ATP-dependent Clp protease proteolytic subunit [Pannonibacter indicus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| SDH_sah super family | cl26734 | Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ... |
3-268 | 2.84e-114 | |||||
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. The actual alignment was detected with superfamily member pfam01972: Pssm-ID: 110924 Cd Length: 286 Bit Score: 330.27 E-value: 2.84e-114
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| Name | Accession | Description | Interval | E-value | |||||
| SDH_sah | pfam01972 | Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ... |
3-268 | 2.84e-114 | |||||
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: 330.27 E-value: 2.84e-114
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| Clp_protease_NfeD_like | cd07021 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
88-150 | 1.79e-15 | |||||
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: 72.62 E-value: 1.79e-15
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| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
88-158 | 3.45e-11 | |||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 62.95 E-value: 3.45e-11
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| SppA_dom | TIGR00706 | signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ... |
92-145 | 4.50e-04 | |||||
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: 40.43 E-value: 4.50e-04
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| PRK11778 | PRK11778 | putative inner membrane peptidase; Provisional |
90-137 | 3.69e-03 | |||||
putative inner membrane peptidase; Provisional Pssm-ID: 236978 [Multi-domain] Cd Length: 330 Bit Score: 38.27 E-value: 3.69e-03
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| Name | Accession | Description | Interval | E-value | |||||
| SDH_sah | pfam01972 | Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ... |
3-268 | 2.84e-114 | |||||
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: 330.27 E-value: 2.84e-114
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| Clp_protease_NfeD_like | cd07021 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
88-150 | 1.79e-15 | |||||
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: 72.62 E-value: 1.79e-15
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| S14_ClpP_1 | cd07016 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
87-144 | 1.96e-12 | |||||
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: 63.71 E-value: 1.96e-12
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| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
88-158 | 3.45e-11 | |||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 62.95 E-value: 3.45e-11
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| Clp_protease_NfeD_1 | cd07020 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
88-166 | 4.84e-08 | |||||
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: 51.79 E-value: 4.84e-08
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| Clp_protease_NfeD | cd07015 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
88-160 | 1.85e-07 | |||||
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: 50.08 E-value: 1.85e-07
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| Clp_protease_like | cd00394 | Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ... |
57-152 | 1.70e-06 | |||||
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: 47.00 E-value: 1.70e-06
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| SppA | COG0616 | Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, ... |
88-138 | 1.97e-06 | |||||
Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440381 [Multi-domain] Cd Length: 215 Bit Score: 47.48 E-value: 1.97e-06
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| S49_Sppa_N_C | cd07023 | Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal ... |
88-145 | 4.36e-06 | |||||
Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. Pssm-ID: 132934 [Multi-domain] Cd Length: 208 Bit Score: 46.33 E-value: 4.36e-06
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| SppA_dom | TIGR00706 | signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ... |
92-145 | 4.50e-04 | |||||
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: 40.43 E-value: 4.50e-04
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| S14_ClpP | cd07013 | Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Clp ... |
65-135 | 5.35e-04 | |||||
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: 39.56 E-value: 5.35e-04
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| PRK11778 | PRK11778 | putative inner membrane peptidase; Provisional |
90-137 | 3.69e-03 | |||||
putative inner membrane peptidase; Provisional Pssm-ID: 236978 [Multi-domain] Cd Length: 330 Bit Score: 38.27 E-value: 3.69e-03
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| Blast search parameters | ||||
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