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Conserved domains on  [gi|488933899|ref|WP_002844974|]
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SsrA-binding protein SmpB [Peptostreptococcus anaerobius]

Protein Classification

SsrA-binding protein( domain architecture ID 10786349)

SsrA-binding protein SmpB, together with SsrA RNA, mediate trans-translation in prokaryotes for translational surveillance and ribosome rescue

CATH:  2.40.280.10
Gene Ontology:  GO:0003723
PubMed:  10393194

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
3-150 3.11e-87

tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 440455  Cd Length: 153  Bit Score: 251.10  E-value: 3.11e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899   3 GIKVLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKL 82
Cdd:COG0691    6 GIKVIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488933899  83 LLHKSEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKDR 150
Cdd:COG0691   86 LLHKKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKRR 153
 
Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
3-150 3.11e-87

tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440455  Cd Length: 153  Bit Score: 251.10  E-value: 3.11e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899   3 GIKVLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKL 82
Cdd:COG0691    6 GIKVIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488933899  83 LLHKSEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKDR 150
Cdd:COG0691   86 LLHKKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKRR 153
SmpB pfam01668
SmpB protein;
7-149 1.52e-86

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 249.16  E-value: 1.52e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899    7 LATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLHK 86
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYEQGNHFNHDPRRTRKLLLHK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488933899   87 SEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKD 149
Cdd:pfam01668  81 REIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMKR 143
smpB PRK05422
SsrA-binding protein SmpB;
3-149 4.28e-84

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 243.02  E-value: 4.28e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899   3 GIKVLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKL 82
Cdd:PRK05422   2 GSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYEQGNHFNHDPRRTRKL 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488933899  83 LLHKSEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKD 149
Cdd:PRK05422  82 LLHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 10-125 2.06e-68

Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Trans-translation system is composed of a ribonucleoprotein complex of tmRNA, a specialized RNA with properties of both tRNA and mRNA, and SmpB. SmpB is highly conserved and present in all bacterial kingdoms and is also found in some chloroplasts and mitochondria. This is suggesting Trans-translation arose early in bacterial evolution and its mechanism is a quality control for protein synthesis in spite of challenges such as transcription errors, mRNA damage, and translation frame shifting. SmpB deletion results in phage development defects phenotype and absence of tagged proteins translated from defective mRNAs.


Pssm-ID: 187755  Cd Length: 116  Bit Score: 202.20  E-value: 2.06e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899  10 NKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLHKSEI 89
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRFNHDPKRPRKLLLHKKEI 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488933899  90 RKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGK 125
Cdd:cd09294   81 DKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 6-148 1.98e-62

SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes. [Protein synthesis, Other]


Pssm-ID: 129194  Cd Length: 144  Bit Score: 188.21  E-value: 1.98e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899    6 VLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLH 85
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPYKFGNYFNHDPRRPRKLLLH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488933899   86 KSEIRKLIGATTIKGYSLVPMRMYLKN-GKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESK 148
Cdd:TIGR00086  81 KKEIDKLQGKVKEKGLTLVPLKLYFKNkGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 144
 
Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
3-150 3.11e-87

tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440455  Cd Length: 153  Bit Score: 251.10  E-value: 3.11e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899   3 GIKVLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKL 82
Cdd:COG0691    6 GIKVIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488933899  83 LLHKSEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKDR 150
Cdd:COG0691   86 LLHKKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKRR 153
SmpB pfam01668
SmpB protein;
7-149 1.52e-86

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 249.16  E-value: 1.52e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899    7 LATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLHK 86
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYEQGNHFNHDPRRTRKLLLHK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488933899   87 SEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKD 149
Cdd:pfam01668  81 REIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMKR 143
smpB PRK05422
SsrA-binding protein SmpB;
3-149 4.28e-84

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 243.02  E-value: 4.28e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899   3 GIKVLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKL 82
Cdd:PRK05422   2 GSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYEQGNHFNHDPRRTRKL 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488933899  83 LLHKSEIRKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESKD 149
Cdd:PRK05422  82 LLHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 10-125 2.06e-68

Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Trans-translation system is composed of a ribonucleoprotein complex of tmRNA, a specialized RNA with properties of both tRNA and mRNA, and SmpB. SmpB is highly conserved and present in all bacterial kingdoms and is also found in some chloroplasts and mitochondria. This is suggesting Trans-translation arose early in bacterial evolution and its mechanism is a quality control for protein synthesis in spite of challenges such as transcription errors, mRNA damage, and translation frame shifting. SmpB deletion results in phage development defects phenotype and absence of tagged proteins translated from defective mRNAs.


Pssm-ID: 187755  Cd Length: 116  Bit Score: 202.20  E-value: 2.06e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899  10 NKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLHKSEI 89
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRFNHDPKRPRKLLLHKKEI 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488933899  90 RKLIGATTIKGYSLVPMRMYLKNGKVKLELGLAKGK 125
Cdd:cd09294   81 DKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 6-148 1.98e-62

SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes. [Protein synthesis, Other]


Pssm-ID: 129194  Cd Length: 144  Bit Score: 188.21  E-value: 1.98e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488933899    6 VLATNKKARHDYFIDEVYECGIELKGTEVKSIRQGRINLKEGYASVENSEVFLKQVHISPYEQGNRFNVDPLRVRKLLLH 85
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPYKFGNYFNHDPRRPRKLLLH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488933899   86 KSEIRKLIGATTIKGYSLVPMRMYLKN-GKVKLELGLAKGKKLYDKRQDLAKKDAMRRIERESK 148
Cdd:TIGR00086  81 KKEIDKLQGKVKEKGLTLVPLKLYFKNkGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 144
 
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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