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Conserved domains on  [gi|1705307672|ref|WP_142657802|]
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ArdC-like ssDNA-binding domain-containing protein [Enterococcus faecalis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ArdC super family cl39143
Antirestriction protein ArdC [Replication, recombination and repair];
447-635 1.24e-17

Antirestriction protein ArdC [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG4227:

Pssm-ID: 443371 [Multi-domain]  Cd Length: 303  Bit Score: 84.13  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 447 YNAWKKLDRQVKKGSKALYVYapYFKdKVDKNGKKVTDENGEIVKETRYFLT--PVFDVEQTTGaeLPQLVYNLEENLSD 524
Cdd:COG4227    77 FKQAKELGGQVRKGEKGTLVV--YYK-RFEKEDEDEEDEEGEEVERRIPFLKayTVFNAEQIDG--LPEEYYPLPEPLPE 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 525 GKTFTRTyNALVEICPVPVTVtsiaSGANGYYDPTKKEIVL---------QQHLGevmtlkVLLHEMTHAMLHP-----D 590
Cdd:COG4227   152 SERIERA-EAFIAATGADIRH----GGDRAFYSPSTDRIQMppreqfkdaEDYYA------TLLHELGHWTGHKsrlnrD 220

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1705307672 591 SQAIFGDDVYSRQEFEAESVAYIVSRHLGL--DTSSYSFGYLSSWTK 635
Cdd:COG4227   221 LGGRFGSEAYAFEELVAELGSAFLCAELGIapEPRENHAAYIASWLK 267
Toprim_2 super family cl48160
Toprim-like; This is a family or Toprim-like proteins.
 223-338 1.69e-09

Toprim-like; This is a family or Toprim-like proteins.


The actual alignment was detected with superfamily member pfam13155:

Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 54.88  E-value: 1.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 223 IVFEAPIDLMSYYELKKEtigdAVLFCA-NGLkkgavstlianeigsyvkeeekPTVLEQLEKSKLTTEKVqlVLAVDND 301
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIK----NVLYVAtLGT----------------------ALTEAQIKLLKRYPKEV--ILAFDND 52

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1705307672 302 EAGKKFIQQF-----SNNWCPITLDQPkliEGKsktDWNDIL 338
Cdd:pfam13155  53 EAGRKAAKRLaellkEAGVDVKIRLLP---DGK---DWNEYL 88
 
Name Accession Description Interval E-value
ArdC COG4227
Antirestriction protein ArdC [Replication, recombination and repair];
447-635 1.24e-17

Antirestriction protein ArdC [Replication, recombination and repair];


Pssm-ID: 443371 [Multi-domain]  Cd Length: 303  Bit Score: 84.13  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 447 YNAWKKLDRQVKKGSKALYVYapYFKdKVDKNGKKVTDENGEIVKETRYFLT--PVFDVEQTTGaeLPQLVYNLEENLSD 524
Cdd:COG4227    77 FKQAKELGGQVRKGEKGTLVV--YYK-RFEKEDEDEEDEEGEEVERRIPFLKayTVFNAEQIDG--LPEEYYPLPEPLPE 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 525 GKTFTRTyNALVEICPVPVTVtsiaSGANGYYDPTKKEIVL---------QQHLGevmtlkVLLHEMTHAMLHP-----D 590
Cdd:COG4227   152 SERIERA-EAFIAATGADIRH----GGDRAFYSPSTDRIQMppreqfkdaEDYYA------TLLHELGHWTGHKsrlnrD 220

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1705307672 591 SQAIFGDDVYSRQEFEAESVAYIVSRHLGL--DTSSYSFGYLSSWTK 635
Cdd:COG4227   221 LGGRFGSEAYAFEELVAELGSAFLCAELGIapEPRENHAAYIASWLK 267
ArdcN pfam08401
N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of ...
 419-501 2.74e-11

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: 61.59  E-value: 2.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 419 FASKFHKYSSKNIRLLLAQNP----NIRRVAGYNAWKKLDRQVKKGSKALYV--YAPYFKDKVDKNGKKVTDENGEIVKE 492
Cdd:pfam08401  37 NAATGRPYSGINVLLLWLAAPeagyTSPRWLTFKQAKELGGQVRKGEKGTPVvyYKFFVKEDEDDKDYKEADEEGEEEER 116

                          90
                  ....*....|.
gi 1705307672 493 TRYFLT--PVF 501
Cdd:pfam08401 117 EIPFLKtyTVF 127
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 223-338 1.69e-09

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 54.88  E-value: 1.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 223 IVFEAPIDLMSYYELKKEtigdAVLFCA-NGLkkgavstlianeigsyvkeeekPTVLEQLEKSKLTTEKVqlVLAVDND 301
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIK----NVLYVAtLGT----------------------ALTEAQIKLLKRYPKEV--ILAFDND 52

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1705307672 302 EAGKKFIQQF-----SNNWCPITLDQPkliEGKsktDWNDIL 338
Cdd:pfam13155  53 EAGRKAAKRLaellkEAGVDVKIRLLP---DGK---DWNEYL 88
 
Name Accession Description Interval E-value
ArdC COG4227
Antirestriction protein ArdC [Replication, recombination and repair];
447-635 1.24e-17

Antirestriction protein ArdC [Replication, recombination and repair];


Pssm-ID: 443371 [Multi-domain]  Cd Length: 303  Bit Score: 84.13  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 447 YNAWKKLDRQVKKGSKALYVYapYFKdKVDKNGKKVTDENGEIVKETRYFLT--PVFDVEQTTGaeLPQLVYNLEENLSD 524
Cdd:COG4227    77 FKQAKELGGQVRKGEKGTLVV--YYK-RFEKEDEDEEDEEGEEVERRIPFLKayTVFNAEQIDG--LPEEYYPLPEPLPE 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 525 GKTFTRTyNALVEICPVPVTVtsiaSGANGYYDPTKKEIVL---------QQHLGevmtlkVLLHEMTHAMLHP-----D 590
Cdd:COG4227   152 SERIERA-EAFIAATGADIRH----GGDRAFYSPSTDRIQMppreqfkdaEDYYA------TLLHELGHWTGHKsrlnrD 220

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1705307672 591 SQAIFGDDVYSRQEFEAESVAYIVSRHLGL--DTSSYSFGYLSSWTK 635
Cdd:COG4227   221 LGGRFGSEAYAFEELVAELGSAFLCAELGIapEPRENHAAYIASWLK 267
ArdcN pfam08401
N-terminal domain of anti-restriction factor ArdC; This is the ssDNA binding domain of ...
 419-501 2.74e-11

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: 61.59  E-value: 2.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 419 FASKFHKYSSKNIRLLLAQNP----NIRRVAGYNAWKKLDRQVKKGSKALYV--YAPYFKDKVDKNGKKVTDENGEIVKE 492
Cdd:pfam08401  37 NAATGRPYSGINVLLLWLAAPeagyTSPRWLTFKQAKELGGQVRKGEKGTPVvyYKFFVKEDEDDKDYKEADEEGEEEER 116

                          90
                  ....*....|.
gi 1705307672 493 TRYFLT--PVF 501
Cdd:pfam08401 117 EIPFLKtyTVF 127
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 223-338 1.69e-09

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 54.88  E-value: 1.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1705307672 223 IVFEAPIDLMSYYELKKEtigdAVLFCA-NGLkkgavstlianeigsyvkeeekPTVLEQLEKSKLTTEKVqlVLAVDND 301
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIK----NVLYVAtLGT----------------------ALTEAQIKLLKRYPKEV--ILAFDND 52

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1705307672 302 EAGKKFIQQF-----SNNWCPITLDQPkliEGKsktDWNDIL 338
Cdd:pfam13155  53 EAGRKAAKRLaellkEAGVDVKIRLLP---DGK---DWNEYL 88
DUF6782 pfam20573
Putative metallopeptidase family (DUF6782); This family of proteins is functionally ...
 550-585 2.41e-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: 40.07  E-value: 2.41e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1705307672 550 SGANGYYDPTKKEIVLQQHLGEVMTLKVLLHEMTHA 585
Cdd:pfam20573  66 GNARGYYDPETNRIVLNADLPFGLQVATLVHELRHL 101
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 555-612 8.52e-03

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: 37.01  E-value: 8.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1705307672 555 YYDPTKKEIVLQQHLGEVMTLKVLLHEMTHAMLHPD---SQAIFGDDVYSRQEFEAESVAY 612
Cdd:pfam06114  22 RFDRHTPVIFLNENLSPTRQRFTLAHELGHLLLHEGgdtLSDQFDFKTAEAREREANIFAA 82
 
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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