translation elongation factor EF1-alpha, partial [Holtermannia corniformis]
Protein Classification
P-loop NTPase family protein( domain architecture ID 1562424)
P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| P-loop_NTPase super family | cl38936 | P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ... |
1-344 | 0e+00 | ||||||
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families. The actual alignment was detected with superfamily member PTZ00141: Pssm-ID: 476819 [Multi-domain] Cd Length: 446 Bit Score: 661.83 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||
| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
1-344 | 0e+00 | ||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 661.83 E-value: 0e+00
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| EF-1_alpha | TIGR00483 | translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ... |
1-344 | 0e+00 | ||||||
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels. [Protein synthesis, Translation factors] Pssm-ID: 129574 [Multi-domain] Cd Length: 426 Bit Score: 557.55 E-value: 0e+00
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
1-344 | 0e+00 | ||||||
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: 507.93 E-value: 0e+00
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| EF1_alpha | cd01883 | Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ... |
1-145 | 1.12e-83 | ||||||
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: 252.41 E-value: 1.12e-83
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| GTP_EFTU_D3 | pfam03143 | Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ... |
240-344 | 3.59e-33 | ||||||
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889. Pssm-ID: 397314 [Multi-domain] Cd Length: 105 Bit Score: 118.52 E-value: 3.59e-33
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| Name | Accession | Description | Interval | E-value | ||||||
| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
1-344 | 0e+00 | ||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 661.83 E-value: 0e+00
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| EF-1_alpha | TIGR00483 | translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ... |
1-344 | 0e+00 | ||||||
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels. [Protein synthesis, Translation factors] Pssm-ID: 129574 [Multi-domain] Cd Length: 426 Bit Score: 557.55 E-value: 0e+00
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
1-344 | 0e+00 | ||||||
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: 507.93 E-value: 0e+00
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| PLN00043 | PLN00043 | elongation factor 1-alpha; Provisional |
1-344 | 1.25e-180 | ||||||
elongation factor 1-alpha; Provisional Pssm-ID: 165621 [Multi-domain] Cd Length: 447 Bit Score: 507.32 E-value: 1.25e-180
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| PRK12317 | PRK12317 | elongation factor 1-alpha; Reviewed |
1-344 | 1.48e-178 | ||||||
elongation factor 1-alpha; Reviewed Pssm-ID: 237055 [Multi-domain] Cd Length: 425 Bit Score: 501.38 E-value: 1.48e-178
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| EF1_alpha | cd01883 | Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ... |
1-145 | 1.12e-83 | ||||||
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: 252.41 E-value: 1.12e-83
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| CysN | COG2895 | Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and ... |
1-343 | 4.43e-71 | ||||||
Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and metabolism]; Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family is part of the Pathway/BioSystem: Cysteine biosynthesis Pssm-ID: 442140 [Multi-domain] Cd Length: 430 Bit Score: 227.28 E-value: 4.43e-71
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| EF1_alpha_III | cd03705 | Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for ... |
242-344 | 1.04e-67 | ||||||
Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 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 model represents the alpha subunit, which is the counterpart of bacterial EF-Tu for archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha). Pssm-ID: 294004 [Multi-domain] Cd Length: 104 Bit Score: 207.82 E-value: 1.04e-67
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| EF1_alpha_II | cd03693 | Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ... |
149-239 | 4.47e-62 | ||||||
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor 1-alpha (EF-1A) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF-1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF-1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression. Pssm-ID: 293894 [Multi-domain] Cd Length: 91 Bit Score: 192.79 E-value: 4.47e-62
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| CysN | TIGR02034 | sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic ... |
1-343 | 2.69e-44 | ||||||
sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase). [Central intermediary metabolism, Sulfur metabolism] Pssm-ID: 213679 [Multi-domain] Cd Length: 406 Bit Score: 156.76 E-value: 2.69e-44
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| tufA | CHL00071 | elongation factor Tu |
2-344 | 1.40e-42 | ||||||
elongation factor Tu Pssm-ID: 177010 [Multi-domain] Cd Length: 409 Bit Score: 152.42 E-value: 1.40e-42
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| TufA | COG0050 | Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ... |
1-232 | 1.77e-42 | ||||||
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors Pssm-ID: 439820 [Multi-domain] Cd Length: 396 Bit Score: 151.46 E-value: 1.77e-42
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| PRK05506 | PRK05506 | bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional |
2-252 | 8.84e-42 | ||||||
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional Pssm-ID: 180120 [Multi-domain] Cd Length: 632 Bit Score: 153.93 E-value: 8.84e-42
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| cysN | PRK05124 | sulfate adenylyltransferase subunit 1; Provisional |
2-252 | 1.36e-40 | ||||||
sulfate adenylyltransferase subunit 1; Provisional Pssm-ID: 235349 [Multi-domain] Cd Length: 474 Bit Score: 148.14 E-value: 1.36e-40
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| PLN03127 | PLN03127 | Elongation factor Tu; Provisional |
2-344 | 1.90e-40 | ||||||
Elongation factor Tu; Provisional Pssm-ID: 178673 [Multi-domain] Cd Length: 447 Bit Score: 147.28 E-value: 1.90e-40
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| PRK00049 | PRK00049 | elongation factor Tu; Reviewed |
2-232 | 2.83e-40 | ||||||
elongation factor Tu; Reviewed Pssm-ID: 234596 [Multi-domain] Cd Length: 396 Bit Score: 145.72 E-value: 2.83e-40
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| PLN03126 | PLN03126 | Elongation factor Tu; Provisional |
2-344 | 1.05e-39 | ||||||
Elongation factor Tu; Provisional Pssm-ID: 215592 [Multi-domain] Cd Length: 478 Bit Score: 145.91 E-value: 1.05e-39
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| PRK12736 | PRK12736 | elongation factor Tu; Reviewed |
1-344 | 1.34e-39 | ||||||
elongation factor Tu; Reviewed Pssm-ID: 237184 [Multi-domain] Cd Length: 394 Bit Score: 143.93 E-value: 1.34e-39
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| CysN_ATPS | cd04166 | CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ... |
1-146 | 1.90e-39 | ||||||
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: 138.47 E-value: 1.90e-39
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| PRK12735 | PRK12735 | elongation factor Tu; Reviewed |
2-232 | 9.34e-38 | ||||||
elongation factor Tu; Reviewed Pssm-ID: 183708 [Multi-domain] Cd Length: 396 Bit Score: 139.20 E-value: 9.34e-38
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| EF-Tu | TIGR00485 | translation elongation factor TU; This model models orthologs of translation elongation factor ... |
2-232 | 7.15e-36 | ||||||
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: 134.13 E-value: 7.15e-36
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| SelB | COG3276 | Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ... |
2-344 | 3.76e-35 | ||||||
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors Pssm-ID: 442507 [Multi-domain] Cd Length: 630 Bit Score: 135.04 E-value: 3.76e-35
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| GTP_EFTU_D3 | pfam03143 | Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ... |
240-344 | 3.59e-33 | ||||||
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889. Pssm-ID: 397314 [Multi-domain] Cd Length: 105 Bit Score: 118.52 E-value: 3.59e-33
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
1-110 | 7.78e-33 | ||||||
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: 120.32 E-value: 7.78e-33
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| Translation_factor_III | cd01513 | Domain III of Elongation factor (EF) Tu (EF-TU) and related proteins; Elongation factor (EF) ... |
242-344 | 2.04e-32 | ||||||
Domain III of Elongation factor (EF) Tu (EF-TU) and related proteins; Elongation factor (EF) EF-Tu participates in the elongation phase during protein biosynthesis on the ribosome. Its functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental findings indicate an essential contribution of domain III to activation of GTP hydrolysis. This domain III, which is distinct from the domain III in EFG and related elongation factors, is found in several eukaryotic translation factors, like peptide chain release factors RF3, elongation factor 1, selenocysteine (Sec)-specific elongation factor, and in GT-1 family of GTPase (GTPBP1). Pssm-ID: 275447 [Multi-domain] Cd Length: 102 Bit Score: 116.72 E-value: 2.04e-32
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| eRF3_C_III | cd03704 | C-terminal domain of eRF3; This model represents the eEF1alpha-like C-terminal region of eRF3, ... |
242-344 | 1.73e-26 | ||||||
C-terminal domain of eRF3; This model represents the eEF1alpha-like C-terminal region of eRF3, which is homologous to the domain III of EF-Tu. eRF3 is a GTPase which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions: N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. Pssm-ID: 294003 [Multi-domain] Cd Length: 108 Bit Score: 101.09 E-value: 1.73e-26
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| selB | TIGR00475 | selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ... |
1-242 | 1.42e-24 | ||||||
selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors] Pssm-ID: 129567 [Multi-domain] Cd Length: 581 Bit Score: 104.57 E-value: 1.42e-24
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| GTP_translation_factor | cd00881 | GTP translation factor family primarily contains translation initiation, elongation and ... |
1-146 | 2.90e-24 | ||||||
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: 97.75 E-value: 2.90e-24
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| EF_Tu | cd01884 | Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ... |
2-145 | 6.99e-21 | ||||||
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: 88.79 E-value: 6.99e-21
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| Translation_Factor_II_like | cd01342 | Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ... |
153-234 | 2.59e-19 | ||||||
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: 81.16 E-value: 2.59e-19
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| HBS1_C_III | cd04093 | C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the ... |
240-344 | 3.77e-18 | ||||||
C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1), which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, which together with Dom34, promotes the No-go decay (NGD) of mRNA. The NGD targets mRNAs whose elongation stalled for degradation initiated by endonucleolytic cleavage in the vicinity of the stalled ribosome. Pssm-ID: 294008 [Multi-domain] Cd Length: 109 Bit Score: 78.74 E-value: 3.77e-18
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| SelB_II | cd03696 | Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ... |
153-233 | 6.72e-17 | ||||||
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. Pssm-ID: 293897 [Multi-domain] Cd Length: 83 Bit Score: 74.49 E-value: 6.72e-17
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| EFTU_II | cd03697 | Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ... |
155-232 | 4.39e-16 | ||||||
Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven alpha helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Both non-catalytic domains are composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA; and an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher affinity for GDP than for GTP. Pssm-ID: 293898 [Multi-domain] Cd Length: 87 Bit Score: 72.55 E-value: 4.39e-16
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
2-106 | 1.25e-15 | ||||||
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: 73.79 E-value: 1.25e-15
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| GTP_EFTU_D2 | pfam03144 | Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ... |
167-232 | 5.05e-15 | ||||||
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: 69.22 E-value: 5.05e-15
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| HBS1-like_II | cd16267 | Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class ... |
152-232 | 6.23e-14 | ||||||
Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class II release factor (eRF3). Hbs1, together with Dom34 (pelota), plays an important role in termination and recycling, but in contrast to eRF3/eRF1, Hbs1, together with Dom34 (pelota), functions on mRNA-bound ribosomes in a codon-independent manner and promotes subunit splitting on completely empty ribosomes. Pssm-ID: 293912 [Multi-domain] Cd Length: 84 Bit Score: 66.38 E-value: 6.23e-14
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| eRF3_II | cd04089 | Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is ... |
152-232 | 4.54e-11 | ||||||
Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. Pssm-ID: 293906 [Multi-domain] Cd Length: 82 Bit Score: 58.27 E-value: 4.54e-11
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| eRF3_II_like | cd03698 | Domain II of the eukaryotic class II release factor-like proteins; This model represents the ... |
152-232 | 9.47e-10 | ||||||
Domain II of the eukaryotic class II release factor-like proteins; This model represents the domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. This group also contains proteins similar to S. cerevisiae Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation 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: 293899 [Multi-domain] Cd Length: 84 Bit Score: 54.81 E-value: 9.47e-10
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| GTPBP_II | cd03694 | Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to ... |
159-232 | 4.44e-09 | ||||||
Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution. Pssm-ID: 293895 [Multi-domain] Cd Length: 87 Bit Score: 52.99 E-value: 4.44e-09
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| CysN_NodQ_II | cd03695 | Domain II of the large subunit of ATP sulfurylase; This subfamily represents domain II of the ... |
153-217 | 7.30e-09 | ||||||
Domain II of the large subunit of ATP sulfurylase; This subfamily represents domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction, APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sulfation of a nodulation factor. In Rhizobium meliloti, the heterodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, archaea, and eukaryotes use a different ATP sulfurylase, which shows no amino acid sequence similarity to CysN or NodQ. CysN and the N-terminal portion of NodQ show similarity to GTPases involved in translation, in particular, EF-Tu and EF-1alpha. Pssm-ID: 293896 [Multi-domain] Cd Length: 81 Bit Score: 52.18 E-value: 7.30e-09
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| PRK04000 | PRK04000 | translation initiation factor IF-2 subunit gamma; Validated |
1-216 | 2.43e-08 | ||||||
translation initiation factor IF-2 subunit gamma; Validated Pssm-ID: 235194 [Multi-domain] Cd Length: 411 Bit Score: 55.24 E-value: 2.43e-08
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| PRK10512 | PRK10512 | selenocysteinyl-tRNA-specific translation factor; Provisional |
2-77 | 3.73e-06 | ||||||
selenocysteinyl-tRNA-specific translation factor; Provisional Pssm-ID: 182508 [Multi-domain] Cd Length: 614 Bit Score: 48.51 E-value: 3.73e-06
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| GTPBP_III | cd03708 | Domain III of the GP-1 family of GTPases; This family includes proteins similar to GTPBP1 and ... |
242-311 | 4.96e-06 | ||||||
Domain III of the GP-1 family of GTPases; This family includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in the cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution. Pssm-ID: 294007 [Multi-domain] Cd Length: 87 Bit Score: 44.05 E-value: 4.96e-06
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| PTZ00327 | PTZ00327 | eukaryotic translation initiation factor 2 gamma subunit; Provisional |
2-101 | 1.65e-05 | ||||||
eukaryotic translation initiation factor 2 gamma subunit; Provisional Pssm-ID: 240362 [Multi-domain] Cd Length: 460 Bit Score: 46.54 E-value: 1.65e-05
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| Translation_Factor_II | cd16265 | Proteins related to domain II of EF-Tu and related translation factors; Elongation factor Tu ... |
158-216 | 1.68e-04 | ||||||
Proteins related to domain II of EF-Tu and related translation factors; Elongation factor Tu consists of three structural domains; this family represents single domain proteins that are related to the second domain of EF-Tu. Domain II of EF-Tu adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is also found in other proteins such as elongation factor G and translation initiation factor IF-2. Pssm-ID: 293910 [Multi-domain] Cd Length: 80 Bit Score: 39.59 E-value: 1.68e-04
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
2-108 | 2.39e-04 | ||||||
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: 41.30 E-value: 2.39e-04
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| FERM_C_CCM1 | cd13197 | FERM domain C-lobe of Cerebral cavernous malformation 1; CCM1 (also called KRIT-1/Krev ... |
306-336 | 2.25e-03 | ||||||
FERM domain C-lobe of Cerebral cavernous malformation 1; CCM1 (also called KRIT-1/Krev interaction trapped 1;ankyrin repeat-containing protein Krit1; CAM), a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins. Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of proteins, mutations of which are found in cerebral cavernous malformations which are characterized by cerebral hemorrhages and vascular malformations in the central nervous system. KRIT-1 possesses four ankyrin repeats, a FERM domain, and multiple NPXY sequences, one of which is essential for integrin cytoplasmic domain-associated protein-1alpha (ICAP1alpha) binding and all of which mediate binding of CCM2. KRIT-1 localization is mediated by its FERM domain. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. Pssm-ID: 270018 Cd Length: 100 Bit Score: 37.21 E-value: 2.25e-03
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