Score: 102.28 E-value: 1.07e-22
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| EF2 | cd01885 | Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a ... |
12-144 | 3.24e-22 | ||||||||
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. Pssm-ID: 206672 [Multi-domain] Cd Length: 218 Bit Score: 94.99 E-value: 3.24e-22
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| PRK07560 | PRK07560 | elongation factor EF-2; Reviewed |
12-466 | 3.52e-22 | ||||||||
elongation factor EF-2; Reviewed Pssm-ID: 236047 [Multi-domain] Cd Length: 731 Bit Score: 100.71 E-value: 3.52e-22
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| TypA | COG1217 | Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction ... |
12-156 | 9.40e-22 | ||||||||
Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction mechanisms]; Pssm-ID: 440830 [Multi-domain] Cd Length: 606 Bit Score: 98.94 E-value: 9.40e-22
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| PRK10218 | PRK10218 | translational GTPase TypA; |
12-156 | 2.06e-21 | ||||||||
translational GTPase TypA; Pssm-ID: 104396 [Multi-domain] Cd Length: 607 Bit Score: 97.86 E-value: 2.06e-21
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| EFG_III-like | cd16257 | Domain III of Elongation factor G (EF-G) and related proteins; Bacterial Elongation factor G ... |
393-462 | 2.87e-21 | ||||||||
Domain III of Elongation factor G (EF-G) and related proteins; Bacterial Elongation factor G (EF-G) and related proteins play a role in translation and share a similar domain architecture. Elongation factor EFG participates in the elongation phase during protein biosynthesis on the ribosome by stimulating translocation. Its functional cycles depend on GTP binding and its hydrolysis. Domain III is involved in the activation of GTP hydrolysis. This domain III, which is different from domain III in EF-TU and related elongation factors, is found in several translation factors, like bacterial release factors RF3, elongation factor 4, elongation factor 2, GTP-binding protein BipA and tetracycline resistance protein Tet. Pssm-ID: 293914 [Multi-domain] Cd Length: 71 Bit Score: 87.40 E-value: 2.87e-21
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| Snu114p | cd04167 | Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ... |
12-144 | 2.56e-19 | ||||||||
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. Pssm-ID: 206730 [Multi-domain] Cd Length: 213 Bit Score: 86.55 E-value: 2.56e-19
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| PTZ00416 | PTZ00416 | elongation factor 2; Provisional |
1-159 | 4.03e-17 | ||||||||
elongation factor 2; Provisional Pssm-ID: 240409 [Multi-domain] Cd Length: 836 Bit Score: 84.71 E-value: 4.03e-17
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
15-148 | 1.23e-15 | ||||||||
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] Pssm-ID: 272973 [Multi-domain] Cd Length: 162 Bit Score: 74.33 E-value: 1.23e-15
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| PLN00116 | PLN00116 | translation elongation factor EF-2 subunit; Provisional |
12-144 | 1.08e-13 | ||||||||
translation elongation factor EF-2 subunit; Provisional Pssm-ID: 177730 [Multi-domain] Cd Length: 843 Bit Score: 73.99 E-value: 1.08e-13
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| EF-Tu | TIGR00485 | translation elongation factor TU; This model models orthologs of translation elongation factor ... |
17-157 | 1.95e-09 | ||||||||
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] Pssm-ID: 129576 [Multi-domain] Cd Length: 394 Bit Score: 59.41 E-value: 1.95e-09
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| PLN03126 | PLN03126 | Elongation factor Tu; Provisional |
17-157 | 2.29e-09 | ||||||||
Elongation factor Tu; Provisional Pssm-ID: 215592 [Multi-domain] Cd Length: 478 Bit Score: 59.63 E-value: 2.29e-09
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
15-167 | 3.08e-09 | ||||||||
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. Pssm-ID: 206648 [Multi-domain] Cd Length: 161 Bit Score: 55.93 E-value: 3.08e-09
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
15-161 | 3.98e-09 | ||||||||
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. Pssm-ID: 206674 [Multi-domain] Cd Length: 169 Bit Score: 55.94 E-value: 3.98e-09
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| EFG_mtEFG_II | cd04088 | Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation ... |
294-379 | 2.45e-08 | ||||||||
Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation factors G1 and G2; This family represents the domain II of bacterial Elongation factor G (EF-G)and mitochondrial Elongation factors G1 (mtEFG1) and G2 (mtEFG2). 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 homolog of mtEFG2, MEF2. Pssm-ID: 293905 [Multi-domain] Cd Length: 83 Bit Score: 51.37 E-value: 2.45e-08
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| infB | CHL00189 | translation initiation factor 2; Provisional |
2-160 | 3.31e-08 | ||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 56.38 E-value: 3.31e-08
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| tufA | CHL00071 | elongation factor Tu |
17-157 | 1.15e-07 | ||||||||
elongation factor Tu Pssm-ID: 177010 [Multi-domain] Cd Length: 409 Bit Score: 54.19 E-value: 1.15e-07
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
15-121 | 1.62e-07 | ||||||||
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors Pssm-ID: 444074 [Multi-domain] Cd Length: 423 Bit Score: 53.78 E-value: 1.62e-07
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| PRK12317 | PRK12317 | elongation factor 1-alpha; Reviewed |
15-121 | 2.00e-07 | ||||||||
elongation factor 1-alpha; Reviewed Pssm-ID: 237055 [Multi-domain] Cd Length: 425 Bit Score: 53.39 E-value: 2.00e-07
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| EF1_alpha | cd01883 | Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ... |
14-125 | 2.34e-07 | ||||||||
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. Pssm-ID: 206670 [Multi-domain] Cd Length: 219 Bit Score: 51.72 E-value: 2.34e-07
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
19-160 | 2.40e-07 | ||||||||
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. Pssm-ID: 206734 [Multi-domain] Cd Length: 170 Bit Score: 50.68 E-value: 2.40e-07
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
16-149 | 3.76e-07 | ||||||||
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] Pssm-ID: 273102 [Multi-domain] Cd Length: 587 Bit Score: 52.85 E-value: 3.76e-07
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| PLN03127 | PLN03127 | Elongation factor Tu; Provisional |
17-157 | 7.71e-07 | ||||||||
Elongation factor Tu; Provisional Pssm-ID: 178673 [Multi-domain] Cd Length: 447 Bit Score: 51.75 E-value: 7.71e-07
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| EF_Tu | cd01884 | Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ... |
17-157 | 2.18e-06 | ||||||||
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. Pssm-ID: 206671 [Multi-domain] Cd Length: 195 Bit Score: 48.35 E-value: 2.18e-06
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| Translation_Factor_II_like | cd01342 | Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ... |
294-378 | 2.30e-06 | ||||||||
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. 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. Pssm-ID: 293888 [Multi-domain] Cd Length: 80 Bit Score: 45.72 E-value: 2.30e-06
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
13-141 | 3.21e-06 | ||||||||
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide. Pssm-ID: 460387 [Multi-domain] Cd Length: 113 Bit Score: 46.07 E-value: 3.21e-06
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| EFG_III | pfam14492 | Elongation Factor G, domain III; This domain is found in Elongation Factor G. It shares a ... |
407-463 | 6.76e-06 | ||||||||
Elongation Factor G, domain III; This domain is found in Elongation Factor G. It shares a similar structure with domain V (pfam00679). Structural studies in drosophila indicate this is domain 3. Pssm-ID: 464188 [Multi-domain] Cd Length: 75 Bit Score: 44.01 E-value: 6.76e-06
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| EFG_III | cd16262 | Domain III of Elongation Factor G (EFG); This model represents domain III of bacterial ... |
407-464 | 1.17e-05 | ||||||||
Domain III of Elongation Factor G (EFG); This model represents domain III of bacterial Elongation factor G (EF-G), and mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2), which play an important role during peptide synthesis and tRNA site changes. 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 of the yeast homolog of mtEFG2, MEF2. Pssm-ID: 293919 [Multi-domain] Cd Length: 76 Bit Score: 43.21 E-value: 1.17e-05
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| PLN00043 | PLN00043 | elongation factor 1-alpha; Provisional |
16-116 | 1.25e-05 | ||||||||
elongation factor 1-alpha; Provisional Pssm-ID: 165621 [Multi-domain] Cd Length: 447 Bit Score: 47.78 E-value: 1.25e-05
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| PRK12736 | PRK12736 | elongation factor Tu; Reviewed |
17-157 | 1.87e-05 | ||||||||
elongation factor Tu; Reviewed Pssm-ID: 237184 [Multi-domain] Cd Length: 394 Bit Score: 46.86 E-value: 1.87e-05
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| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
16-116 | 1.93e-05 | ||||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 47.05 E-value: 1.93e-05
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| SelB_euk | cd01889 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
16-143 | 3.22e-05 | ||||||||
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. Pssm-ID: 206676 [Multi-domain] Cd Length: 192 Bit Score: 45.05 E-value: 3.22e-05
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| GTP_EFTU_D2 | pfam03144 | Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ... |
312-378 | 4.14e-05 | ||||||||
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. Pssm-ID: 427163 [Multi-domain] Cd Length: 73 Bit Score: 41.87 E-value: 4.14e-05
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
15-167 | 5.96e-05 | ||||||||
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Pssm-ID: 206646 [Multi-domain] Cd Length: 161 Bit Score: 43.39 E-value: 5.96e-05
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| PRK04004 | PRK04004 | translation initiation factor IF-2; Validated |
15-144 | 1.32e-04 | ||||||||
translation initiation factor IF-2; Validated Pssm-ID: 235195 [Multi-domain] Cd Length: 586 Bit Score: 44.79 E-value: 1.32e-04
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| PRK12735 | PRK12735 | elongation factor Tu; Reviewed |
17-157 | 1.82e-04 | ||||||||
elongation factor Tu; Reviewed Pssm-ID: 183708 [Multi-domain] Cd Length: 396 Bit Score: 44.06 E-value: 1.82e-04
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
15-157 | 3.12e-04 | ||||||||
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA. Pssm-ID: 206726 [Multi-domain] Cd Length: 168 Bit Score: 41.68 E-value: 3.12e-04
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| PRK14845 | PRK14845 | translation initiation factor IF-2; Provisional |
78-144 | 4.17e-04 | ||||||||
translation initiation factor IF-2; Provisional Pssm-ID: 237833 [Multi-domain] Cd Length: 1049 Bit Score: 43.33 E-value: 4.17e-04
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| PRK00049 | PRK00049 | elongation factor Tu; Reviewed |
17-157 | 2.79e-03 | ||||||||
elongation factor Tu; Reviewed Pssm-ID: 234596 [Multi-domain] Cd Length: 396 Bit Score: 40.17 E-value: 2.79e-03
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| CysN_ATPS | cd04166 | CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ... |
14-143 | 3.04e-03 | ||||||||
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. Pssm-ID: 206729 [Multi-domain] Cd Length: 209 Bit Score: 39.09 E-value: 3.04e-03
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| mtEFG1_II_like | cd04091 | Domain II of mitochondrial elongation factor G1-like proteins found in eukaryotes; Eukaryotic ... |
294-378 | 3.78e-03 | ||||||||
Domain II of mitochondrial elongation factor G1-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. Pssm-ID: 293908 [Multi-domain] Cd Length: 81 Bit Score: 36.50 E-value: 3.78e-03
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
15-157 | 4.06e-03 | ||||||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 38.42 E-value: 4.06e-03
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