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Conserved domains on  [gi|501165428|ref|WP_012209633|]
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MULTISPECIES: ribosome silencing factor [Petrotoga]

Protein Classification

RsfS/YbeB/iojap family protein( domain architecture ID 10015471)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 10-107 2.80e-37

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: 121.42  E-value: 2.80e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428   10 VKEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFI 89
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVKEELKEAGLKPLGVEGLEEGDWVLVDLGDVV 81

                          90
                  ....*....|....*...
gi 501165428   90 VHIFSEESREFYDLEGLW 107
Cdd:TIGR00090  82 VHIFTPEAREFYDLEKLW 99
 
Name Accession Description Interval E-value
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 10-107 2.80e-37

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: 121.42  E-value: 2.80e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428   10 VKEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFI 89
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVKEELKEAGLKPLGVEGLEEGDWVLVDLGDVV 81

                          90
                  ....*....|....*...
gi 501165428   90 VHIFSEESREFYDLEGLW 107
Cdd:TIGR00090  82 VHIFTPEAREFYDLEKLW 99
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 10-109 7.64e-34

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 113.29  E-value: 7.64e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428  10 VKEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFI 89
Cdd:COG0799    9 LKLIAKALDDKKAEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKPLRVEGLDEGEWVLLDYGDVV 88

                         90       100
                 ....*....|....*....|
gi 501165428  90 VHIFSEESREFYDLEGLWGE 109
Cdd:COG0799   89 VHIFQPEVREFYNLERLWGD 108
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 11-107 4.37e-33

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: 110.99  E-value: 4.37e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428   11 KEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFIV 90
Cdd:pfam02410   1 ELIAEALDDKKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGDWVLLDYGDVVV 80

                          90
                  ....*....|....*..
gi 501165428   91 HIFSEESREFYDLEGLW 107
Cdd:pfam02410  81 HIFTPEAREFYNLERLW 97
PRK11538 PRK11538
ribosome silencing factor;
13-108 2.50e-14

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 63.27  E-value: 2.50e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428  13 IVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFIVHI 92
Cdd:PRK11538  10 VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVVDLGDVIVHV 89

                         90
                 ....*....|....*.
gi 501165428  93 FSEESREFYDLEGLWG 108
Cdd:PRK11538  90 MQEESRRLYELEKLWS 105
 
Name Accession Description Interval E-value
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
 10-107 2.80e-37

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: 121.42  E-value: 2.80e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428   10 VKEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFI 89
Cdd:TIGR00090   2 LELIVEALDDKKAEDIVVLDVRGKSSIADYFVIASGTSSRHVKAIADNVKEELKEAGLKPLGVEGLEEGDWVLVDLGDVV 81

                          90
                  ....*....|....*...
gi 501165428   90 VHIFSEESREFYDLEGLW 107
Cdd:TIGR00090  82 VHIFTPEAREFYDLEKLW 99
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
 10-109 7.64e-34

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


Pssm-ID: 440562  Cd Length: 113  Bit Score: 113.29  E-value: 7.64e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428  10 VKEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFI 89
Cdd:COG0799    9 LKLIAKALDDKKAEDIVVLDVRGLSSIADYFVIASGTSDRQVKAIADEVEEKLKEAGIKPLRVEGLDEGEWVLLDYGDVV 88

                         90       100
                 ....*....|....*....|
gi 501165428  90 VHIFSEESREFYDLEGLWGE 109
Cdd:COG0799   89 VHIFQPEVREFYNLERLWGD 108
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
 11-107 4.37e-33

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: 110.99  E-value: 4.37e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428   11 KEIVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFIV 90
Cdd:pfam02410   1 ELIAEALDDKKAEDIVVLDVRGKSSIADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGDWVLLDYGDVVV 80

                          90
                  ....*....|....*..
gi 501165428   91 HIFSEESREFYDLEGLW 107
Cdd:pfam02410  81 HIFTPEAREFYNLERLW 97
PRK11538 PRK11538
ribosome silencing factor;
13-108 2.50e-14

ribosome silencing factor;


Pssm-ID: 183184  Cd Length: 105  Bit Score: 63.27  E-value: 2.50e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501165428  13 IVELLEEKDGENIVVLDMENSELMVDYFVIVTGNSEPHRVALRDQVVRYLKDEDIPITFYDKGKSTDWMIIDAGIFIVHI 92
Cdd:PRK11538  10 VIDKIDDLKGQDIIALDVQGKSSITDCMIICTGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVVDLGDVIVHV 89

                         90
                 ....*....|....*.
gi 501165428  93 FSEESREFYDLEGLWG 108
Cdd:PRK11538  90 MQEESRRLYELEKLWS 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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