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MULTISPECIES: 50S ribosomal protein L25 [Enterobacter]

Protein Classification

50S ribosomal protein L25( domain architecture ID 10792702)

50S ribosomal protein L25 is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance

Gene Ontology:  GO:0006412|GO:0005840|GO:0003735
PubMed:  9799245|24524803

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 1-94 3.47e-57

50S ribosomal protein L25; Reviewed


:

Pssm-ID: 180318  Cd Length: 94  Bit Score: 170.85  E-value: 3.47e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492  1 MFTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQTKAEFYSEVLTIVVGGKEEKVKVQAVQRH 80
Cdd:PRK05943  1 MFTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRH 80

                        90
                ....*....|....
gi 658548492 81 PFKPKLSHIDFVRA 94
Cdd:PRK05943 81 PFKPKLEHIDFVRA 94
 
Name Accession Description Interval E-value
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 1-94 3.47e-57

50S ribosomal protein L25; Reviewed


Pssm-ID: 180318  Cd Length: 94  Bit Score: 170.85  E-value: 3.47e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492  1 MFTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQTKAEFYSEVLTIVVGGKEEKVKVQAVQRH 80
Cdd:PRK05943  1 MFTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRH 80

                        90
                ....*....|....
gi 658548492 81 PFKPKLSHIDFVRA 94
Cdd:PRK05943 81 PFKPKLEHIDFVRA 94
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 2-93 1.58e-36

Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]; Ribosomal protein L25 (general stress protein Ctc) is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 441430 [Multi-domain]  Cd Length: 182  Bit Score: 121.54  E-value: 1.58e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492   2 FTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHP 81
Cdd:COG1825    4 ITLKAEKREETGKGAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLL-RKEGENTLITLDIDGKKEKVLIKDVQRHP 82

                         90
                 ....*....|..
gi 658548492  82 FKPKLSHIDFVR 93
Cdd:COG1825   83 VKDEILHVDFLR 94
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 4-91 1.94e-34

Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress.


Pssm-ID: 460185  Cd Length: 87  Bit Score: 112.92  E-value: 1.94e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492   4 IEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHPFK 83
Cdd:pfam01386  1 LKAEKRTEFGKGAARRLRREGKVPAVLYGGGKEPISISVDAKELRKLL-RTEGENTVIELDIDGKKYKVLIKDVQRHPVK 79


                 ....*...
gi 658548492  84 PKLSHIDF 91
Cdd:pfam01386 80 DEILHVDF 87
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 3-93 3.49e-32

Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23.


Pssm-ID: 198379  Cd Length: 90  Bit Score: 107.56  E-value: 3.49e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492  3 TIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHPF 82
Cdd:cd00495   1 TLKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLL-RKEGENTVIELEIDGKKENVLIKDVQRHPV 79

                        90
                ....*....|.
gi 658548492 83 KPKLSHIDFVR 93
Cdd:cd00495  80 KDEILHVDFLR 90
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 4-92 2.29e-15

ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273237 [Multi-domain]  Cd Length: 176  Bit Score: 67.00  E-value: 2.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492    4 IEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELD-HDKLWNLQTKAEfySEVLTIVVGGKEEKVKVQAVQRHPF 82
Cdd:TIGR00731   1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKsKEFIKYLRKGAT--STVLTLEIGGKEFKVLVKDYQYNPV 78

                          90
                  ....*....|
gi 658548492   83 KPKLSHIDFV 92
Cdd:TIGR00731  79 TNEVIHVDFL 88
 
Name Accession Description Interval E-value
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 1-94 3.47e-57

50S ribosomal protein L25; Reviewed


Pssm-ID: 180318  Cd Length: 94  Bit Score: 170.85  E-value: 3.47e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492  1 MFTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQTKAEFYSEVLTIVVGGKEEKVKVQAVQRH 80
Cdd:PRK05943  1 MFTINAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRH 80

                        90
                ....*....|....
gi 658548492 81 PFKPKLSHIDFVRA 94
Cdd:PRK05943 81 PFKPKLEHIDFVRA 94
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 2-93 1.58e-36

Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]; Ribosomal protein L25 (general stress protein Ctc) is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 441430 [Multi-domain]  Cd Length: 182  Bit Score: 121.54  E-value: 1.58e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492   2 FTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHP 81
Cdd:COG1825    4 ITLKAEKREETGKGAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLL-RKEGENTLITLDIDGKKEKVLIKDVQRHP 82

                         90
                 ....*....|..
gi 658548492  82 FKPKLSHIDFVR 93
Cdd:COG1825   83 VKDEILHVDFLR 94
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 4-91 1.94e-34

Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress.


Pssm-ID: 460185  Cd Length: 87  Bit Score: 112.92  E-value: 1.94e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492   4 IEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHPFK 83
Cdd:pfam01386  1 LKAEKRTEFGKGAARRLRREGKVPAVLYGGGKEPISISVDAKELRKLL-RTEGENTVIELDIDGKKYKVLIKDVQRHPVK 79


                 ....*...
gi 658548492  84 PKLSHIDF 91
Cdd:pfam01386 80 DEILHVDF 87
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-93 5.88e-34

50S ribosomal protein L25/general stress protein Ctc; Reviewed


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 115.30  E-value: 5.88e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492   1 MFTIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQTKAEFYSEVLTIVVGGKEEKVKVQAVQRH 80
Cdd:PRK05618   3 TITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGAFLSTLLDLEVGGKKQKVLVKDVQRH 82

                         90
                 ....*....|...
gi 658548492  81 PFKPKLSHIDFVR 93
Cdd:PRK05618  83 PVKDFILHVDFLR 95
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 3-93 3.49e-32

Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23.


Pssm-ID: 198379  Cd Length: 90  Bit Score: 107.56  E-value: 3.49e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492  3 TIEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELDHDKLWNLQtKAEFYSEVLTIVVGGKEEKVKVQAVQRHPF 82
Cdd:cd00495   1 TLKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLL-RKEGENTVIELEIDGKKENVLIKDVQRHPV 79

                        90
                ....*....|.
gi 658548492 83 KPKLSHIDFVR 93
Cdd:cd00495  80 KDEILHVDFLR 90
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 4-92 2.29e-15

ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273237 [Multi-domain]  Cd Length: 176  Bit Score: 67.00  E-value: 2.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 658548492    4 IEAEVRNVQGKGASRRLRNANKFPAIVYGGEAAPVAIELD-HDKLWNLQTKAEfySEVLTIVVGGKEEKVKVQAVQRHPF 82
Cdd:TIGR00731   1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKsKEFIKYLRKGAT--STVLTLEIGGKEFKVLVKDYQYNPV 78

                          90
                  ....*....|
gi 658548492   83 KPKLSHIDFV 92
Cdd:TIGR00731  79 TNEVIHVDFL 88
 
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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