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Conserved domains on  [gi|193785409|dbj|BAG54562|]
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unnamed protein product [Homo sapiens]

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

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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 ...
 98-194 4.55e-38

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: 127.94  E-value: 4.55e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409   98 VSLLRQENARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHlkcKRDPHVKIEGKDTDDWLCVDFGSMVI 177
Cdd:pfam02410   4 AEALDDKKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKE---AGGKPLRIEGLREGDWVLLDYGDVVV 80

                          90
                  ....*....|....*..
gi 193785409  178 HLMLPETREIYELEKLW 194
Cdd:pfam02410  81 HIFTPEAREFYNLERLW 97
 
Name Accession Description Interval E-value
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 98-194 4.55e-38

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: 127.94  E-value: 4.55e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409   98 VSLLRQENARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHlkcKRDPHVKIEGKDTDDWLCVDFGSMVI 177
Cdd:pfam02410   4 AEALDDKKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKE---AGGKPLRIEGLREGDWVLLDYGDVVV 80

                          90
                  ....*....|....*..
gi 193785409  178 HLMLPETREIYELEKLW 194
Cdd:pfam02410  81 HIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 106-194 1.36e-27

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 101.35  E-value: 1.36e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409 106 ARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLCVDFGSMVIHLMLPETR 185
Cdd:COG0799   21 AEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKP---LRVEGLDEGEWVLLDYGDVVVHIFQPEVR 97


                 ....*....
gi 193785409 186 EIYELEKLW 194
Cdd:COG0799   98 EFYNLERLW 106
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 94-194 9.01e-27

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: 99.07  E-value: 9.01e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409   94 IDMMVSLLRQENARDICVIqvppEMR----YTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLC 169
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVL----DVRgkssIADYFVIASGTSSRHVKAIADNVKEELKEAGLKP---LGVEGLEEGDWVL 74

                          90       100
                  ....*....|....*....|....*
gi 193785409  170 VDFGSMVIHLMLPETREIYELEKLW 194
Cdd:TIGR00090  75 VDLGDVVVHIFTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
95-195 1.28e-16

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 72.90  E-value: 1.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409  95 DMMVSLLRQENARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLCVDFGS 174
Cdd:PRK11538   8 DFVIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLP---LGVEGENAADWIVVDLGD 84

                         90       100
                 ....*....|....*....|.
gi 193785409 175 MVIHLMLPETREIYELEKLWT 195
Cdd:PRK11538  85 VIVHVMQEESRRLYELEKLWS 105
 
Name Accession Description Interval E-value
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 98-194 4.55e-38

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: 127.94  E-value: 4.55e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409   98 VSLLRQENARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHlkcKRDPHVKIEGKDTDDWLCVDFGSMVI 177
Cdd:pfam02410   4 AEALDDKKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKE---AGGKPLRIEGLREGDWVLLDYGDVVV 80

                          90
                  ....*....|....*..
gi 193785409  178 HLMLPETREIYELEKLW 194
Cdd:pfam02410  81 HIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 106-194 1.36e-27

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 101.35  E-value: 1.36e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409 106 ARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLCVDFGSMVIHLMLPETR 185
Cdd:COG0799   21 AEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKP---LRVEGLDEGEWVLLDYGDVVVHIFQPEVR 97


                 ....*....
gi 193785409 186 EIYELEKLW 194
Cdd:COG0799   98 EFYNLERLW 106
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 94-194 9.01e-27

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: 99.07  E-value: 9.01e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409   94 IDMMVSLLRQENARDICVIqvppEMR----YTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLC 169
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVL----DVRgkssIADYFVIASGTSSRHVKAIADNVKEELKEAGLKP---LGVEGLEEGDWVL 74

                          90       100
                  ....*....|....*....|....*
gi 193785409  170 VDFGSMVIHLMLPETREIYELEKLW 194
Cdd:TIGR00090  75 VDLGDVVVHIFTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
95-195 1.28e-16

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 72.90  E-value: 1.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193785409  95 DMMVSLLRQENARDICVIQVPPEMRYTDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRdphVKIEGKDTDDWLCVDFGS 174
Cdd:PRK11538   8 DFVIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLP---LGVEGENAADWIVVDLGD 84

                         90       100
                 ....*....|....*....|.
gi 193785409 175 MVIHLMLPETREIYELEKLWT 195
Cdd:PRK11538  85 VIVHVMQEESRRLYELEKLWS 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.
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