NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|501454725|ref|WP_012478170|]
View 

type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family [Helicobacter pylori]

Protein Classification

type II toxin-antitoxin system YafQ family toxin( domain architecture ID 11239005)

type II toxin-antitoxin (TA) system YafQ family toxin similar to Escherichia coli YafQ, which functions as a sequence-specific mRNA endoribonuclease that inhibits translation elongation and induces bacterial stasis, and is the toxin component of the YafQ-DinJ TA module that plays a role in biofilm formation

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YafQ_toxin pfam15738
Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ...
 2-88 2.82e-34

Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, pfam02604.


:

Pssm-ID: 434896  Cd Length: 88  Bit Score: 112.57  E-value: 2.82e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   2 LDIEYHNIFRKDYKKYLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLLRL 81
Cdd:pfam15738  1 YKIKYTKQFKKDYKRAKKRGYDIEKLKEVIDLLAEGEPLPEKYRDHALKGNWKGHRECHIKPDWLLIYRIDDDELILVRT 80


                 ....*..
gi 501454725  82 GSHSELF 88
Cdd:pfam15738 81 GSHSDLF 87
 
Name Accession Description Interval E-value
YafQ_toxin pfam15738
Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ...
 2-88 2.82e-34

Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, pfam02604.


Pssm-ID: 434896  Cd Length: 88  Bit Score: 112.57  E-value: 2.82e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   2 LDIEYHNIFRKDYKKYLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLLRL 81
Cdd:pfam15738  1 YKIKYTKQFKKDYKRAKKRGYDIEKLKEVIDLLAEGEPLPEKYRDHALKGNWKGHRECHIKPDWLLIYRIDDDELILVRT 80


                 ....*..
gi 501454725  82 GSHSELF 88
Cdd:pfam15738 81 GSHSDLF 87
YafQ COG3041
mRNA-degrading endonuclease YafQ (mRNA interferase), toxin component of the YafQ-DinJ ...
 1-88 1.64e-32

mRNA-degrading endonuclease YafQ (mRNA interferase), toxin component of the YafQ-DinJ toxin-antitoxin module [Translation, ribosomal structure and biogenesis, Defense mechanisms];


Pssm-ID: 442275  Cd Length: 88  Bit Score: 107.96  E-value: 1.64e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725  1 MLDIEYHNIFRKDYKKYLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLLR 80
Cdd:COG3041   1 MLKIVYTKQFKKDLKKLKKRGPDIEKLKKVLRLLAEGNPLPPSLRDHALKGNLKGYRECHINPDWRLIYRIEDDVLILVR 80


                ....*...
gi 501454725 81 LGSHSELF 88
Cdd:COG3041  81 IGSHSELF 88
TIGR00053 TIGR00053
addiction module toxin component, YafQ family; This model represents a cluster of eubacterial ...
 1-88 4.76e-25

addiction module toxin component, YafQ family; This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component. [Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 272877  Cd Length: 90  Bit Score: 89.07  E-value: 4.76e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   1 MLDIEYHNIFRKDYKKYLKN-GFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLL 79
Cdd:TIGR00053  1 MLKIEYSKQFDKDLKKLQKRdGKDLKKLKKKMEELINTLPLPEHYKDHPLRGSWKGFRDCHIKPDVILIYKVKDDTLIFV 80


                 ....*....
gi 501454725  80 RLGSHSELF 88
Cdd:TIGR00053 81 RLGHHSELF 89
 
Name Accession Description Interval E-value
YafQ_toxin pfam15738
Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ...
 2-88 2.82e-34

Bacterial toxin of type II toxin-antitoxin system, YafQ; YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, pfam02604.


Pssm-ID: 434896  Cd Length: 88  Bit Score: 112.57  E-value: 2.82e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   2 LDIEYHNIFRKDYKKYLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLLRL 81
Cdd:pfam15738  1 YKIKYTKQFKKDYKRAKKRGYDIEKLKEVIDLLAEGEPLPEKYRDHALKGNWKGHRECHIKPDWLLIYRIDDDELILVRT 80


                 ....*..
gi 501454725  82 GSHSELF 88
Cdd:pfam15738 81 GSHSDLF 87
YafQ COG3041
mRNA-degrading endonuclease YafQ (mRNA interferase), toxin component of the YafQ-DinJ ...
 1-88 1.64e-32

mRNA-degrading endonuclease YafQ (mRNA interferase), toxin component of the YafQ-DinJ toxin-antitoxin module [Translation, ribosomal structure and biogenesis, Defense mechanisms];


Pssm-ID: 442275  Cd Length: 88  Bit Score: 107.96  E-value: 1.64e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725  1 MLDIEYHNIFRKDYKKYLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLLR 80
Cdd:COG3041   1 MLKIVYTKQFKKDLKKLKKRGPDIEKLKKVLRLLAEGNPLPPSLRDHALKGNLKGYRECHINPDWRLIYRIEDDVLILVR 80


                ....*...
gi 501454725 81 LGSHSELF 88
Cdd:COG3041  81 IGSHSELF 88
TIGR00053 TIGR00053
addiction module toxin component, YafQ family; This model represents a cluster of eubacterial ...
 1-88 4.76e-25

addiction module toxin component, YafQ family; This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component. [Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 272877  Cd Length: 90  Bit Score: 89.07  E-value: 4.76e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   1 MLDIEYHNIFRKDYKKYLKN-GFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVYIVKNNTLWLL 79
Cdd:TIGR00053  1 MLKIEYSKQFDKDLKKLQKRdGKDLKKLKKKMEELINTLPLPEHYKDHPLRGSWKGFRDCHIKPDVILIYKVKDDTLIFV 80


                 ....*....
gi 501454725  80 RLGSHSELF 88
Cdd:TIGR00053 81 RLGHHSELF 89
RelE_StbE TIGR02385
addiction module toxin, RelE/StbE family; Plasmids may be maintained stably in bacterial ...
 4-88 9.73e-18

addiction module toxin, RelE/StbE family; Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all are found adjacent to RelB/DinJ family antitoxin genes (TIGR02384), as are most genes found by the resulting model. StbE from Morganella morganii plasmid R485 shows typical behaviour for an addiction module toxin. It cannot be cloned without its partner (the antitoxin), whereas its partner cannot confer plasmid stability without StbE. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 211740  Cd Length: 88  Bit Score: 70.42  E-value: 9.73e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501454725   4 IEYHNIFRKDYKK-YLKNGFDSKLLDEVVLELRQQKPLAQKHKDHILKGEWYPCRECHIRPDVLLVY-IVKNNTLWLLRL 81
Cdd:TIGR02385  2 IVYTEQFKKDLKKiKKYIRKDLPKLLEVIELLINGKPLERRYRDHPLTGSWKGTRECHIEPDYLLVYqVEDEVVIRLVRV 81


                 ....*..
gi 501454725  82 GSHSELF 88
Cdd:TIGR02385 82 GSHSQLF 88
 
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