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Conserved domains on  [gi|1308796190|gb|PKN37047|]
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ribosome silencing factor [Deltaproteobacteria bacterium HGW-Deltaproteobacteria-2]

Protein Classification

RsfS/YbeB/iojap family protein( domain architecture ID 10002731)

RsfS/YbeB/iojap family protein similar to bacterial ribosome silencing factor RsfS that represses translation by preventing the association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 1-101 2.08e-47

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


:

Pssm-ID: 440562  Cd Length: 113  Bit Score: 147.57  E-value: 2.08e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   1 MCINATLQKKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVIS 80
Cdd:COG0799    11 LIAKALDDKKAEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKPLRVEGLDEGEWVLLDYGDVVVH 90

                          90       100
                  ....*....|....*....|..
gi 1308796190  81 VFYEPAREFYNIENLW-DAPRM 101
Cdd:COG0799    91 IFQPEVREFYNLERLWgDAPRI 112
 
Name Accession Description Interval E-value
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 1-101 2.08e-47

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 147.57  E-value: 2.08e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   1 MCINATLQKKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVIS 80
Cdd:COG0799    11 LIAKALDDKKAEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKPLRVEGLDEGEWVLLDYGDVVVH 90

                          90       100
                  ....*....|....*....|..
gi 1308796190  81 VFYEPAREFYNIENLW-DAPRM 101
Cdd:COG0799    91 IFQPEVREFYNLERLWgDAPRI 112
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 9-96 2.56e-44

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: 139.50  E-value: 2.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   9 KKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISVFYEPARE 88
Cdd:pfam02410  10 KKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGDWVLLDYGDVVVHIFTPEARE 89


                  ....*...
gi 1308796190  89 FYNIENLW 96
Cdd:pfam02410  90 FYNLERLW 97
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 2-96 1.30e-42

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: 135.28  E-value: 1.30e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   2 CINATLQKKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISV 81
Cdd:TIGR00090   5 IVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVKEELKEAGLKPLGVEGLEEGDWVLVDLGDVVVHI 84

                          90
                  ....*....|....*
gi 1308796190  82 FYEPAREFYNIENLW 96
Cdd:TIGR00090  85 FTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
10-96 1.16e-24

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 89.85  E-value: 1.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190  10 KAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISVFYEPAREF 89
Cdd:PRK11538   18 KGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVVDLGDVIVHVMQEESRRL 97


                  ....*..
gi 1308796190  90 YNIENLW 96
Cdd:PRK11538   98 YELEKLW 104
 
Name Accession Description Interval E-value
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 1-101 2.08e-47

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 147.57  E-value: 2.08e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   1 MCINATLQKKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVIS 80
Cdd:COG0799    11 LIAKALDDKKAEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKPLRVEGLDEGEWVLLDYGDVVVH 90

                          90       100
                  ....*....|....*....|..
gi 1308796190  81 VFYEPAREFYNIENLW-DAPRM 101
Cdd:COG0799    91 IFQPEVREFYNLERLWgDAPRI 112
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 9-96 2.56e-44

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: 139.50  E-value: 2.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   9 KKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISVFYEPARE 88
Cdd:pfam02410  10 KKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGDWVLLDYGDVVVHIFTPEARE 89


                  ....*...
gi 1308796190  89 FYNIENLW 96
Cdd:pfam02410  90 FYNLERLW 97
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 2-96 1.30e-42

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: 135.28  E-value: 1.30e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190   2 CINATLQKKAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISV 81
Cdd:TIGR00090   5 IVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVKEELKEAGLKPLGVEGLEEGDWVLVDLGDVVVHI 84

                          90
                  ....*....|....*
gi 1308796190  82 FYEPAREFYNIENLW 96
Cdd:TIGR00090  85 FTPEAREFYDLEKLW 99
PRK11538 PRK11538
ribosome silencing factor;
10-96 1.16e-24

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 89.85  E-value: 1.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308796190  10 KAKEIVVLNLKEISAFTDYMIICSGTSEREVQAIAQAIQQFLKKAGIRPMGIEGETNGQWILLDYDDVVISVFYEPAREF 89
Cdd:PRK11538   18 KGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVVDLGDVIVHVMQEESRRL 97


                  ....*..
gi 1308796190  90 YNIENLW 96
Cdd:PRK11538   98 YELEKLW 104
 
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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