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Conserved domains on  [gi|2714511237|ref|WP_341048960|]
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ArdC-like ssDNA-binding domain-containing protein [Carnobacterium sp. FSL W8-0810]

Protein Classification

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, ...
 335-411 9.55e-07

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: 48.18  E-value: 9.55e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2714511237 335 NIPIIKEPFRDSAAKG-YYMPSTHSITLNTKNTETENIHTLIHELAHAEMHNDKKLKNKELTMQAAPVLEYQAEMTAY 411
Cdd:pfam06114   5 GIRVFFLPLGAEDGDGrRFDRHTPVIFLNENLSPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFAA 82
ArdcN pfam08401
N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of ...
 162-290 2.22e-06

N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin. This domain is also found in the N-terminal region of the RP4 TraC1 primase, together with the Toprim domain (pfam01751, pfam13362 and pfam13662).


:

Pssm-ID: 429975  Cd Length: 127  Bit Score: 46.95  E-value: 2.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 162 KKEIDQLTEKMTTQVQTYTE------TPEQMTELLDFMSQFRDYSIRNQFMI--RSQHKG--ANGVASYQRFKELGFPVQ 231
Cdd:pfam08401   1 KDLYERITDQIIEALEAGVGpwqkpwSTGGAGGLPRNAATGRPYSGINVLLLwlAAPEAGytSPRWLTFKQAKELGGQVR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2714511237 232 KGEKGIKI--WVPMTVTQfktKDGEWKNQTKATIEEKEwikknqstdnvKTFTRFKLGTVF 290
Cdd:pfam08401  81 KGEKGTPVvyYKFFVKED---EDDKDYKEADEEGEEEE-----------REIPFLKTYTVF 127
 
Name Accession Description Interval E-value
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 335-411 9.55e-07

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: 48.18  E-value: 9.55e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2714511237 335 NIPIIKEPFRDSAAKG-YYMPSTHSITLNTKNTETENIHTLIHELAHAEMHNDKKLKNKELTMQAAPVLEYQAEMTAY 411
Cdd:pfam06114   5 GIRVFFLPLGAEDGDGrRFDRHTPVIFLNENLSPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFAA 82
ArdcN pfam08401
N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of ...
 162-290 2.22e-06

N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin. This domain is also found in the N-terminal region of the RP4 TraC1 primase, together with the Toprim domain (pfam01751, pfam13362 and pfam13662).


Pssm-ID: 429975  Cd Length: 127  Bit Score: 46.95  E-value: 2.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 162 KKEIDQLTEKMTTQVQTYTE------TPEQMTELLDFMSQFRDYSIRNQFMI--RSQHKG--ANGVASYQRFKELGFPVQ 231
Cdd:pfam08401   1 KDLYERITDQIIEALEAGVGpwqkpwSTGGAGGLPRNAATGRPYSGINVLLLwlAAPEAGytSPRWLTFKQAKELGGQVR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2714511237 232 KGEKGIKI--WVPMTVTQfktKDGEWKNQTKATIEEKEwikknqstdnvKTFTRFKLGTVF 290
Cdd:pfam08401  81 KGEKGTPVvyYKFFVKED---EDDKDYKEADEEGEEEE-----------REIPFLKTYTVF 127
ArdC COG4227
Antirestriction protein ArdC [Replication, recombination and repair];
224-472 2.30e-05

Antirestriction protein ArdC [Replication, recombination and repair];


Pssm-ID: 443371 [Multi-domain]  Cd Length: 303  Bit Score: 46.77  E-value: 2.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 224 KELGFPVQKGEKGIKI--WVPMTVTQFKTKDgewknqtkatiEEKEwikknqstDNVKTFTRFKLGTVFDVTQTHAKPED 301
Cdd:COG4227    81 KELGGQVRKGEKGTLVvyYKRFEKEDEDEED-----------EEGE--------EVERRIPFLKAYTVFNAEQIDGLPEE 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 302 YPAIfPNKKNQFDfggkdldlLNQSLLEYSNSTNIPIIKEPfrDSAakgYYMPSTHSITLNTKNT--ETENIH-TLIHEL 378
Cdd:COG4227   142 YYPL-PEPLPESE--------RIERAEAFIAATGADIRHGG--DRA---FYSPSTDRIQMPPREQfkDAEDYYaTLLHEL 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 379 AHAEMHN---DKKLKNK---------ELTmqaapvleyqAEMTAYVVGKYYGLDTEKH--SLRYISNWTDNLEkvEDK-- 442
Cdd:COG4227   208 GHWTGHKsrlNRDLGGRfgseayafeELV----------AELGSAFLCAELGIAPEPRenHAAYIASWLKVLK--EDKra 275

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2714511237 443 -INSLSEVKKASgklidhlDLIIEQTTESKQ 472
Cdd:COG4227   276 iFRAASKAQKAA-------DYLLGLQPEAAE 299
 
Name Accession Description Interval E-value
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 335-411 9.55e-07

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: 48.18  E-value: 9.55e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2714511237 335 NIPIIKEPFRDSAAKG-YYMPSTHSITLNTKNTETENIHTLIHELAHAEMHNDKKLKNKELTMQAAPVLEYQAEMTAY 411
Cdd:pfam06114   5 GIRVFFLPLGAEDGDGrRFDRHTPVIFLNENLSPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREANIFAA 82
ArdcN pfam08401
N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of ...
 162-290 2.22e-06

N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin. This domain is also found in the N-terminal region of the RP4 TraC1 primase, together with the Toprim domain (pfam01751, pfam13362 and pfam13662).


Pssm-ID: 429975  Cd Length: 127  Bit Score: 46.95  E-value: 2.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 162 KKEIDQLTEKMTTQVQTYTE------TPEQMTELLDFMSQFRDYSIRNQFMI--RSQHKG--ANGVASYQRFKELGFPVQ 231
Cdd:pfam08401   1 KDLYERITDQIIEALEAGVGpwqkpwSTGGAGGLPRNAATGRPYSGINVLLLwlAAPEAGytSPRWLTFKQAKELGGQVR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2714511237 232 KGEKGIKI--WVPMTVTQfktKDGEWKNQTKATIEEKEwikknqstdnvKTFTRFKLGTVF 290
Cdd:pfam08401  81 KGEKGTPVvyYKFFVKED---EDDKDYKEADEEGEEEE-----------REIPFLKTYTVF 127
ArdC COG4227
Antirestriction protein ArdC [Replication, recombination and repair];
224-472 2.30e-05

Antirestriction protein ArdC [Replication, recombination and repair];


Pssm-ID: 443371 [Multi-domain]  Cd Length: 303  Bit Score: 46.77  E-value: 2.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 224 KELGFPVQKGEKGIKI--WVPMTVTQFKTKDgewknqtkatiEEKEwikknqstDNVKTFTRFKLGTVFDVTQTHAKPED 301
Cdd:COG4227    81 KELGGQVRKGEKGTLVvyYKRFEKEDEDEED-----------EEGE--------EVERRIPFLKAYTVFNAEQIDGLPEE 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 302 YPAIfPNKKNQFDfggkdldlLNQSLLEYSNSTNIPIIKEPfrDSAakgYYMPSTHSITLNTKNT--ETENIH-TLIHEL 378
Cdd:COG4227   142 YYPL-PEPLPESE--------RIERAEAFIAATGADIRHGG--DRA---FYSPSTDRIQMPPREQfkDAEDYYaTLLHEL 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714511237 379 AHAEMHN---DKKLKNK---------ELTmqaapvleyqAEMTAYVVGKYYGLDTEKH--SLRYISNWTDNLEkvEDK-- 442
Cdd:COG4227   208 GHWTGHKsrlNRDLGGRfgseayafeELV----------AELGSAFLCAELGIAPEPRenHAAYIASWLKVLK--EDKra 275

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2714511237 443 -INSLSEVKKASgklidhlDLIIEQTTESKQ 472
Cdd:COG4227   276 iFRAASKAQKAA-------DYLLGLQPEAAE 299
DUF6782 pfam20573
Putative metallopeptidase family (DUF6782); This family of proteins is functionally ...
 348-382 8.01e-03

Putative metallopeptidase family (DUF6782); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 256 and 362 amino acids in length. There is a conserved HEXRH sequence motif which is characteriztic of metallopeptidase enzymes.


Pssm-ID: 466722  Cd Length: 241  Bit Score: 38.52  E-value: 8.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2714511237 348 AKGYYMPSTHSITLNTKNTETENIHTLIHELAHAE 382
Cdd:pfam20573  68 ARGYYDPETNRIVLNADLPFGLQVATLVHELRHLQ 102
 
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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