NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446510099|ref|WP_000587617|]
View 

MULTISPECIES: type II toxin-antitoxin system Phd/YefM family antitoxin [Staphylococcus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 1-81 1.29e-20

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


:

Pssm-ID: 441764  Cd Length: 83  Bit Score: 77.52  E-value: 1.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446510099  1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQETIY-LESTGTMDKVREREKDS-SGTTNID 78
Cdd:COG2161   1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGP-AAVLISAEDYESLQETLYlLSSPANAERLLESLAELeAGEVSLD 79


                ...
gi 446510099 79 DID 81
Cdd:COG2161  80 ELI 82
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-81 1.29e-20

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 77.52  E-value: 1.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446510099  1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQETIY-LESTGTMDKVREREKDS-SGTTNID 78
Cdd:COG2161   1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGP-AAVLISAEDYESLQETLYlLSSPANAERLLESLAELeAGEVSLD 79


                ...
gi 446510099 79 DID 81
Cdd:COG2161  80 ELI 82
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-67 1.80e-14

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: 61.50  E-value: 1.80e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446510099   1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQE-TIYLESTGTMDKVRER 67
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKP-VAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 7-55 1.22e-06

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: 41.12  E-value: 1.22e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446510099   7 TEARKDFYQLLKNVNNNhEPIYISgNNAENNAVIIGLEDWKSIQETIYL 55
Cdd:TIGR01552  5 SEAKNKLGELLKRVRDG-EPVTIT-KRGRPVAVLVSAADYDRLQETLRL 51
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-55 4.42e-04

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 35.67  E-value: 4.42e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 446510099  1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQETIYL 55
Cdd:PRK11409  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGE-ACVLMSLEEYNSLEETAYL 54
 
Name Accession Description Interval E-value
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-81 1.29e-20

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 77.52  E-value: 1.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446510099  1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQETIY-LESTGTMDKVREREKDS-SGTTNID 78
Cdd:COG2161   1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGP-AAVLISAEDYESLQETLYlLSSPANAERLLESLAELeAGEVSLD 79


                ...
gi 446510099 79 DID 81
Cdd:COG2161  80 ELI 82
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-67 1.80e-14

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: 61.50  E-value: 1.80e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446510099   1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQE-TIYLESTGTMDKVRER 67
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKP-VAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 7-55 1.22e-06

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: 41.12  E-value: 1.22e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446510099   7 TEARKDFYQLLKNVNNNhEPIYISgNNAENNAVIIGLEDWKSIQETIYL 55
Cdd:TIGR01552  5 SEAKNKLGELLKRVRDG-EPVTIT-KRGRPVAVLVSAADYDRLQETLRL 51
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-55 4.42e-04

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 35.67  E-value: 4.42e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 446510099  1 MIITSPTEARKDFYQLLKNVNNNHEPIYISGNNAEnNAVIIGLEDWKSIQETIYL 55
Cdd:PRK11409  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGE-ACVLMSLEEYNSLEETAYL 54
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH