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Conserved domains on  [gi|45686334|ref|YP_003919|]
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tail fiber protein [Escherichia phage T1]

Protein Classification

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 ...
 359-461 6.42e-12

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: 61.58  E-value: 6.42e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334 359 RTNLGEKHLDSITGegdgPGIYMQSSSALATASRGYPEATAGMLEVLPNGANGasaCIQRFTPFTYlgtapesgnsqney 438
Cdd:cd19958   2 GTLLGTTDLNTLTT----PGFYYQSANANATTALNYPVAGAGYLEVYRYGGGG---VTQIYTPYNS-------------- 60

                        90       100
                ....*....|....*....|...
gi 45686334 439 aragrGTFYIRMKNGNNakFSPW 461
Cdd:cd19958  61 -----GRIYVRTRYNGT--WSAW 76
PHA00430 super family cl28018
tail fiber protein
 143-277 5.67e-03

tail fiber protein


The actual alignment was detected with superfamily member PHA00430:

Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 39.87  E-value: 5.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334  143 ARDSANSARDESISIKNQTQQISDSAigSINAAKDKAITNVQQKENSAVTHINSEEAAAIQAINDAKGDLSGYVNDAQTA 222
Cdd:PHA00430 164 ARNEANRSRNEADRARNQAERFNNES--GASATNTKQWRSEADGSNSEANRFKGYADSMTSSVEAAKGQAESSSKEANTA 241

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 45686334  223 AQTATSAKNDAQAARDAAVSAKDAAAVSAQEAQDAANSVN-ADNLLTKDGNLSGLA 277
Cdd:PHA00430 242 GDYATKAAASASAAHASEVNAANSATAAATSANRAKQQADrAKTEADKLGNMNGFA 297
 
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 ...
 359-461 6.42e-12

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: 61.58  E-value: 6.42e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334 359 RTNLGEKHLDSITGegdgPGIYMQSSSALATASRGYPEATAGMLEVLPNGANGasaCIQRFTPFTYlgtapesgnsqney 438
Cdd:cd19958   2 GTLLGTTDLNTLTT----PGFYYQSANANATTALNYPVAGAGYLEVYRYGGGG---VTQIYTPYNS-------------- 60

                        90       100
                ....*....|....*....|...
gi 45686334 439 aragrGTFYIRMKNGNNakFSPW 461
Cdd:cd19958  61 -----GRIYVRTRYNGT--WSAW 76
PHA00430 PHA00430
tail fiber protein
 143-277 5.67e-03

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 39.87  E-value: 5.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334  143 ARDSANSARDESISIKNQTQQISDSAigSINAAKDKAITNVQQKENSAVTHINSEEAAAIQAINDAKGDLSGYVNDAQTA 222
Cdd:PHA00430 164 ARNEANRSRNEADRARNQAERFNNES--GASATNTKQWRSEADGSNSEANRFKGYADSMTSSVEAAKGQAESSSKEANTA 241

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 45686334  223 AQTATSAKNDAQAARDAAVSAKDAAAVSAQEAQDAANSVN-ADNLLTKDGNLSGLA 277
Cdd:PHA00430 242 GDYATKAAASASAAHASEVNAANSATAAATSANRAKQQADrAKTEADKLGNMNGFA 297
 
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 ...
 359-461 6.42e-12

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: 61.58  E-value: 6.42e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334 359 RTNLGEKHLDSITGegdgPGIYMQSSSALATASRGYPEATAGMLEVLPNGANGasaCIQRFTPFTYlgtapesgnsqney 438
Cdd:cd19958   2 GTLLGTTDLNTLTT----PGFYYQSANANATTALNYPVAGAGYLEVYRYGGGG---VTQIYTPYNS-------------- 60

                        90       100
                ....*....|....*....|...
gi 45686334 439 aragrGTFYIRMKNGNNakFSPW 461
Cdd:cd19958  61 -----GRIYVRTRYNGT--WSAW 76
PHA00430 PHA00430
tail fiber protein
 143-277 5.67e-03

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 39.87  E-value: 5.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45686334  143 ARDSANSARDESISIKNQTQQISDSAigSINAAKDKAITNVQQKENSAVTHINSEEAAAIQAINDAKGDLSGYVNDAQTA 222
Cdd:PHA00430 164 ARNEANRSRNEADRARNQAERFNNES--GASATNTKQWRSEADGSNSEANRFKGYADSMTSSVEAAKGQAESSSKEANTA 241

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 45686334  223 AQTATSAKNDAQAARDAAVSAKDAAAVSAQEAQDAANSVN-ADNLLTKDGNLSGLA 277
Cdd:PHA00430 242 GDYATKAAASASAAHASEVNAANSATAAATSANRAKQQADrAKTEADKLGNMNGFA 297
 
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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