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Conserved domains on  [gi|939535550|ref|YP_009130750|]
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holin [Staphylococcus phage StB12]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Holin_SPP1 super family cl23882
SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group ...
 1-63 1.55e-21

SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes.


The actual alignment was detected with superfamily member TIGR01592:

Pssm-ID: 420075  Cd Length: 75  Bit Score: 80.21  E-value: 1.55e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939535550   1 MEVKVIARYIVLIMAIVNQFLANRGLSPIPVDEETISTIVLA----GIGLYTAWKDNPTSKEGQWAN 63
Cdd:TIGR01592  1 MDAGTIVRTILLIIALVNQFLAMKGISPIPVDEEGISTVVDAvftiGVSLWTWWKNNYITRKGKKQK 67
 
Name Accession Description Interval E-value
holin_SPP1 TIGR01592
holin, SPP1 family; This model represents one of more than 30 families of phage proteins, all ...
 1-63 1.55e-21

holin, SPP1 family; This model represents one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 130653  Cd Length: 75  Bit Score: 80.21  E-value: 1.55e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939535550   1 MEVKVIARYIVLIMAIVNQFLANRGLSPIPVDEETISTIVLA----GIGLYTAWKDNPTSKEGQWAN 63
Cdd:TIGR01592  1 MDAGTIVRTILLIIALVNQFLAMKGISPIPVDEEGISTVVDAvftiGVSLWTWWKNNYITRKGKKQK 67
Holin_SPP1 pfam04688
SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group ...
 6-60 7.31e-10

SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes.


Pssm-ID: 398388  Cd Length: 74  Bit Score: 50.40  E-value: 7.31e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 939535550   6 IARYIVLIMAIVNQFLANRGLSPIPVDEET----ISTIVLAGIGLYTAWKDNPTSKEGQ 60
Cdd:pfam04688  7 LVRTILLLLALLNQLLTMFGKNPLPIDEEQlytaITTVFTVGAALYAWWKNNYVTKKAK 65
 
Name Accession Description Interval E-value
holin_SPP1 TIGR01592
holin, SPP1 family; This model represents one of more than 30 families of phage proteins, all ...
 1-63 1.55e-21

holin, SPP1 family; This model represents one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 130653  Cd Length: 75  Bit Score: 80.21  E-value: 1.55e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939535550   1 MEVKVIARYIVLIMAIVNQFLANRGLSPIPVDEETISTIVLA----GIGLYTAWKDNPTSKEGQWAN 63
Cdd:TIGR01592  1 MDAGTIVRTILLIIALVNQFLAMKGISPIPVDEEGISTVVDAvftiGVSLWTWWKNNYITRKGKKQK 67
Holin_SPP1 pfam04688
SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group ...
 6-60 7.31e-10

SPP1 phage holin; This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes.


Pssm-ID: 398388  Cd Length: 74  Bit Score: 50.40  E-value: 7.31e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 939535550   6 IARYIVLIMAIVNQFLANRGLSPIPVDEET----ISTIVLAGIGLYTAWKDNPTSKEGQ 60
Cdd:pfam04688  7 LVRTILLLLALLNQLLTMFGKNPLPIDEEQlytaITTVFTVGAALYAWWKNNYVTKKAK 65
 
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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