NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1254254498|ref|WP_097172963.1|]
View 

head maturation protease, ClpP-related

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
EC:  3.4.21.92
Gene Ontology:  GO:0004176|GO:0006508|GO:0004252
MEROPS:  S14
PubMed:  17499722
SCOP:  4003574

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 8-166 9.11e-54

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: 173.88  E-value: 9.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   8 GKLRLTGYVGEyyyDDGFTSSDVIVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIA 87
Cdd:cd07016     1 AEIYIYGDIGS---DWGVTAKEFKDALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1254254498  88 MAGATVTMTAGSVMMIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd07016    78 MAGDEVEMPPNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISALMDAETWLTAQEAVELGF 156
 
Name Accession Description Interval E-value
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 8-166 9.11e-54

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: 173.88  E-value: 9.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   8 GKLRLTGYVGEyyyDDGFTSSDVIVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIA 87
Cdd:cd07016     1 AEIYIYGDIGS---DWGVTAKEFKDALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1254254498  88 MAGATVTMTAGSVMMIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd07016    78 MAGDEVEMPPNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISALMDAETWLTAQEAVELGF 156
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
 1-166 1.54e-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: 98.41  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   1 MAAILEDGKLRLTGYVGEyyyddgFTSSDVI---VALSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIe 76
Cdd:pfam00574  10 YSRLLKERIIFLGGEIDD------EVANLIIaqlLFLEAEDPDKDIYLYINSPGGSVTAGLAIYdTMQYIKPDVSTICL- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  77 GIAASAGSLIAMAGATVT--MTAGSVMMIHDPSGFTFGNSSE---HSKTIEALEALAtsyARVYAAKSGQSVEDCREIMK 151
Cdd:pfam00574  83 GLAASMGSFLLAAGAKGKrfALPNARIMIHQPLGGAQGQASDieiQAKEILKIKERL---NEIYAKHTGQSLEKIEKDTD 159

                         170
                  ....*....|....*
gi 1254254498 152 AERWFTPDQAVAEGF 166
Cdd:pfam00574 160 RDFFMSAEEAKEYGL 174
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
 5-166 2.22e-20

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


Pssm-ID: 440503  Cd Length: 194  Bit Score: 87.45  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   5 LEDGKLRLTGYVgeyyydDGFTSSDVI---VALSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIeGIAA 80
Cdd:COG0740    24 LKERIIFLGGEI------DDHVANLIIaqlLFLEAEDPDKDILLYINSPGGSVTAGLAIYdTMQFIKPDVSTICL-GQAA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  81 SAGSLIAMAGATV--TMTAGSVMMIHDPSGFTFGNSSE---HSKTIEALEALatsYARVYAAKSGQSVEDCREIMKAERW 155
Cdd:COG0740    97 SMGAFLLAAGTKGkrFALPNARIMIHQPSGGAQGQASDieiQAREILKMRER---LNEILAEHTGQPLEKIEKDTDRDTW 173

                         170
                  ....*....|.
gi 1254254498 156 FTPDQAVAEGF 166
Cdd:COG0740   174 MTAEEAVEYGL 184
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
 44-166 3.27e-13

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 178955  Cd Length: 200  Bit Score: 67.50  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  44 DVHL--NSPGGVATEGAAIH-ALFSARPGITNIVIeGIAASAGSLIAMAGAtvtmtAG-------SVMMIHDPSGFTFGN 113
Cdd:PRK00277   63 DIYLyiNSPGGSVTAGLAIYdTMQFIKPDVSTICI-GQAASMGAFLLAAGA-----KGkrfalpnSRIMIHQPLGGFQGQ 136

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1254254498 114 SSEHSktIEALEALAT--SYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:PRK00277  137 ATDIE--IHAREILKLkkRLNEILAEHTGQPLEKIEKDTDRDNFMSAEEAKEYGL 189
 
Name Accession Description Interval E-value
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 8-166 9.11e-54

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: 173.88  E-value: 9.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   8 GKLRLTGYVGEyyyDDGFTSSDVIVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIA 87
Cdd:cd07016     1 AEIYIYGDIGS---DWGVTAKEFKDALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1254254498  88 MAGATVTMTAGSVMMIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd07016    78 MAGDEVEMPPNAMLMIHNPSTGAAGNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISALMDAETWLTAQEAVELGF 156
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
 1-166 1.54e-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: 98.41  E-value: 1.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   1 MAAILEDGKLRLTGYVGEyyyddgFTSSDVI---VALSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIe 76
Cdd:pfam00574  10 YSRLLKERIIFLGGEIDD------EVANLIIaqlLFLEAEDPDKDIYLYINSPGGSVTAGLAIYdTMQYIKPDVSTICL- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  77 GIAASAGSLIAMAGATVT--MTAGSVMMIHDPSGFTFGNSSE---HSKTIEALEALAtsyARVYAAKSGQSVEDCREIMK 151
Cdd:pfam00574  83 GLAASMGSFLLAAGAKGKrfALPNARIMIHQPLGGAQGQASDieiQAKEILKIKERL---NEIYAKHTGQSLEKIEKDTD 159

                         170
                  ....*....|....*
gi 1254254498 152 AERWFTPDQAVAEGF 166
Cdd:pfam00574 160 RDFFMSAEEAKEYGL 174
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
 5-166 2.22e-20

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


Pssm-ID: 440503  Cd Length: 194  Bit Score: 87.45  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   5 LEDGKLRLTGYVgeyyydDGFTSSDVI---VALSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIeGIAA 80
Cdd:COG0740    24 LKERIIFLGGEI------DDHVANLIIaqlLFLEAEDPDKDILLYINSPGGSVTAGLAIYdTMQFIKPDVSTICL-GQAA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  81 SAGSLIAMAGATV--TMTAGSVMMIHDPSGFTFGNSSE---HSKTIEALEALatsYARVYAAKSGQSVEDCREIMKAERW 155
Cdd:COG0740    97 SMGAFLLAAGTKGkrFALPNARIMIHQPSGGAQGQASDieiQAREILKMRER---LNEILAEHTGQPLEKIEKDTDRDTW 173

                         170
                  ....*....|.
gi 1254254498 156 FTPDQAVAEGF 166
Cdd:COG0740   174 MTAEEAVEYGL 184
S14_ClpP cd07013
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
 31-166 1.98e-17

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: 78.46  E-value: 1.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  31 IVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIAMAGATVT--MTAGSVMMIHDPSG 108
Cdd:cd07013    21 LLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKADVVTIIDGLAASMGSVIAMAGAKGKrfILPNAMMMIHQPWG 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1254254498 109 FTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd07013   101 GTLGDATDMRIYADLLLKVEGNLVSAYAHKTGQSEEELHADLERDTWLSAREAVEYGF 158
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
 44-166 3.27e-13

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 178955  Cd Length: 200  Bit Score: 67.50  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  44 DVHL--NSPGGVATEGAAIH-ALFSARPGITNIVIeGIAASAGSLIAMAGAtvtmtAG-------SVMMIHDPSGFTFGN 113
Cdd:PRK00277   63 DIYLyiNSPGGSVTAGLAIYdTMQFIKPDVSTICI-GQAASMGAFLLAAGA-----KGkrfalpnSRIMIHQPLGGFQGQ 136

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1254254498 114 SSEHSktIEALEALAT--SYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:PRK00277  137 ATDIE--IHAREILKLkkRLNEILAEHTGQPLEKIEKDTDRDNFMSAEEAKEYGL 189
clpP CHL00028
ATP-dependent Clp protease proteolytic subunit
 34-166 4.76e-13

ATP-dependent Clp protease proteolytic subunit


Pssm-ID: 214340  Cd Length: 200  Bit Score: 67.19  E-value: 4.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  34 LSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIeGIAASAGSLIaMAGATVT---MTAGSVMMIHDP-SG 108
Cdd:CHL00028   54 LSIEDDTKDLYLFINSPGGSVISGLAIYdTMQFVKPDVHTICL-GLAASMASFI-LAGGEITkrlAFPHARVMIHQPaSS 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1254254498 109 FTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:CHL00028  132 FYEGQASEFVLEAEELLKLRETITRVYAQRTGKPLWVISEDMERDVFMSATEAKAYGI 189
PRK12553 PRK12553
ATP-dependent Clp protease proteolytic subunit; Reviewed
 1-165 5.77e-12

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 237133  Cd Length: 207  Bit Score: 64.20  E-value: 5.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498   1 MAAILEDGKLRLTGYVgeyyyDDGfTSSDVI---VALSQIDGESELDVHLNSPGGVATEGAAIH-ALFSARPGITNIVIe 76
Cdd:PRK12553   29 YNKLFEERIIFLGGQV-----DDA-SANDVMaqlLVLESIDPDRDITLYINSPGGSVTAGDAIYdTIQFIRPDVQTVCT- 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  77 GIAASAGSLIAMAGatvtmTAG-------SVMMIHDPS--GFTFGNSSEHSktIEALEALATSYA--RVYAAKSGQSVED 145
Cdd:PRK12553  102 GQAASAGAVLLAAG-----TPGkrfalpnARILIHQPSlgGGIRGQASDLE--IQAREILRMRERleRILAEHTGQSVEK 174

                         170       180
                  ....*....|....*....|
gi 1254254498 146 CREIMKAERWFTPDQAVAEG 165
Cdd:PRK12553  175 IRKDTDRDKWLTAEEAKDYG 194
Clp_protease_like cd00394
Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ...
 47-166 2.53e-10

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: 58.56  E-value: 2.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  47 LNSPGGVATEGAAI-HALFSARPGITNIViEGIAASAGSLIAMAGATVTMTAGSVMMIHDPSGFTFGNSSEHSKTI--EA 123
Cdd:cd00394    36 VNTPGGRVDAGMNIvDALQASRKPVIAYV-GGQAASAGYYIATAANKIVMAPGTRVGSHGPIGGYGGNGNPTAQEAdqRI 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1254254498 124 LEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd00394   115 ILYFIARFISLVAENRGQTTEKLEEDIEKDLVLTAQEALEYGL 157
PRK12551 PRK12551
ATP-dependent Clp protease proteolytic subunit; Reviewed
 15-165 8.92e-07

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 139060  Cd Length: 196  Bit Score: 48.67  E-value: 8.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  15 YVGEYYYDDgftSSDVIVA----LSQIDGESELDVHLNSPGGVATEGAAI-HALFSARPGITNIVIeGIAASAGSLIAMA 89
Cdd:PRK12551   29 FLGEPVTSD---SANRIVAqllfLEAEDPEKDIYLYINSPGGSVYDGLGIfDTMQHVKPDVHTVCV-GLAASMGAFLLCA 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1254254498  90 GATVTMTA--GSVMMIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEG 165
Cdd:PRK12551  105 GAKGKRSSlqHSRIMIHQPLGGARGQASDIRIQADEILFLKERLNTELSERTGQPLERIQEDTDRDFFMSPSEAVEYG 182
PRK14514 PRK14514
ATP-dependent Clp endopeptidase proteolytic subunit ClpP;
23-165 2.62e-06

ATP-dependent Clp endopeptidase proteolytic subunit ClpP;


Pssm-ID: 184722  Cd Length: 221  Bit Score: 47.60  E-value: 2.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  23 DGFTSSDV---IVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIAMAGATVTMTA-- 97
Cdd:PRK14514   64 DDYTANTIqaqLLYLDSVDPGKDISIYINSPGGSVYAGLGIYDTMQFISSDVATICTGMAASMASVLLVAGTKGKRSAlp 143

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1254254498  98 GSVMMIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEG 165
Cdd:PRK14514  144 HSRVMIHQPLGGAQGQASDIEITAREIQKLKKELYTIIADHSGTPFDKVWADSDRDYWMTAQEAKEYG 211
PRK14513 PRK14513
ATP-dependent Clp protease proteolytic subunit; Provisional
 28-166 3.94e-06

ATP-dependent Clp protease proteolytic subunit; Provisional


Pssm-ID: 237742 [Multi-domain]  Cd Length: 201  Bit Score: 46.85  E-value: 3.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  28 SDVIVA----LSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIAMAGATVTMTA--GSVM 101
Cdd:PRK14513   41 ANTIVAqlllLDSQNPEQEIQMYINCPGGEVYAGLAIYDTMRYIKAPVSTICVGIAMSMGSVLLMAGDKGKRMAlpNSRI 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1254254498 102 MIHDPSGFTFGNSSEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:PRK14513  121 MIHQGSAGFRGNTPDLEVQAKEVLFLRDTLVDIYHRHTDLPHEKLLRDMERDYFMSPEEAKAYGL 185
COG3904 COG3904
Predicted periplasmic protein [Function unknown];
45-166 2.94e-05

Predicted periplasmic protein [Function unknown];


Pssm-ID: 443110 [Multi-domain]  Cd Length: 197  Bit Score: 44.25  E-value: 2.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  45 VHLNSPGGVATEGAAIHALFSARpGITNIVIEG-IAASAGSLIAMAGATVTMTAGSVMMIHdpsGFTFGNsSEHSKTIEA 123
Cdd:COG3904    67 VVLNSPGGSVAEALALGRLIRAR-GLDTAVPAGaYCASACVLAFAGGVERYVEPGARVGVH---QPYLGG-GDALPAAEA 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1254254498 124 LEALATSYARV--YAAKSGQSVEDCREIMKAE----RWFTPDQAVAEGF 166
Cdd:COG3904   142 VSDTQRATARLarYLREMGVDPELLELALSTPpddmRYLTPEELLRYGL 190
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 45-166 2.19e-04

Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 42.92  E-value: 2.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  45 VHLNSPGGVATEGAAI-HALFSAR-PGITNIVIEGIAASAGSLIAMAGATVTMTAGSVMMIHDPSGFTFGNSSE-HSKTI 121
Cdd:COG1030    62 LELDTPGGLVDSAREIvDAILASPvPVIVYVASGARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGIDEAmEEKVI 141

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1254254498 122 EALEAlatsYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:COG1030   142 NDAVA----YIRSLAELRGRNADWAEAMVRESVSLTAEEALELGV 182
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 45-132 1.91e-03

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: 38.72  E-value: 1.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  45 VHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIAMAGATVTMTAGSVMMIHDPSGFTfGNSSEHSKTIEAL 124
Cdd:cd07021    35 LDIDTPGGRVDSALEIVDLILNSPIPTIAYVNDRAASAGALIALAADEIYMAPGATIGAAEPIPGD-GNGAADEKVQSYW 113


                  ....*...
gi 1254254498 125 EALATSYA 132
Cdd:cd07021   114 RAKMRAAA 121
Clp_protease_NfeD cd07015
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 38-166 2.86e-03

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: 132926  Cd Length: 172  Bit Score: 38.14  E-value: 2.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  38 DGESELDVHLNSPGG-VATEGAAIHALFSARPGITNIVIEGI--AASAGSLIAMAGATVTMTAGSVMMIHDPSgFTFGNS 114
Cdd:cd07015    28 DNAEAIIIELDTPGGrADAAGNIVQRIQQSKIPVIIYVYPPGasAASAGTYIALGSHLIAMAPGTSIGACRPI-LGYSQN 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1254254498 115 SEHSKTIEALEALATSYARVYAAKSGQSVEDCREIMKAERWFTPDQAVAEGF 166
Cdd:cd07015   107 GSIIEAPPKITNYFIAYIKSLAQESGRNATIAEEFITKDLSLTPEEALKYGV 158
SDH_sah pfam01972
Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ...
 27-106 4.38e-03

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: 38.29  E-value: 4.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1254254498  27 SSDVIVALSQIDGESELDVHLNSPGGVATEGAAIHALFSARPGITNIVIEGIAASAGSLIAMAGATVTMTAGSVMMIHDP 106
Cdd:pfam01972  78 SEEILRAIRLTPKDMPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADEIIMDENAVLGPVDP 157
 
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