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Conserved domains on  [gi|2463612026|pdb|8CRX|u]
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Chain u, 50S ribosomal protein L25

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

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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
 2-191 6.31e-65

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


:

Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 198.50  E-value: 6.31e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         2 ADIIHLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE---NPLLSIEIEGQKpMLALPKDV 78
Cdd:PRK05618   1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGaflSTLLDLEVGGKK-QKVLVKDV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        79 QRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAP-----GTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIY 153
Cdd:PRK05618  80 QRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGvgvklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIH 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
8CRX_u       154 LGDLKLPEGTSLLGDAEDVAATVAFPETEPVEDEESAG 191
Cdd:PRK05618 160 VSDLKLPEGVKLLDDPDEVVATVVAPRGEEEEEEEEAA 197
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 2-191 6.31e-65

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 198.50  E-value: 6.31e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         2 ADIIHLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE---NPLLSIEIEGQKpMLALPKDV 78
Cdd:PRK05618   1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGaflSTLLDLEVGGKK-QKVLVKDV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        79 QRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAP-----GTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIY 153
Cdd:PRK05618  80 QRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGvgvklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIH 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
8CRX_u       154 LGDLKLPEGTSLLGDAEDVAATVAFPETEPVEDEESAG 191
Cdd:PRK05618 160 VSDLKLPEGVKLLDDPDEVVATVVAPRGEEEEEEEEAA 197
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-179 3.66e-50

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: 160.45  E-value: 3.66e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        1 MADIIhLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE--NPLLSIEIEGQKpMLALPKDV 78
Cdd:COG1825   1 MESIT-LKAEKREETGKGAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLLRKEgeNTLITLDIDGKK-EKVLIKDV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u       79 QRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAPGTIAMTEFN---EIEVQADLLNIPEVIEIDVTGLEAGTTIYLG 155
Cdd:COG1825  79 QRHPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLtlhELEVEALPPDIPEPIEVDVSDLGLGDSISVH 158

                       170       180
                ....*....|....*....|....
8CRX_u      156 DLKLPEGTSLLGDAEDVAATVAFP 179
Cdd:COG1825 159 DLDLPLLVGVVEDPDVVVVVVVTP 182
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 7-177 1.08e-46

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: 151.75  E-value: 1.08e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u          7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALR--TENPLLSIEIEGqKPMLALPKDVQRDVLK 84
Cdd:TIGR00731   1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRkgATSTVLTLEIGG-KEFKVLVKDYQYNPVT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         85 GFVRHVDLLTVRRGEKVDVNVALRITGES---APGTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIYLGDLKLPE 161
Cdd:TIGR00731  80 NEVIHVDFLEVVEGVKLKVEVPIKLIGTPigvKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPA 159

                         170
                  ....*....|....*.
8CRX_u        162 GTSLLGDAEDVAATVA 177
Cdd:TIGR00731 160 GVSFITDDDEVVVTVI 175
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 7-92 1.89e-32

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: 112.15  E-value: 1.89e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u          7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE--NPLLSIEIEGQKpMLALPKDVQRDVLK 84
Cdd:pfam01386   1 LKAEKRTEFGKGAARRLRREGKVPAVLYGGGKEPISISVDAKELRKLLRTEgeNTVIELDIDGKK-YKVLIKDVQRHPVK 79


                  ....*...
8CRX_u         85 GFVRHVDL 92
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, ...
 7-93 8.29e-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: 108.33  E-value: 8.29e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRT--ENPLLSIEIEGQKpMLALPKDVQRDVLK 84
Cdd:cd00495   2 LKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKegENTVIELEIDGKK-ENVLIKDVQRHPVK 80


                ....*....
8CRX_u       85 GFVRHVDLL 93
Cdd:cd00495  81 DEILHVDFL 89
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 2-191 6.31e-65

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


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 198.50  E-value: 6.31e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         2 ADIIHLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE---NPLLSIEIEGQKpMLALPKDV 78
Cdd:PRK05618   1 METITLEAEVREEFGKGAARRLRRAGKVPAVIYGKGKEPVSISVDEKELIKALKKGaflSTLLDLEVGGKK-QKVLVKDV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        79 QRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAP-----GTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIY 153
Cdd:PRK05618  80 QRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGvgvklGGVLNQVLHELEVECLPEDIPEFIEVDVSGLEIGDSIH 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
8CRX_u       154 LGDLKLPEGTSLLGDAEDVAATVAFPETEPVEDEESAG 191
Cdd:PRK05618 160 VSDLKLPEGVKLLDDPDEVVATVVAPRGEEEEEEEEAA 197
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 1-179 3.66e-50

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: 160.45  E-value: 3.66e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        1 MADIIhLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE--NPLLSIEIEGQKpMLALPKDV 78
Cdd:COG1825   1 MESIT-LKAEKREETGKGAARRLRREGKVPAVIYGGGKEPVSISVDAKELRKLLRKEgeNTLITLDIDGKK-EKVLIKDV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u       79 QRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAPGTIAMTEFN---EIEVQADLLNIPEVIEIDVTGLEAGTTIYLG 155
Cdd:COG1825  79 QRHPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLtlhELEVEALPPDIPEPIEVDVSDLGLGDSISVH 158

                       170       180
                ....*....|....*....|....
8CRX_u      156 DLKLPEGTSLLGDAEDVAATVAFP 179
Cdd:COG1825 159 DLDLPLLVGVVEDPDVVVVVVVTP 182
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 7-177 1.08e-46

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: 151.75  E-value: 1.08e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u          7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALR--TENPLLSIEIEGqKPMLALPKDVQRDVLK 84
Cdd:TIGR00731   1 LEVKSRTSFGKSAARRIRKEGRIPAVVYGKGKENVNLELKSKEFIKYLRkgATSTVLTLEIGG-KEFKVLVKDYQYNPVT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         85 GFVRHVDLLTVRRGEKVDVNVALRITGES---APGTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIYLGDLKLPE 161
Cdd:TIGR00731  80 NEVIHVDFLEVVEGVKLKVEVPIKLIGTPigvKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPA 159

                         170
                  ....*....|....*.
8CRX_u        162 GTSLLGDAEDVAATVA 177
Cdd:TIGR00731 160 GVSFITDDDEVVVTVI 175
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 7-92 1.89e-32

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: 112.15  E-value: 1.89e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u          7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTE--NPLLSIEIEGQKpMLALPKDVQRDVLK 84
Cdd:pfam01386   1 LKAEKRTEFGKGAARRLRREGKVPAVLYGGGKEPISISVDAKELRKLLRTEgeNTVIELDIDGKK-YKVLIKDVQRHPVK 79


                  ....*...
8CRX_u         85 GFVRHVDL 92
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, ...
 7-93 8.29e-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: 108.33  E-value: 8.29e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRT--ENPLLSIEIEGQKpMLALPKDVQRDVLK 84
Cdd:cd00495   2 LKAEKREETGKGAARRLRREGKVPAVIYGKGEEPIPISVDAKELEKLLRKegENTVIELEIDGKK-ENVLIKDVQRHPVK 80


                ....*....
8CRX_u       85 GFVRHVDLL 93
Cdd:cd00495  81 DEILHVDFL 89
Ribosomal_TL5_C pfam14693
Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ...
 100-180 1.17e-21

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: 84.38  E-value: 1.17e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u        100 KVDVNVALRITGESAP---GTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIYLGDLKLPEGTSLLGDAEDVAATV 176
Cdd:pfam14693   1 KVTVEVPVHFVGEAPGvkkGGVLNQVLRELEVECLPKDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVELLTDPDTVVVSV 80


                  ....
8CRX_u        177 AFPE 180
Cdd:pfam14693  81 VAPR 84
PRK05943 PRK05943
50S ribosomal protein L25; Reviewed
 7-91 6.18e-16

50S ribosomal protein L25; Reviewed


Pssm-ID: 180318  Cd Length: 94  Bit Score: 69.93  E-value: 6.18e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u         7 LKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTENPL---LSIEIEGqKPMLALPKDVQRDVL 83
Cdd:PRK05943   4 INAEVRPEQGKGASRRLRRAGKFPAIIYGGNEAPVSIVLDHKDVINLQAKAEFYkevITLVIDG-KEVKVKVQAVQRHPF 82


                 ....*...
8CRX_u        84 KGFVRHVD 91
Cdd:PRK05943  83 KPKLEHID 90
YbbR COG4856
Cyclic di-AMP synthase regulator CdaR, YbbR domain [Signal transduction mechanisms];
94-176 3.71e-03

Cyclic di-AMP synthase regulator CdaR, YbbR domain [Signal transduction mechanisms];


Pssm-ID: 443884 [Multi-domain]  Cd Length: 392  Bit Score: 37.34  E-value: 3.71e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8CRX_u       94 TVRRGEKVDVNVALRITGESAPG---TIAMTEFNEIEV---QADLLNIPEV--IEIDVTGLEAGTTIYLgDLKLPEGTSL 165
Cdd:COG4856 215 TVPVLPSKTVPVKVNTTGEPAEGysvTSITVSPSTVTIygpEEVLDSISSIetEPIDLSGLTESTTVEV-KLKLPEGVTL 293

                        90
                ....*....|.
8CRX_u      166 LGDAEDVAATV 176
Cdd:COG4856 294 VDPPSTVTVTV 304
 
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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