NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2524575980|gb|WJK06760|]
View 

type II toxin-antitoxin system Phd/YefM family antitoxin (plasmid) [Escherichia coli]

Protein Classification

type II toxin-antitoxin system Phd/YefM family antitoxin( domain architecture ID 10008295)

type II toxin-antitoxin (TA) system Phd/YefM family antitoxin similar to Mycobacterium tuberculosis VapB antitoxins, which are the antitoxin components of TA modules; VapB toxins bind to and neutralize the effect of their cognate VapC toxins

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Phd COG4118
Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor ...
 1-63 4.30e-13

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


:

Pssm-ID: 443294 [Multi-domain]  Cd Length: 65  Bit Score: 57.64  E-value: 4.30e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524575980  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKK-AALDAEFASLFDTL 63
Cdd:COG4118    1 MKTVTVREAKAHLSELLDRVEAGEEVVITRRGKPVARLVPVEPPRRPRAlGLLKGRLSDDFDEP 64
 
Name Accession Description Interval E-value
Phd COG4118
Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor ...
 1-63 4.30e-13

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


Pssm-ID: 443294 [Multi-domain]  Cd Length: 65  Bit Score: 57.64  E-value: 4.30e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524575980  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKK-AALDAEFASLFDTL 63
Cdd:COG4118    1 MKTVTVREAKAHLSELLDRVEAGEEVVITRRGKPVARLVPVEPPRRPRAlGLLKGRLSDDFDEP 64
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-55 4.24e-09

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: 47.25  E-value: 4.24e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2524575980  1 MQSINFRTARGNLSEVLNNVEAGEE-VEITRRGREPAVIVSKATFEAYKKAALDAE 55
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEpVIITRRGKPVAVLLSLEDYERLQELTLYLL 56
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 3-54 1.20e-08

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: 45.74  E-value: 1.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2524575980  3 SINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDA 54
Cdd:TIGR01552  1 SVSLSEAKNKLGELLKRVRDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
 
Name Accession Description Interval E-value
Phd COG4118
Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor ...
 1-63 4.30e-13

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


Pssm-ID: 443294 [Multi-domain]  Cd Length: 65  Bit Score: 57.64  E-value: 4.30e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524575980  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKK-AALDAEFASLFDTL 63
Cdd:COG4118    1 MKTVTVREAKAHLSELLDRVEAGEEVVITRRGKPVARLVPVEPPRRPRAlGLLKGRLSDDFDEP 64
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-48 2.42e-09

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 48.25  E-value: 2.42e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 2524575980  1 MQSINFRTARGNLSEVLNNV-EAGEEVEITRRGREPAVIVSKATFEAYK 48
Cdd:COG2161    1 MTTISYSEARKNLASLLDQVvEDHEPVIITRRNGPAAVLISAEDYESLQ 49
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-55 4.24e-09

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: 47.25  E-value: 4.24e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2524575980  1 MQSINFRTARGNLSEVLNNVEAGEE-VEITRRGREPAVIVSKATFEAYKKAALDAE 55
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEpVIITRRGKPVAVLLSLEDYERLQELTLYLL 56
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 3-54 1.20e-08

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: 45.74  E-value: 1.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2524575980  3 SINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDA 54
Cdd:TIGR01552  1 SVSLSEAKNKLGELLKRVRDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH