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Conserved domains on  [gi|672720487|gb|AIJ52365|]
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hypothetical protein DK48_731 [Brucella abortus]

Protein Classification

SspB family protein( domain architecture ID 10008038)

SspB family protein similar to Escherichia coli stringent starvation protein B (SspB), which is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SspB2 COG3814
SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein ...
 1-189 1.22e-97

SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 443026  Cd Length: 166  Bit Score: 279.78  E-value: 1.22e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   1 MVQDLIRYDILAQEALRGVIRKVLAEAAKAGLPGNHHFFITFLTGAPGVRISSRLKEKYPEQMTIVLQHQFWDMHVTDQL 80
Cdd:COG3814    1 MAEDLIRYDLLVQDALRGVVRKVLEEVAREGLPGEHHFYITFDTDAPGVEISDRLRERYPEEMTIVLQHQFWDLKVTEDG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487  81 FEVGLSFGDIPEKLTIPFSAIRGFYDPSVNFELEFDVAVFQPASDNDEGnispieemaPEKADKPKAKTRKPaagkkesa 160
Cdd:COG3814   81 FSVGLSFGGVPERLVIPFDAITGFVDPSVQFGLQFEVAEEDDDEEEEED---------DPEDAEPAEEDDAP-------- 143

                        170       180
                 ....*....|....*....|....*....
gi 672720487 161 stdseqEDGEDKAPKPTADVVSLDAFRKK 189
Cdd:COG3814  144 ------EDDDPPPPEGGAEVVSLDAFRKK 166
 
Name Accession Description Interval E-value
SspB2 COG3814
SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein ...
 1-189 1.22e-97

SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443026  Cd Length: 166  Bit Score: 279.78  E-value: 1.22e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   1 MVQDLIRYDILAQEALRGVIRKVLAEAAKAGLPGNHHFFITFLTGAPGVRISSRLKEKYPEQMTIVLQHQFWDMHVTDQL 80
Cdd:COG3814    1 MAEDLIRYDLLVQDALRGVVRKVLEEVAREGLPGEHHFYITFDTDAPGVEISDRLRERYPEEMTIVLQHQFWDLKVTEDG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487  81 FEVGLSFGDIPEKLTIPFSAIRGFYDPSVNFELEFDVAVFQPASDNDEGnispieemaPEKADKPKAKTRKPaagkkesa 160
Cdd:COG3814   81 FSVGLSFGGVPERLVIPFDAITGFVDPSVQFGLQFEVAEEDDDEEEEED---------DPEDAEPAEEDDAP-------- 143

                        170       180
                 ....*....|....*....|....*....
gi 672720487 161 stdseqEDGEDKAPKPTADVVSLDAFRKK 189
Cdd:COG3814  144 ------EDDDPPPPEGGAEVVSLDAFRKK 166
SspB pfam04386
Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is ...
 10-181 3.94e-44

Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates.


Pssm-ID: 427913  Cd Length: 144  Bit Score: 143.44  E-value: 3.94e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   10 ILAQEALRGVIRKVLAEAAkagLPgnhhfFITFLTGAPGVRISsrlkEKYPEQMTIVLQ---HQFWDMHVTDQLFEVGLS 86
Cdd:pfam04386   1 SLRPYALRAVYRWVLDNGL---TP-----YITFDTDAPGVRVP----EQYPEEGTIVLNispHAFWDLVVGNDGFEFGLR 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   87 FGDIPEKLTIPFSAIRGFYDPSVNFELEFDVAvfQPASDNDEgnispiEEMAPEKADKPkaktrkpaagkKESASTDSEQ 166
Cdd:pfam04386  69 FGGVPERLVVPFAAVLAFYDPENGFGLQFEPP--EPAYEEDD------EAEAAEEEPPP-----------AADEDAEDPD 129

                         170
                  ....*....|....*
gi 672720487  167 EDGEDKAPKPTADVV 181
Cdd:pfam04386 130 DEPPKPPPRPGLKVV 144
 
Name Accession Description Interval E-value
SspB2 COG3814
SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein ...
 1-189 1.22e-97

SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443026  Cd Length: 166  Bit Score: 279.78  E-value: 1.22e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   1 MVQDLIRYDILAQEALRGVIRKVLAEAAKAGLPGNHHFFITFLTGAPGVRISSRLKEKYPEQMTIVLQHQFWDMHVTDQL 80
Cdd:COG3814    1 MAEDLIRYDLLVQDALRGVVRKVLEEVAREGLPGEHHFYITFDTDAPGVEISDRLRERYPEEMTIVLQHQFWDLKVTEDG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487  81 FEVGLSFGDIPEKLTIPFSAIRGFYDPSVNFELEFDVAVFQPASDNDEGnispieemaPEKADKPKAKTRKPaagkkesa 160
Cdd:COG3814   81 FSVGLSFGGVPERLVIPFDAITGFVDPSVQFGLQFEVAEEDDDEEEEED---------DPEDAEPAEEDDAP-------- 143

                        170       180
                 ....*....|....*....|....*....
gi 672720487 161 stdseqEDGEDKAPKPTADVVSLDAFRKK 189
Cdd:COG3814  144 ------EDDDPPPPEGGAEVVSLDAFRKK 166
SspB pfam04386
Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is ...
 10-181 3.94e-44

Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates.


Pssm-ID: 427913  Cd Length: 144  Bit Score: 143.44  E-value: 3.94e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   10 ILAQEALRGVIRKVLAEAAkagLPgnhhfFITFLTGAPGVRISsrlkEKYPEQMTIVLQ---HQFWDMHVTDQLFEVGLS 86
Cdd:pfam04386   1 SLRPYALRAVYRWVLDNGL---TP-----YITFDTDAPGVRVP----EQYPEEGTIVLNispHAFWDLVVGNDGFEFGLR 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672720487   87 FGDIPEKLTIPFSAIRGFYDPSVNFELEFDVAvfQPASDNDEgnispiEEMAPEKADKPkaktrkpaagkKESASTDSEQ 166
Cdd:pfam04386  69 FGGVPERLVVPFAAVLAFYDPENGFGLQFEPP--EPAYEEDD------EAEAAEEEPPP-----------AADEDAEDPD 129

                         170
                  ....*....|....*
gi 672720487  167 EDGEDKAPKPTADVV 181
Cdd:pfam04386 130 DEPPKPPPRPGLKVV 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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