translation initiation factor IF-2 [Cytophaga hutchinsonii]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
508-1008 | 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: 979.11 E-value: 0e+00
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| PBP1 super family | cl34930 | PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ... |
77-481 | 6.53e-12 | ||||||||
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; The actual alignment was detected with superfamily member COG5180: Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 69.32 E-value: 6.53e-12
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| Name | Accession | Description | Interval | E-value | |||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
508-1008 | 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: 979.11 E-value: 0e+00
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
426-1008 | 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: 788.58 E-value: 0e+00
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| infB | CHL00189 | translation initiation factor 2; Provisional |
393-1008 | 0e+00 | |||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 546.74 E-value: 0e+00
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
510-674 | 7.29e-94 | |||||||||
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: 294.77 E-value: 7.29e-94
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| IF-2 | pfam11987 | Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main ... |
782-898 | 6.00e-50 | |||||||||
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: 171.85 E-value: 6.00e-50
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| PBP1 | COG5180 | PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ... |
77-481 | 6.53e-12 | |||||||||
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 69.32 E-value: 6.53e-12
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| IF2_N | pfam04760 | Translation initiation factor IF-2, N-terminal region; This conserved feature at the ... |
432-482 | 1.06e-11 | |||||||||
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: 60.56 E-value: 1.06e-11
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| rne | PRK10811 | ribonuclease E; Reviewed |
78-272 | 2.67e-06 | |||||||||
ribonuclease E; Reviewed Pssm-ID: 236766 [Multi-domain] Cd Length: 1068 Bit Score: 51.58 E-value: 2.67e-06
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| PspC_subgroup_2 | NF033839 | pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ... |
85-368 | 1.46e-04 | |||||||||
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. Pssm-ID: 468202 [Multi-domain] Cd Length: 557 Bit Score: 45.53 E-value: 1.46e-04
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| Name | Accession | Description | Interval | E-value | |||||||||
| InfB | COG0532 | Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
508-1008 | 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: 979.11 E-value: 0e+00
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| IF-2 | TIGR00487 | translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ... |
426-1008 | 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: 788.58 E-value: 0e+00
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| infB | CHL00189 | translation initiation factor 2; Provisional |
393-1008 | 0e+00 | |||||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 546.74 E-value: 0e+00
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
510-674 | 7.29e-94 | |||||||||
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: 294.77 E-value: 7.29e-94
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| PRK04004 | PRK04004 | translation initiation factor IF-2; Validated |
508-997 | 7.97e-60 | |||||||||
translation initiation factor IF-2; Validated Pssm-ID: 235195 [Multi-domain] Cd Length: 586 Bit Score: 215.43 E-value: 7.97e-60
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| IF-2 | pfam11987 | Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main ... |
782-898 | 6.00e-50 | |||||||||
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: 171.85 E-value: 6.00e-50
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| aIF-2 | TIGR00491 | translation initiation factor aIF-2/yIF-2; This model describes archaeal and eukaryotic ... |
508-997 | 2.56e-49 | |||||||||
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: 185.02 E-value: 2.56e-49
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| IF2_mtIF2_II | cd03702 | Domain II of bacterial and mitochondrial Initiation Factor 2; This family represents domain II ... |
683-778 | 2.63e-45 | |||||||||
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: 157.97 E-value: 2.63e-45
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| mtIF2_IVc | cd03692 | C2 subdomain of domain IV in mitochondrial translation initiation factor 2; This model ... |
915-998 | 1.76e-39 | |||||||||
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: 140.71 E-value: 1.76e-39
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| PRK14845 | PRK14845 | translation initiation factor IF-2; Provisional |
523-986 | 3.54e-39 | |||||||||
translation initiation factor IF-2; Provisional Pssm-ID: 237833 [Multi-domain] Cd Length: 1049 Bit Score: 158.12 E-value: 3.54e-39
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
507-667 | 5.53e-37 | |||||||||
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: 137.66 E-value: 5.53e-37
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| GTP_translation_factor | cd00881 | GTP translation factor family primarily contains translation initiation, elongation and ... |
511-665 | 4.10e-30 | |||||||||
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: 117.78 E-value: 4.10e-30
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
512-668 | 1.56e-26 | |||||||||
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: 106.69 E-value: 1.56e-26
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| selB | TIGR00475 | selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ... |
511-731 | 1.82e-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: 96.87 E-value: 1.82e-20
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
514-668 | 6.33e-20 | |||||||||
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: 87.90 E-value: 6.33e-20
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
511-663 | 3.82e-19 | |||||||||
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: 85.73 E-value: 3.82e-19
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| TypA_BipA | cd01891 | Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ... |
512-633 | 2.25e-18 | |||||||||
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: 84.18 E-value: 2.25e-18
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| PRK10512 | PRK10512 | selenocysteinyl-tRNA-specific translation factor; Provisional |
511-720 | 2.79e-18 | |||||||||
selenocysteinyl-tRNA-specific translation factor; Provisional Pssm-ID: 182508 [Multi-domain] Cd Length: 614 Bit Score: 89.72 E-value: 2.79e-18
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| SelB | COG3276 | Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ... |
516-741 | 1.81e-17 | |||||||||
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: 87.28 E-value: 1.81e-17
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
514-668 | 4.24e-17 | |||||||||
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: 79.60 E-value: 4.24e-17
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| LepA | cd01890 | LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ... |
514-667 | 3.22e-16 | |||||||||
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: 77.57 E-value: 3.22e-16
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| TypA_BipA | TIGR01394 | GTP-binding protein TypA/BipA; This bacterial (and Arabidopsis) protein, termed TypA or BipA, ... |
512-632 | 9.11e-16 | |||||||||
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: 81.96 E-value: 9.11e-16
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| SelB_euk | cd01889 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
512-663 | 8.23e-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 eukaryotic SelBs and some from archaea. Pssm-ID: 206676 [Multi-domain] Cd Length: 192 Bit Score: 73.94 E-value: 8.23e-15
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| Snu114p | cd04167 | Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ... |
512-621 | 1.12e-14 | |||||||||
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: 74.23 E-value: 1.12e-14
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| TEF1 | COG5256 | Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ... |
514-741 | 2.03e-14 | |||||||||
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: 76.51 E-value: 2.03e-14
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| Arf_Arl | cd00878 | ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ... |
521-668 | 5.80e-14 | |||||||||
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: 70.30 E-value: 5.80e-14
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| EF2 | cd01885 | Elongation Factor 2 (EF2) in archaea and eukarya; Translocation requires hydrolysis of a ... |
512-621 | 2.92e-13 | |||||||||
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: 69.95 E-value: 2.92e-13
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| PRK12740 | PRK12740 | elongation factor G-like protein EF-G2; |
515-633 | 2.95e-13 | |||||||||
elongation factor G-like protein EF-G2; Pssm-ID: 237186 [Multi-domain] Cd Length: 668 Bit Score: 74.01 E-value: 2.95e-13
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| PRK12317 | PRK12317 | elongation factor 1-alpha; Reviewed |
512-741 | 6.20e-13 | |||||||||
elongation factor 1-alpha; Reviewed Pssm-ID: 237055 [Multi-domain] Cd Length: 425 Bit Score: 71.88 E-value: 6.20e-13
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| PLN03127 | PLN03127 | Elongation factor Tu; Provisional |
512-821 | 9.32e-13 | |||||||||
Elongation factor Tu; Provisional Pssm-ID: 178673 [Multi-domain] Cd Length: 447 Bit Score: 71.78 E-value: 9.32e-13
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| PRK13351 | PRK13351 | elongation factor G-like protein; |
512-640 | 3.69e-12 | |||||||||
elongation factor G-like protein; Pssm-ID: 237358 [Multi-domain] Cd Length: 687 Bit Score: 70.37 E-value: 3.69e-12
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| FusA | COG0480 | Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ... |
514-633 | 4.87e-12 | |||||||||
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: 70.07 E-value: 4.87e-12
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
512-618 | 4.95e-12 | |||||||||
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: 63.41 E-value: 4.95e-12
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| PBP1 | COG5180 | PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ... |
77-481 | 6.53e-12 | |||||||||
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 69.32 E-value: 6.53e-12
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| EF-G_bact | cd04170 | Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ... |
512-633 | 9.63e-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: 66.46 E-value: 9.63e-12
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| TetM_like | cd04168 | Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline ... |
514-638 | 1.04e-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: 65.72 E-value: 1.04e-11
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| IF2_N | pfam04760 | Translation initiation factor IF-2, N-terminal region; This conserved feature at the ... |
432-482 | 1.06e-11 | |||||||||
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: 60.56 E-value: 1.06e-11
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| TypA | COG1217 | Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction ... |
512-632 | 1.51e-11 | |||||||||
Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction mechanisms]; Pssm-ID: 440830 [Multi-domain] Cd Length: 606 Bit Score: 68.12 E-value: 1.51e-11
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| EF_Tu | cd01884 | Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ... |
511-620 | 1.78e-11 | |||||||||
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: 64.14 E-value: 1.78e-11
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| PRK12736 | PRK12736 | elongation factor Tu; Reviewed |
515-620 | 6.73e-11 | |||||||||
elongation factor Tu; Reviewed Pssm-ID: 237184 [Multi-domain] Cd Length: 394 Bit Score: 65.35 E-value: 6.73e-11
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| PRK10218 | PRK10218 | translational GTPase TypA; |
505-633 | 6.73e-11 | |||||||||
translational GTPase TypA; Pssm-ID: 104396 [Multi-domain] Cd Length: 607 Bit Score: 66.27 E-value: 6.73e-11
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| PRK00049 | PRK00049 | elongation factor Tu; Reviewed |
511-620 | 1.06e-10 | |||||||||
elongation factor Tu; Reviewed Pssm-ID: 234596 [Multi-domain] Cd Length: 396 Bit Score: 64.82 E-value: 1.06e-10
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| EF-Tu | TIGR00485 | translation elongation factor TU; This model models orthologs of translation elongation factor ... |
512-714 | 1.17e-10 | |||||||||
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: 64.80 E-value: 1.17e-10
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| EF1_alpha | cd01883 | Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ... |
511-635 | 1.20e-10 | |||||||||
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: 62.51 E-value: 1.20e-10
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| PRK07560 | PRK07560 | elongation factor EF-2; Reviewed |
514-621 | 2.24e-10 | |||||||||
elongation factor EF-2; Reviewed Pssm-ID: 236047 [Multi-domain] Cd Length: 731 Bit Score: 64.50 E-value: 2.24e-10
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| PRK12735 | PRK12735 | elongation factor Tu; Reviewed |
511-620 | 5.97e-10 | |||||||||
elongation factor Tu; Reviewed Pssm-ID: 183708 [Multi-domain] Cd Length: 396 Bit Score: 62.55 E-value: 5.97e-10
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| TufA | COG0050 | Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ... |
515-620 | 8.41e-10 | |||||||||
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: 62.09 E-value: 8.41e-10
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
295-360 | 9.91e-10 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 58.51 E-value: 9.91e-10
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| CysN_ATPS | cd04166 | CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ... |
516-620 | 1.74e-09 | |||||||||
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: 58.74 E-value: 1.74e-09
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| Era | COG1159 | GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; |
559-668 | 1.99e-09 | |||||||||
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440773 [Multi-domain] Cd Length: 290 Bit Score: 60.00 E-value: 1.99e-09
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| Translation_Factor_II_like | cd01342 | Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ... |
917-997 | 2.57e-09 | |||||||||
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: 54.58 E-value: 2.57e-09
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| RF3 | cd04169 | Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; ... |
514-633 | 1.10e-08 | |||||||||
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: 57.22 E-value: 1.10e-08
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| aEF-2 | TIGR00490 | translation elongation factor aEF-2; This model represents archaeal elongation factor 2, a ... |
512-621 | 1.83e-08 | |||||||||
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: 58.37 E-value: 1.83e-08
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
294-353 | 3.49e-08 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 53.89 E-value: 3.49e-08
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| YeeP | COG3596 | Predicted GTPase [General function prediction only]; |
508-621 | 3.61e-08 | |||||||||
Predicted GTPase [General function prediction only]; Pssm-ID: 442815 [Multi-domain] Cd Length: 318 Bit Score: 56.31 E-value: 3.61e-08
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| tufA | CHL00071 | elongation factor Tu |
511-621 | 3.69e-08 | |||||||||
elongation factor Tu Pssm-ID: 177010 [Multi-domain] Cd Length: 409 Bit Score: 56.89 E-value: 3.69e-08
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| PLN03126 | PLN03126 | Elongation factor Tu; Provisional |
510-621 | 3.85e-08 | |||||||||
Elongation factor Tu; Provisional Pssm-ID: 215592 [Multi-domain] Cd Length: 478 Bit Score: 56.93 E-value: 3.85e-08
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
396-668 | 5.17e-08 | |||||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 57.11 E-value: 5.17e-08
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| era | PRK00089 | GTPase Era; Reviewed |
559-668 | 6.10e-08 | |||||||||
GTPase Era; Reviewed Pssm-ID: 234624 [Multi-domain] Cd Length: 292 Bit Score: 55.44 E-value: 6.10e-08
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
512-675 | 7.79e-08 | |||||||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 53.06 E-value: 7.79e-08
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
559-668 | 8.67e-08 | |||||||||
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: 52.85 E-value: 8.67e-08
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| PRK04000 | PRK04000 | translation initiation factor IF-2 subunit gamma; Validated |
516-620 | 1.39e-07 | |||||||||
translation initiation factor IF-2 subunit gamma; Validated Pssm-ID: 235194 [Multi-domain] Cd Length: 411 Bit Score: 54.86 E-value: 1.39e-07
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| YihA_EngB | cd01876 | YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ... |
521-668 | 1.48e-07 | |||||||||
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: 52.13 E-value: 1.48e-07
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| eIF2_gamma | cd01888 | Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation ... |
511-637 | 1.56e-07 | |||||||||
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: 52.66 E-value: 1.56e-07
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| EngA2 | cd01895 | EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ... |
512-668 | 1.83e-07 | |||||||||
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: 52.05 E-value: 1.83e-07
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| prfC | TIGR00503 | peptide chain release factor 3; This translation releasing factor, RF-3 (prfC) was originally ... |
506-659 | 2.43e-07 | |||||||||
peptide chain release factor 3; This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus. [Protein synthesis, Translation factors] Pssm-ID: 129594 [Multi-domain] Cd Length: 527 Bit Score: 54.53 E-value: 2.43e-07
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| EF-G | cd01886 | Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling ... |
514-633 | 4.22e-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: 52.49 E-value: 4.22e-07
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| GTPBP1_like | cd04165 | GTP binding protein 1 (GTPBP1)-like family includes GTPBP2; Mammalian GTP binding protein 1 ... |
512-625 | 4.72e-07 | |||||||||
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: 51.91 E-value: 4.72e-07
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| Arl3 | cd04155 | Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ... |
507-662 | 1.58e-06 | |||||||||
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation. Pssm-ID: 206721 [Multi-domain] Cd Length: 174 Bit Score: 49.32 E-value: 1.58e-06
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| Sar1 | cd00879 | Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ... |
521-652 | 1.80e-06 | |||||||||
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation. Pssm-ID: 206645 [Multi-domain] Cd Length: 191 Bit Score: 49.58 E-value: 1.80e-06
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| EngA1 | cd01894 | EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ... |
556-668 | 1.82e-06 | |||||||||
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: 48.59 E-value: 1.82e-06
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| IF2_IF5B_II | cd03701 | Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ... |
686-762 | 2.18e-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: 46.89 E-value: 2.18e-06
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| CysN | COG2895 | Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and ... |
563-743 | 2.43e-06 | |||||||||
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: 51.24 E-value: 2.43e-06
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| rne | PRK10811 | ribonuclease E; Reviewed |
78-272 | 2.67e-06 | |||||||||
ribonuclease E; Reviewed Pssm-ID: 236766 [Multi-domain] Cd Length: 1068 Bit Score: 51.58 E-value: 2.67e-06
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| Arl10_like | cd04159 | Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ... |
512-665 | 3.71e-06 | |||||||||
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: 48.08 E-value: 3.71e-06
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| SR_beta | cd04105 | Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ... |
510-642 | 4.43e-06 | |||||||||
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. Pssm-ID: 206691 [Multi-domain] Cd Length: 202 Bit Score: 48.47 E-value: 4.43e-06
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
294-360 | 4.63e-06 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 47.73 E-value: 4.63e-06
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
293-360 | 1.29e-05 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 46.57 E-value: 1.29e-05
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
582-672 | 1.29e-05 | |||||||||
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: 46.33 E-value: 1.29e-05
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| CysN | TIGR02034 | sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic ... |
563-821 | 1.43e-05 | |||||||||
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: 48.52 E-value: 1.43e-05
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| YjeQ_EngC | cd01854 | Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ... |
582-665 | 2.11e-05 | |||||||||
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: 46.62 E-value: 2.11e-05
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| GTP_EFTU_D2 | pfam03144 | Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ... |
929-996 | 2.13e-05 | |||||||||
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain. Pssm-ID: 427163 [Multi-domain] Cd Length: 73 Bit Score: 43.41 E-value: 2.13e-05
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
556-668 | 2.15e-05 | |||||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 48.10 E-value: 2.15e-05
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| Obg_like | cd01881 | Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ... |
514-667 | 2.24e-05 | |||||||||
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: 45.85 E-value: 2.24e-05
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| Arl6 | cd04157 | Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ... |
512-665 | 2.98e-05 | |||||||||
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: 45.50 E-value: 2.98e-05
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| PRK05506 | PRK05506 | bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional |
563-743 | 3.16e-05 | |||||||||
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional Pssm-ID: 180120 [Multi-domain] Cd Length: 632 Bit Score: 48.00 E-value: 3.16e-05
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
556-683 | 5.12e-05 | |||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 46.97 E-value: 5.12e-05
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
556-668 | 6.02e-05 | |||||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 46.56 E-value: 6.02e-05
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| SRPRB | pfam09439 | Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ... |
508-636 | 6.12e-05 | |||||||||
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane. Pssm-ID: 462797 [Multi-domain] Cd Length: 181 Bit Score: 44.74 E-value: 6.12e-05
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| PspC_subgroup_2 | NF033839 | pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ... |
85-368 | 1.46e-04 | |||||||||
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. Pssm-ID: 468202 [Multi-domain] Cd Length: 557 Bit Score: 45.53 E-value: 1.46e-04
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| cysN | PRK05124 | sulfate adenylyltransferase subunit 1; Provisional |
563-620 | 1.84e-04 | |||||||||
sulfate adenylyltransferase subunit 1; Provisional Pssm-ID: 235349 [Multi-domain] Cd Length: 474 Bit Score: 45.29 E-value: 1.84e-04
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| Obg | cd01898 | Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ... |
611-670 | 2.04e-04 | |||||||||
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: 43.18 E-value: 2.04e-04
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
293-360 | 3.82e-04 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 42.33 E-value: 3.82e-04
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
521-668 | 3.90e-04 | |||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 43.89 E-value: 3.90e-04
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| HflX | cd01878 | HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ... |
554-667 | 4.21e-04 | |||||||||
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: 42.83 E-value: 4.21e-04
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
102-350 | 4.27e-04 | |||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 44.46 E-value: 4.27e-04
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| Arl2l1_Arl13_like | cd04161 | Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ... |
583-670 | 4.39e-04 | |||||||||
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene. Pssm-ID: 133361 [Multi-domain] Cd Length: 167 Bit Score: 41.99 E-value: 4.39e-04
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| Pro-rich | pfam15240 | Proline-rich protein; This family includes several eukaryotic proline-rich proteins. |
295-338 | 4.57e-04 | |||||||||
Proline-rich protein; This family includes several eukaryotic proline-rich proteins. Pssm-ID: 464580 [Multi-domain] Cd Length: 167 Bit Score: 41.95 E-value: 4.57e-04
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
510-668 | 4.76e-04 | |||||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 43.81 E-value: 4.76e-04
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| PHA03264 | PHA03264 | envelope glycoprotein D; Provisional |
294-357 | 5.58e-04 | |||||||||
envelope glycoprotein D; Provisional Pssm-ID: 223029 [Multi-domain] Cd Length: 416 Bit Score: 43.46 E-value: 5.58e-04
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| Innate_immun | pfam12782 | Invertebrate innate immunity transcript family; The immune response of the purple sea urchin ... |
297-395 | 1.03e-03 | |||||||||
Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge. Pssm-ID: 432781 [Multi-domain] Cd Length: 291 Bit Score: 42.45 E-value: 1.03e-03
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| Ras_dva | cd04147 | Ras - dorsal-ventral anterior localization (Ras-dva) family; Ras-dva subfamily. Ras-dva (Ras - ... |
559-673 | 1.25e-03 | |||||||||
Ras - dorsal-ventral anterior localization (Ras-dva) family; Ras-dva subfamily. Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. 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: 206714 [Multi-domain] Cd Length: 197 Bit Score: 41.36 E-value: 1.25e-03
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| PTZ00327 | PTZ00327 | eukaryotic translation initiation factor 2 gamma subunit; Provisional |
559-620 | 1.25e-03 | |||||||||
eukaryotic translation initiation factor 2 gamma subunit; Provisional Pssm-ID: 240362 [Multi-domain] Cd Length: 460 Bit Score: 42.68 E-value: 1.25e-03
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| PRK00098 | PRK00098 | GTPase RsgA; Reviewed |
582-666 | 1.26e-03 | |||||||||
GTPase RsgA; Reviewed Pssm-ID: 234631 [Multi-domain] Cd Length: 298 Bit Score: 42.11 E-value: 1.26e-03
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| prfC | PRK00741 | peptide chain release factor 3; Provisional |
556-633 | 1.29e-03 | |||||||||
peptide chain release factor 3; Provisional Pssm-ID: 179105 [Multi-domain] Cd Length: 526 Bit Score: 42.43 E-value: 1.29e-03
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| HflX | COG2262 | 50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]; ... |
551-677 | 1.38e-03 | |||||||||
50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441863 [Multi-domain] Cd Length: 419 Bit Score: 42.38 E-value: 1.38e-03
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| PTZ00416 | PTZ00416 | elongation factor 2; Provisional |
513-621 | 1.56e-03 | |||||||||
elongation factor 2; Provisional Pssm-ID: 240409 [Multi-domain] Cd Length: 836 Bit Score: 42.34 E-value: 1.56e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
202-365 | 1.62e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 42.62 E-value: 1.62e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
101-367 | 1.63e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 42.62 E-value: 1.63e-03
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| obgE | PRK12297 | GTPase CgtA; Reviewed |
600-675 | 1.68e-03 | |||||||||
GTPase CgtA; Reviewed Pssm-ID: 237046 [Multi-domain] Cd Length: 424 Bit Score: 42.01 E-value: 1.68e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
102-369 | 1.78e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 42.62 E-value: 1.78e-03
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| PRK11633 | PRK11633 | cell division protein DedD; Provisional |
88-236 | 2.44e-03 | |||||||||
cell division protein DedD; Provisional Pssm-ID: 236940 [Multi-domain] Cd Length: 226 Bit Score: 40.76 E-value: 2.44e-03
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| EFTU_II | cd03697 | Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ... |
919-993 | 2.80e-03 | |||||||||
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: 37.88 E-value: 2.80e-03
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| PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
102-378 | 3.51e-03 | |||||||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 41.61 E-value: 3.51e-03
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| PTZ00141 | PTZ00141 | elongation factor 1- alpha; Provisional |
512-635 | 3.58e-03 | |||||||||
elongation factor 1- alpha; Provisional Pssm-ID: 185474 [Multi-domain] Cd Length: 446 Bit Score: 40.89 E-value: 3.58e-03
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
203-410 | 3.72e-03 | |||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 41.21 E-value: 3.72e-03
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| Ras | pfam00071 | Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ... |
516-672 | 3.72e-03 | |||||||||
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Pssm-ID: 425451 [Multi-domain] Cd Length: 162 Bit Score: 39.03 E-value: 3.72e-03
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| PRK07994 | PRK07994 | DNA polymerase III subunits gamma and tau; Validated |
101-237 | 4.04e-03 | |||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 41.00 E-value: 4.04e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
293-367 | 4.85e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.08 E-value: 4.85e-03
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| DLP_2 | cd09912 | Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ... |
512-656 | 6.86e-03 | |||||||||
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: 38.68 E-value: 6.86e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
106-360 | 9.05e-03 | |||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 9.05e-03
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| Rab | cd00154 | Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ... |
521-667 | 9.18e-03 | |||||||||
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. 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 mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. 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. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. Pssm-ID: 206640 [Multi-domain] Cd Length: 159 Bit Score: 37.82 E-value: 9.18e-03
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| PHA03377 | PHA03377 | EBNA-3C; Provisional |
197-359 | 9.40e-03 | |||||||||
EBNA-3C; Provisional Pssm-ID: 177614 [Multi-domain] Cd Length: 1000 Bit Score: 40.04 E-value: 9.40e-03
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