NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|546770877|ref|WP_021892596|]
View 

MULTISPECIES: SsrA-binding protein [Barnesiella]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
6-150 1.97e-76

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


:

Pssm-ID: 440455  Cd Length: 153  Bit Score: 223.75  E-value: 1.97e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877   6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:COG0691    9 VIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKLLLH 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 546770877  86 HKEIQKIERAAKESGFSIIPTRVFINeKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:COG0691   89 KKEIDKLIGKVKEKGYTLVPLKLYFK-DGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKR 152
 
Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
6-150 1.97e-76

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 223.75  E-value: 1.97e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877   6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:COG0691    9 VIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKLLLH 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 546770877  86 HKEIQKIERAAKESGFSIIPTRVFINeKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:COG0691   89 KKEIDKLIGKVKEKGYTLVPLKLYFK-DGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKR 152
SmpB pfam01668
SmpB protein;
7-150 7.60e-76

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 222.20  E-value: 7.60e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877    7 NIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLTH 86
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYEQGNHFNHDPRRTRKLLLHK 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 546770877   87 KEIQKIERAAKESGFSIIPTRVFINeKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:pfam01668  81 REIDKLIGKVEQKGLTLVPLKLYFK-NGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMKR 143
smpB PRK05422
SsrA-binding protein SmpB;
6-150 2.58e-71

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 210.66  E-value: 2.58e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877   6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:PRK05422   5 VIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYEQGNHFNHDPRRTRKLLLH 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 546770877  86 HKEIQKIERAAKESGFSIIPTRVFInEKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:PRK05422  85 KKEIDKLIGKVERKGYTLVPLKLYF-KNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
6-149 1.03e-64

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: 193.99  E-value: 1.03e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877    6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPYKFGNYFNHDPRRPRKLLLH 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 546770877   86 HKEIQKIERAAKESGFSIIPTRVFINEKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFK 149
Cdd:TIGR00086  81 KKEIDKLQGKVKEKGLTLVPLKLYFKNKGKVKVEIALAKGKKLHDKRESIKKRDAKRELKRALK 144
 
Name Accession Description Interval E-value
SmpB COG0691
tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones];
6-150 1.97e-76

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


Pssm-ID: 440455  Cd Length: 153  Bit Score: 223.75  E-value: 1.97e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877   6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:COG0691    9 VIAQNRKARHDYFIEETYEAGIVLTGTEVKSLRAGKANLKDSYARIKNGELWLINAHISPYEQGNHFNHDPRRTRKLLLH 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 546770877  86 HKEIQKIERAAKESGFSIIPTRVFINeKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:COG0691   89 KKEIDKLIGKVKEKGYTLVPLKLYFK-DGRAKVEIALAKGKKLYDKRETIKERDWKREKERALKR 152
SmpB pfam01668
SmpB protein;
7-150 7.60e-76

SmpB protein;


Pssm-ID: 460287  Cd Length: 143  Bit Score: 222.20  E-value: 7.60e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877    7 NIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLTH 86
Cdd:pfam01668   1 IAQNKKARHDYFIEETYEAGIVLTGTEVKSIRAGKVNLKDSYVRIKNGEAWLINMHISPYEQGNHFNHDPRRTRKLLLHK 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 546770877   87 KEIQKIERAAKESGFSIIPTRVFINeKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:pfam01668  81 REIDKLIGKVEQKGLTLVPLKLYFK-NGRAKVEIALAKGKKLYDKRETIKERDAKREIERAMKR 143
smpB PRK05422
SsrA-binding protein SmpB;
6-150 2.58e-71

SsrA-binding protein SmpB;


Pssm-ID: 235455  Cd Length: 148  Bit Score: 210.66  E-value: 2.58e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877   6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:PRK05422   5 VIAQNKKARHDYFIEETFEAGIVLTGTEVKSLRAGKANLKDSYVLIKNGEAWLFNAHISPYEQGNHFNHDPRRTRKLLLH 84
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 546770877  86 HKEIQKIERAAKESGFSIIPTRVFInEKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFKR 150
Cdd:PRK05422  85 KKEIDKLIGKVERKGYTLVPLKLYF-KNGRAKVEIGLAKGKKLHDKRETIKERDWKREKARAMKA 148
smpB TIGR00086
SsrA-binding protein; This model describes the SsrA-binding protein, also called tmRNA binding ...
6-149 1.03e-64

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: 193.99  E-value: 1.03e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 546770877    6 INIKNKRASFDYELLDTFHAGIVLSGTEIKSIRLGKAGLTDSFCYINNGEIWIKNMYIAEYFYGSYNNHSSRRDRKLLLT 85
Cdd:TIGR00086   1 LIASNKKAFFDYEILDTYEAGIVLKGSEVKSIRAGKVSLKDSYVIIKKGELWLKNMHIAPYKFGNYFNHDPRRPRKLLLH 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 546770877   86 HKEIQKIERAAKESGFSIIPTRVFINEKGLAKVVIAIAKGKKEYDKRDSIKEREDKRQMDRMFK 149
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH