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Conserved domains on  [gi|502189552|ref|WP_012728771|]
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type II toxin-antitoxin system Phd/YefM family antitoxin [Tolumonas auensis]

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 ...
 10-83 2.11e-13

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


:

Pssm-ID: 441764  Cd Length: 83  Bit Score: 59.03  E-value: 2.11e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 502189552 10 AASITELKKNPMGTAMEG--EGQPVAILNRNEPAFYIVPPALFGYFQE---LAEDAELNRIADERMNNPEFIEISIDDL 83
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 ...
 10-83 2.11e-13

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 59.03  E-value: 2.11e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 502189552 10 AASITELKKNPMGTAMEG--EGQPVAILNRNEPAFYIVPPALFGYFQE---LAEDAELNRIADERMNNPEFIEISIDDL 83
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQEtlyLLSSPANAERLLESLAELEAGEVSLDEL 81
PRK02854 PRK02854
primosomal protein DnaT;
1-79 3.22e-06

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 42.49  E-value: 3.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 502189552   1 MAYQILTSVAASITELKKNPMGTAMEGEGQPVAILNRNEPAFYIVPPALFGyfQELAEDAELNRIADERMNNPEFIEIS 79
Cdd:PRK02854   1 MSSRILTSDVIGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLA--ELLALEEKLARPGSDVALDDQLYQEP 77
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 12-69 3.25e-03

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: 32.61  E-value: 3.25e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502189552  12 SITELKKNP--MGTAMEGEGQPVAILNRNEPAFYIVPPALFGYFQELAEDAELNRIADER 69
Cdd:pfam02604  5 SISEARNNLseLLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAER 64
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 12-60 7.92e-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: 31.49  E-value: 7.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502189552  12 SITELKKNP---MGTAMEGEgqPVAILNRNEPAFYIVPPALFGYFQELAEDA 60
Cdd:TIGR01552  3 SLSEAKNKLgelLKRVRDGE--PVTITKRGRPVAVLVSAADYDRLQETLRLL 52
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 10-83 2.11e-13

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 59.03  E-value: 2.11e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 502189552 10 AASITELKKNPMGTAMEG--EGQPVAILNRNEPAFYIVPPALFGYFQE---LAEDAELNRIADERMNNPEFIEISIDDL 83
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQEtlyLLSSPANAERLLESLAELEAGEVSLDEL 81
PRK02854 PRK02854
primosomal protein DnaT;
1-79 3.22e-06

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 42.49  E-value: 3.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 502189552   1 MAYQILTSVAASITELKKNPMGTAMEGEGQPVAILNRNEPAFYIVPPALFGyfQELAEDAELNRIADERMNNPEFIEIS 79
Cdd:PRK02854   1 MSSRILTSDVIGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLA--ELLALEEKLARPGSDVALDDQLYQEP 77
PRK09778 PRK09778
type I toxin-antitoxin system antitoxin YafN;
3-64 2.60e-05

type I toxin-antitoxin system antitoxin YafN;


Pssm-ID: 170091  Cd Length: 97  Bit Score: 38.80  E-value: 2.60e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502189552  3 YQILTSVAASITELKKNPmgtAMEGEGQPVAILNRNEPAFYIVPPALFGYFQELAEDAELNR 64
Cdd:PRK09778  2 HRILAEKSVNITELRKNP---AKYFIDQPVAVLSNNRPAGYLLSASAFEALMDMLAEQEEKK 60
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 12-69 3.25e-03

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: 32.61  E-value: 3.25e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502189552  12 SITELKKNP--MGTAMEGEGQPVAILNRNEPAFYIVPPALFGYFQELAEDAELNRIADER 69
Cdd:pfam02604  5 SISEARNNLseLLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAER 64
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 12-60 7.92e-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: 31.49  E-value: 7.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502189552  12 SITELKKNP---MGTAMEGEgqPVAILNRNEPAFYIVPPALFGYFQELAEDA 60
Cdd:TIGR01552  3 SLSEAKNKLgelLKRVRDGE--PVTITKRGRPVAVLVSAADYDRLQETLRLL 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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