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Conserved domains on  [gi|1317788215|gb|AUI29955|]
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hypothetical protein CO999_00809 [Enterococcus faecium]

Protein Classification

M78 family metallopeptidase domain-containing protein( domain architecture ID 1522)

M78 family metallopeptidase domain-containing protein which includes the catalytic domain of ImmA/IrrE family metallo-endopeptidase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_M78 super family cl01076
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 11-92 1.80e-04

IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC.


The actual alignment was detected with superfamily member pfam06114:

Pssm-ID: 470062  Cd Length: 122  Bit Score: 38.94  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317788215  11 EYNLKVVYM---EMKEPGFYYPKPR-IIFLNENLyGETAEAFHLSHELAHFSASHFEFSVLYDTSTTFHSKFETEADKIA 86
Cdd:pfam06114   3 RLGIRVFFLplgAEDGDGRRFDRHTpVIFLNENL-SPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFA 81


                  ....*.
gi 1317788215  87 ILILLN 92
Cdd:pfam06114  82 AALLMP 87
 
Name Accession Description Interval E-value
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 11-92 1.80e-04

IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC.


Pssm-ID: 399250  Cd Length: 122  Bit Score: 38.94  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317788215  11 EYNLKVVYM---EMKEPGFYYPKPR-IIFLNENLyGETAEAFHLSHELAHFSASHFEFSVLYDTSTTFHSKFETEADKIA 86
Cdd:pfam06114   3 RLGIRVFFLplgAEDGDGRRFDRHTpVIFLNENL-SPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFA 81


                  ....*.
gi 1317788215  87 ILILLN 92
Cdd:pfam06114  82 AALLMP 87
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 34-114 3.88e-03

Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442104  Cd Length: 105  Bit Score: 34.64  E-value: 3.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317788215  34 IFLNENLyGETAEAFHLSHELAHFSASHFEFSVLYDTSttfHSKFETEADKIAILILLNIY-IENELTDKSQFNLEKFME 112
Cdd:COG2856     1 IVLNSNL-SPERQRFTLAHELGHLLLHRGGETDLFLSS---DDKIEREANAFAAELLMPEEaLRELLKEKLSEDLEELAK 76


                  ..
gi 1317788215 113 YY 114
Cdd:COG2856    77 RF 78
M48C_Oma1-like cd07324
Oma1 peptidase-like, integral membrane metallopeptidase; This family contains peptidase M48 ...
 47-90 7.04e-03

Oma1 peptidase-like, integral membrane metallopeptidase; This family contains peptidase M48 subfamily C (also known as Oma1 peptidase or mitochondrial metalloendopeptidase OMA1), including similar peptidases containing tetratricopeptide (TPR) repeats, as well as uncharacterized proteins such as E. coli bepA (formerly yfgC), ycaL and loiP (formerly yggG), considered to be putative metallopeptidases. Oma1 peptidase is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Homologs of Oma1 are present in higher eukaryotes, eubacteria and archaebacteria, suggesting that Oma1 is the founding member of a conserved family of membrane-embedded metallopeptidases, all containing the zinc metalloprotease motif (HEXXH). M48 peptidases proteolytically remove the C-terminal three residues of farnesylated proteins.


Pssm-ID: 320683 [Multi-domain]  Cd Length: 142  Bit Score: 34.46  E-value: 7.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1317788215  47 AFHLSHELAHFSASHFEfsvlyDTSTTFHSKFETEADKIAILIL 90
Cdd:cd07324    57 AAVLAHEIGHVTLRHIA-----RQLERYSRDQEREADRLGLQLL 95
 
Name Accession Description Interval E-value
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 11-92 1.80e-04

IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC.


Pssm-ID: 399250  Cd Length: 122  Bit Score: 38.94  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317788215  11 EYNLKVVYM---EMKEPGFYYPKPR-IIFLNENLyGETAEAFHLSHELAHFSASHFEFSVLYDTSTTFHSKFETEADKIA 86
Cdd:pfam06114   3 RLGIRVFFLplgAEDGDGRRFDRHTpVIFLNENL-SPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFA 81


                  ....*.
gi 1317788215  87 ILILLN 92
Cdd:pfam06114  82 AALLMP 87
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 34-114 3.88e-03

Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442104  Cd Length: 105  Bit Score: 34.64  E-value: 3.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1317788215  34 IFLNENLyGETAEAFHLSHELAHFSASHFEFSVLYDTSttfHSKFETEADKIAILILLNIY-IENELTDKSQFNLEKFME 112
Cdd:COG2856     1 IVLNSNL-SPERQRFTLAHELGHLLLHRGGETDLFLSS---DDKIEREANAFAAELLMPEEaLRELLKEKLSEDLEELAK 76


                  ..
gi 1317788215 113 YY 114
Cdd:COG2856    77 RF 78
M48C_Oma1-like cd07324
Oma1 peptidase-like, integral membrane metallopeptidase; This family contains peptidase M48 ...
 47-90 7.04e-03

Oma1 peptidase-like, integral membrane metallopeptidase; This family contains peptidase M48 subfamily C (also known as Oma1 peptidase or mitochondrial metalloendopeptidase OMA1), including similar peptidases containing tetratricopeptide (TPR) repeats, as well as uncharacterized proteins such as E. coli bepA (formerly yfgC), ycaL and loiP (formerly yggG), considered to be putative metallopeptidases. Oma1 peptidase is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Homologs of Oma1 are present in higher eukaryotes, eubacteria and archaebacteria, suggesting that Oma1 is the founding member of a conserved family of membrane-embedded metallopeptidases, all containing the zinc metalloprotease motif (HEXXH). M48 peptidases proteolytically remove the C-terminal three residues of farnesylated proteins.


Pssm-ID: 320683 [Multi-domain]  Cd Length: 142  Bit Score: 34.46  E-value: 7.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1317788215  47 AFHLSHELAHFSASHFEfsvlyDTSTTFHSKFETEADKIAILIL 90
Cdd:cd07324    57 AAVLAHEIGHVTLRHIA-----RQLERYSRDQEREADRLGLQLL 95
 
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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