translation initiation factor IF-2 [Haemophilus parahaemolyticus]
Protein Classification
translation initiation factor IF-2( domain architecture ID 12057539)
translation initiation factor IF-2 protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits; also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
348-850 | 0e+00 | ||||||||
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors : Pssm-ID: 440298 [Multi-domain] Cd Length: 502 Bit Score: 987.97 E-value: 0e+00
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| IF2_N | pfam04760 | Translation initiation factor IF-2, N-terminal region; This conserved feature at the ... |
274-324 | 3.99e-17 | ||||||||
Translation initiation factor IF-2, N-terminal region; This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. : Pssm-ID: 428110 [Multi-domain] Cd Length: 52 Bit Score: 75.58 E-value: 3.99e-17
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| PTZ00121 super family | cl31754 | MAEBL; Provisional |
3-351 | 7.72e-03 | ||||||||
MAEBL; Provisional The actual alignment was detected with superfamily member PTZ00121: Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 40.12 E-value: 7.72e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
348-850 | 0e+00 | ||||||||||
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors Pssm-ID: 440298 [Multi-domain] Cd Length: 502 Bit Score: 987.97 E-value: 0e+00
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
265-850 | 0e+00 | ||||||||||
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: 977.33 E-value: 0e+00
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| infB | CHL00189 | translation initiation factor 2; Provisional |
185-850 | 0e+00 | ||||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 599.51 E-value: 0e+00
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
352-516 | 4.50e-103 | ||||||||||
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: 315.57 E-value: 4.50e-103
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
354-510 | 9.41e-45 | ||||||||||
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: 159.23 E-value: 9.41e-45
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| IF2_N | pfam04760 | Translation initiation factor IF-2, N-terminal region; This conserved feature at the ... |
274-324 | 3.99e-17 | ||||||||||
Translation initiation factor IF-2, N-terminal region; This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. Pssm-ID: 428110 [Multi-domain] Cd Length: 52 Bit Score: 75.58 E-value: 3.99e-17
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3-351 | 7.72e-03 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 40.12 E-value: 7.72e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
348-850 | 0e+00 | ||||||||||
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors Pssm-ID: 440298 [Multi-domain] Cd Length: 502 Bit Score: 987.97 E-value: 0e+00
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
265-850 | 0e+00 | ||||||||||
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: 977.33 E-value: 0e+00
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| infB | CHL00189 | translation initiation factor 2; Provisional |
185-850 | 0e+00 | ||||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 599.51 E-value: 0e+00
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
352-516 | 4.50e-103 | ||||||||||
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: 315.57 E-value: 4.50e-103
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| PRK04004 | PRK04004 | translation initiation factor IF-2; Validated |
350-843 | 3.77e-68 | ||||||||||
translation initiation factor IF-2; Validated Pssm-ID: 235195 [Multi-domain] Cd Length: 586 Bit Score: 237.00 E-value: 3.77e-68
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| aIF-2 | TIGR00491 | translation initiation factor aIF-2/yIF-2; This model describes archaeal and eukaryotic ... |
350-839 | 7.32e-51 | ||||||||||
translation initiation factor aIF-2/yIF-2; This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; the alignment generated by this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region. [Protein synthesis, Translation factors] Pssm-ID: 273104 [Multi-domain] Cd Length: 591 Bit Score: 188.49 E-value: 7.32e-51
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| IF2_mtIF2_II | cd03702 | Domain II of bacterial and mitochondrial Initiation Factor 2; This family represents domain II ... |
526-619 | 3.15e-47 | ||||||||||
Domain II of bacterial and mitochondrial Initiation Factor 2; This family represents domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homolog mtIF2. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2. Pssm-ID: 293903 [Multi-domain] Cd Length: 96 Bit Score: 162.98 E-value: 3.15e-47
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
354-510 | 9.41e-45 | ||||||||||
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: 159.23 E-value: 9.41e-45
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| IF-2 | pfam11987 | Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main ... |
624-740 | 6.24e-42 | ||||||||||
Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation. Pssm-ID: 463421 [Multi-domain] Cd Length: 116 Bit Score: 148.74 E-value: 6.24e-42
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| mtIF2_IVc | cd03692 | C2 subdomain of domain IV in mitochondrial translation initiation factor 2; This model ... |
757-840 | 4.53e-41 | ||||||||||
C2 subdomain of domain IV in mitochondrial translation initiation factor 2; This model represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 has been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits. Pssm-ID: 293893 [Multi-domain] Cd Length: 84 Bit Score: 144.94 E-value: 4.53e-41
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| PRK14845 | PRK14845 | translation initiation factor IF-2; Provisional |
365-846 | 4.97e-41 | ||||||||||
translation initiation factor IF-2; Provisional Pssm-ID: 237833 [Multi-domain] Cd Length: 1049 Bit Score: 163.13 E-value: 4.97e-41
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| GTP_translation_factor | cd00881 | GTP translation factor family primarily contains translation initiation, elongation and ... |
354-512 | 2.17e-37 | ||||||||||
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: 138.20 E-value: 2.17e-37
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
358-509 | 2.10e-26 | ||||||||||
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: 106.54 E-value: 2.10e-26
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
352-510 | 2.14e-25 | ||||||||||
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: 103.22 E-value: 2.14e-25
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| SelB | COG3276 | Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ... |
358-583 | 5.27e-23 | ||||||||||
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: 104.61 E-value: 5.27e-23
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| TypA_BipA | cd01891 | Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ... |
354-510 | 1.68e-21 | ||||||||||
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: 93.04 E-value: 1.68e-21
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
356-510 | 2.60e-21 | ||||||||||
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: 91.36 E-value: 2.60e-21
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| PRK10512 | PRK10512 | selenocysteinyl-tRNA-specific translation factor; Provisional |
358-582 | 5.85e-21 | ||||||||||
selenocysteinyl-tRNA-specific translation factor; Provisional Pssm-ID: 182508 [Multi-domain] Cd Length: 614 Bit Score: 98.20 E-value: 5.85e-21
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| LepA | cd01890 | LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ... |
356-510 | 6.61e-21 | ||||||||||
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: 90.67 E-value: 6.61e-21
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| selB | TIGR00475 | selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ... |
353-574 | 4.85e-20 | ||||||||||
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: 94.94 E-value: 4.85e-20
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
356-510 | 1.42e-19 | ||||||||||
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: 86.53 E-value: 1.42e-19
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| TypA_BipA | TIGR01394 | GTP-binding protein TypA/BipA; This bacterial (and Arabidopsis) protein, termed TypA or BipA, ... |
354-593 | 1.90e-19 | ||||||||||
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: 93.13 E-value: 1.90e-19
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| SelB_euk | cd01889 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
354-505 | 4.75e-18 | ||||||||||
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: 83.18 E-value: 4.75e-18
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| PRK12736 | PRK12736 | elongation factor Tu; Reviewed |
357-558 | 6.04e-18 | ||||||||||
elongation factor Tu; Reviewed Pssm-ID: 237184 [Multi-domain] Cd Length: 394 Bit Score: 86.92 E-value: 6.04e-18
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| PRK12740 | PRK12740 | elongation factor G-like protein EF-G2; |
357-583 | 2.44e-17 | ||||||||||
elongation factor G-like protein EF-G2; Pssm-ID: 237186 [Multi-domain] Cd Length: 668 Bit Score: 86.72 E-value: 2.44e-17
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| PLN03127 | PLN03127 | Elongation factor Tu; Provisional |
354-558 | 3.72e-17 | ||||||||||
Elongation factor Tu; Provisional Pssm-ID: 178673 [Multi-domain] Cd Length: 447 Bit Score: 84.88 E-value: 3.72e-17
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| IF2_N | pfam04760 | Translation initiation factor IF-2, N-terminal region; This conserved feature at the ... |
274-324 | 3.99e-17 | ||||||||||
Translation initiation factor IF-2, N-terminal region; This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. Pssm-ID: 428110 [Multi-domain] Cd Length: 52 Bit Score: 75.58 E-value: 3.99e-17
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| PRK12317 | PRK12317 | elongation factor 1-alpha; Reviewed |
354-504 | 1.38e-16 | ||||||||||
elongation factor 1-alpha; Reviewed Pssm-ID: 237055 [Multi-domain] Cd Length: 425 Bit Score: 83.05 E-value: 1.38e-16
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| EF_Tu | cd01884 | Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ... |
355-509 | 2.31e-16 | ||||||||||
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: 78.39 E-value: 2.31e-16
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| TufA | COG0050 | Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ... |
357-558 | 2.55e-16 | ||||||||||
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: 81.74 E-value: 2.55e-16
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| EF1_alpha | cd01883 | Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ... |
356-504 | 3.02e-16 | ||||||||||
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: 78.69 E-value: 3.02e-16
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| FusA | COG0480 | Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
356-583 | 4.77e-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: 82.40 E-value: 4.77e-16
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
356-502 | 1.67e-15 | ||||||||||
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: 79.59 E-value: 1.67e-15
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| TypA | COG1217 | Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction ... |
354-476 | 2.44e-15 | ||||||||||
Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction mechanisms]; Pssm-ID: 440830 [Multi-domain] Cd Length: 606 Bit Score: 80.06 E-value: 2.44e-15
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| tufA | CHL00071 | elongation factor Tu |
355-558 | 2.53e-15 | ||||||||||
elongation factor Tu Pssm-ID: 177010 [Multi-domain] Cd Length: 409 Bit Score: 78.85 E-value: 2.53e-15
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| PRK00049 | PRK00049 | elongation factor Tu; Reviewed |
355-558 | 4.02e-15 | ||||||||||
elongation factor Tu; Reviewed Pssm-ID: 234596 [Multi-domain] Cd Length: 396 Bit Score: 78.31 E-value: 4.02e-15
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| PLN03126 | PLN03126 | Elongation factor Tu; Provisional |
350-558 | 1.24e-14 | ||||||||||
Elongation factor Tu; Provisional Pssm-ID: 215592 [Multi-domain] Cd Length: 478 Bit Score: 77.35 E-value: 1.24e-14
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| EF2 | cd01885 | Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a ... |
354-463 | 1.30e-14 | ||||||||||
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: 73.80 E-value: 1.30e-14
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| Era | COG1159 | GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; |
363-510 | 2.75e-14 | ||||||||||
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440773 [Multi-domain] Cd Length: 290 Bit Score: 74.25 E-value: 2.75e-14
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| YeeP | COG3596 | Predicted GTPase [General function prediction only]; |
350-510 | 4.45e-14 | ||||||||||
Predicted GTPase [General function prediction only]; Pssm-ID: 442815 [Multi-domain] Cd Length: 318 Bit Score: 74.03 E-value: 4.45e-14
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| PRK12735 | PRK12735 | elongation factor Tu; Reviewed |
353-558 | 1.17e-13 | ||||||||||
elongation factor Tu; Reviewed Pssm-ID: 183708 [Multi-domain] Cd Length: 396 Bit Score: 73.72 E-value: 1.17e-13
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| Snu114p | cd04167 | Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ... |
354-463 | 1.32e-13 | ||||||||||
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: 70.76 E-value: 1.32e-13
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| EF-Tu | TIGR00485 | translation elongation factor TU; This model models orthologs of translation elongation factor ... |
354-558 | 1.48e-13 | ||||||||||
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: 73.27 E-value: 1.48e-13
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| era | PRK00089 | GTPase Era; Reviewed |
349-510 | 7.49e-13 | ||||||||||
GTPase Era; Reviewed Pssm-ID: 234624 [Multi-domain] Cd Length: 292 Bit Score: 70.08 E-value: 7.49e-13
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| PRK13351 | PRK13351 | elongation factor G-like protein; |
354-539 | 7.75e-13 | ||||||||||
elongation factor G-like protein; Pssm-ID: 237358 [Multi-domain] Cd Length: 687 Bit Score: 72.29 E-value: 7.75e-13
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| EF-G_bact | cd04170 | Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ... |
354-561 | 3.45e-12 | ||||||||||
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: 67.62 E-value: 3.45e-12
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| PRK10218 | PRK10218 | translational GTPase TypA; |
354-476 | 6.65e-12 | ||||||||||
translational GTPase TypA; Pssm-ID: 104396 [Multi-domain] Cd Length: 607 Bit Score: 68.97 E-value: 6.65e-12
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
363-510 | 8.78e-12 | ||||||||||
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: 64.02 E-value: 8.78e-12
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| TetM_like | cd04168 | Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline ... |
356-475 | 2.30e-11 | ||||||||||
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: 64.57 E-value: 2.30e-11
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| Translation_Factor_II_like | cd01342 | Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ... |
761-839 | 3.36e-11 | ||||||||||
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: 59.97 E-value: 3.36e-11
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| PRK04000 | PRK04000 | translation initiation factor IF-2 subunit gamma; Validated |
352-509 | 3.61e-11 | ||||||||||
translation initiation factor IF-2 subunit gamma; Validated Pssm-ID: 235194 [Multi-domain] Cd Length: 411 Bit Score: 66.03 E-value: 3.61e-11
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
354-509 | 5.58e-11 | ||||||||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 62.31 E-value: 5.58e-11
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| Arf_Arl | cd00878 | ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ... |
363-507 | 7.26e-11 | ||||||||||
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. Pssm-ID: 206644 [Multi-domain] Cd Length: 158 Bit Score: 61.44 E-value: 7.26e-11
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| eIF2_gamma | cd01888 | Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation ... |
358-510 | 8.08e-11 | ||||||||||
Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. Pssm-ID: 206675 [Multi-domain] Cd Length: 197 Bit Score: 62.29 E-value: 8.08e-11
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| EngA2 | cd01895 | EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ... |
354-509 | 1.20e-10 | ||||||||||
EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. 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. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability. Pssm-ID: 206682 [Multi-domain] Cd Length: 174 Bit Score: 60.91 E-value: 1.20e-10
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| CysN_ATPS | cd04166 | CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ... |
358-499 | 1.70e-10 | ||||||||||
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: 61.43 E-value: 1.70e-10
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
354-460 | 2.15e-10 | ||||||||||
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: 58.78 E-value: 2.15e-10
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| cysN | PRK05124 | sulfate adenylyltransferase subunit 1; Provisional |
405-514 | 3.87e-10 | ||||||||||
sulfate adenylyltransferase subunit 1; Provisional Pssm-ID: 235349 [Multi-domain] Cd Length: 474 Bit Score: 63.01 E-value: 3.87e-10
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| EngA1 | cd01894 | EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ... |
397-510 | 4.45e-10 | ||||||||||
EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. 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. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability. Pssm-ID: 206681 [Multi-domain] Cd Length: 157 Bit Score: 58.99 E-value: 4.45e-10
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| YihA_EngB | cd01876 | YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ... |
426-509 | 7.81e-10 | ||||||||||
YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target. Pssm-ID: 206665 [Multi-domain] Cd Length: 170 Bit Score: 58.68 E-value: 7.81e-10
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| RF3 | cd04169 | Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; ... |
397-475 | 1.29e-09 | ||||||||||
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: 59.92 E-value: 1.29e-09
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
397-510 | 1.82e-09 | ||||||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 60.81 E-value: 1.82e-09
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| aEF-2 | TIGR00490 | translation elongation factor aEF-2; This model represents archaeal elongation factor 2, a ... |
354-463 | 9.33e-09 | ||||||||||
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: 59.14 E-value: 9.33e-09
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| PRK07560 | PRK07560 | elongation factor EF-2; Reviewed |
356-463 | 1.48e-08 | ||||||||||
elongation factor EF-2; Reviewed Pssm-ID: 236047 [Multi-domain] Cd Length: 731 Bit Score: 58.34 E-value: 1.48e-08
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| CysN | COG2895 | Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and ... |
405-558 | 2.36e-08 | ||||||||||
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: 57.40 E-value: 2.36e-08
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
424-510 | 4.17e-08 | ||||||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 56.57 E-value: 4.17e-08
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
424-510 | 7.49e-08 | ||||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 55.83 E-value: 7.49e-08
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| PRK05506 | PRK05506 | bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional |
405-589 | 1.23e-07 | ||||||||||
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional Pssm-ID: 180120 [Multi-domain] Cd Length: 632 Bit Score: 55.32 E-value: 1.23e-07
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| FeoB | cd01879 | Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ... |
363-510 | 1.39e-07 | ||||||||||
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Pssm-ID: 206667 [Multi-domain] Cd Length: 159 Bit Score: 51.69 E-value: 1.39e-07
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| EF-G | cd01886 | Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling ... |
356-475 | 2.72e-07 | ||||||||||
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: 52.88 E-value: 2.72e-07
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
397-510 | 3.31e-07 | ||||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 53.52 E-value: 3.31e-07
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
291-513 | 3.91e-07 | ||||||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 53.64 E-value: 3.91e-07
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| HflX | cd01878 | HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ... |
393-509 | 5.33e-07 | ||||||||||
HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms. Pssm-ID: 206666 [Multi-domain] Cd Length: 204 Bit Score: 50.92 E-value: 5.33e-07
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| Obg_like | cd01881 | Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ... |
356-510 | 6.28e-07 | ||||||||||
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified. Pssm-ID: 206668 [Multi-domain] Cd Length: 167 Bit Score: 50.09 E-value: 6.28e-07
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| PTZ00416 | PTZ00416 | elongation factor 2; Provisional |
355-463 | 6.46e-07 | ||||||||||
elongation factor 2; Provisional Pssm-ID: 240409 [Multi-domain] Cd Length: 836 Bit Score: 53.13 E-value: 6.46e-07
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
416-510 | 7.01e-07 | ||||||||||
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification Pssm-ID: 440253 [Multi-domain] Cd Length: 448 Bit Score: 52.76 E-value: 7.01e-07
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| Srp102 | COG2229 | Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, ... |
406-510 | 1.06e-06 | ||||||||||
Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, secretion, and vesicular transport]; Pssm-ID: 441830 [Multi-domain] Cd Length: 189 Bit Score: 49.82 E-value: 1.06e-06
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| GTPBP1_like | cd04165 | GTP binding protein 1 (GTPBP1)-like family includes GTPBP2; Mammalian GTP binding protein 1 ... |
354-476 | 1.65e-06 | ||||||||||
GTP binding protein 1 (GTPBP1)-like family includes GTPBP2; Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and survival. This fusion product may contribute to the onset of GBM. Pssm-ID: 206728 [Multi-domain] Cd Length: 224 Bit Score: 49.98 E-value: 1.65e-06
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| YjeQ_EngC | cd01854 | Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ... |
424-509 | 2.76e-06 | ||||||||||
Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. Pssm-ID: 206747 [Multi-domain] Cd Length: 211 Bit Score: 48.93 E-value: 2.76e-06
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| IF2_IF5B_II | cd03701 | Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ... |
526-605 | 5.12e-06 | ||||||||||
Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents domain II of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma. Pssm-ID: 293902 [Multi-domain] Cd Length: 96 Bit Score: 45.74 E-value: 5.12e-06
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
416-510 | 7.82e-06 | ||||||||||
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance. Pssm-ID: 206727 [Multi-domain] Cd Length: 159 Bit Score: 46.72 E-value: 7.82e-06
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| Obg | cd01898 | Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ... |
453-509 | 1.18e-05 | ||||||||||
Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain. Pssm-ID: 206685 [Multi-domain] Cd Length: 170 Bit Score: 46.26 E-value: 1.18e-05
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| DLP_2 | cd09912 | Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ... |
354-518 | 1.18e-05 | ||||||||||
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner. Pssm-ID: 206739 [Multi-domain] Cd Length: 180 Bit Score: 46.77 E-value: 1.18e-05
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| prfC | PRK00741 | peptide chain release factor 3; Provisional |
397-475 | 2.84e-05 | ||||||||||
peptide chain release factor 3; Provisional Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 47.44 E-value: 2.84e-05
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| Arf | pfam00025 | ADP-ribosylation factor family; Pfam combines a number of different Prosite families together |
422-507 | 3.36e-05 | ||||||||||
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together Pssm-ID: 459636 [Multi-domain] Cd Length: 160 Bit Score: 44.91 E-value: 3.36e-05
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| Arl10_like | cd04159 | Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ... |
405-510 | 4.19e-05 | ||||||||||
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. Pssm-ID: 206724 [Multi-domain] Cd Length: 159 Bit Score: 44.62 E-value: 4.19e-05
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| MnmE_helical | pfam12631 | MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ... |
416-531 | 4.97e-05 | ||||||||||
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain. Pssm-ID: 463649 [Multi-domain] Cd Length: 326 Bit Score: 46.32 E-value: 4.97e-05
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| YqeH | cd01855 | Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ... |
426-509 | 5.07e-05 | ||||||||||
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. Pssm-ID: 206748 [Multi-domain] Cd Length: 191 Bit Score: 44.95 E-value: 5.07e-05
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| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
416-509 | 5.37e-05 | ||||||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 46.64 E-value: 5.37e-05
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| PRK04213 | PRK04213 | GTP-binding protein EngB; |
350-509 | 1.26e-04 | ||||||||||
GTP-binding protein EngB; Pssm-ID: 179790 [Multi-domain] Cd Length: 201 Bit Score: 44.14 E-value: 1.26e-04
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| RocCOR | cd09914 | Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ... |
444-510 | 1.77e-04 | ||||||||||
Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease. Pssm-ID: 206741 [Multi-domain] Cd Length: 161 Bit Score: 42.71 E-value: 1.77e-04
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| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
354-499 | 1.89e-04 | ||||||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 44.74 E-value: 1.89e-04
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| HflX | COG2262 | 50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]; ... |
393-509 | 3.41e-04 | ||||||||||
50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441863 [Multi-domain] Cd Length: 419 Bit Score: 43.92 E-value: 3.41e-04
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| PTZ00327 | PTZ00327 | eukaryotic translation initiation factor 2 gamma subunit; Provisional |
401-512 | 4.24e-04 | ||||||||||
eukaryotic translation initiation factor 2 gamma subunit; Provisional Pssm-ID: 240362 [Multi-domain] Cd Length: 460 Bit Score: 43.84 E-value: 4.24e-04
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| obgE | PRK12297 | GTPase CgtA; Reviewed |
363-509 | 4.81e-04 | ||||||||||
GTPase CgtA; Reviewed Pssm-ID: 237046 [Multi-domain] Cd Length: 424 Bit Score: 43.55 E-value: 4.81e-04
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| Rab7 | cd01862 | Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ... |
354-514 | 7.69e-04 | ||||||||||
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Pssm-ID: 206655 [Multi-domain] Cd Length: 172 Bit Score: 41.11 E-value: 7.69e-04
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
332-510 | 7.78e-04 | ||||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 43.03 E-value: 7.78e-04
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| Rhes_like | cd04143 | Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); ... |
387-509 | 1.22e-03 | ||||||||||
Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression levels in other tissues. Dexras1 localizes primarily to the cytoplasm, and is a critical regulator of the circadian master clock to photic and nonphotic input. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Pssm-ID: 133343 [Multi-domain] Cd Length: 247 Bit Score: 41.66 E-value: 1.22e-03
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
351-509 | 1.66e-03 | ||||||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 42.09 E-value: 1.66e-03
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| Arl6 | cd04157 | Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ... |
354-507 | 2.08e-03 | ||||||||||
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily. Pssm-ID: 206722 [Multi-domain] Cd Length: 162 Bit Score: 39.72 E-value: 2.08e-03
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| PRK13768 | PRK13768 | GTPase; Provisional |
451-509 | 2.26e-03 | ||||||||||
GTPase; Provisional Pssm-ID: 237498 [Multi-domain] Cd Length: 253 Bit Score: 40.62 E-value: 2.26e-03
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| obgE | PRK12299 | GTPase CgtA; Reviewed |
453-509 | 3.45e-03 | ||||||||||
GTPase CgtA; Reviewed Pssm-ID: 237048 [Multi-domain] Cd Length: 335 Bit Score: 40.44 E-value: 3.45e-03
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| Arfrp1 | cd04160 | Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ... |
354-510 | 6.75e-03 | ||||||||||
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development. Pssm-ID: 206725 [Multi-domain] Cd Length: 168 Bit Score: 38.48 E-value: 6.75e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
3-351 | 7.72e-03 | ||||||||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 40.12 E-value: 7.72e-03
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| GPN1 | cd17870 | GPN-loop GTPase 1; GPN-loop GTPase 1 (GPN1, also kown as MBD2-interacting protein or MBDin, ... |
451-509 | 8.24e-03 | ||||||||||
GPN-loop GTPase 1; GPN-loop GTPase 1 (GPN1, also kown as MBD2-interacting protein or MBDin, RNAPII-associated protein 4, and XPA-binding protein 1) is a GTPase is required for nuclear targeting of RNA polymerase II. It forms heterodimers with GPN3. Pssm-ID: 349779 [Multi-domain] Cd Length: 241 Bit Score: 38.70 E-value: 8.24e-03
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
397-509 | 8.82e-03 | ||||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 39.57 E-value: 8.82e-03
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| IF2_aeIF5B_IV | cd16266 | Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ... |
764-839 | 9.14e-03 | ||||||||||
Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents the domain IV of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologs IF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma. Pssm-ID: 293911 [Multi-domain] Cd Length: 87 Bit Score: 35.98 E-value: 9.14e-03
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| Ras | cd00876 | Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ... |
397-512 | 9.75e-03 | ||||||||||
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Pssm-ID: 206642 [Multi-domain] Cd Length: 160 Bit Score: 37.51 E-value: 9.75e-03
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