NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|499722962|ref|WP_011403696|]
View 

elongation factor P [Salinibacter ruber]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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, ...
 1-187 8.02e-93

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: 268.43  E-value: 8.02e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQV-EGREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGA 159
Cdd:COG0231   81 VFMDTETYEQIELPKEVVgDAAKFLKEGMEVTVLF--YNGKPISVELPNFVELEVTETEPGVKGDTATGGTKPATLETGA 158

                        170       180
                 ....*....|....*....|....*...
gi 499722962 160 TIDVPLFINEGDVVRLNTETEEYETRVS 187
Cdd:COG0231  159 VVQVPLFIEEGDKIKVDTRTGEYVERAK 186
 
Name Accession Description Interval E-value
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-187 8.02e-93

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: 268.43  E-value: 8.02e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQV-EGREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGA 159
Cdd:COG0231   81 VFMDTETYEQIELPKEVVgDAAKFLKEGMEVTVLF--YNGKPISVELPNFVELEVTETEPGVKGDTATGGTKPATLETGA 158

                        170       180
                 ....*....|....*....|....*...
gi 499722962 160 TIDVPLFINEGDVVRLNTETEEYETRVS 187
Cdd:COG0231  159 VVQVPLFIEEGDKIKVDTRTGEYVERAK 186
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 2-186 2.78e-92

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: 267.02  E-value: 2.78e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962    2 ADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGLH 81
Cdd:TIGR00038   1 ISANDLRKGLKIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   82 FMDQESYEQFSMPPEQV-EGREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGAT 160
Cdd:TIGR00038  81 FMDTETYEQIELPKDLLgDAAKFLKENMEVSVVF--YNGEPIGVELPNFVELEVTETEPGVKGDTASGSTKPATLETGAV 158

                         170       180
                  ....*....|....*....|....*.
gi 499722962  161 IDVPLFINEGDVVRLNTETEEYETRV 186
Cdd:TIGR00038 159 VQVPLFIEEGEKIKVDTRTGEYVERA 184
PRK00529 PRK00529
elongation factor P; Validated
 1-186 1.14e-89

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 260.37  E-value: 1.14e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:PRK00529   1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQVE-GREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGA 159
Cdd:PRK00529  81 VFMDTETYEQIEVPADQVGdAAKFLKEGMEVTVVF--YNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGA 158

                        170       180
                 ....*....|....*....|....*..
gi 499722962 160 TIDVPLFINEGDVVRLNTETEEYETRV 186
Cdd:PRK00529 159 VVQVPLFINEGEKIKVDTRTGEYVERA 185
Elong-fact-P_C pfam09285
Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are ...
 130-185 4.71e-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: 94.37  E-value: 4.71e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 499722962  130 VDLEVTETTPGVKGDTAQGGDKPATLESGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:pfam09285   1 VELEVTETEPGVKGDTASGATKPATLETGAEVQVPLFINEGDKIKVDTRTGEYVER 56
S1_EF-P_repeat_2 cd05794
S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 130-185 1.29e-24

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: 91.05  E-value: 1.29e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499722962 130 VDLEVTETTPGVKGDTAQGGDKPATLESGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:cd05794    1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 130-185 3.90e-24

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: 89.82  E-value: 3.90e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 499722962   130 VDLEVTETTPGVKGDTAQGGDK-PATLESGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:smart00841   1 VELEVTETEPGVKGDTASGGTKkPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 57
 
Name Accession Description Interval E-value
Efp COG0231
Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ...
 1-187 8.02e-93

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: 268.43  E-value: 8.02e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:COG0231    1 MISANDLRKGLVIEIDGEPYVVVEFQHVKPGKGGAFVRTKLKNLLTGKVVEKTFKSGDKVEEADLERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQV-EGREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGA 159
Cdd:COG0231   81 VFMDTETYEQIELPKEVVgDAAKFLKEGMEVTVLF--YNGKPISVELPNFVELEVTETEPGVKGDTATGGTKPATLETGA 158

                        170       180
                 ....*....|....*....|....*...
gi 499722962 160 TIDVPLFINEGDVVRLNTETEEYETRVS 187
Cdd:COG0231  159 VVQVPLFIEEGDKIKVDTRTGEYVERAK 186
efp TIGR00038
translation elongation factor P; function: involved in peptide bond synthesis. stimulate ...
 2-186 2.78e-92

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: 267.02  E-value: 2.78e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962    2 ADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGLH 81
Cdd:TIGR00038   1 ISANDLRKGLKIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   82 FMDQESYEQFSMPPEQV-EGREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGAT 160
Cdd:TIGR00038  81 FMDTETYEQIELPKDLLgDAAKFLKENMEVSVVF--YNGEPIGVELPNFVELEVTETEPGVKGDTASGSTKPATLETGAV 158

                         170       180
                  ....*....|....*....|....*.
gi 499722962  161 IDVPLFINEGDVVRLNTETEEYETRV 186
Cdd:TIGR00038 159 VQVPLFIEEGEKIKVDTRTGEYVERA 184
PRK00529 PRK00529
elongation factor P; Validated
 1-186 1.14e-89

elongation factor P; Validated


Pssm-ID: 234788 [Multi-domain]  Cd Length: 186  Bit Score: 260.37  E-value: 1.14e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:PRK00529   1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQVE-GREFLKEGGDVDIVFraDTEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLESGA 159
Cdd:PRK00529  81 VFMDTETYEQIEVPADQVGdAAKFLKEGMEVTVVF--YNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGA 158

                        170       180
                 ....*....|....*....|....*..
gi 499722962 160 TIDVPLFINEGDVVRLNTETEEYETRV 186
Cdd:PRK00529 159 VVQVPLFINEGEKIKVDTRTGEYVERA 185
PRK04542 PRK04542
elongation factor P; Provisional
 1-185 6.33e-31

elongation factor P; Provisional


Pssm-ID: 179863 [Multi-domain]  Cd Length: 189  Bit Score: 111.21  E-value: 6.33e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDF-LHVKPGKGGAFV-RTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDY 78
Cdd:PRK04542   1 MPKANEIKKGMVVEYNGKLLLVKDIdRQSPSGRGGATLyKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  79 GLHFMDQESYEQFSMPPEQVEGRE-FLKEGGDVDIVFRADtEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLES 157
Cdd:PRK04542  81 EYVFMDNEDYTPYTFKKDQIEDELlFIPEGMPGMQVLTVD-GQPVALELPQTVDLEIVETAPSIKGASASARTKPATLST 159

                        170       180
                 ....*....|....*....|....*...
gi 499722962 158 GATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:PRK04542 160 GLVIQVPEYISTGEKIRINTEERKFMGR 187
PRK12426 PRK12426
elongation factor P; Provisional
 1-186 4.38e-29

elongation factor P; Provisional


Pssm-ID: 183522 [Multi-domain]  Cd Length: 185  Bit Score: 106.47  E-value: 4.38e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGL 80
Cdd:PRK12426   1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  81 HFMDQESYEQFSMPPEQVEGR-EFLKEGGDVDIVFRADTeePLRTEVPQKVDLEVTETT-PGVKGDTAqGGDKPATLESG 158
Cdd:PRK12426  81 LFLDLGNYDKIYIPKEIMKDNfLFLKAGVTVSALVYDGT--VFSVELPHFLELMVSKTDfPGDSLSLS-GGAKKALLETG 157

                        170       180
                 ....*....|....*....|....*...
gi 499722962 159 ATIDVPLFINEGDVVRLNTETEEYETRV 186
Cdd:PRK12426 158 VEVLVPPFVEIGDVIKVDTRTCEYIQRV 185
PRK14578 PRK14578
elongation factor P; Provisional
 1-185 2.85e-28

elongation factor P; Provisional


Pssm-ID: 173042 [Multi-domain]  Cd Length: 187  Bit Score: 104.15  E-value: 2.85e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962   1 MADTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGA--FVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDY 78
Cdd:PRK14578   1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGAntMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  79 GLHFMDQESYEQFSMPPEQVEG-REFLKEGGDVDI-VFRadtEEPLRTEVPQKVDLEVTETTPGVKGDTAQGGDKPATLE 156
Cdd:PRK14578  81 RGVFMDLETYEQFEMEEDAFSAiAPFLLDGTEVQLgLFQ---GRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLE 157

                        170       180
                 ....*....|....*....|....*....
gi 499722962 157 SGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:PRK14578 158 TGLRLQVPPYLESGEKIKVDTRDGRFISR 186
Elong-fact-P_C pfam09285
Elongation factor P, C-terminal; Members of this family of nucleic acid binding domains are ...
 130-185 4.71e-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: 94.37  E-value: 4.71e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 499722962  130 VDLEVTETTPGVKGDTAQGGDKPATLESGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:pfam09285   1 VELEVTETEPGVKGDTASGATKPATLETGAEVQVPLFINEGDKIKVDTRTGEYVER 56
EFP_N pfam08207
Elongation factor P (EF-P) KOW-like domain;
3-60 7.54e-25

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


Pssm-ID: 429864 [Multi-domain]  Cd Length: 58  Bit Score: 91.34  E-value: 7.54e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 499722962    3 DTSDFRNGMTFIWKDDLWEIVDFLHVKPGKGGAFVRTTLKNVKDGHEVEETFRAGAKV 60
Cdd:pfam08207   1 SANELRKGNVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKAGDKV 58
S1_EF-P_repeat_2 cd05794
S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. ...
 130-185 1.29e-24

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: 91.05  E-value: 1.29e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499722962 130 VDLEVTETTPGVKGDTAQGGDKPATLESGATIDVPLFINEGDVVRLNTETEEYETR 185
Cdd:cd05794    1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56
Elong-fact-P_C smart00841
Elongation factor P, C-terminal; These nucleic acid binding domains are predominantly found in ...
 130-185 3.90e-24

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: 89.82  E-value: 3.90e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 499722962   130 VDLEVTETTPGVKGDTAQGGDK-PATLESGATIDVPLFINEGDVVRLNTETEEYETR 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. ...
 66-127 5.55e-17

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: 71.34  E-value: 5.55e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499722962  66 ERREHQYLYEDDYGLHFMDQESYEQFSMPPEQVEGRE-FLKEGGDVDIVFRADteEPLRTEVP 127
Cdd:cd04470    1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAkFLKEGMEVIVLFYNG--EPIGVELP 61
EFP pfam01132
Elongation factor P (EF-P) OB domain;
68-114 4.48e-15

Elongation factor P (EF-P) OB domain;


Pssm-ID: 460077 [Multi-domain]  Cd Length: 54  Bit Score: 66.27  E-value: 4.48e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 499722962   68 REHQYLYEDDYGLHFMDQESYEQFSMPPEQVEGRE-FLKEGGDVDIVF 114
Cdd:pfam01132   1 REMQYLYNDGDDYVFMDNETYEQIELPKEQLGDAAkFLKEGMEVTVLF 48
eIF_5A TIGR00037
translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes ...
 5-113 7.61e-08

translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes and aIF5A in archaea, hypusine-containing proteins, from translation initiation factor to translation elongation factor. [Protein synthesis, Translation factors]


Pssm-ID: 272866 [Multi-domain]  Cd Length: 130  Bit Score: 49.05  E-value: 7.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962    5 SDFRNGMTFIWKDDLWEIVDFLHVKPGK-GGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGLHFM 83
Cdd:TIGR00037  10 SALRVGGYVVIDGEPCKIVDISTSKPGKhGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLAIMGGMVQLM 89

                          90       100       110
                  ....*....|....*....|....*....|.
gi 499722962   84 DQESYEQFSMP-PEqvEGREFLKEGGDVDIV 113
Cdd:TIGR00037  90 DLETYETFELPiPE--ELGDSLEPGFEVEYI 118
S1_EF_like cd04463
S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the ...
 68-119 2.43e-04

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: 37.60  E-value: 2.43e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499722962  68 REHQYLYEDDYGLHFMDQESYEQFSMPPEQVEGREFLKEGGDVDIVFRADTE 119
Cdd:cd04463    1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVDQSFESFEPGEVVLVDTRTGQY 52
PRK03999 PRK03999
translation initiation factor IF-5A; Provisional
 21-110 3.10e-04

translation initiation factor IF-5A; Provisional


Pssm-ID: 235193 [Multi-domain]  Cd Length: 129  Bit Score: 39.12  E-value: 3.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499722962  21 EIVDFLHVKPGK-GGAFVRTTLKNVKDGHEVEETFRAGAKVDEVRVERREHQYLYEDDYGLHFMDQESYEQFSMP-PEQV 98
Cdd:PRK03999  25 KIVEISKSKPGKhGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGDVVQLMDLETYETFEIPiPEEL 104

                         90
                 ....*....|..
gi 499722962  99 EGRefLKEGGDV 110
Cdd:PRK03999 105 KDK--LEPGVEV 114
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH