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Conserved domains on  [gi|1681982575|dbj|BBL08996|]
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50S ribosomal protein L25 [Alistipes onderdonkii subsp. vulgaris]

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|GO:0005840
PubMed:  24524803|12432960
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
 1-189 3.85e-59

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


:

Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 183.48  E-value: 3.85e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   1 MKTISVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYTPNSY--IVEFDFDGKKEQAVLREAQ 77
Cdd:PRK05618    1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGkEPVSISVDEKELIKALKKGAFLstLLDLEVGGKKQKVLVKDVQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  78 FHPIREQILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKV--GGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFV 155
Cdd:PRK05618   81 RHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHV 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1681982575 156 GDLAF-ENLKFVTPASTAVCAVRVTRASRGAAAQA 189
Cdd:PRK05618  161 SDLKLpEGVKLLDDPDEVVATVVAPRGEEEEEEEE 195
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-189 3.85e-59

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 183.48  E-value: 3.85e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   1 MKTISVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYTPNSY--IVEFDFDGKKEQAVLREAQ 77
Cdd:PRK05618    1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGkEPVSISVDEKELIKALKKGAFLstLLDLEVGGKKQKVLVKDVQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  78 FHPIREQILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKV--GGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFV 155
Cdd:PRK05618   81 RHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHV 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1681982575 156 GDLAF-ENLKFVTPASTAVCAVRVTRASRGAAAQA 189
Cdd:PRK05618  161 SDLKLpEGVKLLDDPDEVVATVVAPRGEEEEEEEE 195
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-180 1.89e-57

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: 178.55  E-value: 1.89e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   1 MKTISVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYT-PNSYIVEFDFDGKKEQAVLREAQF 78
Cdd:COG1825     1 MESITLKAEKREETGKGAARRLRREGKVPAVIYGGGkEPVSISVDAKELRKLLRKeGENTLITLDIDGKKEKVLIKDVQR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  79 HPIREQILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKVGGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFVGDL 158
Cdd:COG1825    81 HPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLTLHELEVEALPPDIPEPIEVDVSDLGLGDSISVHDL 160

                         170       180
                  ....*....|....*....|..
gi 1681982575 159 AFENLKFVTPASTAVCAVRVTR 180
Cdd:COG1825   161 DLPLLVGVVEDPDVVVVVVVTP 182
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 7-176 1.51e-33

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: 117.47  E-value: 1.51e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   7 KAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPRE-IKALIYTPNSYIVEFDFDGKKEQAVLREAQFHPIREQ 84
Cdd:TIGR00731   2 EVKSRTSFGKSAARRIRKEGRIPAVVYGKGkENVNLELKSKEfIKYLRKGATSTVLTLEIGGKEFKVLVKDYQYNPVTNE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  85 ILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKVGGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFVGDLAF-ENL 163
Cdd:TIGR00731  82 VIHVDFLEVVEGVKLKVEVPIKLIGTPIGVKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELpAGV 161

                         170
                  ....*....|...
gi 1681982575 164 KFVTPASTAVCAV 176
Cdd:TIGR00731 162 SFITDDDEVVVTV 174
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 5-92 7.29e-31

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: 107.94  E-value: 7.29e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   5 SVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYTPN-SYIVEFDFDGKKEQAVLREAQFHPIR 82
Cdd:cd00495     1 TLKAEKREETGKGAARRLRREGKVPAVIYGKGeEPIPISVDAKELEKLLRKEGeNTVIELEIDGKKENVLIKDVQRHPVK 80

                          90
                  ....*....|
gi 1681982575  83 EQILHLDFYR 92
Cdd:cd00495    81 DEILHVDFLR 90
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 7-90 1.76e-30

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: 106.75  E-value: 1.76e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   7 KAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYT-PNSYIVEFDFDGKKEQAVLREAQFHPIREQ 84
Cdd:pfam01386   2 KAEKRTEFGKGAARRLRREGKVPAVLYGGGkEPISISVDAKELRKLLRTeGENTVIELDIDGKKYKVLIKDVQRHPVKDE 81


                  ....*.
gi 1681982575  85 ILHLDF 90
Cdd:pfam01386  82 ILHVDF 87
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 1-189 3.85e-59

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 183.48  E-value: 3.85e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   1 MKTISVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYTPNSY--IVEFDFDGKKEQAVLREAQ 77
Cdd:PRK05618    1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGkEPVSISVDEKELIKALKKGAFLstLLDLEVGGKKQKVLVKDVQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  78 FHPIREQILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKV--GGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFV 155
Cdd:PRK05618   81 RHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIHV 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1681982575 156 GDLAF-ENLKFVTPASTAVCAVRVTRASRGAAAQA 189
Cdd:PRK05618  161 SDLKLpEGVKLLDDPDEVVATVVAPRGEEEEEEEE 195
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-180 1.89e-57

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: 178.55  E-value: 1.89e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   1 MKTISVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYT-PNSYIVEFDFDGKKEQAVLREAQF 78
Cdd:COG1825     1 MESITLKAEKREETGKGAARRLRREGKVPAVIYGGGkEPVSISVDAKELRKLLRKeGENTLITLDIDGKKEKVLIKDVQR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  79 HPIREQILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKVGGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFVGDL 158
Cdd:COG1825    81 HPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLTLHELEVEALPPDIPEPIEVDVSDLGLGDSISVHDL 160

                         170       180
                  ....*....|....*....|..
gi 1681982575 159 AFENLKFVTPASTAVCAVRVTR 180
Cdd:COG1825   161 DLPLLVGVVEDPDVVVVVVVTP 182
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 7-176 1.51e-33

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: 117.47  E-value: 1.51e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   7 KAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPRE-IKALIYTPNSYIVEFDFDGKKEQAVLREAQFHPIREQ 84
Cdd:TIGR00731   2 EVKSRTSFGKSAARRIRKEGRIPAVVYGKGkENVNLELKSKEfIKYLRKGATSTVLTLEIGGKEFKVLVKDYQYNPVTNE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  85 ILHLDFYRIAEGKPVSIAIPVRLTGNAEGVKVGGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFVGDLAF-ENL 163
Cdd:TIGR00731  82 VIHVDFLEVVEGVKLKVEVPIKLIGTPIGVKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELpAGV 161

                         170
                  ....*....|...
gi 1681982575 164 KFVTPASTAVCAV 176
Cdd:TIGR00731 162 SFITDDDEVVVTV 174
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 5-92 7.29e-31

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: 107.94  E-value: 7.29e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   5 SVKAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYTPN-SYIVEFDFDGKKEQAVLREAQFHPIR 82
Cdd:cd00495     1 TLKAEKREETGKGAARRLRREGKVPAVIYGKGeEPIPISVDAKELEKLLRKEGeNTVIELEIDGKKENVLIKDVQRHPVK 80

                          90
                  ....*....|
gi 1681982575  83 EQILHLDFYR 92
Cdd:cd00495    81 DEILHVDFLR 90
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 7-90 1.76e-30

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: 106.75  E-value: 1.76e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   7 KAVKRDEYGKKAAKAVRREGMVPCVLSGNG-ESVSFSVDPREIKALIYT-PNSYIVEFDFDGKKEQAVLREAQFHPIREQ 84
Cdd:pfam01386   2 KAEKRTEFGKGAARRLRREGKVPAVLYGGGkEPISISVDAKELRKLLRTeGENTVIELDIDGKKYKVLIKDVQRHPVKDE 81


                  ....*.
gi 1681982575  85 ILHLDF 90
Cdd:pfam01386  82 ILHVDF 87
Ribosomal_TL5_C pfam14693
Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ...
 98-180 3.29e-23

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: 87.85  E-value: 3.29e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575  98 PVSIAIPVRLTGNAEGVKVGGKLTLSARKLVVSALVENLPDELVVDVTELGVGKTIFVGDLAF-ENLKFVTPASTAVCAV 176
Cdd:pfam14693   1 KVTVEVPVHFVGEAPGVKKGGVLNQVLRELEVECLPKDIPEFIEVDVSGLEIGDSIHVSDLKLpEGVELLTDPDTVVVSV 80


                  ....
gi 1681982575 177 RVTR 180
Cdd:pfam14693  81 VAPR 84
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 4-93 3.60e-16

50S ribosomal protein L25; Reviewed


Pssm-ID: 180318  Cd Length: 94  Bit Score: 69.93  E-value: 3.60e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681982575   4 ISVKAVKRDEYGKKAAKAVRREGMVPCVLSG-NGESVSFSVDPREIKALI--YTPNSYIVEFDFDGKKEQAVLREAQFHP 80
Cdd:PRK05943    2 FTINAEVRPEQGKGASRRLRRAGKFPAIIYGgNEAPVSIVLDHKDVINLQakAEFYKEVITLVIDGKEVKVKVQAVQRHP 81

                          90
                  ....*....|...
gi 1681982575  81 IREQILHLDFYRI 93
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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