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Conserved domains on  [gi|500159977|ref|WP_011834647|]
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MULTISPECIES: ATP-dependent Clp protease proteolytic subunit [Lactobacillales]

Protein Classification

ATP-dependent Clp protease proteolytic subunit( domain architecture ID 10791868)

ATP-dependent Clp protease proteolytic subunit is a serine protease that catalyzes the hydrolysis of proteins to small peptides in the presence of ATP and Mg2+

CATH:  3.90.226.10
Gene Ontology:  GO:0004176|GO:0004252|GO:0006508
PubMed:  17499722
SCOP:  4003574

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
1-199 2.07e-128

ATP-dependent Clp protease proteolytic subunit; Reviewed


:

Pssm-ID: 178955  Cd Length: 200  Bit Score: 359.09  E-value: 2.07e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   1 MGYLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVD 80
Cdd:PRK00277   4 MMNLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYD 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  81 TMNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADN 160
Cdd:PRK00277  84 TMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRIMIHQPLGGF-QG-QATDIEIHAREILKLKKRLNEILAEH 161
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 500159977 161 SNRSLEQIHKDAERDHWMDAKETLEYGFIDEIMENNSLK 199
Cdd:PRK00277 162 TGQPLEKIEKDTDRDNFMSAEEAKEYGLIDEVLTKRKEA 200
 
Name Accession Description Interval E-value
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
1-199 2.07e-128

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 178955  Cd Length: 200  Bit Score: 359.09  E-value: 2.07e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   1 MGYLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVD 80
Cdd:PRK00277   4 MMNLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYD 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  81 TMNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADN 160
Cdd:PRK00277  84 TMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRIMIHQPLGGF-QG-QATDIEIHAREILKLKKRLNEILAEH 161
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 500159977 161 SNRSLEQIHKDAERDHWMDAKETLEYGFIDEIMENNSLK 199
Cdd:PRK00277 162 TGQPLEKIEKDTDRDNFMSAEEAKEYGLIDEVLTKRKEA 200
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
3-195 3.51e-114

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


Pssm-ID: 440503  Cd Length: 194  Bit Score: 323.19  E-value: 3.51e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   3 YLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTM 82
Cdd:COG0740    1 YLVPMVVEQTPRGERAYDIYSRLLKERIIFLGGEIDDHVANLIIAQLLFLEAEDPDKDILLYINSPGGSVTAGLAIYDTM 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  83 NFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNSN 162
Cdd:COG0740   81 QFIKPDVSTICLGQAASMGAFLLAAGTKGKRFALPNARIMIHQPSGGA-QG-QASDIEIQAREILKMRERLNEILAEHTG 158
                        170       180       190
                 ....*....|....*....|....*....|...
gi 500159977 163 RSLEQIHKDAERDHWMDAKETLEYGFIDEIMEN 195
Cdd:COG0740  159 QPLEKIEKDTDRDTWMTAEEAVEYGLIDEVIES 191
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
13-195 1.58e-103

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: 295.63  E-value: 1.58e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   13 SRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTI 92
Cdd:pfam00574   1 SRGERAYDIYSRLLKERIIFLGGEIDDEVANLIIAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYDTMQYIKPDVSTI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   93 VMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAGQgtQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDA 172
Cdd:pfam00574  81 CLGLAASMGSFLLAAGAKGKRFALPNARIMIHQPLGGAQG--QASDIEIQAKEILKIKERLNEIYAKHTGQSLEKIEKDT 158
                         170       180
                  ....*....|....*....|...
gi 500159977  173 ERDHWMDAKETLEYGFIDEIMEN 195
Cdd:pfam00574 159 DRDFFMSAEEAKEYGLIDEVIER 181
clpP TIGR00493
ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic ...
4-193 3.31e-95

ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores well with this model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 188055  Cd Length: 192  Bit Score: 275.13  E-value: 3.31e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977    4 LVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMN 83
Cdd:TIGR00493   3 LIPTVIEQTGRGERSFDIYSRLLKERIIFLSGEVNDNVANSIVAQLLFLEAEDPEKDIYLYINSPGGSITAGLAIYDTMQ 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   84 FIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNSNR 163
Cdd:TIGR00493  83 FIKPDVSTICIGQAASMGAFLLAAGAKGKRFSLPNSRIMIHQPLGGA-QG-QATDIEIQANEILRLKGLLNDILAEHTGQ 160
                         170       180       190
                  ....*....|....*....|....*....|
gi 500159977  164 SLEQIHKDAERDHWMDAKETLEYGFIDEIM 193
Cdd:TIGR00493 161 SLEQIERDTERDFFMSAEEAKEYGLIDKVL 190
S14_ClpP_2 cd07017
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
20-192 4.60e-93

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: 268.93  E-value: 4.60e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  20 DIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAAS 99
Cdd:cd07017    1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIYDTMQYIKPPVSTICLGLAAS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 100 MGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgqGTQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMD 179
Cdd:cd07017   81 MGALLLAAGTKGKRYALPNSRIMIHQPLGGA--GGQASDIEIQAKEILRLRRRLNEILAKHTGQPLEKIEKDTDRDRYMS 158
                        170
                 ....*....|...
gi 500159977 180 AKETLEYGFIDEI 192
Cdd:cd07017  159 AEEAKEYGLIDKI 171
 
Name Accession Description Interval E-value
clpP PRK00277
ATP-dependent Clp protease proteolytic subunit; Reviewed
1-199 2.07e-128

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 178955  Cd Length: 200  Bit Score: 359.09  E-value: 2.07e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   1 MGYLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVD 80
Cdd:PRK00277   4 MMNLVPMVIEQTSRGERSYDIYSRLLKERIIFLGGEVEDHMANLIVAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYD 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  81 TMNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADN 160
Cdd:PRK00277  84 TMQFIKPDVSTICIGQAASMGAFLLAAGAKGKRFALPNSRIMIHQPLGGF-QG-QATDIEIHAREILKLKKRLNEILAEH 161
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 500159977 161 SNRSLEQIHKDAERDHWMDAKETLEYGFIDEIMENNSLK 199
Cdd:PRK00277 162 TGQPLEKIEKDTDRDNFMSAEEAKEYGLIDEVLTKRKEA 200
ClpP COG0740
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ...
3-195 3.51e-114

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


Pssm-ID: 440503  Cd Length: 194  Bit Score: 323.19  E-value: 3.51e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   3 YLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTM 82
Cdd:COG0740    1 YLVPMVVEQTPRGERAYDIYSRLLKERIIFLGGEIDDHVANLIIAQLLFLEAEDPDKDILLYINSPGGSVTAGLAIYDTM 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  83 NFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNSN 162
Cdd:COG0740   81 QFIKPDVSTICLGQAASMGAFLLAAGTKGKRFALPNARIMIHQPSGGA-QG-QASDIEIQAREILKMRERLNEILAEHTG 158
                        170       180       190
                 ....*....|....*....|....*....|...
gi 500159977 163 RSLEQIHKDAERDHWMDAKETLEYGFIDEIMEN 195
Cdd:COG0740  159 QPLEKIEKDTDRDTWMTAEEAVEYGLIDEVIES 191
CLP_protease pfam00574
Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ...
13-195 1.58e-103

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: 295.63  E-value: 1.58e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   13 SRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTI 92
Cdd:pfam00574   1 SRGERAYDIYSRLLKERIIFLGGEIDDEVANLIIAQLLFLEAEDPDKDIYLYINSPGGSVTAGLAIYDTMQYIKPDVSTI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   93 VMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAGQgtQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDA 172
Cdd:pfam00574  81 CLGLAASMGSFLLAAGAKGKRFALPNARIMIHQPLGGAQG--QASDIEIQAKEILKIKERLNEIYAKHTGQSLEKIEKDT 158
                         170       180
                  ....*....|....*....|...
gi 500159977  173 ERDHWMDAKETLEYGFIDEIMEN 195
Cdd:pfam00574 159 DRDFFMSAEEAKEYGLIDEVIER 181
clpP TIGR00493
ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic ...
4-193 3.31e-95

ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores well with this model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 188055  Cd Length: 192  Bit Score: 275.13  E-value: 3.31e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977    4 LVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMN 83
Cdd:TIGR00493   3 LIPTVIEQTGRGERSFDIYSRLLKERIIFLSGEVNDNVANSIVAQLLFLEAEDPEKDIYLYINSPGGSITAGLAIYDTMQ 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   84 FIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNSNR 163
Cdd:TIGR00493  83 FIKPDVSTICIGQAASMGAFLLAAGAKGKRFSLPNSRIMIHQPLGGA-QG-QATDIEIQANEILRLKGLLNDILAEHTGQ 160
                         170       180       190
                  ....*....|....*....|....*....|
gi 500159977  164 SLEQIHKDAERDHWMDAKETLEYGFIDEIM 193
Cdd:TIGR00493 161 SLEQIERDTERDFFMSAEEAKEYGLIDKVL 190
S14_ClpP_2 cd07017
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
20-192 4.60e-93

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: 268.93  E-value: 4.60e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  20 DIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAAS 99
Cdd:cd07017    1 DIYSRLLKERIIFLGGPIDDEVANLIIAQLLYLESEDPKKPIYLYINSPGGSVTAGLAIYDTMQYIKPPVSTICLGLAAS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 100 MGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgqGTQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMD 179
Cdd:cd07017   81 MGALLLAAGTKGKRYALPNSRIMIHQPLGGA--GGQASDIEIQAKEILRLRRRLNEILAKHTGQPLEKIEKDTDRDRYMS 158
                        170
                 ....*....|...
gi 500159977 180 AKETLEYGFIDEI 192
Cdd:cd07017  159 AEEAKEYGLIDKI 171
PRK12553 PRK12553
ATP-dependent Clp protease proteolytic subunit; Reviewed
1-192 4.96e-87

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 237133  Cd Length: 207  Bit Score: 254.88  E-value: 4.96e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   1 MGYLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVD 80
Cdd:PRK12553   8 SRYILPSFIERTSYGVKESDPYNKLFEERIIFLGGQVDDASANDVMAQLLVLESIDPDRDITLYINSPGGSVTAGDAIYD 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  81 TMNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAGQGTQQTDMAIVAEQLLKTRKRLEQILADN 160
Cdd:PRK12553  88 TIQFIRPDVQTVCTGQAASAGAVLLAAGTPGKRFALPNARILIHQPSLGGGIRGQASDLEIQAREILRMRERLERILAEH 167
                        170       180       190
                 ....*....|....*....|....*....|..
gi 500159977 161 SNRSLEQIHKDAERDHWMDAKETLEYGFIDEI 192
Cdd:PRK12553 168 TGQSVEKIRKDTDRDKWLTAEEAKDYGLVDQI 199
S14_ClpP cd07013
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
29-192 2.05e-77

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: 229.08  E-value: 2.05e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  29 RIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAASMGTIIASSG 108
Cdd:cd07013    1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLYINSPGGDVFAGMAIYDTIKFIKADVVTIIDGLAASMGSVIAMAG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 109 TKGKRFMLPNAEYLIHQPMGGAgqGTQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMDAKETLEYGF 188
Cdd:cd07013   81 AKGKRFILPNAMMMIHQPWGGT--LGDATDMRIYADLLLKVEGNLVSAYAHKTGQSEEELHADLERDTWLSAREAVEYGF 158

                 ....
gi 500159977 189 IDEI 192
Cdd:cd07013  159 ADTI 162
PRK12551 PRK12551
ATP-dependent Clp protease proteolytic subunit; Reviewed
4-199 6.55e-72

ATP-dependent Clp protease proteolytic subunit; Reviewed


Pssm-ID: 139060  Cd Length: 196  Bit Score: 216.23  E-value: 6.55e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   4 LVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMN 83
Cdd:PRK12551   1 MIPIVIEESGRGERAFDIYSRLLRERIIFLGEPVTSDSANRIVAQLLFLEAEDPEKDIYLYINSPGGSVYDGLGIFDTMQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  84 FIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNSNR 163
Cdd:PRK12551  81 HVKPDVHTVCVGLAASMGAFLLCAGAKGKRSSLQHSRIMIHQPLGGA-RG-QASDIRIQADEILFLKERLNTELSERTGQ 158
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 500159977 164 SLEQIHKDAERDHWMDAKETLEYGFIDEIMENNSLK 199
Cdd:PRK12551 159 PLERIQEDTDRDFFMSPSEAVEYGLIDLVIDKRPVK 194
clpP CHL00028
ATP-dependent Clp protease proteolytic subunit
20-196 1.31e-68

ATP-dependent Clp protease proteolytic subunit


Pssm-ID: 214340  Cd Length: 200  Bit Score: 207.79  E-value: 1.31e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  20 DIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAAS 99
Cdd:CHL00028  22 DLYNRLYRERLLFLGQEVDDEIANQLIGLMVYLSIEDDTKDLYLFINSPGGSVISGLAIYDTMQFVKPDVHTICLGLAAS 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 100 MGTIIASSGTKGKRFMLPNAEYLIHQPMGGAGQGtQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMD 179
Cdd:CHL00028 102 MASFILAGGEITKRLAFPHARVMIHQPASSFYEG-QASEFVLEAEELLKLRETITRVYAQRTGKPLWVISEDMERDVFMS 180
                        170
                 ....*....|....*..
gi 500159977 180 AKETLEYGFIDEIMENN 196
Cdd:CHL00028 181 ATEAKAYGIVDLVAVNN 197
PRK14514 PRK14514
ATP-dependent Clp endopeptidase proteolytic subunit ClpP;
2-196 3.74e-68

ATP-dependent Clp endopeptidase proteolytic subunit ClpP;


Pssm-ID: 184722  Cd Length: 221  Bit Score: 207.46  E-value: 3.74e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   2 GYLVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDT 81
Cdd:PRK14514  28 SYLNPYILEERQLNVTQMDVFSRLMMDRIIFLGTQIDDYTANTIQAQLLYLDSVDPGKDISIYINSPGGSVYAGLGIYDT 107
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  82 MNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADNS 161
Cdd:PRK14514 108 MQFISSDVATICTGMAASMASVLLVAGTKGKRSALPHSRVMIHQPLGGA-QG-QASDIEITAREIQKLKKELYTIIADHS 185
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 500159977 162 NRSLEQIHKDAERDHWMDAKETLEYGFIDEIMENN 196
Cdd:PRK14514 186 GTPFDKVWADSDRDYWMTAQEAKEYGMIDEVLIKK 220
PRK14513 PRK14513
ATP-dependent Clp protease proteolytic subunit; Provisional
4-199 4.30e-66

ATP-dependent Clp protease proteolytic subunit; Provisional


Pssm-ID: 237742 [Multi-domain]  Cd Length: 201  Bit Score: 201.70  E-value: 4.30e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   4 LVPTVIEQSSRGERAYDIYSRLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMN 83
Cdd:PRK14513   3 VIPYVIEQTGRGERMYDIYSRLLKDRIIFVGTPIESQMANTIVAQLLLLDSQNPEQEIQMYINCPGGEVYAGLAIYDTMR 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  84 FIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQpmGGAGQGTQQTDMAIVAEQLLKTRKRLEQILADNSNR 163
Cdd:PRK14513  83 YIKAPVSTICVGIAMSMGSVLLMAGDKGKRMALPNSRIMIHQ--GSAGFRGNTPDLEVQAKEVLFLRDTLVDIYHRHTDL 160
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 500159977 164 SLEQIHKDAERDHWMDAKETLEYGFIDEIMENNSLK 199
Cdd:PRK14513 161 PHEKLLRDMERDYFMSPEEAKAYGLIDSVIEPTRVK 196
Clp_protease_like cd00394
Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ...
30-192 2.52e-58

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: 180.67  E-value: 2.52e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  30 IIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAASMGTIIASSGT 109
Cdd:cd00394    1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQASRKPVIAYVGGQAASAGYYIATAAN 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 110 kgKRFMLPNAEYLIHQPMGGAGQGTQQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMDAKETLEYGFI 189
Cdd:cd00394   81 --KIVMAPGTRVGSHGPIGGYGGNGNPTAQEADQRIILYFIARFISLVAENRGQTTEKLEEDIEKDLVLTAQEALEYGLV 158

                 ...
gi 500159977 190 DEI 192
Cdd:cd00394  159 DAL 161
PRK14512 PRK14512
ATP-dependent Clp protease proteolytic subunit; Provisional
24-195 1.58e-50

ATP-dependent Clp protease proteolytic subunit; Provisional


Pssm-ID: 237741  Cd Length: 197  Bit Score: 161.89  E-value: 1.58e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  24 RLLKDRIIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAASMGTI 103
Cdd:PRK14512  19 KFLKSRSIVIAGEINKDLSELFQEKILLLEALDSKKPIFVYIDSEGGDIDAGFAIFNMIRFVKPKVFTIGVGLVASAAAL 98
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 104 IASSGTKGKRFMLPNAEYLIHQPMGGAgQGTqQTDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMDAKET 183
Cdd:PRK14512  99 IFLAAKKESRFSLPNARYLLHQPLSGF-KGV-ATDIEIYANELNKVKSELNDIIAKETGQELDKVEKDTDRDFWLDSSSA 176
                        170
                 ....*....|..
gi 500159977 184 LEYGFIDEIMEN 195
Cdd:PRK14512 177 VKYGLVFEVVET 188
PRK12552 PRK12552
ATP-dependent Clp protease proteolytic subunit;
20-194 2.32e-45

ATP-dependent Clp protease proteolytic subunit;


Pssm-ID: 183588  Cd Length: 222  Bit Score: 149.50  E-value: 2.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  20 DIYSRLLKDRIIMLTGP-VEDGMANS---------IIAQLLFLDAQDNTKDIYLYVNTPGGSVSAG---------LAIVD 80
Cdd:PRK12552  22 DLPSLLLKERIVYLGLPlFSDDDAKRqvgmdvtelIIAQLLYLEFDDPEKPIYFYINSTGTSWYTGdaigfeteaFAICD 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  81 TMNFIKSDVQTIVMGMAASMGTIIASSGTKGKRFMLPNAEYLIHQPMGGAgQGtQQTDMAIVAEQLLKTRKRLEQILADN 160
Cdd:PRK12552 102 TMRYIKPPVHTICIGQAMGTAAMILSAGTKGQRASLPHATIVLHQPRSGA-RG-QATDIQIRAKEVLHNKRTMLEILSRN 179
                        170       180       190
                 ....*....|....*....|....*....|....
gi 500159977 161 SNRSLEQIHKDAERDHWMDAKETLEYGFIDEIME 194
Cdd:PRK12552 180 TGQTVEKLSKDTDRMFYLTPQEAKEYGLIDRVLE 213
S14_ClpP_1 cd07016
Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ...
31-192 1.80e-32

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: 114.55  E-value: 1.80e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  31 IMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAASMGTIIASSGTk 110
Cdd:cd07016    3 IYIYGDIGSDWGVTAKEFKDALDALGDDSDITVRINSPGGDVFAGLAIYNALKRHKGKVTVKIDGLAASAASVIAMAGD- 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 111 gKRFMLPNAEYLIHQPMGGAgQGTQQtDMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWMDAKETLEYGFID 190
Cdd:cd07016   82 -EVEMPPNAMLMIHNPSTGA-AGNAD-DLRKAADLLDKIDESIANAYAEKTGLSEEEISALMDAETWLTAQEAVELGFAD 158

                 ..
gi 500159977 191 EI 192
Cdd:cd07016  159 EI 160
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
30-195 1.00e-07

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 51.01  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  30 IIMLTGPVEDGMANSIIAQLLflDAQDNTKD-IYLYVNTPGGSVSAGLAIVDTMnfIKSDVQTIVM----GMAASMGTII 104
Cdd:COG1030   30 VIPIDGAIGPATADYLERALE--EAEEEGADaVVLELDTPGGLVDSAREIVDAI--LASPVPVIVYvasgARAASAGAYI 105
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 105 ASSGTKGkrFMLPNAEylihqpMGGA----GQGTQQTDMAIVAEQLLKTRKRleqILADNSNRSLEQIHKDAERDHWMDA 180
Cdd:COG1030  106 LLASHIA--AMAPGTN------IGAAtpvqIGGGIDEAMEEKVINDAVAYIR---SLAELRGRNADWAEAMVRESVSLTA 174
                        170
                 ....*....|....*
gi 500159977 181 KETLEYGFIDEIMEN 195
Cdd:COG1030  175 EEALELGVIDLIAED 189
SppA_67K TIGR00705
signal peptide peptidase SppA, 67K type; This model represents the signal peptide peptidase A ...
6-192 2.03e-06

signal peptide peptidase SppA, 67K type; This model represents the signal peptide peptidase A (SppA, protease IV) as found in E. coli, Treponema pallidum, Mycobacterium leprae, and several other species, in which it has a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half. This enzyme was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273226 [Multi-domain]  Cd Length: 584  Bit Score: 47.13  E-value: 2.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977    6 PTVIEQSSRGER---AYDIYSRLLKDR--------IIMLTGPVEDG------MANSIIAQLLFLDAQDNT-KDIYLYVNT 67
Cdd:TIGR00705 277 KFLFEDDYDKAKnfiSLDDYNRDRPQRhdvqdkigIVHLEGPIADGrdtegnTGGDTVAALLRVARSDPDiKAVVLRINS 356
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   68 PGGSVSAGLAIVDTMNFIKSDVQTIV--MG-MAASMGTIIAS------------SGTKGKRFMLPNAEYLIHQpMGGAGQ 132
Cdd:TIGR00705 357 PGGSVFASEIIRRELARAQARGKPVIvsMGaMAASGGYWIASaadyivaspntiTGSIGVFSVLPTFENSLDR-IGVHVD 435
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500159977  133 GTQQT--------------DMAIVAEQLLKTRKRLEQILADNSNRSLEQIHKDAERDHWM--DAKETleyGFIDEI 192
Cdd:TIGR00705 436 GVSTHelanvsllrpltaeDQAIMQLSVEAGYRRFLSVVSAGRNLTPTQVDKVAQGRVWTgeDAVSN---GLVDAL 508
S49_Sppa_N_C cd07023
Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal ...
30-192 4.34e-05

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: 42.47  E-value: 4.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  30 IIMLTGPVEDG---MANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIV---MGMAASMGTI 103
Cdd:cd07023    4 VIDIEGTISDGggiGADSLIEQLRKAREDDSVKAVVLRINSPGGSVVASEEIYREIRRLRKAKKPVVasmGDVAASGGYY 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 104 IASSGTK------------GKRFMLPNAEYLI--------------HQPMGGAGQGTQQTDMAIVAEQLLKTRKRLEQIL 157
Cdd:cd07023   84 IAAAADKivanpttitgsiGVIGQGPNLEELLdklgierdtiksgpGKDKGSPDRPLTEEERAILQALVDDIYDQFVDVV 163
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 500159977 158 ADNSNRSLEQIHKDAERDHWmDAKETLEYGFIDEI 192
Cdd:cd07023  164 AEGRGMSGERLDKLADGRVW-TGRQALELGLVDEL 197
Clp_protease_NfeD cd07015
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
36-195 5.10e-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: 132926  Cd Length: 172  Bit Score: 42.00  E-value: 5.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  36 PVEDGMANSIIAQL---LFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVM---GMAASMGTIIASSGT 109
Cdd:cd07015    5 QIKGQITSYTYDQFdryITIAEQDNAEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVYppgASAASAGTYIALGSH 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977 110 kgKRFMLPNAEYLIHQPMGGAGQGTQ--QTDMAIVAEQLLKTRKrleqiLADNSNRSLEQIHKDAERDHWMDAKETLEYG 187
Cdd:cd07015   85 --LIAMAPGTSIGACRPILGYSQNGSiiEAPPKITNYFIAYIKS-----LAQESGRNATIAEEFITKDLSLTPEEALKYG 157

                 ....*...
gi 500159977 188 FIDEIMEN 195
Cdd:cd07015  158 VIEVVARD 165
SppA COG0616
Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, ...
30-192 1.40e-04

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


Pssm-ID: 440381 [Multi-domain]  Cd Length: 215  Bit Score: 40.93  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  30 IIMLTGPVEDGM--------ANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDT-MNFIKSDVQTIV--MGMAA 98
Cdd:COG0616   14 VIDLEGTIVDGGgppsgeigLEDILAALRKAAEDPDVKAVVLRINSPGGSVAASEEIRDAlRRLRAKGKPVVAsmGDVAA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  99 SMGTIIASSgtkgkrfmlpnAEYLIHQPMGGAG------QGTQQTDMA----IVAEQL----LKT------------RKR 152
Cdd:COG0616   94 SGGYYIASA-----------ADKIYANPTTITGsigviaQGPNFKGLLeklgVEVEVVtageYKDalspfrplseeeREQ 162
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 500159977 153 LEQIL-----------ADNSNRSLEQIHKDAERDHWMdAKETLEYGFIDEI 192
Cdd:COG0616  163 LQALLddiydqfvedvAEGRGLSLEEVREIADGRVWT-GEQALELGLVDEL 212
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
30-120 3.57e-04

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: 39.49  E-value: 3.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977  30 IIMLTGPVEDGMANSIIAQLLflDAQDNTKD-IYLYVNTPGGSVSAGLAIVDTMNfiKSDVQTI--VMGMAASMGTIIAS 106
Cdd:cd07021    3 VIPIEGEIDPGLAAFVERALK--EAKEEGADaVVLDIDTPGGRVDSALEIVDLIL--NSPIPTIayVNDRAASAGALIAL 78
                         90
                 ....*....|....
gi 500159977 107 SGTkgKRFMLPNAE 120
Cdd:cd07021   79 AAD--EIYMAPGAT 90
PRK10949 PRK10949
signal peptide peptidase SppA;
56-109 3.94e-03

signal peptide peptidase SppA;


Pssm-ID: 182860 [Multi-domain]  Cd Length: 618  Bit Score: 37.34  E-value: 3.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500159977  56 DNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSDVQTIVM---GMAASMG--------TIIASSGT 109
Cdd:PRK10949 363 PKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVsmgGMAASGGywistpanYIVASPST 427
Clp_protease_NfeD_1 cd07020
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
55-104 7.28e-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: 132931 [Multi-domain]  Cd Length: 187  Bit Score: 35.99  E-value: 7.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 500159977  55 QDNTKDIYLYVNTPGGSVSAGLAIVDTmnFIKSDVQTIVM-----GMAASMGTII 104
Cdd:cd07020   27 EGGADALIIELDTPGGLLDSTREIVQA--ILASPVPVVVYvypsgARAASAGTYI 79
SppA_dom TIGR00706
signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ...
30-110 8.28e-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: 35.81  E-value: 8.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500159977   30 IIMLTGPVEDGMANSIIAQLLFLDAQDNTKDIYLYVNTPGGSVSAGLAIVDTMNFIKSD--VQTIVMGMAASMGTIIASS 107
Cdd:TIGR00706   4 VLEVSGAIADVSPEDFDKKLERIKDDKTIKALVLRINSPGGTVVASEEIYKKLEKLKAKkpVVASMGGMAASGGYYISMA 83

                  ...
gi 500159977  108 GTK 110
Cdd:TIGR00706  84 ADE 86
 
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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