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Conserved domains on  [gi|952345726|gb|KRT67844|]
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50S ribosomal protein L25, large subunit ribosomal protein L25 [candidate division WWE3 bacterium CSP1-7]

Protein Classification

50S ribosomal protein L25/general stress protein Ctc( domain architecture ID 11481318)

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

CATH:  2.170.120.20|2.40.240.10
Gene Ontology:  GO:0003735|GO:0008097|GO:0006412
PubMed:  24524803
SCOP:  4002376

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-159 7.08e-48

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


:

Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 156.90  E-value: 7.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGKK-VRSLRRGGVLPAILFGGDEGSTPVELDLNIFRR-VYEEAGESTLLDLELGGKKEKILIADVQRDP 78
Cdd:PRK05618   4 ITLEAEVREEFGKGaARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKaLKKGAFLSTLLDLEVGGKKQKVLVKDVQRHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726  79 L-GKLLHADLRRVAAGEKITATVPVEVVGESIPVR-SGEGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKD 156
Cdd:PRK05618  84 VkDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGvKLGGVLNQVLHELEVECLPEDIPEFIEVDVSGL-EIGDSIHVSD 162


                 ...
gi 952345726 157 LPI 159
Cdd:PRK05618 163 LKL 165
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-159 7.08e-48

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 156.90  E-value: 7.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGKK-VRSLRRGGVLPAILFGGDEGSTPVELDLNIFRR-VYEEAGESTLLDLELGGKKEKILIADVQRDP 78
Cdd:PRK05618   4 ITLEAEVREEFGKGaARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKaLKKGAFLSTLLDLEVGGKKQKVLVKDVQRHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726  79 L-GKLLHADLRRVAAGEKITATVPVEVVGESIPVR-SGEGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKD 156
Cdd:PRK05618  84 VkDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGvKLGGVLNQVLHELEVECLPEDIPEFIEVDVSGL-EIGDSIHVSD 162


                 ...
gi 952345726 157 LPI 159
Cdd:PRK05618 163 LKL 165
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-176 1.92e-44

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: 147.35  E-value: 1.92e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGK-KVRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL 79
Cdd:COG1825    4 ITLKAEKREETGKgAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLLRKEGENTLITLDIDGKKEKVLIKDVQRHPV 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726  80 -GKLLHADLRRVAAGEKITATVPVEVVGESIPVRSGeGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKDLP 158
Cdd:COG1825   84 kDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVG-GGLVLTLHELEVEALPPDIPEPIEVDVSDL-GLGDSISVHDLD 161

                        170
                 ....*....|....*...
gi 952345726 159 IDLAKVTIVGHELDELAV 176
Cdd:COG1825  162 LPLLVGVVEDPDVVVVVV 179
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 3-176 3.18e-30

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: 110.92  E-value: 3.18e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726    3 LKAEKRKILGKKV-RSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPLGK 81
Cdd:TIGR00731   1 LEVKSRTSFGKSAaRRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGATSTVLTLEIGGKEFKVLVKDYQYNPVTN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   82 LL-HADLRRVAAGEKITATVPVEVVGESIPVRSGeGVLLTLLDEIEVECFPQDLPQKITVDISGLNeVGTGIAIKDLPID 160
Cdd:TIGR00731  81 EViHVDFLEVVEGVKLKVEVPIKLIGTPIGVKNG-GILTQVKRRIEVECKPKDIPDFLELDVSSLG-VGESLKLSDLELP 158

                         170
                  ....*....|....*.
gi 952345726  161 lAKVTIVgHELDELAV 176
Cdd:TIGR00731 159 -AGVSFI-TDDDEVVV 172
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 3-87 2.18e-25

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: 95.20  E-value: 2.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726    3 LKAEKRKILGKK-VRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL-G 80
Cdd:pfam01386   1 LKAEKRTEFGKGaARRLRREGKVPAVLYGGGKEPISISVDAKELRKLLRTEGENTVIELDIDGKKYKVLIKDVQRHPVkD 80


                  ....*..
gi 952345726   81 KLLHADL 87
Cdd:pfam01386  81 EILHVDF 87
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 2-89 9.40e-25

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: 93.69  E-value: 9.40e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   2 ELKAEKRKILGK-KVRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL- 79
Cdd:cd00495    1 TLKAEKREETGKgAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKEGENTVIELEIDGKKENVLIKDVQRHPVk 80

                         90
                 ....*....|
gi 952345726  80 GKLLHADLRR 89
Cdd:cd00495   81 DEILHVDFLR 90
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-159 7.08e-48

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 156.90  E-value: 7.08e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGKK-VRSLRRGGVLPAILFGGDEGSTPVELDLNIFRR-VYEEAGESTLLDLELGGKKEKILIADVQRDP 78
Cdd:PRK05618   4 ITLEAEVREEFGKGaARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKaLKKGAFLSTLLDLEVGGKKQKVLVKDVQRHP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726  79 L-GKLLHADLRRVAAGEKITATVPVEVVGESIPVR-SGEGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKD 156
Cdd:PRK05618  84 VkDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGvKLGGVLNQVLHELEVECLPEDIPEFIEVDVSGL-EIGDSIHVSD 162


                 ...
gi 952345726 157 LPI 159
Cdd:PRK05618 163 LKL 165
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-176 1.92e-44

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: 147.35  E-value: 1.92e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGK-KVRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL 79
Cdd:COG1825    4 ITLKAEKREETGKgAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLLRKEGENTLITLDIDGKKEKVLIKDVQRHPV 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726  80 -GKLLHADLRRVAAGEKITATVPVEVVGESIPVRSGeGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKDLP 158
Cdd:COG1825   84 kDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVG-GGLVLTLHELEVEALPPDIPEPIEVDVSDL-GLGDSISVHDLD 161

                        170
                 ....*....|....*...
gi 952345726 159 IDLAKVTIVGHELDELAV 176
Cdd:COG1825  162 LPLLVGVVEDPDVVVVVV 179
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 3-176 3.18e-30

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: 110.92  E-value: 3.18e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726    3 LKAEKRKILGKKV-RSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPLGK 81
Cdd:TIGR00731   1 LEVKSRTSFGKSAaRRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRKGATSTVLTLEIGGKEFKVLVKDYQYNPVTN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   82 LL-HADLRRVAAGEKITATVPVEVVGESIPVRSGeGVLLTLLDEIEVECFPQDLPQKITVDISGLNeVGTGIAIKDLPID 160
Cdd:TIGR00731  81 EViHVDFLEVVEGVKLKVEVPIKLIGTPIGVKNG-GILTQVKRRIEVECKPKDIPDFLELDVSSLG-VGESLKLSDLELP 158

                         170
                  ....*....|....*.
gi 952345726  161 lAKVTIVgHELDELAV 176
Cdd:TIGR00731 159 -AGVSFI-TDDDEVVV 172
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 3-87 2.18e-25

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: 95.20  E-value: 2.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726    3 LKAEKRKILGKK-VRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL-G 80
Cdd:pfam01386   1 LKAEKRTEFGKGaARRLRREGKVPAVLYGGGKEPISISVDAKELRKLLRTEGENTVIELDIDGKKYKVLIKDVQRHPVkD 80


                  ....*..
gi 952345726   81 KLLHADL 87
Cdd:pfam01386  81 EILHVDF 87
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 2-89 9.40e-25

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: 93.69  E-value: 9.40e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   2 ELKAEKRKILGK-KVRSLRRGGVLPAILFGGDEGSTPVELDLNIFRRVYEEAGESTLLDLELGGKKEKILIADVQRDPL- 79
Cdd:cd00495    1 TLKAEKREETGKgAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKEGENTVIELEIDGKKENVLIKDVQRHPVk 80

                         90
                 ....*....|
gi 952345726  80 GKLLHADLRR 89
Cdd:cd00495   81 DEILHVDFLR 90
Ribosomal_TL5_C pfam14693
Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ...
 95-170 5.13e-17

Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, pfam01386. Full length (N- and C-terminal domain) homologs of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family pfam01386). The function of the C-terminal domain of TLC is at present unknown.


Pssm-ID: 464265  Cd Length: 84  Bit Score: 73.21  E-value: 5.13e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 952345726   95 KITATVPVEVVGESIPVRSGeGVLLTLLDEIEVECFPQDLPQKITVDISGLnEVGTGIAIKDLPIDlAKVTIVGHE 170
Cdd:pfam14693   1 KVTVEVPVHFVGEAPGVKKG-GVLNQVLRELEVECLPKDIPEFIEVDVSGL-EIGDSIHVSDLKLP-EGVELLTDP 73
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 1-90 9.79e-12

50S ribosomal protein L25; Reviewed


Pssm-ID: 180318  Cd Length: 94  Bit Score: 59.53  E-value: 9.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 952345726   1 MELKAEKRKILGK-KVRSLRRGGVLPAILFGGDEGSTPVELDLN-IFRRVYEEAGESTLLDLELGGKKEKILIADVQRDP 78
Cdd:PRK05943   2 FTINAEVRPEQGKgASRRLRRAGKFPAIIYGGNEAPVSIVLDHKdVINLQAKAEFYKEVITLVIDGKEVKVKVQAVQRHP 81

                         90
                 ....*....|...
gi 952345726  79 L-GKLLHADLRRV 90
Cdd:PRK05943  82 FkPKLEHIDFVRA 94
 
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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