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Conserved domains on  [gi|1124053261|ref|WP_074436594|]
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MULTISPECIES: Clp protease ClpP [Bacillota]

Protein Classification

Clp protease ClpP( domain architecture ID 10161508)

Clp protease ClpP is a serine protease, involved in several cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins

CATH:  3.90.226.10
Gene Ontology:  GO:0004176|GO:0006508|GO:0004252
MEROPS:  S14
SCOP:  4003574

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 20-190 1.72e-60

Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function.


:

Pssm-ID: 132927 [Multi-domain]  Cd Length: 160  Bit Score: 187.74  E-value: 1.72e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  20 ADLFFYGDIVcdEWDAWTEEDqyplaIKDFLAQ-EQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIA 98
Cdd:cd07016     1 AEIYIYGDIG--SDWGVTAKE-----FKDALDAlGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  99 SVIALAGDRVVIPQNAYFMIHKPWIGLCGayNSDKLIKAAEDLDRIEEGILNVYQDNLkeEIDIEEIKEKLSEETWFTGK 178
Cdd:cd07016    74 SVIAMAGDEVEMPPNAMLMIHNPSTGAAG--NADDLRKAADLLDKIDESIANAYAEKT--GLSEEEISALMDAETWLTAQ 149

                         170
                  ....*....|..
gi 1124053261 179 EASNYFNfeVDE 190
Cdd:cd07016   150 EAVELGF--ADE 159
 
Name Accession Description Interval E-value
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 20-190 1.72e-60

Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function.


Pssm-ID: 132927 [Multi-domain]  Cd Length: 160  Bit Score: 187.74  E-value: 1.72e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  20 ADLFFYGDIVcdEWDAWTEEDqyplaIKDFLAQ-EQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIA 98
Cdd:cd07016     1 AEIYIYGDIG--SDWGVTAKE-----FKDALDAlGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  99 SVIALAGDRVVIPQNAYFMIHKPWIGLCGayNSDKLIKAAEDLDRIEEGILNVYQDNLkeEIDIEEIKEKLSEETWFTGK 178
Cdd:cd07016    74 SVIAMAGDEVEMPPNAMLMIHNPSTGAAG--NADDLRKAADLLDKIDESIANAYAEKT--GLSEEEISALMDAETWLTAQ 149

                         170
                  ....*....|..
gi 1124053261 179 EASNYFNfeVDE 190
Cdd:cd07016   150 EAVELGF--ADE 159
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
 51-152 3.18e-24

Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.


Pssm-ID: 425759 [Multi-domain]  Cd Length: 181  Bit Score: 95.32  E-value: 3.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWiGLCG 127
Cdd:pfam00574  42 AEDPDKDIYLYINSPGGSVTAGLAIYDTMQYIKPDVSTICLGLAASMGSFLLAAGAkgkRFALP-NARIMIHQPL-GGAQ 119

                          90       100
                  ....*....|....*....|....*
gi 1124053261 128 AYNSDKLIKAAEdLDRIEEGILNVY 152
Cdd:pfam00574 120 GQASDIEIQAKE-ILKIKERLNEIY 143
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
 49-183 5.27e-19

ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440503  Cd Length: 194  Bit Score: 81.67  E-value: 5.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  49 FLAQE-QGKDLNIYINSGGGSVFAGMAIYNMLKRHEgfKTV--YVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPW 122
Cdd:COG0740    49 FLEAEdPDKDILLYINSPGGSVTAGLAIYDTMQFIK--PDVstICLGQAASMGAFLLAAGTkgkRFALP-NARIMIHQPS 125

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261 123 IGLCGAYnSDKLIkAAEDLDRIEEGILNVYQDNlkeeidieeikEKLSEE---------TWFTGKEASNY 183
Cdd:COG0740   126 GGAQGQA-SDIEI-QAREILKMRERLNEILAEH-----------TGQPLEkiekdtdrdTWMTAEEAVEY 182
PRK12553 PRK12553
ATP-dependent Clp protease proteolytic subunit; Reviewed
 51-146 2.84e-15

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 237133  Cd Length: 207  Bit Score: 71.91  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWI-GLC 126
Cdd:PRK12553   61 SIDPDRDITLYINSPGGSVTAGDAIYDTIQFIRPDVQTVCTGQAASAGAVLLAAGTpgkRFALP-NARILIHQPSLgGGI 139

                          90       100
                  ....*....|....*....|...
gi 1124053261 127 GAYNSDKLIKAAEDL---DRIEE 146
Cdd:PRK12553  140 RGQASDLEIQAREILrmrERLER 162
SppA_dom TIGR00706
signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ...
 56-109 1.05e-03

signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein SppA (protease IV) of E. coli was shown experimentally to degrade signal peptides as are released by protein processing and secretion. This protein shows stronger homology to the C-terminal region of SppA than to the N-terminal domain or to the related putative protease SuhB. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273227 [Multi-domain]  Cd Length: 208  Bit Score: 38.89  E-value: 1.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1124053261  56 KDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTV--YVDGIAASIASVIALAGDRVV 109
Cdd:TIGR00706  33 KALVLRINSPGGTVVASEEIYKKLEKLKAKKPVvaSMGGMAASGGYYISMAADEIF 88
 
Name Accession Description Interval E-value
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 20-190 1.72e-60

Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function.


Pssm-ID: 132927 [Multi-domain]  Cd Length: 160  Bit Score: 187.74  E-value: 1.72e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  20 ADLFFYGDIVcdEWDAWTEEDqyplaIKDFLAQ-EQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIA 98
Cdd:cd07016     1 AEIYIYGDIG--SDWGVTAKE-----FKDALDAlGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  99 SVIALAGDRVVIPQNAYFMIHKPWIGLCGayNSDKLIKAAEDLDRIEEGILNVYQDNLkeEIDIEEIKEKLSEETWFTGK 178
Cdd:cd07016    74 SVIAMAGDEVEMPPNAMLMIHNPSTGAAG--NADDLRKAADLLDKIDESIANAYAEKT--GLSEEEISALMDAETWLTAQ 149

                         170
                  ....*....|..
gi 1124053261 179 EASNYFNfeVDE 190
Cdd:cd07016   150 EAVELGF--ADE 159
S14_ClpP cd07013
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 51-183 1.11e-26

Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. Additionally, they are implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function.


Pssm-ID: 132924 [Multi-domain]  Cd Length: 162  Bit Score: 101.19  E-value: 1.11e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWIGLCG 127
Cdd:cd07013    26 AVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKADVVTIIDGLAASMGSVIAMAGAkgkRFILP-NAMMMIHQPWGGTLG 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1124053261 128 ayNSDKLIKAAEDLDRIEEGILNVYQDNlkEEIDIEEIKEKLSEETWFTGKEASNY 183
Cdd:cd07013   105 --DATDMRIYADLLLKVEGNLVSAYAHK--TGQSEEELHADLERDTWLSAREAVEY 156
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
 51-152 3.18e-24

Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.


Pssm-ID: 425759 [Multi-domain]  Cd Length: 181  Bit Score: 95.32  E-value: 3.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWiGLCG 127
Cdd:pfam00574  42 AEDPDKDIYLYINSPGGSVTAGLAIYDTMQYIKPDVSTICLGLAASMGSFLLAAGAkgkRFALP-NARIMIHQPL-GGAQ 119

                          90       100
                  ....*....|....*....|....*
gi 1124053261 128 AYNSDKLIKAAEdLDRIEEGILNVY 152
Cdd:pfam00574 120 GQASDIEIQAKE-ILKIKERLNEIY 143
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
 49-183 5.27e-19

ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440503  Cd Length: 194  Bit Score: 81.67  E-value: 5.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  49 FLAQE-QGKDLNIYINSGGGSVFAGMAIYNMLKRHEgfKTV--YVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPW 122
Cdd:COG0740    49 FLEAEdPDKDILLYINSPGGSVTAGLAIYDTMQFIK--PDVstICLGQAASMGAFLLAAGTkgkRFALP-NARIMIHQPS 125

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261 123 IGLCGAYnSDKLIkAAEDLDRIEEGILNVYQDNlkeeidieeikEKLSEE---------TWFTGKEASNY 183
Cdd:COG0740   126 GGAQGQA-SDIEI-QAREILKMRERLNEILAEH-----------TGQPLEkiekdtdrdTWMTAEEAVEY 182
PRK12553 PRK12553
ATP-dependent Clp protease proteolytic subunit; Reviewed
 51-146 2.84e-15

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 237133  Cd Length: 207  Bit Score: 71.91  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWI-GLC 126
Cdd:PRK12553   61 SIDPDRDITLYINSPGGSVTAGDAIYDTIQFIRPDVQTVCTGQAASAGAVLLAAGTpgkRFALP-NARILIHQPSLgGGI 139

                          90       100
                  ....*....|....*....|...
gi 1124053261 127 GAYNSDKLIKAAEDL---DRIEE 146
Cdd:PRK12553  140 RGQASDLEIQAREILrmrERLER 162
clpP CHL00028
ATP-dependent Clp protease proteolytic subunit
 51-152 8.73e-15

ATP-dependent Clp protease proteolytic subunit


Pssm-ID: 214340  Cd Length: 200  Bit Score: 70.27  E-value: 8.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKR-HEGFKTVYVdGIAASIASVIALAGD---RVVIPqNAYFMIHKPWIGLC 126
Cdd:CHL00028   56 IEDDTKDLYLFINSPGGSVISGLAIYDTMQFvKPDVHTICL-GLAASMASFILAGGEitkRLAFP-HARVMIHQPASSFY 133

                          90       100
                  ....*....|....*....|....*.
gi 1124053261 127 GAYNSDkLIKAAEDLDRIEEGILNVY 152
Cdd:CHL00028  134 EGQASE-FVLEAEELLKLRETITRVY 158
S14_ClpP_2 cd07017
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 49-152 1.01e-14

Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function.


Pssm-ID: 132928 [Multi-domain]  Cd Length: 171  Bit Score: 69.78  E-value: 1.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  49 FLAQE-QGKDLNIYINSGGGSVFAGMAIYNMLKrhegfktvYVD--------GIAASIASVIALAGD---RVVIPqNAYF 116
Cdd:cd07017    32 YLESEdPKKPIYLYINSPGGSVTAGLAIYDTMQ--------YIKppvsticlGLAASMGALLLAAGTkgkRYALP-NSRI 102

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1124053261 117 MIHKPWIGlCGAYNSDKLIKAAEdLDRIEEGILNVY 152
Cdd:cd07017   103 MIHQPLGG-AGGQASDIEIQAKE-ILRLRRRLNEIL 136
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
 49-146 3.85e-12

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 178955  Cd Length: 200  Bit Score: 63.26  E-value: 3.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  49 FL-AQEQGKDLNIYINSGGGSVFAGMAIYNMLKrhegF-----KTVYVdGIAASIASVIALAGD---RVVIPqNAYFMIH 119
Cdd:PRK00277   54 FLeAEDPDKDIYLYINSPGGSVTAGLAIYDTMQ----FikpdvSTICI-GQAASMGAFLLAAGAkgkRFALP-NSRIMIH 127

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1124053261 120 KPWIGLCG-AynSDKLIKAAEDL---DRIEE 146
Cdd:PRK00277  128 QPLGGFQGqA--TDIEIHAREILklkKRLNE 156
PRK14514 PRK14514
ATP-dependent Clp endopeptidase proteolytic subunit ClpP;
53-183 2.35e-11

ATP-dependent Clp endopeptidase proteolytic subunit ClpP;


Pssm-ID: 184722  Cd Length: 221  Bit Score: 61.47  E-value: 2.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  53 EQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALA---GDRVVIPqNAYFMIHKPWIGLCGAy 129
Cdd:PRK14514   82 DPGKDISIYINSPGGSVYAGLGIYDTMQFISSDVATICTGMAASMASVLLVAgtkGKRSALP-HSRVMIHQPLGGAQGQ- 159

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1124053261 130 NSDKLIKAAEDLdRIEEGILNVYQDNLKEEIDIEEIKEklSEETWFTGKEASNY 183
Cdd:PRK14514  160 ASDIEITAREIQ-KLKKELYTIIADHSGTPFDKVWADS--DRDYWMTAQEAKEY 210
PRK14513 PRK14513
ATP-dependent Clp protease proteolytic subunit; Provisional
 51-153 2.44e-10

ATP-dependent Clp protease proteolytic subunit; Provisional


Pssm-ID: 237742 [Multi-domain]  Cd Length: 201  Bit Score: 58.40  E-value: 2.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGD---RVVIPqNAYFMIHKPWIGLCG 127
Cdd:PRK14513   53 SQNPEQEIQMYINCPGGEVYAGLAIYDTMRYIKAPVSTICVGIAMSMGSVLLMAGDkgkRMALP-NSRIMIHQGSAGFRG 131

                          90       100
                  ....*....|....*....|....*.
gi 1124053261 128 ayNSDKLIKAAEDLDRIEEGILNVYQ 153
Cdd:PRK14513  132 --NTPDLEVQAKEVLFLRDTLVDIYH 155
Clp_protease_like cd00394
Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ...
 46-183 7.93e-09

Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad.


Pssm-ID: 132923 [Multi-domain]  Cd Length: 161  Bit Score: 53.17  E-value: 7.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  46 IKDFLAQEQGKDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGDRVVIPQNAYFMIHKPWIGL 125
Cdd:cd00394    20 IRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPVIAYVGGQAASAGYYIATAANKIVMAPGTRVGSHGPIGGY 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124053261 126 CGAYNSDKLIKAAEDLDRIEEGILNVYQDNlkEEIDIEEIKEKLSEETWFTGKEASNY 183
Cdd:cd00394   100 GGNGNPTAQEADQRIILYFIARFISLVAEN--RGQTTEKLEEDIEKDLVLTAQEALEY 155
COG3904 COG3904
Predicted periplasmic protein [Function unknown];
43-139 3.25e-08

Predicted periplasmic protein [Function unknown];


Pssm-ID: 443110 [Multi-domain]  Cd Length: 197  Bit Score: 51.95  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  43 PLAIKDFLAQEQGKDLNIYINSGGGSVFAGMAIYNMLkRHEGFKT-VYVDGIAASiASVIALAG--DRVVIPQnAYFMIH 119
Cdd:COG3904    50 AARLEALLETRGPGVATVVLNSPGGSVAEALALGRLI-RARGLDTaVPAGAYCAS-ACVLAFAGgvERYVEPG-ARVGVH 126

                          90       100
                  ....*....|....*....|
gi 1124053261 120 KPWIGLCGAYNSDKLIKAAE 139
Cdd:COG3904   127 QPYLGGGDALPAAEAVSDTQ 146
PRK12551 PRK12551
ATP-dependent Clp protease proteolytic subunit; Reviewed
 49-141 1.75e-06

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 139060  Cd Length: 196  Bit Score: 47.13  E-value: 1.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  49 FL-AQEQGKDLNIYINSGGGSVFAGMAIYNMLKR-HEGFKTVYVdGIAASIASVIALA---GDRVVIpQNAYFMIHKPWI 123
Cdd:PRK12551   48 FLeAEDPEKDIYLYINSPGGSVYDGLGIFDTMQHvKPDVHTVCV-GLAASMGAFLLCAgakGKRSSL-QHSRIMIHQPLG 125

                          90
                  ....*....|....*...
gi 1124053261 124 GLCGAyNSDKLIKAAEDL 141
Cdd:PRK12551  126 GARGQ-ASDIRIQADEIL 142
S49_Sppa_N_C cd07023
Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal ...
 60-109 1.79e-06

Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain.


Pssm-ID: 132934 [Multi-domain]  Cd Length: 208  Bit Score: 47.10  E-value: 1.79e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1124053261  60 IYINSGGGSVFAGMAIYNMLKR--HEGFK-TVYVDGIAASIASVIALAGDRVV 109
Cdd:cd07023    40 LRINSPGGSVVASEEIYREIRRlrKAKKPvVASMGDVAASGGYYIAAAADKIV 92
PRK14512 PRK14512
ATP-dependent Clp protease proteolytic subunit; Provisional
 56-127 4.78e-06

ATP-dependent Clp protease proteolytic subunit; Provisional


Pssm-ID: 237741  Cd Length: 197  Bit Score: 45.94  E-value: 4.78e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1124053261  56 KDLNIYINSGGGSVFAGMAIYNMLK--RHEGFkTVYVdGIAASIASVIALAGD---RVVIPqNAYFMIHKPWIGLCG 127
Cdd:PRK14512   54 KPIFVYIDSEGGDIDAGFAIFNMIRfvKPKVF-TIGV-GLVASAAALIFLAAKkesRFSLP-NARYLLHQPLSGFKG 127
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 51-139 4.02e-05

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132932 [Multi-domain]  Cd Length: 178  Bit Score: 42.96  E-value: 4.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  51 AQEQGKDLNI-YINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGDRVVIPQNAYfmihkpwIGLCGAY 129
Cdd:cd07021    25 AKEEGADAVVlDIDTPGGRVDSALEIVDLILNSPIPTIAYVNDRAASAGALIALAADEIYMAPGAT-------IGAAEPI 97

                          90
                  ....*....|
gi 1124053261 130 NSDKLIKAAE 139
Cdd:cd07021    98 PGDGNGAADE 107
SppA COG0616
Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, ...
 60-114 9.51e-05

Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440381 [Multi-domain]  Cd Length: 215  Bit Score: 42.09  E-value: 9.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1124053261  60 IYINSGGGSVFAGMAIYNMLKRhegFK------TVYVDGIAASIASVIALAGDRVVIPQNA 114
Cdd:COG0616    55 LRINSPGGSVAASEEIRDALRR---LRakgkpvVASMGDVAASGGYYIASAADKIYANPTT 112
SDH_sah pfam01972
Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ...
 56-139 1.19e-04

Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan.


Pssm-ID: 110924  Cd Length: 286  Bit Score: 42.53  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  56 KDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTVYVDGIAASIASVIALAGDRVVIPQNAYFMIHKPWIglcGAYNSDKLI 135
Cdd:pfam01972  92 MPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADEIIMDENAVLGPVDPQI---GQYPAASIL 168


                  ....
gi 1124053261 136 KAAE 139
Cdd:pfam01972 169 KAVE 172
SppA_dom TIGR00706
signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ...
 56-109 1.05e-03

signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein SppA (protease IV) of E. coli was shown experimentally to degrade signal peptides as are released by protein processing and secretion. This protein shows stronger homology to the C-terminal region of SppA than to the N-terminal domain or to the related putative protease SuhB. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273227 [Multi-domain]  Cd Length: 208  Bit Score: 38.89  E-value: 1.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1124053261  56 KDLNIYINSGGGSVFAGMAIYNMLKRHEGFKTV--YVDGIAASIASVIALAGDRVV 109
Cdd:TIGR00706  33 KALVLRINSPGGTVVASEEIYKKLEKLKAKKPVvaSMGGMAASGGYYISMAADEIF 88
S49_Sppa_36K_type cd07022
Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; ...
 62-114 7.18e-03

Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.


Pssm-ID: 132933 [Multi-domain]  Cd Length: 214  Bit Score: 36.77  E-value: 7.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124053261  62 INSGGGSVfAGM-----AIYNMLKRhegfKTV--YVDGIAASIASVIALAGDRVVIPQNA 114
Cdd:cd07022    50 IDSPGGEV-AGVfeladAIRAARAG----KPIvaFVNGLAASAAYWIASAADRIVVTPTA 104
 
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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