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Conserved domains on  [gi|818607436|gb|KKS56397|]
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MAG: Elongation factor P [Candidatus Magasanikbacteria bacterium GW2011_GWA2_42_32]

Protein Classification

elongation factor P( domain architecture ID 11415475)

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
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-186 7.51e-96

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: 275.75  E-value: 7.51e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHI 160
Cdd:COG0231   81 VFMDTETYEQIELPKEVVGDAAKFLKEGMEVTVLFYNGKPISVELPNFVELEVTETEPGVKGDTATG-GTKPATLETGAV 159

                        170       180
                 ....*....|....*....|....*.
gi 818607436 161 IRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:COG0231  160 VQVPLFIEEGDKIKVDTRTGEYVERA 185
 
Name Accession Description Interval E-value
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-186 7.51e-96

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: 275.75  E-value: 7.51e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHI 160
Cdd:COG0231   81 VFMDTETYEQIELPKEVVGDAAKFLKEGMEVTVLFYNGKPISVELPNFVELEVTETEPGVKGDTATG-GTKPATLETGAV 159

                        170       180
                 ....*....|....*....|....*.
gi 818607436 161 IRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:COG0231  160 VQVPLFIEEGDKIKVDTRTGEYVERA 185
PRK00529 PRK00529
elongation factor P; Validated
 1-186 8.63e-94

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 270.77  E-value: 8.63e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:PRK00529   1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHI 160
Cdd:PRK00529  81 VFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASG-GTKPATLETGAV 159

                        170       180
                 ....*....|....*....|....*.
gi 818607436 161 IRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:PRK00529 160 VQVPLFINEGEKIKVDTRTGEYVERA 185
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 2-186 2.05e-90

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: 262.01  E-value: 2.05e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436    2 ASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMYT 81
Cdd:TIGR00038   1 ISANDLRKGLKIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   82 FMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHII 161
Cdd:TIGR00038  81 FMDTETYEQIELPKDLLGDAAKFLKENMEVSVVFYNGEPIGVELPNFVELEVTETEPGVKGDTASG-STKPATLETGAVV 159

                         170       180
                  ....*....|....*....|....*
gi 818607436  162 RVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:TIGR00038 160 QVPLFIEEGEKIKVDTRTGEYVERA 184
Elong-fact-P_C pfam09285
Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are ...
 129-185 8.54e-26

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: 93.60  E-value: 8.54e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 818607436  129 VAYKIIQAEPGVKGDTASGnVSKEATLETGHIIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:pfam09285   1 VELEVTETEPGVKGDTASG-ATKPATLETGAEVQVPLFINEGDKIKVDTRTGEYVER 56
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 129-185 4.35e-25

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: 91.75  E-value: 4.35e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 818607436   129 VAYKIIQAEPGVKGDTASGNVSKEATLETGHIIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:smart00841   1 VELEVTETEPGVKGDTASGGTKKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 57
S1_EF-P_repeat_1 cd04470
S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 66-126 1.29e-23

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: 88.28  E-value: 1.29e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818607436  66 ERRKMQYLYNNGEMYTFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLP 126
Cdd:cd04470    1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61
 
Name Accession Description Interval E-value
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-186 7.51e-96

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: 275.75  E-value: 7.51e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHI 160
Cdd:COG0231   81 VFMDTETYEQIELPKEVVGDAAKFLKEGMEVTVLFYNGKPISVELPNFVELEVTETEPGVKGDTATG-GTKPATLETGAV 159

                        170       180
                 ....*....|....*....|....*.
gi 818607436 161 IRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:COG0231  160 VQVPLFIEEGDKIKVDTRTGEYVERA 185
PRK00529 PRK00529
elongation factor P; Validated
 1-186 8.63e-94

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 270.77  E-value: 8.63e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:PRK00529   1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHI 160
Cdd:PRK00529  81 VFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASG-GTKPATLETGAV 159

                        170       180
                 ....*....|....*....|....*.
gi 818607436 161 IRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:PRK00529 160 VQVPLFINEGEKIKVDTRTGEYVERA 185
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 2-186 2.05e-90

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: 262.01  E-value: 2.05e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436    2 ASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMYT 81
Cdd:TIGR00038   1 ISANDLRKGLKIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   82 FMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGnVSKEATLETGHII 161
Cdd:TIGR00038  81 FMDTETYEQIELPKDLLGDAAKFLKENMEVSVVFYNGEPIGVELPNFVELEVTETEPGVKGDTASG-STKPATLETGAVV 159

                         170       180
                  ....*....|....*....|....*
gi 818607436  162 RVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:TIGR00038 160 QVPLFIEEGEKIKVDTRTGEYVERA 184
PRK04542 PRK04542
elongation factor P; Provisional
 1-186 4.56e-39

elongation factor P; Provisional


Pssm-ID: 179863 [Multi-domain]  Cd Length: 189  Bit Score: 132.01  E-value: 4.56e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGK--GSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGE 78
Cdd:PRK04542   1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGrgGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  79 MYTFMDNSTYEQLEINVSLLEGKKEFLKEGL-DVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGNvSKEATLET 157
Cdd:PRK04542  81 EYVFMDNEDYTPYTFKKDQIEDELLFIPEGMpGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASAR-TKPATLST 159

                        170       180
                 ....*....|....*....|....*....
gi 818607436 158 GHIIRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:PRK04542 160 GLVIQVPEYISTGEKIRINTEERKFMGRA 188
PRK14578 PRK14578
elongation factor P; Provisional
 1-186 8.08e-34

elongation factor P; Provisional


Pssm-ID: 173042 [Multi-domain]  Cd Length: 187  Bit Score: 118.40  E-value: 8.08e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTE--FQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGE 78
Cdd:PRK14578   1 MYTTSDFKKGLVIQLDGAPCLLLDvtFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  79 MYTFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAEPGVKGDTASGNvSKEATLETG 158
Cdd:PRK14578  81 RGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQ-TKEAVLETG 159

                        170       180
                 ....*....|....*....|....*...
gi 818607436 159 HIIRVPLFIKEGEEIIVNTETGEYVERA 186
Cdd:PRK14578 160 LRLQVPPYLESGEKIKVDTRDGRFISRA 187
PRK12426 PRK12426
elongation factor P; Provisional
 1-185 7.09e-27

elongation factor P; Provisional


Pssm-ID: 183522 [Multi-domain]  Cd Length: 185  Bit Score: 100.30  E-value: 7.09e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436   1 MASINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMY 80
Cdd:PRK12426   1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  81 TFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLPNKVAYKIIQAE-PGVKGDTASGnvSKEATLETGH 159
Cdd:PRK12426  81 LFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMVSKTDfPGDSLSLSGG--AKKALLETGV 158

                        170       180
                 ....*....|....*....|....*.
gi 818607436 160 IIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:PRK12426 159 EVLVPPFVEIGDVIKVDTRTCEYIQR 184
Elong-fact-P_C pfam09285
Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are ...
 129-185 8.54e-26

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: 93.60  E-value: 8.54e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 818607436  129 VAYKIIQAEPGVKGDTASGnVSKEATLETGHIIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:pfam09285   1 VELEVTETEPGVKGDTASG-ATKPATLETGAEVQVPLFINEGDKIKVDTRTGEYVER 56
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 129-185 4.35e-25

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: 91.75  E-value: 4.35e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 818607436   129 VAYKIIQAEPGVKGDTASGNVSKEATLETGHIIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:smart00841   1 VELEVTETEPGVKGDTASGGTKKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 57
S1_EF-P_repeat_1 cd04470
S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 66-126 1.29e-23

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: 88.28  E-value: 1.29e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818607436  66 ERRKMQYLYNNGEMYTFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPLSIQLP 126
Cdd:cd04470    1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61
S1_EF-P_repeat_2 cd05794
S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 129-185 5.30e-22

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: 84.11  E-value: 5.30e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 818607436 129 VAYKIIQAEPGVKGDTASgNVSKEATLETGHIIRVPLFIKEGEEIIVNTETGEYVER 185
Cdd:cd05794    1 VELEVTETEPGVKGDTAS-SGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56
EFP pfam01132
Elongation factor P (EF-P) OB domain;
68-121 1.95e-19

Elongation factor P (EF-P) OB domain;


Pssm-ID: 460077 [Multi-domain]  Cd Length: 54  Bit Score: 77.44  E-value: 1.95e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 818607436   68 RKMQYLYNNGEMYTFMDNSTYEQLEINVSLLEGKKEFLKEGLDVMVIKFESIPL 121
Cdd:pfam01132   1 REMQYLYNDGDDYVFMDNETYEQIELPKEQLGDAAKFLKEGMEVTVLFYEGKPI 54
EFP_N pfam08207
Elongation factor P (EF-P) KOW-like domain;
3-60 4.42e-19

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


Pssm-ID: 429864 [Multi-domain]  Cd Length: 58  Bit Score: 76.32  E-value: 4.42e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 818607436    3 SINEISKETILRLNGEIYLVTEFQHVNPGKGSAFVRTRLRGIKTGKTMELTFKSNESV 60
Cdd:pfam08207   1 SANELRKGNVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKAGDKV 58
PRK03999 PRK03999
translation initiation factor IF-5A; Provisional
 17-117 9.40e-07

translation initiation factor IF-5A; Provisional


Pssm-ID: 235193 [Multi-domain]  Cd Length: 129  Bit Score: 46.06  E-value: 9.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607436  17 GEIYLVTEFQHVNPGK-GSAFVRTRLRGIKTGKTMELTFKSNESVEIVEVERRKMQYLYNNGEMYTFMDNSTYEQLEINV 95
Cdd:PRK03999  21 GEPCKIVEISKSKPGKhGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGDVVQLMDLETYETFEIPI 100

                         90       100
                 ....*....|....*....|..
gi 818607436  96 SllEGKKEFLKEGLDVMVIKFE 117
Cdd:PRK03999 101 P--EELKDKLEPGVEVEYWEAM 120
S1_EF_like cd04463
S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the ...
 68-114 3.12e-03

S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.


Pssm-ID: 239910  Cd Length: 55  Bit Score: 34.52  E-value: 3.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 818607436  68 RKMQYLYNNGEMYTFMDNSTYEQLEINVSLLEGkKEFLKEGLDVMVI 114
Cdd:cd04463    1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVDQS-FESFEPGEVVLVD 46
 
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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