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Conserved domains on  [gi|849253404|ref|YP_009149999|]
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baseplate protein [Leuconostoc phage Ln-9]

Protein Classification

pyocin knob domain-containing protein( domain architecture ID 15331322)

pyocin knob domain-containing protein similar to Bacillus subtilis protein YqcC and to R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species; R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 33-110 2.33e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


:

Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 50.03  E-value: 2.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 849253404  33 VSISNGTDFNTLKSNGRYFGSGIFPNSPA---PTTSWqWVIDVSKSV-TFISQRAIqlTASTPNVFFRNLVGGTWQAWQK 108
Cdd:cd19958    2 GTLLGTTDLNTLTTPGFYYQSANANATTAlnyPVAGA-GYLEVYRYGgGGVTQIYT--PYNSGRIYVRTRYNGTWSAWKE 78


                 ..
gi 849253404 109 QA 110
Cdd:cd19958   79 IA 80
 
Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 33-110 2.33e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 50.03  E-value: 2.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 849253404  33 VSISNGTDFNTLKSNGRYFGSGIFPNSPA---PTTSWqWVIDVSKSV-TFISQRAIqlTASTPNVFFRNLVGGTWQAWQK 108
Cdd:cd19958    2 GTLLGTTDLNTLTTPGFYYQSANANATTAlnyPVAGA-GYLEVYRYGgGGVTQIYT--PYNSGRIYVRTRYNGTWSAWKE 78


                 ..
gi 849253404 109 QA 110
Cdd:cd19958   79 IA 80
 
Name Accession Description Interval E-value
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 33-110 2.33e-08

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 50.03  E-value: 2.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 849253404  33 VSISNGTDFNTLKSNGRYFGSGIFPNSPA---PTTSWqWVIDVSKSV-TFISQRAIqlTASTPNVFFRNLVGGTWQAWQK 108
Cdd:cd19958    2 GTLLGTTDLNTLTTPGFYYQSANANATTAlnyPVAGA-GYLEVYRYGgGGVTQIYT--PYNSGRIYVRTRYNGTWSAWKE 78


                 ..
gi 849253404 109 QA 110
Cdd:cd19958   79 IA 80
 
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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