MULTISPECIES: tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE [Staphylococcus]
Protein Classification
tRNA modification GTPase( domain architecture ID 11480540)
tRNA modification GTPase is involved in the modification of the wobble position of certain tRNAs and is one of the G proteins activated by nucleotide-dependent dimerization, such as bacterial MnmE and mitochondrial GTP-binding protein 3
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
1-459 | 0e+00 | |||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; : Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 614.04 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||
| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
1-459 | 0e+00 | |||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 614.04 E-value: 0e+00
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
5-459 | 0e+00 | |||||||
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification Pssm-ID: 440253 [Multi-domain] Cd Length: 448 Bit Score: 583.18 E-value: 0e+00
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| MnmE_helical | pfam12631 | MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ... |
127-456 | 1.80e-141 | |||||||
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain. Pssm-ID: 463649 [Multi-domain] Cd Length: 326 Bit Score: 408.02 E-value: 1.80e-141
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| mnmE_trmE_thdF | TIGR00450 | tRNA modification GTPase TrmE; TrmE, also called MnmE and previously designated ThdF ... |
10-459 | 8.07e-116 | |||||||
tRNA modification GTPase TrmE; TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer. [Protein synthesis, tRNA and rRNA base modification] Pssm-ID: 273083 [Multi-domain] Cd Length: 442 Bit Score: 347.17 E-value: 8.07e-116
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
219-379 | 8.85e-65 | |||||||
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: 205.81 E-value: 8.85e-65
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| Name | Accession | Description | Interval | E-value | |||||||
| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
1-459 | 0e+00 | |||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 614.04 E-value: 0e+00
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
5-459 | 0e+00 | |||||||
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification Pssm-ID: 440253 [Multi-domain] Cd Length: 448 Bit Score: 583.18 E-value: 0e+00
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| MnmE_helical | pfam12631 | MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ... |
127-456 | 1.80e-141 | |||||||
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain. Pssm-ID: 463649 [Multi-domain] Cd Length: 326 Bit Score: 408.02 E-value: 1.80e-141
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| mnmE_trmE_thdF | TIGR00450 | tRNA modification GTPase TrmE; TrmE, also called MnmE and previously designated ThdF ... |
10-459 | 8.07e-116 | |||||||
tRNA modification GTPase TrmE; TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer. [Protein synthesis, tRNA and rRNA base modification] Pssm-ID: 273083 [Multi-domain] Cd Length: 442 Bit Score: 347.17 E-value: 8.07e-116
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
219-379 | 8.85e-65 | |||||||
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: 205.81 E-value: 8.85e-65
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| TrmE_N | pfam10396 | GTP-binding protein TrmE N-terminus; This family represents the shorter, B, chain of the ... |
5-124 | 1.01e-49 | |||||||
GTP-binding protein TrmE N-terminus; This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein. Pssm-ID: 463072 [Multi-domain] Cd Length: 117 Bit Score: 165.22 E-value: 1.01e-49
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| TrmE_N | cd14858 | N-terminal domain of TrmE, a tRNA modification GTPase; This family contains the N-terminal ... |
4-123 | 5.45e-46 | |||||||
N-terminal domain of TrmE, a tRNA modification GTPase; This family contains the N-terminal domain of TrmE (also known as MnmE, ThdF, MSS1), a guanine nucleotide-binding protein conserved in all three kingdoms of life. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. TrmE is a three-domain protein comprising an N-terminal alpha/beta domain, a helical domain, and the GTPase domain which is nested within the helical domain. The N-terminal domain induces dimerization for self-assembly and is topologically homologous to the tetrahydrofolate (THF)-binding domain of N,N-dimethylglycine oxidase (DMGO). However, the THF-binding site in DMGO is encoded on a single polypeptide, while homodimerization would be required to create a similar THF-binding site in TrmE. Dimerization also creates a second, symmetry-related THF-binding site. Biochemical and structural studies show that TrmE indeed binds formyl-THF. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. Pssm-ID: 410986 [Multi-domain] Cd Length: 117 Bit Score: 155.20 E-value: 5.45e-46
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
226-371 | 7.59e-34 | |||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 131.68 E-value: 7.59e-34
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| EngA2 | cd01895 | EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ... |
226-371 | 5.86e-32 | |||||||
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: 119.84 E-value: 5.86e-32
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
226-371 | 6.96e-31 | |||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 123.62 E-value: 6.96e-31
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
225-336 | 4.11e-30 | |||||||
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: 113.10 E-value: 4.11e-30
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| EngA1 | cd01894 | EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ... |
225-344 | 7.30e-30 | |||||||
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: 113.68 E-value: 7.30e-30
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
225-371 | 2.08e-29 | |||||||
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: 112.72 E-value: 2.08e-29
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| GTPase_EngA | TIGR03594 | ribosome-associated GTPase EngA; EngA (YfgK, Der) is a ribosome-associated essential GTPase ... |
225-342 | 6.62e-28 | |||||||
ribosome-associated GTPase EngA; EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability. [Protein synthesis, Other] Pssm-ID: 274667 [Multi-domain] Cd Length: 428 Bit Score: 114.85 E-value: 6.62e-28
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
225-338 | 3.66e-27 | |||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 112.84 E-value: 3.66e-27
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
225-338 | 1.04e-24 | |||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 105.88 E-value: 1.04e-24
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
226-379 | 4.22e-23 | |||||||
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: 95.61 E-value: 4.22e-23
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
225-371 | 5.88e-23 | |||||||
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: 94.83 E-value: 5.88e-23
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| era | PRK00089 | GTPase Era; Reviewed |
226-378 | 1.67e-22 | |||||||
GTPase Era; Reviewed Pssm-ID: 234624 [Multi-domain] Cd Length: 292 Bit Score: 97.04 E-value: 1.67e-22
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| Era | COG1159 | GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; |
226-378 | 1.56e-21 | |||||||
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440773 [Multi-domain] Cd Length: 290 Bit Score: 94.29 E-value: 1.56e-21
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
226-346 | 1.84e-19 | |||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 90.41 E-value: 1.84e-19
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
225-371 | 3.74e-19 | |||||||
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: 84.35 E-value: 3.74e-19
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
213-339 | 8.94e-18 | |||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 86.00 E-value: 8.94e-18
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| era | TIGR00436 | GTP-binding protein Era; Era is an essential GTPase in Escherichia coli and many other ... |
226-376 | 2.36e-16 | |||||||
GTP-binding protein Era; Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein. [Protein synthesis, Other] Pssm-ID: 129528 [Multi-domain] Cd Length: 270 Bit Score: 78.97 E-value: 2.36e-16
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
225-382 | 1.52e-12 | |||||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 65.77 E-value: 1.52e-12
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| YihA_EngB | cd01876 | YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ... |
225-379 | 2.46e-12 | |||||||
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: 64.84 E-value: 2.46e-12
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| feoB | TIGR00437 | ferrous iron transporter FeoB; FeoB (773 amino acids in E. coli), a cytoplasmic membrane ... |
228-376 | 4.98e-12 | |||||||
ferrous iron transporter FeoB; FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum. [Transport and binding proteins, Cations and iron carrying compounds] Pssm-ID: 273077 [Multi-domain] Cd Length: 591 Bit Score: 67.84 E-value: 4.98e-12
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| NOG | cd01897 | Nucleolar GTP-binding protein (NOG); NOG1 is a nucleolar GTP-binding protein present in ... |
225-371 | 1.26e-11 | |||||||
Nucleolar GTP-binding protein (NOG); NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins. Pssm-ID: 206684 [Multi-domain] Cd Length: 167 Bit Score: 62.96 E-value: 1.26e-11
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| YeeP | COG3596 | Predicted GTPase [General function prediction only]; |
225-339 | 3.38e-11 | |||||||
Predicted GTPase [General function prediction only]; Pssm-ID: 442815 [Multi-domain] Cd Length: 318 Bit Score: 64.02 E-value: 3.38e-11
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
226-338 | 6.31e-11 | |||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 64.22 E-value: 6.31e-11
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
219-338 | 1.14e-10 | |||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 63.66 E-value: 1.14e-10
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| Nog1 | COG1084 | GTP-binding protein, GTP1/Obg family [General function prediction only]; |
131-371 | 1.23e-10 | |||||||
GTP-binding protein, GTP1/Obg family [General function prediction only]; Pssm-ID: 440701 [Multi-domain] Cd Length: 330 Bit Score: 62.54 E-value: 1.23e-10
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| FeoB | cd01879 | Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ... |
226-378 | 2.15e-10 | |||||||
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Pssm-ID: 206667 [Multi-domain] Cd Length: 159 Bit Score: 59.01 E-value: 2.15e-10
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| DLP_2 | cd09912 | Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ... |
225-348 | 2.28e-10 | |||||||
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: 59.48 E-value: 2.28e-10
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| YfjP | cd11383 | YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several ... |
225-338 | 4.18e-10 | |||||||
YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They 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. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. Pssm-ID: 206743 [Multi-domain] Cd Length: 140 Bit Score: 57.74 E-value: 4.18e-10
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| Obg_like | cd01881 | Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ... |
225-378 | 1.01e-08 | |||||||
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: 54.32 E-value: 1.01e-08
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| FeoB_N | pfam02421 | Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) ... |
225-371 | 4.33e-08 | |||||||
Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Pssm-ID: 460552 [Multi-domain] Cd Length: 156 Bit Score: 52.45 E-value: 4.33e-08
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| RbgA | COG1161 | Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis]; |
199-279 | 1.02e-06 | |||||||
Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440775 [Multi-domain] Cd Length: 279 Bit Score: 50.11 E-value: 1.02e-06
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| YlqF | cd01856 | Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ... |
194-279 | 2.02e-06 | |||||||
Circularly permuted YlqF GTPase; Proteins of the YlqF 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. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga). Pssm-ID: 206749 [Multi-domain] Cd Length: 171 Bit Score: 47.91 E-value: 2.02e-06
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| Rbg1 | COG1163 | Ribosome-interacting GTPase RBG1 [Translation, ribosomal structure and biogenesis]; |
219-377 | 3.12e-06 | |||||||
Ribosome-interacting GTPase RBG1 [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440777 [Multi-domain] Cd Length: 368 Bit Score: 49.03 E-value: 3.12e-06
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| YqeH | cd01855 | Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH ... |
199-279 | 6.84e-06 | |||||||
Circularly permuted YqeH GTPase; YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. Pssm-ID: 206748 [Multi-domain] Cd Length: 191 Bit Score: 46.49 E-value: 6.84e-06
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| FeoB | COG0370 | Fe2+ transporter FeoB [Inorganic ion transport and metabolism]; |
226-391 | 1.10e-05 | |||||||
Fe2+ transporter FeoB [Inorganic ion transport and metabolism]; Pssm-ID: 440139 [Multi-domain] Cd Length: 662 Bit Score: 47.81 E-value: 1.10e-05
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| DRG | cd01896 | Developmentally Regulated GTP-binding protein (DRG); The developmentally regulated GTP-binding ... |
225-377 | 7.49e-05 | |||||||
Developmentally Regulated GTP-binding protein (DRG); The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding. Pssm-ID: 206683 [Multi-domain] Cd Length: 233 Bit Score: 44.07 E-value: 7.49e-05
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| GTPase_YlqF | TIGR03596 | ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding ... |
199-257 | 1.13e-04 | |||||||
ribosome biogenesis GTP-binding protein YlqF; Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members. [Protein synthesis, Other] Pssm-ID: 274669 [Multi-domain] Cd Length: 276 Bit Score: 43.65 E-value: 1.13e-04
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| Nucleostemin_like | cd04178 | A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein ... |
224-279 | 2.31e-04 | |||||||
A circularly permuted subfamily of the Ras GTPases; Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the protein. Pssm-ID: 206753 [Multi-domain] Cd Length: 171 Bit Score: 41.79 E-value: 2.31e-04
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| HSR1_MMR1 | cd01857 | A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC ... |
227-257 | 6.01e-04 | |||||||
A circularly permuted subfamily of the Ras GTPases; Human HSR1 is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N-terminus. Pssm-ID: 206750 [Multi-domain] Cd Length: 140 Bit Score: 39.91 E-value: 6.01e-04
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| YlqF_related_GTPase | cd01849 | Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ... |
219-279 | 1.09e-03 | |||||||
Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases. Pssm-ID: 206746 [Multi-domain] Cd Length: 146 Bit Score: 39.29 E-value: 1.09e-03
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| M_R_Ras_like | cd04145 | R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, ... |
225-370 | 2.60e-03 | |||||||
R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Pssm-ID: 133345 [Multi-domain] Cd Length: 164 Bit Score: 38.54 E-value: 2.60e-03
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| Toc34_like | cd01853 | Translocon at the Outer-envelope membrane of Chloroplasts 34-like (Toc34-like); The Toc34-like ... |
222-284 | 6.40e-03 | |||||||
Translocon at the Outer-envelope membrane of Chloroplasts 34-like (Toc34-like); The Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts) family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon. Pssm-ID: 206652 Cd Length: 248 Bit Score: 38.07 E-value: 6.40e-03
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| Miro1 | cd01893 | Mitochondrial Rho family 1 (Miro1), N-terminal; Miro1 subfamily. Miro (mitochondrial Rho) ... |
225-339 | 8.74e-03 | |||||||
Mitochondrial Rho family 1 (Miro1), N-terminal; Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Pssm-ID: 206680 [Multi-domain] Cd Length: 168 Bit Score: 36.93 E-value: 8.74e-03
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| Rab | cd00154 | Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ... |
225-371 | 9.31e-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: 36.67 E-value: 9.31e-03
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| Obg | cd01898 | Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ... |
226-371 | 9.36e-03 | |||||||
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: 37.02 E-value: 9.36e-03
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