NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|71988563|ref|NP_498757|]
View 

Mitochondrial Assembly of ribosomal Large Subunit [Caenorhabditis elegans]

Protein Classification

RsfS/YbeB/iojap family protein( domain architecture ID 10493352)

RsfS/YbeB/iojap family protein similar to Arabidopsis thaliana chloroplastic protein Iojap and fungal mitochondrial ATPase synthesis protein 25

CATH:  3.30.460.10
Gene Ontology:  GO:0090071|GO:0017148|GO:0043022
SCOP:  4001878

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 65-167 1.06e-20

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


:

Pssm-ID: 460550  Cd Length: 97  Bit Score: 82.10  E-value: 1.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563    65 ENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVSngsmsHARRSTKRSNGWYVS 143
Cdd:pfam02410   1 ELIAEALDDKKAEDIVVLDvRGKSSIADYF--VIATGTSERHVRAIADEVEEKLKEAGGK-----PLRIEGLREGDWVLL 73

                          90       100
                  ....*....|....*....|....
gi 71988563   144 EVERVQVHVMSEECREKYDLEAIW 167
Cdd:pfam02410  74 DYGDVVVHIFTPEAREFYNLERLW 97
 
Name Accession Description Interval E-value
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 65-167 1.06e-20

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


Pssm-ID: 460550  Cd Length: 97  Bit Score: 82.10  E-value: 1.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563    65 ENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVSngsmsHARRSTKRSNGWYVS 143
Cdd:pfam02410   1 ELIAEALDDKKAEDIVVLDvRGKSSIADYF--VIATGTSERHVRAIADEVEEKLKEAGGK-----PLRIEGLREGDWVLL 73

                          90       100
                  ....*....|....*....|....
gi 71988563   144 EVERVQVHVMSEECREKYDLEAIW 167
Cdd:pfam02410  74 DYGDVVVHIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 64-173 8.22e-13

Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440562  Cd Length: 113  Bit Score: 61.67  E-value: 8.22e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563  64 VENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVSngsmsHARRSTKRSNGW-- 140
Cdd:COG0799   9 LKLIAKALDDKKAEDIVVLDvRGLSSIADYF--VIASGTSDRQVKAIADEVEEKLKEAGIK-----PLRVEGLDEGEWvl 81

                        90       100       110
                ....*....|....*....|....*....|....*
gi 71988563 141 --YVSeverVQVHVMSEECREKYDLEAIWAGDDRI 173
Cdd:COG0799  82 ldYGD----VVVHIFQPEVREFYNLERLWGDAPRI 112
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 64-167 5.06e-12

ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. [Protein synthesis, Translation factors]


Pssm-ID: 272901  Cd Length: 99  Bit Score: 59.40  E-value: 5.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563    64 VENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVsngsmsHARRSTKRSNG-WY 141
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVLDvRGKSSIADYF--VIASGTSSRHVKAIADNVKEELKEAGL------KPLGVEGLEEGdWV 73

                          90       100
                  ....*....|....*....|....*.
gi 71988563   142 VSEVERVQVHVMSEECREKYDLEAIW 167
Cdd:TIGR00090  74 LVDLGDVVVHIFTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
67-168 1.44e-04

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 39.39  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563   67 VVGALTDQRAKDVFVV----KSEETEMTpythkIICSAFNSRQASAISENLRSllkiDGVSNGSMSHARRSTKRSNgWYV 142
Cdd:PRK11538  10 VIDKIDDLKGQDIIALdvqgKSSITDCM-----IICTGTSSRHVMSIADHVVQ----ESRAAGLLPLGVEGENAAD-WIV 79

                         90       100
                 ....*....|....*....|....*.
gi 71988563  143 SEVERVQVHVMSEECREKYDLEAIWA 168
Cdd:PRK11538  80 VDLGDVIVHVMQEESRRLYELEKLWS 105
 
Name Accession Description Interval E-value
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 65-167 1.06e-20

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


Pssm-ID: 460550  Cd Length: 97  Bit Score: 82.10  E-value: 1.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563    65 ENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVSngsmsHARRSTKRSNGWYVS 143
Cdd:pfam02410   1 ELIAEALDDKKAEDIVVLDvRGKSSIADYF--VIATGTSERHVRAIADEVEEKLKEAGGK-----PLRIEGLREGDWVLL 73

                          90       100
                  ....*....|....*....|....
gi 71988563   144 EVERVQVHVMSEECREKYDLEAIW 167
Cdd:pfam02410  74 DYGDVVVHIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 64-173 8.22e-13

Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440562  Cd Length: 113  Bit Score: 61.67  E-value: 8.22e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563  64 VENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVSngsmsHARRSTKRSNGW-- 140
Cdd:COG0799   9 LKLIAKALDDKKAEDIVVLDvRGLSSIADYF--VIASGTSDRQVKAIADEVEEKLKEAGIK-----PLRVEGLDEGEWvl 81

                        90       100       110
                ....*....|....*....|....*....|....*
gi 71988563 141 --YVSeverVQVHVMSEECREKYDLEAIWAGDDRI 173
Cdd:COG0799  82 ldYGD----VVVHIFQPEVREFYNLERLWGDAPRI 112
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 64-167 5.06e-12

ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. [Protein synthesis, Translation factors]


Pssm-ID: 272901  Cd Length: 99  Bit Score: 59.40  E-value: 5.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563    64 VENVVGALTDQRAKDVFVVK-SEETEMTPYThkIICSAFNSRQASAISENLRSLLKIDGVsngsmsHARRSTKRSNG-WY 141
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVLDvRGKSSIADYF--VIASGTSSRHVKAIADNVKEELKEAGL------KPLGVEGLEEGdWV 73

                          90       100
                  ....*....|....*....|....*.
gi 71988563   142 VSEVERVQVHVMSEECREKYDLEAIW 167
Cdd:TIGR00090  74 LVDLGDVVVHIFTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
67-168 1.44e-04

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 39.39  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71988563   67 VVGALTDQRAKDVFVV----KSEETEMTpythkIICSAFNSRQASAISENLRSllkiDGVSNGSMSHARRSTKRSNgWYV 142
Cdd:PRK11538  10 VIDKIDDLKGQDIIALdvqgKSSITDCM-----IICTGTSSRHVMSIADHVVQ----ESRAAGLLPLGVEGENAAD-WIV 79

                         90       100
                 ....*....|....*....|....*.
gi 71988563  143 SEVERVQVHVMSEECREKYDLEAIWA 168
Cdd:PRK11538  80 VDLGDVIVHVMQEESRRLYELEKLWS 105
 
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