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Conserved domains on  [gi|1321811342|gb|PLY16831|]
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MAG: antitoxin, Phd family protein [Sedimenticola sp.]

Protein Classification

type II toxin-antitoxin system Phd/YefM family antitoxin( domain architecture ID 10495655)

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 and neutralizes its ability to phosphorylate host EF-Tu

CATH:  3.40.1620.10
Gene Ontology:  GO:0110001
PubMed:  31932311|33498357
SCOP:  4003460

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 6-70 3.55e-11

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: 53.42  E-value: 3.55e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1321811342  6 QIKPISYLKAHAAEIVRNISSQVEPLVITQNGEAKAVMQDIKSYEQTQE-TMALLKMLALGQRQVE 70
Cdd:pfam02604  2 KIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
 
Name Accession Description Interval E-value
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 6-70 3.55e-11

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: 53.42  E-value: 3.55e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1321811342  6 QIKPISYLKAHAAEIVRNISSQVEPLVITQNGEAKAVMQDIKSYEQTQE-TMALLKMLALGQRQVE 70
Cdd:pfam02604  2 KIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 9-59 1.07e-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: 41.50  E-value: 1.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1321811342  9 PISYLKAHAAEIVRNISSQvEPLVITQNGEAKAVMQDIKSYEQTQETMALL 59
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRDG-EPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 9-76 6.80e-06

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 40.16  E-value: 6.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1321811342  9 PISYLKAHAAEIVRNISSQVEPLVITQNGEAKAVMQDIKSYEQTQETMALLKMLALGQR------QVEDGRVQP 76
Cdd:COG2161    5 SYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERlleslaELEAGEVSL 78
 
Name Accession Description Interval E-value
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 6-70 3.55e-11

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: 53.42  E-value: 3.55e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1321811342  6 QIKPISYLKAHAAEIVRNISSQVEPLVITQNGEAKAVMQDIKSYEQTQE-TMALLKMLALGQRQVE 70
Cdd:pfam02604  2 KIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 9-59 1.07e-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: 41.50  E-value: 1.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1321811342  9 PISYLKAHAAEIVRNISSQvEPLVITQNGEAKAVMQDIKSYEQTQETMALL 59
Cdd:TIGR01552  3 SLSEAKNKLGELLKRVRDG-EPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 9-76 6.80e-06

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


Pssm-ID: 441764  Cd Length: 83  Bit Score: 40.16  E-value: 6.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1321811342  9 PISYLKAHAAEIVRNISSQVEPLVITQNGEAKAVMQDIKSYEQTQETMALLKMLALGQR------QVEDGRVQP 76
Cdd:COG2161    5 SYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERlleslaELEAGEVSL 78
 
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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