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Conserved domains on  [gi|748943313|gb|AJE69868|]
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elongation factor P, partial [Xanthomonas oryzae]

Protein Classification

elongation factor P( domain architecture ID 11478847)

elongation factor P (EF-P) is an essential protein that stimulates ribosomal peptidyltransferase activity

Gene Ontology:  GO:0005737|GO:0005829|GO:0003746
PubMed:  23239624|31178848

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00529 PRK00529
elongation factor P; Validated
 1-130 9.91e-72

elongation factor P; Validated


:

Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 212.22  E-value: 9.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:PRK00529  31 GKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGME 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:PRK00529 111 VTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVV 160
 
Name Accession Description Interval E-value
PRK00529 PRK00529
elongation factor P; Validated
 1-130 9.91e-72

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 212.22  E-value: 9.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:PRK00529  31 GKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGME 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:PRK00529 111 VTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVV 160
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-130 3.65e-71

Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]; Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440001 [Multi-domain]  Cd Length: 186  Bit Score: 211.03  E-value: 3.65e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:COG0231   31 GKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGYVFMDTETYEQIELPKEVVGDAAKFLKEGME 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:COG0231  111 VTVLFYNGKPISVELPNFVELEVTETEPGVKGDTATGGTKPATLETGAVV 160
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 1-130 5.68e-70

translation elongation factor P; function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria. [Protein synthesis, Translation factors]


Pssm-ID: 272867 [Multi-domain]  Cd Length: 184  Bit Score: 207.70  E-value: 5.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313    1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:TIGR00038  30 GKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYVFMDTETYEQIELPKDLLGDAAKFLKENME 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 748943313   81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:TIGR00038 110 VSVVFYNGEPIGVELPNFVELEVTETEPGVKGDTASGSTKPATLETGAVV 159
S1_EF-P_repeat_1 cd04470
S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 37-96 3.73e-26

S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain II (the first S1 domain of EF_P). Domains II and III have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication.


Pssm-ID: 239916 [Multi-domain]  Cd Length: 61  Bit Score: 92.91  E-value: 3.73e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313  37 DTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDCVVTLWNGTPIQVTPP 96
Cdd:cd04470    2 EREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61
EFP pfam01132
Elongation factor P (EF-P) OB domain;
39-91 9.02e-23

Elongation factor P (EF-P) OB domain;


Pssm-ID: 460077 [Multi-domain]  Cd Length: 54  Bit Score: 83.99  E-value: 9.02e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 748943313   39 DMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDCVVTLWNGTPI 91
Cdd:pfam01132   2 EMQYLYNDGDDYVFMDNETYEQIELPKEQLGDAAKFLKEGMEVTVLFYEGKPI 54
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 99-130 8.03e-12

Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.


Pssm-ID: 214849 [Multi-domain]  Cd Length: 57  Bit Score: 55.92  E-value: 8.03e-12
                           10        20        30
                   ....*....|....*....|....*....|...
gi 748943313    99 VELKIVETDPGVRGDTSGGGGK-PATLETGAVV 130
Cdd:smart00841   1 VELEVTETEPGVKGDTASGGTKkPATLETGAVV 33
 
Name Accession Description Interval E-value
PRK00529 PRK00529
elongation factor P; Validated
 1-130 9.91e-72

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 212.22  E-value: 9.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:PRK00529  31 GKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGYVFMDTETYEQIEVPADQVGDAAKFLKEGME 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:PRK00529 111 VTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVV 160
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-130 3.65e-71

Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]; Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440001 [Multi-domain]  Cd Length: 186  Bit Score: 211.03  E-value: 3.65e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:COG0231   31 GKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGYVFMDTETYEQIELPKEVVGDAAKFLKEGME 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:COG0231  111 VTVLFYNGKPISVELPNFVELEVTETEPGVKGDTATGGTKPATLETGAVV 160
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 1-130 5.68e-70

translation elongation factor P; function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria. [Protein synthesis, Translation factors]


Pssm-ID: 272867 [Multi-domain]  Cd Length: 184  Bit Score: 207.70  E-value: 5.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313    1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEED 80
Cdd:TIGR00038  30 GKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYVFMDTETYEQIELPKDLLGDAAKFLKENME 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 748943313   81 CVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:TIGR00038 110 VSVVFYNGEPIGVELPNFVELEVTETEPGVKGDTASGSTKPATLETGAVV 159
S1_EF-P_repeat_1 cd04470
S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 37-96 3.73e-26

S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain II (the first S1 domain of EF_P). Domains II and III have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication.


Pssm-ID: 239916 [Multi-domain]  Cd Length: 61  Bit Score: 92.91  E-value: 3.73e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313  37 DTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDCVVTLWNGTPIQVTPP 96
Cdd:cd04470    2 EREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61
PRK04542 PRK04542
elongation factor P; Provisional
 1-130 4.96e-23

elongation factor P; Provisional


Pssm-ID: 179863 [Multi-domain]  Cd Length: 189  Bit Score: 88.48  E-value: 4.96e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   1 GKGQAfTRVKYRF--IKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWI-KG 77
Cdd:PRK04542  32 GRGGA-TLYKMRFydVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGDEYVFMDNEDYTPYTFKKDQIEDELLFIpEG 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 748943313  78 EEDCVVTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:PRK04542 111 MPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTGLVI 163
EFP pfam01132
Elongation factor P (EF-P) OB domain;
39-91 9.02e-23

Elongation factor P (EF-P) OB domain;


Pssm-ID: 460077 [Multi-domain]  Cd Length: 54  Bit Score: 83.99  E-value: 9.02e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 748943313   39 DMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDCVVTLWNGTPI 91
Cdd:pfam01132   2 EMQYLYNDGDDYVFMDNETYEQIELPKEQLGDAAKFLKEGMEVTVLFYEGKPI 54
PRK14578 PRK14578
elongation factor P; Provisional
 3-127 9.25e-18

elongation factor P; Provisional


Pssm-ID: 173042 [Multi-domain]  Cd Length: 187  Bit Score: 74.87  E-value: 9.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   3 GQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDCV 82
Cdd:PRK14578  35 ANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGDRGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQ 114

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 748943313  83 VTLWNGTPIQVTPPNFVELKIVETDPGVRGDTSGGGGKPATLETG 127
Cdd:PRK14578 115 LGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLETG 159
Elong-fact-P_C pfam09285
Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are ...
 99-130 8.83e-14

Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.


Pssm-ID: 430503 [Multi-domain]  Cd Length: 56  Bit Score: 61.24  E-value: 8.83e-14
                          10        20        30
                  ....*....|....*....|....*....|..
gi 748943313   99 VELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:pfam09285   1 VELEVTETEPGVKGDTASGATKPATLETGAEV 32
PRK12426 PRK12426
elongation factor P; Provisional
 2-130 8.44e-13

elongation factor P; Provisional


Pssm-ID: 183522 [Multi-domain]  Cd Length: 185  Bit Score: 61.78  E-value: 8.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 748943313   2 KGQAFTRVKYRFIKSGRVVEMTMKATDSVEAADVVDTDMQYLYSDGEYWHFMQQETFEQVQADKAGVGDAAKWIKGEEDC 81
Cdd:PRK12426  32 KGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEYLFLDLGNYDKIYIPKEIMKDNFLFLKAGVTV 111

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 748943313  82 VVTLWNGTPIQVTPPNFVELKIVETD-PGVRGDTSgGGGKPATLETGAVV 130
Cdd:PRK12426 112 SALVYDGTVFSVELPHFLELMVSKTDfPGDSLSLS-GGAKKALLETGVEV 160
S1_EF-P_repeat_2 cd05794
S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 99-130 2.99e-12

S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain III (the second S1 domain of EF_P). Domains II and III of have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication.


Pssm-ID: 240220 [Multi-domain]  Cd Length: 56  Bit Score: 57.15  E-value: 2.99e-12
                         10        20        30
                 ....*....|....*....|....*....|..
gi 748943313  99 VELKIVETDPGVRGDTSGGGGKPATLETGAVV 130
Cdd:cd05794    1 VELEVTETEPGVKGDTASSGTKPATLETGAEV 32
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 99-130 8.03e-12

Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.


Pssm-ID: 214849 [Multi-domain]  Cd Length: 57  Bit Score: 55.92  E-value: 8.03e-12
                           10        20        30
                   ....*....|....*....|....*....|...
gi 748943313    99 VELKIVETDPGVRGDTSGGGGK-PATLETGAVV 130
Cdd:smart00841   1 VELEVTETEPGVKGDTASGGTKkPATLETGAVV 33
EFP_N pfam08207
Elongation factor P (EF-P) KOW-like domain;
1-30 3.83e-07

Elongation factor P (EF-P) KOW-like domain;


Pssm-ID: 429864 [Multi-domain]  Cd Length: 58  Bit Score: 43.96  E-value: 3.83e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 748943313    1 GKGQAFTRVKYRFIKSGRVVEMTMKATDSV 30
Cdd:pfam08207  29 GKGQAFVRTKLKNLRTGAKVEKTFKAGDKV 58
 
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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