[FeFe] hydrogenase H-cluster maturation GTPase HydF [Clostridioides difficile]
Protein Classification
GTP-binding protein( domain architecture ID 11498991)
GTP-binding protein similar to the [FeFe] hydrogenase H-cluster maturation GTPase HydF, which is essential for hydrogenase activity; it assembles a di-iron precursor of the 2Fe subcluster and transfers it to HydA (hydrogenase) for maturation
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| GTP_HydF | TIGR03918 | [FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the ... |
6-397 | 0e+00 | ||||||
[FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the [Fe] hydrogenase maturation protein HypF as characterized in Chlamydomonas reinhardtii and found, in an operon with radical SAM proteins HydE and HydG, in numerous bacteria. It has GTPase activity, can bind an 4Fe-4S cluster, and is essential for hydrogenase activity. [Protein fate, Protein modification and repair] : Pssm-ID: 274853 [Multi-domain] Cd Length: 391 Bit Score: 685.78 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||
| GTP_HydF | TIGR03918 | [FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the ... |
6-397 | 0e+00 | ||||||
[FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the [Fe] hydrogenase maturation protein HypF as characterized in Chlamydomonas reinhardtii and found, in an operon with radical SAM proteins HydE and HydG, in numerous bacteria. It has GTPase activity, can bind an 4Fe-4S cluster, and is essential for hydrogenase activity. [Protein fate, Protein modification and repair] Pssm-ID: 274853 [Multi-domain] Cd Length: 391 Bit Score: 685.78 E-value: 0e+00
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| HydF_tetramer | pfam18133 | Hydrogen maturase F tetramerization domain; This is the C-terminal domain found in Hydrogen ... |
282-398 | 8.13e-61 | ||||||
Hydrogen maturase F tetramerization domain; This is the C-terminal domain found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain is known as domain III, and is primarily responsible for homotetramer formation. Interactions between the two FeS cluster-binding domains worth noting are the interactions between beta-2 strands, the initial part of the long loop that connects strand beta-2 to strand beta-3, and the loop that connects strand beta-1 to helix alpha-3. There are three highly conserved cysteine residues (Cys-302, Cys-353, and Cys-356) that represent the FeS cluster-binding site which form a superficial pocket. Pssm-ID: 436296 Cd Length: 118 Bit Score: 192.43 E-value: 8.13e-61
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
15-172 | 4.11e-48 | ||||||
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: 160.87 E-value: 4.11e-48
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
18-178 | 1.48e-32 | ||||||
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: 127.10 E-value: 1.48e-32
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| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
12-175 | 1.50e-27 | ||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 113.28 E-value: 1.50e-27
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| Name | Accession | Description | Interval | E-value | ||||||
| GTP_HydF | TIGR03918 | [FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the ... |
6-397 | 0e+00 | ||||||
[FeFe] hydrogenase H-cluster maturation GTPase HydF; This model describes the family of the [Fe] hydrogenase maturation protein HypF as characterized in Chlamydomonas reinhardtii and found, in an operon with radical SAM proteins HydE and HydG, in numerous bacteria. It has GTPase activity, can bind an 4Fe-4S cluster, and is essential for hydrogenase activity. [Protein fate, Protein modification and repair] Pssm-ID: 274853 [Multi-domain] Cd Length: 391 Bit Score: 685.78 E-value: 0e+00
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| HydF_tetramer | pfam18133 | Hydrogen maturase F tetramerization domain; This is the C-terminal domain found in Hydrogen ... |
282-398 | 8.13e-61 | ||||||
Hydrogen maturase F tetramerization domain; This is the C-terminal domain found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain is known as domain III, and is primarily responsible for homotetramer formation. Interactions between the two FeS cluster-binding domains worth noting are the interactions between beta-2 strands, the initial part of the long loop that connects strand beta-2 to strand beta-3, and the loop that connects strand beta-1 to helix alpha-3. There are three highly conserved cysteine residues (Cys-302, Cys-353, and Cys-356) that represent the FeS cluster-binding site which form a superficial pocket. Pssm-ID: 436296 Cd Length: 118 Bit Score: 192.43 E-value: 8.13e-61
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| HydF_dimer | pfam18128 | Hydrogen maturase F dimerization domain; This domain is found in Hydrogen maturase F (HydF) ... |
181-279 | 1.84e-50 | ||||||
Hydrogen maturase F dimerization domain; This domain is found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain, referred to as domain II, is responsible for HydF dimerization through the formation of a continuous beta-sheet comprising eight beta-strands from two monomers. Pssm-ID: 375576 Cd Length: 99 Bit Score: 164.78 E-value: 1.84e-50
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
15-172 | 4.11e-48 | ||||||
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: 160.87 E-value: 4.11e-48
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
12-172 | 6.03e-33 | ||||||
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: 121.06 E-value: 6.03e-33
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
18-178 | 1.48e-32 | ||||||
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: 127.10 E-value: 1.48e-32
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
15-170 | 2.75e-31 | ||||||
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: 116.79 E-value: 2.75e-31
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| MnmE_helical | pfam12631 | MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ... |
12-172 | 8.65e-31 | ||||||
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: 119.89 E-value: 8.65e-31
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| EngA2 | cd01895 | EngA2 GTPase contains the second domain of EngA; This EngA2 subfamily CD represents the second ... |
12-171 | 9.82e-30 | ||||||
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: 112.91 E-value: 9.82e-30
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| trmE | PRK05291 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; |
12-175 | 1.50e-27 | ||||||
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE; Pssm-ID: 235392 [Multi-domain] Cd Length: 449 Bit Score: 113.28 E-value: 1.50e-27
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
11-171 | 2.75e-26 | ||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 109.34 E-value: 2.75e-26
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
13-128 | 1.48e-25 | ||||||
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: 99.62 E-value: 1.48e-25
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
11-171 | 5.80e-25 | ||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 105.52 E-value: 5.80e-25
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
13-172 | 2.68e-20 | ||||||
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: 87.13 E-value: 2.68e-20
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| era | PRK00089 | GTPase Era; Reviewed |
18-186 | 3.92e-20 | ||||||
GTPase Era; Reviewed Pssm-ID: 234624 [Multi-domain] Cd Length: 292 Bit Score: 89.72 E-value: 3.92e-20
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| EngA1 | cd01894 | EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ... |
18-172 | 1.48e-19 | ||||||
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: 84.79 E-value: 1.48e-19
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| Era | COG1159 | GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; |
14-173 | 8.65e-19 | ||||||
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440773 [Multi-domain] Cd Length: 290 Bit Score: 85.81 E-value: 8.65e-19
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| PRK00093 | PRK00093 | GTP-binding protein Der; Reviewed |
18-178 | 2.28e-17 | ||||||
GTP-binding protein Der; Reviewed Pssm-ID: 234628 [Multi-domain] Cd Length: 435 Bit Score: 83.18 E-value: 2.28e-17
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| YihA_EngB | cd01876 | YihA (EngB) GTPase family; The YihA (EngB) subfamily of GTPases is typified by the E. coli ... |
14-172 | 5.82e-17 | ||||||
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: 77.94 E-value: 5.82e-17
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| Der | COG1160 | Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; |
18-178 | 6.18e-17 | ||||||
Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440774 [Multi-domain] Cd Length: 438 Bit Score: 81.99 E-value: 6.18e-17
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| mnmE_trmE_thdF | TIGR00450 | tRNA modification GTPase TrmE; TrmE, also called MnmE and previously designated ThdF ... |
14-184 | 6.85e-17 | ||||||
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: 82.15 E-value: 6.85e-17
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| YeeP | COG3596 | Predicted GTPase [General function prediction only]; |
14-174 | 1.71e-15 | ||||||
Predicted GTPase [General function prediction only]; Pssm-ID: 442815 [Multi-domain] Cd Length: 318 Bit Score: 76.73 E-value: 1.71e-15
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
14-168 | 3.49e-14 | ||||||
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: 69.71 E-value: 3.49e-14
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| Obg_like | cd01881 | Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ... |
15-172 | 3.10e-12 | ||||||
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: 64.34 E-value: 3.10e-12
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
6-130 | 1.16e-11 | ||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 66.36 E-value: 1.16e-11
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| EngB | COG0218 | GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, ... |
7-172 | 7.06e-11 | ||||||
GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 439988 [Multi-domain] Cd Length: 194 Bit Score: 60.86 E-value: 7.06e-11
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| HflX | cd01878 | HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ... |
14-172 | 9.14e-11 | ||||||
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: 60.94 E-value: 9.14e-11
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| Obg | cd01898 | Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ... |
13-172 | 2.19e-10 | ||||||
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: 58.98 E-value: 2.19e-10
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| PRK09518 | PRK09518 | bifunctional cytidylate kinase/GTPase Der; Reviewed |
14-183 | 2.62e-10 | ||||||
bifunctional cytidylate kinase/GTPase Der; Reviewed Pssm-ID: 236546 [Multi-domain] Cd Length: 712 Bit Score: 62.12 E-value: 2.62e-10
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| GTPase_YsxC | TIGR03598 | ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase ... |
7-162 | 3.45e-10 | ||||||
ribosome biogenesis GTP-binding protein YsxC/EngB; Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes. [Protein synthesis, Other] Pssm-ID: 274670 [Multi-domain] Cd Length: 179 Bit Score: 58.64 E-value: 3.45e-10
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| obgE | PRK12299 | GTPase CgtA; Reviewed |
14-174 | 1.08e-09 | ||||||
GTPase CgtA; Reviewed Pssm-ID: 237048 [Multi-domain] Cd Length: 335 Bit Score: 59.31 E-value: 1.08e-09
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| YfjP | cd11383 | YfjP GTPase; The Era (E. coli Ras-like protein)-like YfjP subfamily includes several ... |
15-172 | 2.01e-09 | ||||||
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: 55.42 E-value: 2.01e-09
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
14-132 | 2.23e-09 | ||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 58.83 E-value: 2.23e-09
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| DLP_2 | cd09912 | Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ... |
13-148 | 3.29e-09 | ||||||
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: 56.02 E-value: 3.29e-09
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| FeoB | cd01879 | Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ... |
16-174 | 4.76e-07 | ||||||
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Pssm-ID: 206667 [Multi-domain] Cd Length: 159 Bit Score: 48.99 E-value: 4.76e-07
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| SelB | cd04171 | SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ... |
92-178 | 5.43e-07 | ||||||
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: 49.14 E-value: 5.43e-07
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| PRK03003 | PRK03003 | GTP-binding protein Der; Reviewed |
18-182 | 2.30e-06 | ||||||
GTP-binding protein Der; Reviewed Pssm-ID: 179525 [Multi-domain] Cd Length: 472 Bit Score: 49.58 E-value: 2.30e-06
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| SelB | COG3276 | Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ... |
92-172 | 6.04e-06 | ||||||
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: 48.37 E-value: 6.04e-06
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| EF-G_bact | cd04170 | Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). ... |
14-130 | 1.13e-05 | ||||||
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: 46.43 E-value: 1.13e-05
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| feoB | PRK09554 | Fe(2+) transporter permease subunit FeoB; |
120-252 | 1.12e-04 | ||||||
Fe(2+) transporter permease subunit FeoB; Pssm-ID: 236563 [Multi-domain] Cd Length: 772 Bit Score: 44.32 E-value: 1.12e-04
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| YjeQ_EngC | cd01854 | Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ... |
92-168 | 5.17e-04 | ||||||
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: 40.84 E-value: 5.17e-04
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| YlqF_related_GTPase | cd01849 | Circularly permuted YlqF-related GTPases; These proteins are found in bacteria, eukaryotes, ... |
14-50 | 5.35e-04 | ||||||
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: 40.06 E-value: 5.35e-04
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| IF2_eIF5B | cd01887 | Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ... |
91-169 | 8.29e-04 | ||||||
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s. Pssm-ID: 206674 [Multi-domain] Cd Length: 169 Bit Score: 39.76 E-value: 8.29e-04
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| YlqF | cd01856 | Circularly permuted YlqF GTPase; Proteins of the YlqF family contain all sequence motifs ... |
21-69 | 1.11e-03 | ||||||
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: 39.43 E-value: 1.11e-03
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| GTP_EFTU | pfam00009 | Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ... |
92-174 | 1.24e-03 | ||||||
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: 39.43 E-value: 1.24e-03
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| infB | CHL00189 | translation initiation factor 2; Provisional |
91-253 | 3.65e-03 | ||||||
translation initiation factor 2; Provisional Pssm-ID: 177089 [Multi-domain] Cd Length: 742 Bit Score: 39.43 E-value: 3.65e-03
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