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Conserved domains on  [gi|978950334|gb|KVS37992|]
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SsrA-binding protein [Burkholderia vietnamiensis]

Protein Classification

SsrA-binding protein( domain architecture ID 10012389)

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 Symbol:  smpB
Gene Ontology:  GO:0003723|GO:0070929
PubMed:  17488812
SCOP:  4002211

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
smpB PRK05422
SsrA-binding protein SmpB;
1-146 7.89e-87

SsrA-binding protein SmpB;


:

Pssm-ID: 235455  Cd Length: 148  Bit Score: 249.95  E-value: 7.89e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   1 MSIIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLL 80
Cdd:PRK05422   4 KVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPY-EQGNHFNHDPRRTRKLL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 978950334  81 LHREEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMRA 146
Cdd:PRK05422  83 LHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
 
Name Accession Description Interval E-value
smpB PRK05422
SsrA-binding protein SmpB;
1-146 7.89e-87

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 249.95  E-value: 7.89e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   1 MSIIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLL 80
Cdd:PRK05422   4 KVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPY-EQGNHFNHDPRRTRKLL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 978950334  81 LHREEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMRA 146
Cdd:PRK05422  83 LHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
3-145 5.62e-86

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 248.01  E-value: 5.62e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLPEAStHIKPDPVRTRKLLLH 82
Cdd:COG0691   10 IAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGN-HFNHDPRRTRKLLLH 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 978950334  83 REEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
Cdd:COG0691   89 KKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALK 151
SmpB pfam01668
SmpB protein;
3-145 1.98e-83

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 241.07  E-value: 1.98e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334    3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLLLH 82
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPY-EQGNHFNHDPRRTRKLLLH 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 978950334   83 REEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
Cdd:pfam01668  80 KREIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMK 142
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 6-122 2.28e-62

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: 186.79  E-value: 2.28e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   6 NRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLPEASTHiKPDPVRTRKLLLHREE 85
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRF-NHDPKRPRKLLLHKKE 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 978950334  86 IKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGK 122
Cdd:cd09294   80 IDKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 3-145 4.87e-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: 187.05  E-value: 4.87e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334    3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLLLH 82
Cdd:TIGR00086   2 IASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPY-KFGNYFNHDPRRPRKLLLH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 978950334   83 REEIKKLIGKVEQRGYTLVPLNFHYK-GGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
Cdd:TIGR00086  81 KKEIDKLQGKVKEKGLTLVPLKLYFKnKGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 144
 
Name Accession Description Interval E-value
smpB PRK05422
SsrA-binding protein SmpB;
1-146 7.89e-87

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 249.95  E-value: 7.89e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   1 MSIIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLL 80
Cdd:PRK05422   4 KVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPY-EQGNHFNHDPRRTRKLL 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 978950334  81 LHREEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMRA 146
Cdd:PRK05422  83 LHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
3-145 5.62e-86

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 248.01  E-value: 5.62e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLPEAStHIKPDPVRTRKLLLH 82
Cdd:COG0691   10 IAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGN-HFNHDPRRTRKLLLH 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 978950334  83 REEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
Cdd:COG0691   89 KKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALK 151
SmpB pfam01668
SmpB protein;
3-145 1.98e-83

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 241.07  E-value: 1.98e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334    3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLLLH 82
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPY-EQGNHFNHDPRRTRKLLLH 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 978950334   83 REEIKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
Cdd:pfam01668  80 KREIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMK 142
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 6-122 2.28e-62

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: 186.79  E-value: 2.28e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334   6 NRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLPEASTHiKPDPVRTRKLLLHREE 85
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRF-NHDPKRPRKLLLHKKE 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 978950334  86 IKKLIGKVEQRGYTLVPLNFHYKGGRVKCDIALAKGK 122
Cdd:cd09294   80 IDKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 3-145 4.87e-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: 187.05  E-value: 4.87e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 978950334    3 IIDNRKAHFDYHIEERYEAGLVLEGWEVKALRAGRGQIKEGYVVVKNAEIFLIGTHISPLpEASTHIKPDPVRTRKLLLH 82
Cdd:TIGR00086   2 IASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPY-KFGNYFNHDPRRPRKLLLH 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 978950334   83 REEIKKLIGKVEQRGYTLVPLNFHYK-GGRVKCDIALAKGKKLHDKRETEKKRDWEREKARIMR 145
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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