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Conserved domains on  [gi|472437244|ref|YP_007676655|]
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holin [Leuconostoc phage LN04]

Protein Classification

phage holin family protein( domain architecture ID 5166)

phage holin family protein may function in the transport of murein hydrolases (endolysins) across the cytoplasmic membrane to the cell wall where these enzymes hydrolyze the cell wall polymer as a prelude to cell lysis; similar to Beecentumtrevirus antiholin

Gene Ontology:  GO:0016020|GO:0005886
PubMed:  7669346

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Phage_holin_4_1 super family cl01989
Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial ...
 17-116 1.93e-08

Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile. The 1.E.10 family is represented by Bacillus subtilis phi29 holin. 1.E.16 represents the Cph1 holin; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis.


The actual alignment was detected with superfamily member pfam05105:

Pssm-ID: 470425  Cd Length: 109  Bit Score: 48.64  E-value: 1.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472437244   17 IFVAIIYASFIDLFLGIIKAVVSKSLNSTISAYGLLKHCLLILIppLTVPIFFALGYGDYWSVFETLVLF----TQALSL 92
Cdd:pfam05105   8 LLYALLLLMVIDYITGLLAAIKEGKLSSKKGFKGIAKKVGILLL--VLVAHLLDVLLGTNGGYIRTAVIIfyiaNEGISI 85

                          90       100
                  ....*....|....*....|....
gi 472437244   93 AENWIALGLPFPEAIAKYLDNEKK 116
Cdd:pfam05105  86 LENAGLMGVPVPEKLKKALEQLKN 109
 
Name Accession Description Interval E-value
Phage_holin_4_1 pfam05105
Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial ...
 17-116 1.93e-08

Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile. The 1.E.10 family is represented by Bacillus subtilis phi29 holin. 1.E.16 represents the Cph1 holin; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis.


Pssm-ID: 428306  Cd Length: 109  Bit Score: 48.64  E-value: 1.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472437244   17 IFVAIIYASFIDLFLGIIKAVVSKSLNSTISAYGLLKHCLLILIppLTVPIFFALGYGDYWSVFETLVLF----TQALSL 92
Cdd:pfam05105   8 LLYALLLLMVIDYITGLLAAIKEGKLSSKKGFKGIAKKVGILLL--VLVAHLLDVLLGTNGGYIRTAVIIfyiaNEGISI 85

                          90       100
                  ....*....|....*....|....
gi 472437244   93 AENWIALGLPFPEAIAKYLDNEKK 116
Cdd:pfam05105  86 LENAGLMGVPVPEKLKKALEQLKN 109
holin_tox_secr TIGR01593
toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar ...
 18-117 1.97e-03

toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species. [Protein fate, Protein and peptide secretion and trafficking, Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273708  Cd Length: 128  Bit Score: 35.75  E-value: 1.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472437244   18 FVAIIYASFIDLFLGIIKAVVSKSLNSTISAYGLLKHCLLILIPPLTVPI--FFALGYGDYWSVFETLVLFTQALSLAEN 95
Cdd:TIGR01593  19 LTLLLVLIIIDFITGVLKAWKNKKLSSKKGIKGLVKKLATLILVILAHPFdvLLPTNGFMLLLVIYNFYILNESLSILEN 98

                          90       100
                  ....*....|....*....|..
gi 472437244   96 WIALGLPFPEAIAKYLDNEKKE 117
Cdd:TIGR01593  99 LALLGVKVPEMLVDILETLKNK 120
 
Name Accession Description Interval E-value
Phage_holin_4_1 pfam05105
Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial ...
 17-116 1.93e-08

Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile. The 1.E.10 family is represented by Bacillus subtilis phi29 holin. 1.E.16 represents the Cph1 holin; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis.


Pssm-ID: 428306  Cd Length: 109  Bit Score: 48.64  E-value: 1.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472437244   17 IFVAIIYASFIDLFLGIIKAVVSKSLNSTISAYGLLKHCLLILIppLTVPIFFALGYGDYWSVFETLVLF----TQALSL 92
Cdd:pfam05105   8 LLYALLLLMVIDYITGLLAAIKEGKLSSKKGFKGIAKKVGILLL--VLVAHLLDVLLGTNGGYIRTAVIIfyiaNEGISI 85

                          90       100
                  ....*....|....*....|....
gi 472437244   93 AENWIALGLPFPEAIAKYLDNEKK 116
Cdd:pfam05105  86 LENAGLMGVPVPEKLKKALEQLKN 109
holin_tox_secr TIGR01593
toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar ...
 18-117 1.97e-03

toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species. [Protein fate, Protein and peptide secretion and trafficking, Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273708  Cd Length: 128  Bit Score: 35.75  E-value: 1.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472437244   18 FVAIIYASFIDLFLGIIKAVVSKSLNSTISAYGLLKHCLLILIPPLTVPI--FFALGYGDYWSVFETLVLFTQALSLAEN 95
Cdd:TIGR01593  19 LTLLLVLIIIDFITGVLKAWKNKKLSSKKGIKGLVKKLATLILVILAHPFdvLLPTNGFMLLLVIYNFYILNESLSILEN 98

                          90       100
                  ....*....|....*....|..
gi 472437244   96 WIALGLPFPEAIAKYLDNEKKE 117
Cdd:TIGR01593  99 LALLGVKVPEMLVDILETLKNK 120
 
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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