nodulation protein NfeD [Vibrio fluvialis]
Protein Classification
NfeD family protein( domain architecture ID 11437047)
NfeD (nodulation formation efficiency D) family protein containing only the C-terminal soluble OB-fold NfeD (NfeDC) domain, may function by associating with neighboring slipin clusters; similar to Bacillus subtilis membrane protein NfeD1b
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
6-446 | 3.11e-164 | |||||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; : Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 468.57 E-value: 3.11e-164
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| Name | Accession | Description | Interval | E-value | |||||||
| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
6-446 | 3.11e-164 | |||||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 468.57 E-value: 3.11e-164
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| Clp_protease_NfeD_1 | cd07020 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
35-232 | 2.23e-89 | |||||||
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: 269.42 E-value: 2.23e-89
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| NfeD | pfam01957 | NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ... |
364-445 | 3.27e-12 | |||||||
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts. Pssm-ID: 460395 Cd Length: 90 Bit Score: 62.21 E-value: 3.27e-12
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| SppA_dom | TIGR00706 | signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ... |
34-131 | 7.35e-05 | |||||||
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: 43.90 E-value: 7.35e-05
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| Name | Accession | Description | Interval | E-value | |||||||
| NfeD | COG1030 | Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ... |
6-446 | 3.11e-164 | |||||||
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440653 [Multi-domain] Cd Length: 413 Bit Score: 468.57 E-value: 3.11e-164
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| Clp_protease_NfeD_1 | cd07020 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
35-232 | 2.23e-89 | |||||||
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: 269.42 E-value: 2.23e-89
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| Clp_protease_NfeD | cd07015 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
35-215 | 2.39e-29 | |||||||
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: 112.87 E-value: 2.39e-29
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| Clp_protease_NfeD_like | cd07021 | Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ... |
35-215 | 7.65e-23 | |||||||
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: 94.96 E-value: 7.65e-23
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| Clp_protease_like | cd00394 | Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ... |
37-207 | 5.11e-16 | |||||||
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: 75.12 E-value: 5.11e-16
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| YbbJ | COG1585 | Membrane protein implicated in regulation of membrane protease activity [Posttranslational ... |
311-446 | 1.98e-15 | |||||||
Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 441193 Cd Length: 143 Bit Score: 72.92 E-value: 1.98e-15
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| NfeD | pfam01957 | NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ... |
364-445 | 3.27e-12 | |||||||
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts. Pssm-ID: 460395 Cd Length: 90 Bit Score: 62.21 E-value: 3.27e-12
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| SppA | COG0616 | Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, ... |
24-130 | 9.19e-06 | |||||||
Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440381 [Multi-domain] Cd Length: 215 Bit Score: 46.33 E-value: 9.19e-06
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| SppA_dom | TIGR00706 | signal peptide peptidase SppA, 36K type; The related but duplicated, double-length protein ... |
34-131 | 7.35e-05 | |||||||
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: 43.90 E-value: 7.35e-05
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| S49_Sppa_N_C | cd07023 | Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Signal ... |
34-130 | 1.63e-03 | |||||||
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: 39.78 E-value: 1.63e-03
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