U5 snRNP GTPase SNU114 [Saccharomyces cerevisiae S288C]
Protein Classification
translation factor GTPase family protein( domain architecture ID 1903461)
translation factor GTPase family protein such as elongation factor G that catalyzes the translocation step of protein synthesis, and TetM/TetW/TetO/TetS family tetracycline resistance ribosomal protection proteins that abolish the inhibitory effect of tetracyclin on protein synthesis
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||||||
| PRK13351 super family | cl46912 | elongation factor G-like protein; |
121-992 | 3.41e-120 | |||||||||||||
elongation factor G-like protein; The actual alignment was detected with superfamily member PTZ00416: Pssm-ID: 481252 [Multi-domain] Cd Length: 836 Bit Score: 387.87 E-value: 3.41e-120
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| Name | Accession | Description | Interval | E-value | |||||||||||||
| PTZ00416 | PTZ00416 | elongation factor 2; Provisional |
121-992 | 3.41e-120 | |||||||||||||
elongation factor 2; Provisional Pssm-ID: 240409 [Multi-domain] Cd Length: 836 Bit Score: 387.87 E-value: 3.41e-120
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| Snu114p | cd04167 | Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ... |
135-331 | 6.96e-101 | |||||||||||||
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: 315.36 E-value: 6.96e-101
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
131-320 | 4.51e-41 | |||||||||||||
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: 149.21 E-value: 4.51e-41
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| FusA | COG0480 | Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
126-272 | 2.28e-16 | |||||||||||||
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: 83.94 E-value: 2.28e-16
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| EFG_IV | smart00889 | Elongation factor G, domain IV; Translation elongation factors are responsible for two main ... |
740-853 | 5.11e-16 | |||||||||||||
Elongation factor G, domain IV; Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. Pssm-ID: 214887 [Multi-domain] Cd Length: 120 Bit Score: 75.27 E-value: 5.11e-16
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
208-272 | 7.18e-04 | |||||||||||||
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: 43.60 E-value: 7.18e-04
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| Name | Accession | Description | Interval | E-value | |||||||||||||
| PTZ00416 | PTZ00416 | elongation factor 2; Provisional |
121-992 | 3.41e-120 | |||||||||||||
elongation factor 2; Provisional Pssm-ID: 240409 [Multi-domain] Cd Length: 836 Bit Score: 387.87 E-value: 3.41e-120
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| Snu114p | cd04167 | Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ... |
135-331 | 6.96e-101 | |||||||||||||
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: 315.36 E-value: 6.96e-101
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| PLN00116 | PLN00116 | translation elongation factor EF-2 subunit; Provisional |
121-976 | 1.01e-99 | |||||||||||||
translation elongation factor EF-2 subunit; Provisional Pssm-ID: 177730 [Multi-domain] Cd Length: 843 Bit Score: 332.84 E-value: 1.01e-99
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| EF2_IV_snRNP | cd01683 | EF-2_domain IV_snRNP domain is a part of 116kD U5-specific protein of the U5 small ... |
672-864 | 8.33e-78 | |||||||||||||
EF-2_domain IV_snRNP domain is a part of 116kD U5-specific protein of the U5 small nucleoprotein (snRNP) particle, essential component of the spliceosome. The protein is structurally closely related to the eukaryotic translational elongation factor EF2. This domain has been also identified in 114kD U5-specific protein of Saccharomyces cerevisiae and may play an important role either in splicing process itself or the recycling of spliceosomal snRNP. Pssm-ID: 238840 [Multi-domain] Cd Length: 178 Bit Score: 251.82 E-value: 8.33e-78
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| PRK07560 | PRK07560 | elongation factor EF-2; Reviewed |
124-994 | 3.32e-76 | |||||||||||||
elongation factor EF-2; Reviewed Pssm-ID: 236047 [Multi-domain] Cd Length: 731 Bit Score: 265.57 E-value: 3.32e-76
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| aeEF2_snRNP_like_IV | cd01681 | This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and ... |
672-863 | 5.88e-55 | |||||||||||||
This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. 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 of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Phe-tRNA, EF-1 (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm. Pssm-ID: 238839 [Multi-domain] Cd Length: 177 Bit Score: 188.55 E-value: 5.88e-55
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| EF2 | cd01885 | Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a ... |
135-331 | 4.29e-41 | |||||||||||||
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: 150.46 E-value: 4.29e-41
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
131-320 | 4.51e-41 | |||||||||||||
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: 149.21 E-value: 4.51e-41
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| eEF2_C_snRNP | cd04098 | eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 ... |
859-941 | 1.43e-36 | |||||||||||||
eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Pssm-ID: 239765 [Multi-domain] Cd Length: 80 Bit Score: 132.37 E-value: 1.43e-36
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| snRNP_III | cd16264 | Domain III of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component; ... |
601-672 | 5.63e-35 | |||||||||||||
Domain III of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component; Domain III of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p is homologous to domain III of the eukaryotic translational elongation factor EF-2. U5-116 kD is a GTPase component of the spliceosome complex which functions in the processing of precursor mRNAs to produce mature mRNAs. Pssm-ID: 293921 [Multi-domain] Cd Length: 72 Bit Score: 127.61 E-value: 5.63e-35
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| eEF2_snRNP_like_C | cd04096 | eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor ... |
859-941 | 6.04e-31 | |||||||||||||
eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Pssm-ID: 239763 [Multi-domain] Cd Length: 80 Bit Score: 116.10 E-value: 6.04e-31
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| EF2_II_snRNP | cd04090 | Domain II of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component; This ... |
468-579 | 2.24e-30 | |||||||||||||
Domain II of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component; This subfamily includes domain II 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. U5-116 kD is a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Pssm-ID: 293907 [Multi-domain] Cd Length: 94 Bit Score: 115.03 E-value: 2.24e-30
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| GTP_translation_factor | cd00881 | GTP translation factor family primarily contains translation initiation, elongation and ... |
135-320 | 5.56e-29 | |||||||||||||
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: 114.31 E-value: 5.56e-29
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| PRK13351 | PRK13351 | elongation factor G-like protein; |
126-947 | 1.50e-28 | |||||||||||||
elongation factor G-like protein; Pssm-ID: 237358 [Multi-domain] Cd Length: 687 Bit Score: 122.75 E-value: 1.50e-28
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| EF2_snRNP_III | cd16261 | Domain III of Elongation Factor 2 (EF2); This model represents domain III of Elongation factor ... |
602-672 | 3.01e-21 | |||||||||||||
Domain III of Elongation Factor 2 (EF2); This model represents domain III of Elongation factor 2 (EF2) found in eukaryotes and archaea, and 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 are important for the function of the U5-116 kD/Snu114p. Pssm-ID: 293918 [Multi-domain] Cd Length: 72 Bit Score: 88.40 E-value: 3.01e-21
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| Elongation_Factor_C | cd01514 | Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of ... |
859-941 | 1.94e-16 | |||||||||||||
Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown. Pssm-ID: 238772 [Multi-domain] Cd Length: 79 Bit Score: 74.83 E-value: 1.94e-16
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| FusA | COG0480 | Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
126-272 | 2.28e-16 | |||||||||||||
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: 83.94 E-value: 2.28e-16
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| EFG_IV | smart00889 | Elongation factor G, domain IV; Translation elongation factors are responsible for two main ... |
740-853 | 5.11e-16 | |||||||||||||
Elongation factor G, domain IV; Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. Pssm-ID: 214887 [Multi-domain] Cd Length: 120 Bit Score: 75.27 E-value: 5.11e-16
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| EF-G_bact | cd04170 | Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ... |
135-272 | 1.30e-15 | |||||||||||||
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: 78.02 E-value: 1.30e-15
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| EFG_C | pfam00679 | Elongation factor G C-terminus; This domain includes the carboxyl terminal regions of ... |
856-947 | 8.78e-15 | |||||||||||||
Elongation factor G C-terminus; This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. Pssm-ID: 425814 [Multi-domain] Cd Length: 88 Bit Score: 70.65 E-value: 8.78e-15
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| PRK12740 | PRK12740 | elongation factor G-like protein EF-G2; |
139-673 | 1.28e-14 | |||||||||||||
elongation factor G-like protein EF-G2; Pssm-ID: 237186 [Multi-domain] Cd Length: 668 Bit Score: 78.24 E-value: 1.28e-14
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| LepA | cd01890 | LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ... |
135-271 | 6.30e-12 | |||||||||||||
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: 65.25 E-value: 6.30e-12
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| EFG_IV | pfam03764 | Elongation factor G, domain IV; This domain is found in elongation factor G, elongation factor ... |
740-853 | 3.47e-11 | |||||||||||||
Elongation factor G, domain IV; This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. Pssm-ID: 397710 [Multi-domain] Cd Length: 121 Bit Score: 61.47 E-value: 3.47e-11
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| TypA_BipA | cd01891 | Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ... |
133-272 | 9.18e-10 | |||||||||||||
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: 59.14 E-value: 9.18e-10
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| EFG_C | smart00838 | Elongation factor G C-terminus; This domain includes the carboxyl terminal regions of ... |
857-946 | 5.00e-08 | |||||||||||||
Elongation factor G C-terminus; This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. Pssm-ID: 197906 [Multi-domain] Cd Length: 85 Bit Score: 51.35 E-value: 5.00e-08
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| PRK10218 | PRK10218 | translational GTPase TypA; |
131-272 | 4.25e-07 | |||||||||||||
translational GTPase TypA; Pssm-ID: 104396 [Multi-domain] Cd Length: 607 Bit Score: 53.94 E-value: 4.25e-07
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| RF3 | cd04169 | Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; ... |
184-276 | 1.04e-06 | |||||||||||||
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: 51.44 E-value: 1.04e-06
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| SelB_euk | cd01889 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
134-271 | 7.36e-06 | |||||||||||||
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: 47.75 E-value: 7.36e-06
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
125-271 | 9.98e-06 | |||||||||||||
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: 49.16 E-value: 9.98e-06
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
203-273 | 1.41e-05 | |||||||||||||
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: 46.31 E-value: 1.41e-05
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
203-269 | 3.96e-05 | |||||||||||||
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: 43.76 E-value: 3.96e-05
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
212-295 | 5.01e-05 | |||||||||||||
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: 44.76 E-value: 5.01e-05
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| prfC | PRK00741 | peptide chain release factor 3; Provisional |
184-283 | 6.81e-05 | |||||||||||||
peptide chain release factor 3; Provisional Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 46.66 E-value: 6.81e-05
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
137-273 | 1.72e-04 | |||||||||||||
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: 43.21 E-value: 1.72e-04
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| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
134-244 | 2.10e-04 | |||||||||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 45.12 E-value: 2.10e-04
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
179-245 | 4.45e-04 | |||||||||||||
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: 42.21 E-value: 4.45e-04
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| EFG_III | pfam14492 | Elongation Factor G, domain III; This domain is found in Elongation Factor G. It shares a ... |
600-670 | 5.82e-04 | |||||||||||||
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: 39.39 E-value: 5.82e-04
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
208-272 | 7.18e-04 | |||||||||||||
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: 43.60 E-value: 7.18e-04
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
133-308 | 7.80e-04 | |||||||||||||
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: 41.20 E-value: 7.80e-04
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| PLN00043 | PLN00043 | elongation factor 1-alpha; Provisional |
134-244 | 1.02e-03 | |||||||||||||
elongation factor 1-alpha; Provisional Pssm-ID: 165621 [Multi-domain] Cd Length: 447 Bit Score: 42.77 E-value: 1.02e-03
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| EF2_II | cd16268 | Domain II of Elongation Factor 2; This subfamily represents domain II of elongation factor 2 ... |
476-577 | 4.95e-03 | |||||||||||||
Domain II of Elongation Factor 2; This subfamily represents domain II of elongation factor 2 (EF-2) found in eukaryotes and archaea. 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. Pssm-ID: 293913 [Multi-domain] Cd Length: 96 Bit Score: 37.20 E-value: 4.95e-03
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| infB | CHL00189 | translation initiation factor 2; Provisional |
205-272 | 6.90e-03 | |||||||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 40.20 E-value: 6.90e-03
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