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Conserved domains on  [gi|446391978|ref|WP_000469833|]
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MULTISPECIES: ImmA/IrrE family metallo-endopeptidase [Staphylococcus]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443576)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|10556324

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 199-308 6.66e-26

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


:

Pssm-ID: 442104  Cd Length: 105  Bit Score: 100.51  E-value: 6.66e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446391978 199 IILGTNRGVAvRRNFDLAHELGHLVLHRHIQFDLLSPEEYKtIEHEADIFASEFLLPEEAFKKDFDQmtkkSNPDYLAVL 278
Cdd:COG2856    1 IVLNSNLSPE-RQRFTLAHELGHLLLHRGGETDLFLSSDDK-IEREANAFAAELLMPEEALRELLKE----KLSEDLEEL 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 446391978 279 KEKWYVSIQAIAMRAYYLGLMSSTQYRYFW 308
Cdd:COG2856   75 AKRFGVSEEALLYRLKELGLIDEPGLGLIL 104
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-78 1.62e-08

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.15  E-value: 1.62e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446391978   1 MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYFISEQPEELLINSVDKHS 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
 
Name Accession Description Interval E-value
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 199-308 6.66e-26

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


Pssm-ID: 442104  Cd Length: 105  Bit Score: 100.51  E-value: 6.66e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446391978 199 IILGTNRGVAvRRNFDLAHELGHLVLHRHIQFDLLSPEEYKtIEHEADIFASEFLLPEEAFKKDFDQmtkkSNPDYLAVL 278
Cdd:COG2856    1 IVLNSNLSPE-RQRFTLAHELGHLLLHRGGETDLFLSSDDK-IEREANAFAAELLMPEEALRELLKE----KLSEDLEEL 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 446391978 279 KEKWYVSIQAIAMRAYYLGLMSSTQYRYFW 308
Cdd:COG2856   75 AKRFGVSEEALLYRLKELGLIDEPGLGLIL 104
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 170-294 1.55e-17

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: 77.85  E-value: 1.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446391978  170 EKAGIVIYEKRINDS-IDAYSFWskDQTPFIILGTNRGVAvRRNFDLAHELGHLVLH-----RHIQFDLLSPEEYktiEH 243
Cdd:pfam06114   2 ERLGIRVFFLPLGAEdGDGRRFD--RHTPVIFLNENLSPT-RQRFTLAHELGHLLLHeggdtLSDQFDFKTAEAR---ER 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446391978  244 EADIFASEFLLPEEafkkDFDQMTKKSNPDYLAVLKEKWYVSIQAIAMRAY 294
Cdd:pfam06114  76 EANIFAAALLMPYE----AFLAAAETLRYDLELLLAERFGVSYEAVAHRLS 122
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-78 1.62e-08

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.15  E-value: 1.62e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446391978   1 MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYFISEQPEELLINSVDKHS 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 2.13e-07

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 47.55  E-value: 2.13e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446391978   4 GKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 4.29e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 4.29e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446391978     6 NLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 3.81e-04

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 37.91  E-value: 3.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446391978    7 LEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
 
Name Accession Description Interval E-value
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 199-308 6.66e-26

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


Pssm-ID: 442104  Cd Length: 105  Bit Score: 100.51  E-value: 6.66e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446391978 199 IILGTNRGVAvRRNFDLAHELGHLVLHRHIQFDLLSPEEYKtIEHEADIFASEFLLPEEAFKKDFDQmtkkSNPDYLAVL 278
Cdd:COG2856    1 IVLNSNLSPE-RQRFTLAHELGHLLLHRGGETDLFLSSDDK-IEREANAFAAELLMPEEALRELLKE----KLSEDLEEL 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 446391978 279 KEKWYVSIQAIAMRAYYLGLMSSTQYRYFW 308
Cdd:COG2856   75 AKRFGVSEEALLYRLKELGLIDEPGLGLIL 104
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 170-294 1.55e-17

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: 77.85  E-value: 1.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446391978  170 EKAGIVIYEKRINDS-IDAYSFWskDQTPFIILGTNRGVAvRRNFDLAHELGHLVLH-----RHIQFDLLSPEEYktiEH 243
Cdd:pfam06114   2 ERLGIRVFFLPLGAEdGDGRRFD--RHTPVIFLNENLSPT-RQRFTLAHELGHLLLHeggdtLSDQFDFKTAEAR---ER 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446391978  244 EADIFASEFLLPEEafkkDFDQMTKKSNPDYLAVLKEKWYVSIQAIAMRAY 294
Cdd:pfam06114  76 EANIFAAALLMPYE----AFLAAAETLRYDLELLLAERFGVSYEAVAHRLS 122
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-78 1.62e-08

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 51.15  E-value: 1.62e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446391978   1 MFIGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYFISEQPEELLINSVDKHS 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 2.13e-07

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 47.55  E-value: 2.13e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446391978   4 GKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 4.29e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 4.29e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446391978     6 NLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 3.81e-04

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 37.91  E-value: 3.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446391978    7 LEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVKSSYF 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-57 6.50e-04

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 38.00  E-value: 6.50e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446391978   3 IGKNLEYVRKLNALSRKELSEKINVSEQAIWQYETKNMMPEISKIYDMTSIFNVK 57
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
 
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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