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Conserved domains on  [gi|296427498|gb|ADH16620|]
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elongation factor G, partial [Cronobacter sakazakii]

Protein Classification

EF-G superfamily protein( domain architecture ID 1002456)

EF-G superfamily protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EF-G super family cl31006
translation elongation factor EF-G; After peptide bond formation, this elongation factor of ...
 3-146 4.02e-88

translation elongation factor EF-G; After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G. [Protein synthesis, Translation factors]


The actual alignment was detected with superfamily member TIGR00484:

Pssm-ID: 129575 [Multi-domain]  Cd Length: 689  Bit Score: 270.14  E-value: 4.02e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498    3 LDDGKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVR 82
Cdd:TIGR00484 290 IDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVR 369

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 296427498   83 AGDIAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:TIGR00484 370 AGDICAAIGLKDTTTGDTLCDPKIDVILERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEED 433
 
Name Accession Description Interval E-value
EF-G TIGR00484
translation elongation factor EF-G; After peptide bond formation, this elongation factor of ...
 3-146 4.02e-88

translation elongation factor EF-G; After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G. [Protein synthesis, Translation factors]


Pssm-ID: 129575 [Multi-domain]  Cd Length: 689  Bit Score: 270.14  E-value: 4.02e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498    3 LDDGKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVR 82
Cdd:TIGR00484 290 IDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVR 369

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 296427498   83 AGDIAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:TIGR00484 370 AGDICAAIGLKDTTTGDTLCDPKIDVILERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEED 433
FusA COG0480
Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 3-146 9.10e-88

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: 269.22  E-value: 9.10e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498   3 LDDGKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVR 82
Cdd:COG0480  289 VDPDTGEEVERKPDDDEPFSALVFKTMTDPFVGKLSFFRVYSGTLKSGSTVYNSTKGKKERIGRLLRMHGNKREEVDEAG 368

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 296427498  83 AGDIAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:COG0480  369 AGDIVAVVKLKDTTTGDTLCDEDHPIVLEPIEFPEPVISVAIEPKTKADEDKLSTALAKLAEED 432
PRK12740 PRK12740
elongation factor G-like protein EF-G2;
9-146 2.24e-67

elongation factor G-like protein EF-G2;


Pssm-ID: 237186 [Multi-domain]  Cd Length: 668  Bit Score: 215.37  E-value: 2.24e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498   9 TPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAA 88
Cdd:PRK12740 277 EGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVA 356

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 296427498  89 AIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PRK12740 357 VAKLKDAATGDTLCDKGDPILLEPMEFPEPVISLAIEPKDKGDEEKLSEALGKLAEED 414
EFG_mtEFG_II cd04088
Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation ...
 21-102 9.38e-49

Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation factors G1 and G2; This family represents the domain II of bacterial Elongation factor G (EF-G)and mitochondrial Elongation factors G1 (mtEFG1) and G2 (mtEFG2). During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homolog of mtEFG2, MEF2.


Pssm-ID: 293905 [Multi-domain]  Cd Length: 83  Bit Score: 151.14  E-value: 9.38e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDT 100
Cdd:cd04088    1 FSALVFKTMADPFVGKLTFFRVYSGTLKSGSTVYNSTKGKKERVGRLLRMHGKKREEVEELGAGDIGAVVGLKDTRTGDT 80


                 ..
gi 296427498 101 LC 102
Cdd:cd04088   81 LC 82
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 35-102 7.94e-17

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 69.99  E-value: 7.94e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 296427498   35 GNLTFFRVYSGVVNSGDTILN-----SVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLC 102
Cdd:pfam03144   1 GTVATGRVESGTLKKGDKVRIlpngtGKKKIVTRVTSLLMFHAPLREAVAGDNAGLILAGVGLEDIRVGDTLT 73
 
Name Accession Description Interval E-value
EF-G TIGR00484
translation elongation factor EF-G; After peptide bond formation, this elongation factor of ...
 3-146 4.02e-88

translation elongation factor EF-G; After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G. [Protein synthesis, Translation factors]


Pssm-ID: 129575 [Multi-domain]  Cd Length: 689  Bit Score: 270.14  E-value: 4.02e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498    3 LDDGKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVR 82
Cdd:TIGR00484 290 IDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVR 369

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 296427498   83 AGDIAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:TIGR00484 370 AGDICAAIGLKDTTTGDTLCDPKIDVILERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEED 433
FusA COG0480
Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 3-146 9.10e-88

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: 269.22  E-value: 9.10e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498   3 LDDGKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVR 82
Cdd:COG0480  289 VDPDTGEEVERKPDDDEPFSALVFKTMTDPFVGKLSFFRVYSGTLKSGSTVYNSTKGKKERIGRLLRMHGNKREEVDEAG 368

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 296427498  83 AGDIAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:COG0480  369 AGDIVAVVKLKDTTTGDTLCDEDHPIVLEPIEFPEPVISVAIEPKTKADEDKLSTALAKLAEED 432
PRK12740 PRK12740
elongation factor G-like protein EF-G2;
9-146 2.24e-67

elongation factor G-like protein EF-G2;


Pssm-ID: 237186 [Multi-domain]  Cd Length: 668  Bit Score: 215.37  E-value: 2.24e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498   9 TPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAA 88
Cdd:PRK12740 277 EGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVA 356

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 296427498  89 AIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PRK12740 357 VAKLKDAATGDTLCDKGDPILLEPMEFPEPVISLAIEPKDKGDEEKLSEALGKLAEED 414
PRK13351 PRK13351
elongation factor G-like protein;
6-146 4.15e-56

elongation factor G-like protein;


Pssm-ID: 237358 [Multi-domain]  Cd Length: 687  Bit Score: 185.93  E-value: 4.15e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498   6 GKDTPAERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGD 85
Cdd:PRK13351 291 DNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDRAKAGD 370

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 296427498  86 IAAAIGLKDVTTGDTLCNPDHPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PRK13351 371 IVAVAGLKELETGDTLHDSADPVLLELLTFPEPVVSLAVEPERRGDEQKLAEALEKLVWED 431
EFG_mtEFG_II cd04088
Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation ...
 21-102 9.38e-49

Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation factors G1 and G2; This family represents the domain II of bacterial Elongation factor G (EF-G)and mitochondrial Elongation factors G1 (mtEFG1) and G2 (mtEFG2). During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homolog of mtEFG2, MEF2.


Pssm-ID: 293905 [Multi-domain]  Cd Length: 83  Bit Score: 151.14  E-value: 9.38e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDT 100
Cdd:cd04088    1 FSALVFKTMADPFVGKLTFFRVYSGTLKSGSTVYNSTKGKKERVGRLLRMHGKKREEVEELGAGDIGAVVGLKDTRTGDT 80


                 ..
gi 296427498 101 LC 102
Cdd:cd04088   81 LC 82
mtEFG2_II_like cd04092
Domain II of mitochondrial elongation factor G2-like proteins found in eukaryotes; Eukaryotic ...
 23-103 4.88e-26

Domain II of mitochondrial elongation factor G2-like proteins found in eukaryotes; Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homolog of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s); mtEFG1s are not present in this group.


Pssm-ID: 293909 [Multi-domain]  Cd Length: 83  Bit Score: 93.92  E-value: 4.88e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  23 ALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLC 102
Cdd:cd04092    3 ALAFKVIHDPQRGPLVFVRVYSGTLKAGSNVYNTTTGKKERISRLLKMHADQTEEVDSLSAGNIGVITGLKVTSTGDTLV 82


                 .
gi 296427498 103 N 103
Cdd:cd04092   83 S 83
mtEFG1_II_like cd04091
Domain II of mitochondrial elongation factor G1-like proteins found in eukaryotes; Eukaryotic ...
 21-102 2.37e-24

Domain II of mitochondrial elongation factor G1-like proteins found in eukaryotes; Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s); mtEFG2s are not present in this group.


Pssm-ID: 293908 [Multi-domain]  Cd Length: 81  Bit Score: 89.27  E-value: 2.37e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIATDPFvGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLkDVTTGDT 100
Cdd:cd04091    1 FVGLAFKLEEGRF-GQLTYMRVYQGVLRKGDTIYNVRTGKKVRVPRLVRMHSDEMEDIEEVYAGDICALFGI-DCASGDT 78


                 ..
gi 296427498 101 LC 102
Cdd:cd04091   79 FT 80
PRK07560 PRK07560
elongation factor EF-2; Reviewed
 11-146 8.18e-19

elongation factor EF-2; Reviewed


Pssm-ID: 236047 [Multi-domain]  Cd Length: 731  Bit Score: 81.45  E-value: 8.18e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  11 AERHASDEEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDT--ILNSVKSARerfgriVQ----MHANKREEIKEVRAG 84
Cdd:PRK07560 281 AMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFSGTLRKGQEvyLVGAKKKNR------VQqvgiYMGPEREEVEEIPAG 354

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 296427498  85 DIAAAIGLKDVTTGDTLCNPDHPIILERME-FPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PRK07560 355 NIAAVTGLKDARAGETVVSVEDMTPFESLKhISEPVVTVAIEAKNPKDLPKLIEVLRQLAKED 417
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 35-102 7.94e-17

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 69.99  E-value: 7.94e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 296427498   35 GNLTFFRVYSGVVNSGDTILN-----SVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLC 102
Cdd:pfam03144   1 GTVATGRVESGTLKKGDKVRIlpngtGKKKIVTRVTSLLMFHAPLREAVAGDNAGLILAGVGLEDIRVGDTLT 73
BipA_TypA_II cd03691
Domain II of BipA; BipA (also called TypA) is a highly conserved protein with global ...
 21-107 4.99e-15

Domain II of BipA; BipA (also called TypA) is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. The domain II of BipA shows similarity to the domain II of the elongation factors (EFs) EF-G and EF-Tu.


Pssm-ID: 293892 [Multi-domain]  Cd Length: 94  Bit Score: 66.06  E-value: 4.99e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHA---NKREEIKEVRAGDIAAAIGLKDVTT 97
Cdd:cd03691    1 FQMLVTTLDYDDYLGRIAIGRIFSGTVKVGQQVTVVDEDGKIEKGRVTKLFGfegLERVEVEEAEAGDIVAIAGLEDITI 80

                         90
                 ....*....|
gi 296427498  98 GDTLCNPDHP 107
Cdd:cd03691   81 GDTICDPEVP 90
EFG_III pfam14492
Elongation Factor G, domain III; This domain is found in Elongation Factor G. It shares a ...
 115-146 5.23e-13

Elongation Factor G, domain III; This domain is found in Elongation Factor G. It shares a similar structure with domain V (pfam00679). Structural studies in drosophila indicate this is domain 3.


Pssm-ID: 464188 [Multi-domain]  Cd Length: 75  Bit Score: 60.19  E-value: 5.23e-13
                          10        20        30
                  ....*....|....*....|....*....|..
gi 296427498  115 FPEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:pfam14492   1 FPEPVISVAIEPKTKGDEDKLSKALNRLLEED 32
EFG_III cd16262
Domain III of Elongation Factor G (EFG); This model represents domain III of bacterial ...
 116-146 8.94e-13

Domain III of Elongation Factor G (EFG); This model represents domain III of bacterial Elongation factor G (EF-G), and mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2), which play an important role during peptide synthesis and tRNA site changes. In bacteria, this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects, and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants of the yeast homolog of mtEFG2, MEF2.


Pssm-ID: 293919 [Multi-domain]  Cd Length: 76  Bit Score: 59.39  E-value: 8.94e-13
                         10        20        30
                 ....*....|....*....|....*....|.
gi 296427498 116 PEPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:cd16262    1 PEPVISLAIEPKTKADEDKLSKALARLAEED 31
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 21-102 9.99e-10

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: 51.88  E-value: 9.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHankrEEIKEVRAGDI--AAAIGLKDVTTG 98
Cdd:cd01342    1 LVMQVFKVFYIPGRGRVAGGRVESGTLKVGDEIRILPKGITGRVTSIERFH----EEVDEAKAGDIvgIGILGVKDILTG 76


                 ....
gi 296427498  99 DTLC 102
Cdd:cd01342   77 DTLT 80
PLN00116 PLN00116
translation elongation factor EF-2 subunit; Provisional
 37-146 5.78e-09

translation elongation factor EF-2 subunit; Provisional


Pssm-ID: 177730 [Multi-domain]  Cd Length: 843  Bit Score: 53.19  E-value: 5.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  37 LTFFRVYSGVVNSGDT--ILNS-----------VKSARerfgRIVQMHANKREEIKEVRAGDIAAAIGL-----KDVTTG 98
Cdd:PLN00116 393 FAFGRVFSGTVATGMKvrIMGPnyvpgekkdlyVKSVQ----RTVIWMGKKQESVEDVPCGNTVAMVGLdqfitKNATLT 468

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 296427498  99 DTLCNPDHPIilERMEFP-EPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PLN00116 469 NEKEVDAHPI--KAMKFSvSPVVRVAVQCKNASDLPKLVEGLKRLAKSD 515
Tet_II cd03690
Domain II of ribosomal protection proteins Tet(M) and Tet(O); This subfamily represents domain ...
 18-101 4.87e-08

Domain II of ribosomal protection proteins Tet(M) and Tet(O); This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.


Pssm-ID: 293891 [Multi-domain]  Cd Length: 86  Bit Score: 47.62  E-value: 4.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  18 EEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTILNSVKSARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTT 97
Cdd:cd03690    1 ESELSGTVFKIEYDPKGERLAYLRLYSGTLRLRDSVRVSGEEEKIKITELRTFENGELVKVDRVYAGDIAILVGLKSLRV 80


                 ....
gi 296427498  98 GDTL 101
Cdd:cd03690   81 GDVL 84
EF2_II cd16268
Domain II of Elongation Factor 2; This subfamily represents domain II of elongation factor 2 ...
 28-102 8.69e-06

Domain II of Elongation Factor 2; This subfamily represents domain II of elongation factor 2 (EF-2) found in eukaryotes and archaea. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site.


Pssm-ID: 293913 [Multi-domain]  Cd Length: 96  Bit Score: 41.82  E-value: 8.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  28 IATDPFVGNLTFFRVYSGVVNSGDTI--------LNSVKSARE-RFGRIVQMHANKREEIKEVRAGDIAAAIGLKD--VT 96
Cdd:cd16268   10 VPTDKGAGFVAFGRVFSGTVRRGQEVyilgpkyvPGKKDDLKKkRIQQTYLMMGREREPVDEVPAGNIVGLVGLDDflAK 89


                 ....*.
gi 296427498  97 TGDTLC 102
Cdd:cd16268   90 SGTTTS 95
PTZ00416 PTZ00416
elongation factor 2; Provisional
 39-146 1.22e-05

elongation factor 2; Provisional


Pssm-ID: 240409 [Multi-domain]  Cd Length: 836  Bit Score: 43.88  E-value: 1.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  39 FFRVYSGVVNSGDTIlnSVKSARERFG-----------RIVQMHANKREEIKEVRAGDIAAAIGLKD--VTTGDTLCNPD 105
Cdd:PTZ00416 391 FGRVFSGTVATGQKV--RIQGPNYVPGkkedlfekniqRTVLMMGRYVEQIEDVPCGNTVGLVGVDQylVKSGTITTSET 468

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 296427498 106 -HPIilERMEFP-EPVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:PTZ00416 469 aHNI--RDMKYSvSPVVRVAVEPKNPKDLPKLVEGLKRLAKSD 509
PRK10218 PRK10218
translational GTPase TypA;
33-122 4.69e-04

translational GTPase TypA;


Pssm-ID: 104396 [Multi-domain]  Cd Length: 607  Bit Score: 38.92  E-value: 4.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  33 FVGNLTFFRVYSGVV--NSGDTILNSVKSARE-RFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLCNPDHPII 109
Cdd:PRK10218 217 YVGVIGIGRIKRGKVkpNQQVTIIDSEGKTRNaKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEA 296

                         90
                 ....*....|...
gi 296427498 110 LERMEFPEPVISI 122
Cdd:PRK10218 297 LPALSVDEPTVSM 309
EF4_II cd03699
Domain II of Elongation Factor 4 (EF4); Elongation factor 4 (EF4 or LepA) is a highly ...
 31-103 5.89e-04

Domain II of Elongation Factor 4 (EF4); Elongation factor 4 (EF4 or LepA) is a highly conserved guanosine triphosphatase found in bacteria and eukaryotic mitochondria and chloroplasts. EF4 functions as a translation factor, which promotes back-translocation of tRNAs on posttranslocational ribosome complexes and competes with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis.


Pssm-ID: 293900 [Multi-domain]  Cd Length: 86  Bit Score: 36.63  E-value: 5.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  31 DPFVGNLTFFRVYSGVVNSGDTIlnsvksareRFgrivqMHANKREEIKEV-------------RAGD---IAAAIG-LK 93
Cdd:cd03699   11 DPYRGVVVLVRVFDGTLKKGDKI---------RF-----MATGKEYEVLEVgvftpkmvptdelSAGEvgyIIAGIKsVK 76

                         90
                 ....*....|
gi 296427498  94 DVTTGDTLCN 103
Cdd:cd03699   77 DARVGDTITL 86
EFG_III-like cd16257
Domain III of Elongation factor G (EF-G) and related proteins; Bacterial Elongation factor G ...
 118-146 3.78e-03

Domain III of Elongation factor G (EF-G) and related proteins; Bacterial Elongation factor G (EF-G) and related proteins play a role in translation and share a similar domain architecture. Elongation factor EFG participates in the elongation phase during protein biosynthesis on the ribosome by stimulating translocation. Its functional cycles depend on GTP binding and its hydrolysis. Domain III is involved in the activation of GTP hydrolysis. This domain III, which is different from domain III in EF-TU and related elongation factors, is found in several translation factors, like bacterial release factors RF3, elongation factor 4, elongation factor 2, GTP-binding protein BipA and tetracycline resistance protein Tet.


Pssm-ID: 293914 [Multi-domain]  Cd Length: 71  Bit Score: 34.25  E-value: 3.78e-03
                         10        20
                 ....*....|....*....|....*....
gi 296427498 118 PVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:cd16257    1 PVVFVTVEVKNPLDQEKLLEGLERLSEED 29
EF2_snRNP_III cd16261
Domain III of Elongation Factor 2 (EF2); This model represents domain III of Elongation factor ...
 118-146 3.98e-03

Domain III of Elongation Factor 2 (EF2); This model represents domain III of Elongation factor 2 (EF2) found in eukaryotes and archaea, and the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis are important for the function of the U5-116 kD/Snu114p.


Pssm-ID: 293918 [Multi-domain]  Cd Length: 72  Bit Score: 34.09  E-value: 3.98e-03
                         10        20
                 ....*....|....*....|....*....
gi 296427498 118 PVISIAVEPKTKADQEKMGLALGRLAKED 146
Cdd:cd16261    1 PVVRVAVEPKNPSDLPKLVEGLKKLAKSD 29
RF3_II cd03689
Domain II of bacterial Release Factor 3; This subfamily represents domain II of bacterial ...
 21-102 5.04e-03

Domain II of bacterial Release Factor 3; This subfamily represents domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.


Pssm-ID: 293890 [Multi-domain]  Cd Length: 87  Bit Score: 34.17  E-value: 5.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296427498  21 FSALAFKIAT--DP-FVGNLTFFRVYSGVVNSGDTIlNSVKSARE-RFGRIVQMHANKREEIKEVRAGDIaaaIGLKDVT 96
Cdd:cd03689    1 FSGFVFKIQAnmDPkHRDRIAFLRVCSGKFERGMKV-KHVRTGKEvRLSNATTFMAQDRETVEEAYPGDI---IGLPNHG 76


                 ....*....
gi 296427498  97 T---GDTLC 102
Cdd:cd03689   77 TfqiGDTFT 85
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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