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Conserved domains on  [gi|499839996|ref|WP_011520730|]
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SsrA-binding protein SmpB [Candidatus Palibaumannia cicadellinicola]

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;
10-157 6.81e-55

SsrA-binding protein SmpB;


:

Pssm-ID: 235455  Cd Length: 148  Bit Score: 169.83  E-value: 6.81e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  10 SKITTITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIvASSHILYSPMRSR 89
Cdd:PRK05422   1 PGSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYE-QGNHFNHDPRRTR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499839996  90 KLLLRRRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:PRK05422  80 KLLLHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMK 147
 
Name Accession Description Interval E-value
smpB PRK05422
SsrA-binding protein SmpB;
10-157 6.81e-55

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 169.83  E-value: 6.81e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  10 SKITTITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIvASSHILYSPMRSR 89
Cdd:PRK05422   1 PGSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYE-QGNHFNHDPRRTR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499839996  90 KLLLRRRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:PRK05422  80 KLLLHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMK 147
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
10-157 6.21e-54

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 167.51  E-value: 6.21e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  10 SKITTITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIVASsHILYSPMRSR 89
Cdd:COG0691    5 PGIKVIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGN-HFNHDPRRTR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499839996  90 KLLLRRRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:COG0691   84 KLLLHKKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALK 151
SmpB pfam01668
SmpB protein;
15-157 2.70e-51

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 160.18  E-value: 2.70e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996   15 ITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIvASSHILYSPMRSRKLLLR 94
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYE-QGNHFNHDPRRTRKLLLH 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499839996   95 RRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:pfam01668  80 KREIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMK 142
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 18-134 3.48e-40

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: 131.32  E-value: 3.48e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  18 NKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIVASSHIlYSPMRSRKLLLRRRE 97
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRFN-HDPKRPRKLLLHKKE 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499839996  98 LDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGK 134
Cdd:cd09294   80 IDKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 14-157 3.47e-38

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: 127.35  E-value: 3.47e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996   14 TITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLrPLIVASSHILYSPMRSRKLLL 93
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHI-APYKFGNYFNHDPRRPRKLLL 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499839996   94 RRRELDTLLGKVHRKGYTIVPISLYWRN-SLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:TIGR00086  80 HKKEIDKLQGKVKEKGLTLVPLKLYFKNkGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 144
 
Name Accession Description Interval E-value
smpB PRK05422
SsrA-binding protein SmpB;
10-157 6.81e-55

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 169.83  E-value: 6.81e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  10 SKITTITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIvASSHILYSPMRSR 89
Cdd:PRK05422   1 PGSKVIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYE-QGNHFNHDPRRTR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499839996  90 KLLLRRRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:PRK05422  80 KLLLHKKEIDKLIGKVERKGYTLVPLKLYFKNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMK 147
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
10-157 6.21e-54

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 167.51  E-value: 6.21e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  10 SKITTITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIVASsHILYSPMRSR 89
Cdd:COG0691    5 PGIKVIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGN-HFNHDPRRTR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499839996  90 KLLLRRRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:COG0691   84 KLLLHKKEIDKLIGKVKEKGYTLVPLKLYFKDGRAKVEIALAKGKKLYDKRETIKERDWKREKERALK 151
SmpB pfam01668
SmpB protein;
15-157 2.70e-51

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 160.18  E-value: 2.70e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996   15 ITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIvASSHILYSPMRSRKLLLR 94
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYE-QGNHFNHDPRRTRKLLLH 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499839996   95 RRELDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:pfam01668  80 KREIDKLIGKVEQKGLTLVPLKLYFKNGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMK 142
SmpB cd09294
Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for ...
 18-134 3.48e-40

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: 131.32  E-value: 3.48e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996  18 NKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLRPLIVASSHIlYSPMRSRKLLLRRRE 97
Cdd:cd09294    1 NKKARHDYEIEETFEAGIVLLGTEVKSLRAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRFN-HDPKRPRKLLLHKKE 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499839996  98 LDTLLGKVHRKGYTIVPISLYWRNSLAKIQLGIAKGK 134
Cdd:cd09294   80 IDKLIGKVEQKGLTIVPLKLYFKNGKAKVEIALAKGK 116
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
 14-157 3.47e-38

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: 127.35  E-value: 3.47e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499839996   14 TITQNKRVRYEYFIEQEFEAGISLLGWEVKSLRAGIVHINDSYILLKDSEAFLLGATLrPLIVASSHILYSPMRSRKLLL 93
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHI-APYKFGNYFNHDPRRPRKLLL 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499839996   94 RRRELDTLLGKVHRKGYTIVPISLYWRN-SLAKIQLGIAKGKKQYDKRHCIKEREWLLNKARITK 157
Cdd:TIGR00086  80 HKKEIDKLQGKVKEKGLTLVPLKLYFKNkGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 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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