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Conserved domains on  [gi|515639669|ref|WP_017072269|]
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type II toxin-antitoxin system Phd/YefM family antitoxin [Vibrio crassostreae]

Protein Classification

type II toxin-antitoxin system Phd/YefM family antitoxin( domain architecture ID 10005482)

type II toxin-antitoxin (TA) system Phd/YefM family antitoxin is the antitoxin component of a TA module that binds to its cognate toxin and neutralizes its mRNA interferase activity; similar to Escherichia virus P1 antitoxin phd (prevent-host-death)

Gene Ontology:  GO:0003677|GO:0097351|GO:0006355|GO:0045927|GO:0110001
PubMed:  9829946|18757857|27159580

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 10-82 1.33e-12

Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms];


:

Pssm-ID: 441764  Cd Length: 83  Bit Score: 57.11  E-value: 1.33e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515639669 10 AASITELKANPMKVATSA--YGEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLE---LLTIAKERESE-ESISVNLDDL 82
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAElEAGEVSLDEL 81
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 10-82 1.33e-12

Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms];


Pssm-ID: 441764  Cd Length: 83  Bit Score: 57.11  E-value: 1.33e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515639669 10 AASITELKANPMKVATSA--YGEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLE---LLTIAKERESE-ESISVNLDDL 82
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAElEAGEVSLDEL 81
PRK09778 PRK09778
type I toxin-antitoxin system antitoxin YafN;
2-61 5.99e-10

type I toxin-antitoxin system antitoxin YafN;


Pssm-ID: 170091  Cd Length: 97  Bit Score: 50.74  E-value: 5.99e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 515639669  2 TTRILADVAASITELKANPMKVATSaygEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLE 61
Cdd:PRK09778  1 MHRILAEKSVNITELRKNPAKYFID---QPVAVLSNNRPAGYLLSASAFEALMDMLAEQE 57
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 12-60 1.46e-04

prevent-host-death family protein; This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 273688  Cd Length: 52  Bit Score: 35.72  E-value: 1.46e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 515639669  12 SITELKANPMKVATSAY-GEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDL 60
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRdGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 12-72 3.36e-04

Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.


Pssm-ID: 460615  Cd Length: 67  Bit Score: 35.31  E-value: 3.36e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515639669  12 SITELKANPMKV--ATSAYGEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLELLTIAKERESE 72
Cdd:pfam02604  5 SISEARNNLSELldEVEDGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAERLAE 67
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 10-82 1.33e-12

Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms];


Pssm-ID: 441764  Cd Length: 83  Bit Score: 57.11  E-value: 1.33e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515639669 10 AASITELKANPMKVATSA--YGEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLE---LLTIAKERESE-ESISVNLDDL 82
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAElEAGEVSLDEL 81
PRK09778 PRK09778
type I toxin-antitoxin system antitoxin YafN;
2-61 5.99e-10

type I toxin-antitoxin system antitoxin YafN;


Pssm-ID: 170091  Cd Length: 97  Bit Score: 50.74  E-value: 5.99e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 515639669  2 TTRILADVAASITELKANPMKVATSaygEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLE 61
Cdd:PRK09778  1 MHRILAEKSVNITELRKNPAKYFID---QPVAVLSNNRPAGYLLSASAFEALMDMLAEQE 57
PRK02854 PRK02854
primosomal protein DnaT;
1-81 1.20e-05

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 40.94  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515639669   1 MTTRILADVAASITELKANPMKVATSAYGEPVAVLNRNEPAFYCVPAEAyemmMDRLEDLElltiakERESEESISVNLD 80
Cdd:PRK02854   1 MSSRILTSDVIGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPAR----LAELLALE------EKLARPGSDVALD 70


                 .
gi 515639669  81 D 81
Cdd:PRK02854  71 D 71
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 12-60 1.46e-04

prevent-host-death family protein; This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 273688  Cd Length: 52  Bit Score: 35.72  E-value: 1.46e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 515639669  12 SITELKANPMKVATSAY-GEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDL 60
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRdGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 12-72 3.36e-04

Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.


Pssm-ID: 460615  Cd Length: 67  Bit Score: 35.31  E-value: 3.36e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 515639669  12 SITELKANPMKV--ATSAYGEPVAVLNRNEPAFYCVPAEAYEMMMDRLEDLELLTIAKERESE 72
Cdd:pfam02604  5 SISEARNNLSELldEVEDGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAERLAE 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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