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Conserved domains on  [gi|2524286953|ref|WP_286473425|]
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MULTISPECIES: type II toxin-antitoxin system Phd/YefM family antitoxin [Empedobacter]

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 ...
 1-83 1.97e-23

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


:

Pssm-ID: 441764  Cd Length: 83  Bit Score: 84.45  E-value: 1.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMATNHELSSRKNEERLDAAIEKLKTQKTFTKE 80
Cdd:COG2161    1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERLLESLAELEAGEVSLDE 80


                 ...
gi 2524286953 81 LIE 83
Cdd:COG2161   81 LIE 83
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-83 1.97e-23

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 84.45  E-value: 1.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMATNHELSSRKNEERLDAAIEKLKTQKTFTKE 80
Cdd:COG2161    1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERLLESLAELEAGEVSLDE 80


                 ...
gi 2524286953 81 LIE 83
Cdd:COG2161   81 LIE 83
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-64 3.57e-12

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: 55.73  E-value: 3.57e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMA-TNHELSSRKNEERL 64
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERL 65
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-83 4.15e-11

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 53.39  E-value: 4.15e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMATNHELSSRKNEERLDAAIEKLKTQKTFTKE 80
Cdd:PRK11409   1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80


                 ...
gi 2524286953 81 LIE 83
Cdd:PRK11409  81 IIE 83
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 5-55 2.49e-03

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: 32.64  E-value: 2.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 2524286953  5 SISEFRKDIKEYFDRVTNNFETLIINRGKNSgVVIMSLEEYNSLMATNHEL 55
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRDGEPVTITKRGRPV-AVLVSAADYDRLQETLRLL 52
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-83 1.97e-23

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 84.45  E-value: 1.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMATNHELSSRKNEERLDAAIEKLKTQKTFTKE 80
Cdd:COG2161    1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERLLESLAELEAGEVSLDE 80


                 ...
gi 2524286953 81 LIE 83
Cdd:COG2161   81 LIE 83
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-64 3.57e-12

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: 55.73  E-value: 3.57e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMA-TNHELSSRKNEERL 64
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERL 65
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-83 4.15e-11

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 53.39  E-value: 4.15e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524286953  1 MLITSISEFRKDIKEYFDRVTNNFETLIINRGKNSGVVIMSLEEYNSLMATNHELSSRKNEERLDAAIEKLKTQKTFTKE 80
Cdd:PRK11409   1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80


                 ...
gi 2524286953 81 LIE 83
Cdd:PRK11409  81 IIE 83
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 5-55 2.49e-03

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: 32.64  E-value: 2.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 2524286953  5 SISEFRKDIKEYFDRVTNNFETLIINRGKNSgVVIMSLEEYNSLMATNHEL 55
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRDGEPVTITKRGRPV-AVLVSAADYDRLQETLRLL 52
 
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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