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Conserved domains on  [gi|469747834|gb|EMQ60332|]
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prevent-host-death family protein [Vibrio cholerae O1 str. NHCC-004A]

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 ...
 9-83 8.44e-14

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


:

Pssm-ID: 441764  Cd Length: 83  Bit Score: 60.19  E-value: 8.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469747834  9 SASISELKKNPTALLNEA--DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDYE---LSQIVDSRRADLAqAVEVNIDDL 83
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAELE-AGEVSLDEL 81
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 9-83 8.44e-14

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 60.19  E-value: 8.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469747834  9 SASISELKKNPTALLNEA--DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDYE---LSQIVDSRRADLAqAVEVNIDDL 83
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAELE-AGEVSLDEL 81
PRK09778 PRK09778
type I toxin-antitoxin system antitoxin YafN;
1-68 4.92e-11

type I toxin-antitoxin system antitoxin YafN;


Pssm-ID: 170091  Cd Length: 97  Bit Score: 53.43  E-value: 4.92e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 469747834  1 MRQVLANCSASISELKKNPTALLNEadgSAIAILNHNKPAAYLVPAETYEYLIDMLDDYELSQIVDSR 68
Cdd:PRK09778  1 MHRILAEKSVNITELRKNPAKYFID---QPVAVLSNNRPAGYLLSASAFEALMDMLAEQEEKKPIKAR 65
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 11-71 1.05e-07

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: 44.17  E-value: 1.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 469747834  11 SISELKKNPTALLNEA--DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDYELSQIVDSRRAD 71
Cdd:pfam02604  5 SISEARNNLSELLDEVedGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 11-59 1.22e-05

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: 38.80  E-value: 1.22e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 469747834  11 SISELKKNPTALLNEA-DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDY 59
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVrDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 9-83 8.44e-14

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 60.19  E-value: 8.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 469747834  9 SASISELKKNPTALLNEA--DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDYE---LSQIVDSRRADLAqAVEVNIDDL 83
Cdd:COG2161   3 TISYSEARKNLASLLDQVveDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSspaNAERLLESLAELE-AGEVSLDEL 81
PRK09778 PRK09778
type I toxin-antitoxin system antitoxin YafN;
1-68 4.92e-11

type I toxin-antitoxin system antitoxin YafN;


Pssm-ID: 170091  Cd Length: 97  Bit Score: 53.43  E-value: 4.92e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 469747834  1 MRQVLANCSASISELKKNPTALLNEadgSAIAILNHNKPAAYLVPAETYEYLIDMLDDYELSQIVDSR 68
Cdd:PRK09778  1 MHRILAEKSVNITELRKNPAKYFID---QPVAVLSNNRPAGYLLSASAFEALMDMLAEQEEKKPIKAR 65
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 11-71 1.05e-07

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: 44.17  E-value: 1.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 469747834  11 SISELKKNPTALLNEA--DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDYELSQIVDSRRAD 71
Cdd:pfam02604  5 SISEARNNLSELLDEVedGGEPVIITRRGKPVAVLLSLEDYERLQELTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 11-59 1.22e-05

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: 38.80  E-value: 1.22e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 469747834  11 SISELKKNPTALLNEA-DGSAIAILNHNKPAAYLVPAETYEYLIDMLDDY 59
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVrDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
Phd COG4118
Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor ...
 1-50 9.00e-05

Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor [Defense mechanisms];


Pssm-ID: 443294 [Multi-domain]  Cd Length: 65  Bit Score: 36.84  E-value: 9.00e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 469747834  1 MRQVlancsaSISELKKNPTALLNEA-DGSAIAILNHNKPAAYLVPAETYE 50
Cdd:COG4118   1 MKTV------TVREAKAHLSELLDRVeAGEEVVITRRGKPVARLVPVEPPR 45
PRK02854 PRK02854
primosomal protein DnaT;
10-46 2.88e-03

primosomal protein DnaT;


Pssm-ID: 179484  Cd Length: 179  Bit Score: 34.40  E-value: 2.88e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 469747834  10 ASISELKKNPTALLNEADGSAIAILNHNKPAAYLV-PA 46
Cdd:PRK02854  11 IGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVtPA 48
 
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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