ATP-dependent Clp protease proteolytic subunit [Rhizobium ruizarguesonis]
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+
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| clpP | PRK00277 | ATP-dependent Clp protease proteolytic subunit; Reviewed |
1-198 | 1.69e-140 | ||||
ATP-dependent Clp protease proteolytic subunit; Reviewed : Pssm-ID: 178955 Cd Length: 200 Bit Score: 389.91 E-value: 1.69e-140
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| Name | Accession | Description | Interval | E-value | ||||
| clpP | PRK00277 | ATP-dependent Clp protease proteolytic subunit; Reviewed |
1-198 | 1.69e-140 | ||||
ATP-dependent Clp protease proteolytic subunit; Reviewed Pssm-ID: 178955 Cd Length: 200 Bit Score: 389.91 E-value: 1.69e-140
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| ClpP | COG0740 | ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ... |
6-198 | 5.24e-122 | ||||
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440503 Cd Length: 194 Bit Score: 342.83 E-value: 5.24e-122
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| CLP_protease | pfam00574 | Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ... |
16-195 | 1.86e-114 | ||||
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: 323.36 E-value: 1.86e-114
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| S14_ClpP_2 | cd07017 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
23-193 | 2.67e-106 | ||||
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: 302.44 E-value: 2.67e-106
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| clpP | TIGR00493 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic ... |
5-195 | 5.77e-103 | ||||
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: 294.77 E-value: 5.77e-103
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| Name | Accession | Description | Interval | E-value | ||||
| clpP | PRK00277 | ATP-dependent Clp protease proteolytic subunit; Reviewed |
1-198 | 1.69e-140 | ||||
ATP-dependent Clp protease proteolytic subunit; Reviewed Pssm-ID: 178955 Cd Length: 200 Bit Score: 389.91 E-value: 1.69e-140
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| ClpP | COG0740 | ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein ... |
6-198 | 5.24e-122 | ||||
ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440503 Cd Length: 194 Bit Score: 342.83 E-value: 5.24e-122
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| CLP_protease | pfam00574 | Clp protease; The Clp protease has an active site catalytic triad. In E. coli Clp protease, ... |
16-195 | 1.86e-114 | ||||
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: 323.36 E-value: 1.86e-114
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| S14_ClpP_2 | cd07017 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
23-193 | 2.67e-106 | ||||
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: 302.44 E-value: 2.67e-106
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| clpP | TIGR00493 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP; This model for the proteolytic ... |
5-195 | 5.77e-103 | ||||
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: 294.77 E-value: 5.77e-103
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| PRK12553 | PRK12553 | ATP-dependent Clp protease proteolytic subunit; Reviewed |
3-195 | 1.93e-94 | ||||
ATP-dependent Clp protease proteolytic subunit; Reviewed Pssm-ID: 237133 Cd Length: 207 Bit Score: 273.75 E-value: 1.93e-94
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| clpP | CHL00028 | ATP-dependent Clp protease proteolytic subunit |
23-200 | 2.63e-78 | ||||
ATP-dependent Clp protease proteolytic subunit Pssm-ID: 214340 Cd Length: 200 Bit Score: 232.83 E-value: 2.63e-78
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| PRK12551 | PRK12551 | ATP-dependent Clp protease proteolytic subunit; Reviewed |
7-197 | 3.23e-74 | ||||
ATP-dependent Clp protease proteolytic subunit; Reviewed Pssm-ID: 139060 Cd Length: 196 Bit Score: 222.40 E-value: 3.23e-74
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| PRK14513 | PRK14513 | ATP-dependent Clp protease proteolytic subunit; Provisional |
5-194 | 5.25e-74 | ||||
ATP-dependent Clp protease proteolytic subunit; Provisional Pssm-ID: 237742 [Multi-domain] Cd Length: 201 Bit Score: 221.73 E-value: 5.25e-74
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| PRK14514 | PRK14514 | ATP-dependent Clp endopeptidase proteolytic subunit ClpP; |
3-195 | 8.35e-68 | ||||
ATP-dependent Clp endopeptidase proteolytic subunit ClpP; Pssm-ID: 184722 Cd Length: 221 Bit Score: 206.69 E-value: 8.35e-68
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| PRK12552 | PRK12552 | ATP-dependent Clp protease proteolytic subunit; |
7-202 | 4.15e-65 | ||||
ATP-dependent Clp protease proteolytic subunit; Pssm-ID: 183588 Cd Length: 222 Bit Score: 199.96 E-value: 4.15e-65
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| S14_ClpP | cd07013 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
32-193 | 5.13e-63 | ||||
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: 192.48 E-value: 5.13e-63
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| PRK14512 | PRK14512 | ATP-dependent Clp protease proteolytic subunit; Provisional |
27-197 | 4.59e-53 | ||||
ATP-dependent Clp protease proteolytic subunit; Provisional Pssm-ID: 237741 Cd Length: 197 Bit Score: 168.43 E-value: 4.59e-53
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| Clp_protease_like | cd00394 | Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ... |
33-193 | 5.33e-44 | ||||
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: 144.07 E-value: 5.33e-44
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| S14_ClpP_1 | cd07016 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
54-193 | 9.68e-37 | ||||
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: 125.73 E-value: 9.68e-37
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| COG3904 | COG3904 | Predicted periplasmic protein [Function unknown]; |
54-194 | 5.15e-08 | ||||
Predicted periplasmic protein [Function unknown]; Pssm-ID: 443110 [Multi-domain] Cd Length: 197 Bit Score: 50.80 E-value: 5.15e-08
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| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
33-193 | 1.02e-06 | ||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 47.93 E-value: 1.02e-06
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| Clp_protease_NfeD_1 | cd07020 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
36-193 | 1.06e-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: 38.30 E-value: 1.06e-03
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| PRK06213 | PRK06213 | crotonase/enoyl-CoA hydratase family protein; |
73-193 | 8.66e-03 | ||||
crotonase/enoyl-CoA hydratase family protein; Pssm-ID: 235744 Cd Length: 229 Bit Score: 36.11 E-value: 8.66e-03
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| Blast search parameters | ||||
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