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Conserved domains on  [gi|501084871|ref|WP_012135360|]
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MULTISPECIES: ClpXP protease specificity-enhancing factor [Citrobacter]

Protein Classification

stringent starvation protein B( domain architecture ID 10013880)

stringent starvation protein B is a ClpXP protease specificity-enhancing factor that plays a role in the degradation of incomplete proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11798 PRK11798
ClpXP protease specificity-enhancing factor; Provisional
 4-121 1.24e-77

ClpXP protease specificity-enhancing factor; Provisional


:

Pssm-ID: 236987  Cd Length: 138  Bit Score: 227.01  E-value: 1.24e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871   4 SQLSPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQV 83
Cdd:PRK11798   2 MQMTSTRPYLLRALYEWIVDNGLTPHLLVDATYPGVQVPMEYVRDGQIVLNISPRAVGNLQLGNDAISFNARFGGVPRQI 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501084871  84 SVPLAAVLAIYARENGAGTMFEPEAAYDEDVASLNDDD 121
Cdd:PRK11798  82 YVPVAAVLAIYARENGQGMMFEPEAAYDEDEHDDDTDP 119
 
Name Accession Description Interval E-value
PRK11798 PRK11798
ClpXP protease specificity-enhancing factor; Provisional
 4-121 1.24e-77

ClpXP protease specificity-enhancing factor; Provisional


Pssm-ID: 236987  Cd Length: 138  Bit Score: 227.01  E-value: 1.24e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871   4 SQLSPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQV 83
Cdd:PRK11798   2 MQMTSTRPYLLRALYEWIVDNGLTPHLLVDATYPGVQVPMEYVRDGQIVLNISPRAVGNLQLGNDAISFNARFGGVPRQI 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501084871  84 SVPLAAVLAIYARENGAGTMFEPEAAYDEDVASLNDDD 121
Cdd:PRK11798  82 YVPVAAVLAIYARENGQGMMFEPEAAYDEDEHDDDTDP 119
SspB COG2969
Stringent starvation protein B, binds SsrA peptide [Posttranslational modification, protein ...
 4-121 4.07e-75

Stringent starvation protein B, binds SsrA peptide [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442209  Cd Length: 138  Bit Score: 220.82  E-value: 4.07e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871   4 SQLSPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQV 83
Cdd:COG2969    1 MQMTSTRPYLIRALYEWIVDNGLTPYLLVDADYPGVQVPREYVKDGQIVLNISPSAVGNLQLGNDAISFSARFGGVPRDI 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501084871  84 SVPLAAVLAIYARENGAGTMFEPEAAYDEDVASLNDDD 121
Cdd:COG2969   81 YVPVAAVLAIYARENGQGMAFEPEEYYEEEADEAPPDD 118
SspB pfam04386
Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is ...
 8-130 7.51e-62

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: 187.36  E-value: 7.51e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871    8 PRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQVSVPL 87
Cdd:pfam04386   1 SLRPYALRAVYRWVLDNGLTPYITFDTDAPGVRVPEQYPEEGTIVLNISPHAFWDLVVGNDGFEFGLRFGGVPERLVVPF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 501084871   88 AAVLAIYARENGAGTMFEP-EAAYDEDVASLNDDDVTPGAESET 130
Cdd:pfam04386  81 AAVLAFYDPENGFGLQFEPpEPAYEEDDEAEAAEEEPPPAADED 124
 
Name Accession Description Interval E-value
PRK11798 PRK11798
ClpXP protease specificity-enhancing factor; Provisional
 4-121 1.24e-77

ClpXP protease specificity-enhancing factor; Provisional


Pssm-ID: 236987  Cd Length: 138  Bit Score: 227.01  E-value: 1.24e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871   4 SQLSPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQV 83
Cdd:PRK11798   2 MQMTSTRPYLLRALYEWIVDNGLTPHLLVDATYPGVQVPMEYVRDGQIVLNISPRAVGNLQLGNDAISFNARFGGVPRQI 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501084871  84 SVPLAAVLAIYARENGAGTMFEPEAAYDEDVASLNDDD 121
Cdd:PRK11798  82 YVPVAAVLAIYARENGQGMMFEPEAAYDEDEHDDDTDP 119
SspB COG2969
Stringent starvation protein B, binds SsrA peptide [Posttranslational modification, protein ...
 4-121 4.07e-75

Stringent starvation protein B, binds SsrA peptide [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442209  Cd Length: 138  Bit Score: 220.82  E-value: 4.07e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871   4 SQLSPRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQV 83
Cdd:COG2969    1 MQMTSTRPYLIRALYEWIVDNGLTPYLLVDADYPGVQVPREYVKDGQIVLNISPSAVGNLQLGNDAISFSARFGGVPRDI 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501084871  84 SVPLAAVLAIYARENGAGTMFEPEAAYDEDVASLNDDD 121
Cdd:COG2969   81 YVPVAAVLAIYARENGQGMAFEPEEYYEEEADEAPPDD 118
SspB pfam04386
Stringent starvation protein B; Escherichia coli stringent starvation protein B (SspB), is ...
 8-130 7.51e-62

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: 187.36  E-value: 7.51e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501084871    8 PRRPYLLRAFYEWLLDNQLTPHLVVDVTLPGVHVPMEYARDGQIVLNIAPRAVGNLELANDEVRFNARFGGVPRQVSVPL 87
Cdd:pfam04386   1 SLRPYALRAVYRWVLDNGLTPYITFDTDAPGVRVPEQYPEEGTIVLNISPHAFWDLVVGNDGFEFGLRFGGVPERLVVPF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 501084871   88 AAVLAIYARENGAGTMFEP-EAAYDEDVASLNDDDVTPGAESET 130
Cdd:pfam04386  81 AAVLAFYDPENGFGLQFEPpEPAYEEDDEAEAAEEEPPPAADED 124
 
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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