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Conserved domains on  [gi|1842001649|ref|YP_009789397|]
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holin [Staphylococcus phage St 134]

Protein Classification

holin family protein( domain architecture ID 10008858)

holin family protein similar to Bacillus subtilis uncharacterized proteins YqxH and YtkC; holin is a lytic phage enzyme necessary for bacterial lysis and release of the virus

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4824 COG4824
Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];
43-159 8.33e-37

Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];


:

Pssm-ID: 443852  Cd Length: 135  Bit Score: 123.79  E-value: 8.33e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  43 AFHTFIYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLLMVTIFF 122
Cdd:COG4824    15 GVLGYLLGGWDGLLYALVILMVIDYITGVLAAIKEKKLSSKKGFKGIAKKVLIFLLVAVAHLLDQVLGTGGFIRTAVIFF 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1842001649 123 YIANEGLSIVENCAEMGVLIPEEIGEKLKVIRSRDNK 159
Cdd:COG4824    95 YIANEGISILENAGRLGLPIPEKLKKALEQLKDKKDE 131
 
Name Accession Description Interval E-value
COG4824 COG4824
Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];
43-159 8.33e-37

Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];


Pssm-ID: 443852  Cd Length: 135  Bit Score: 123.79  E-value: 8.33e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  43 AFHTFIYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLLMVTIFF 122
Cdd:COG4824    15 GVLGYLLGGWDGLLYALVILMVIDYITGVLAAIKEKKLSSKKGFKGIAKKVLIFLLVAVAHLLDQVLGTGGFIRTAVIFF 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1842001649 123 YIANEGLSIVENCAEMGVLIPEEIGEKLKVIRSRDNK 159
Cdd:COG4824    95 YIANEGISILENAGRLGLPIPEKLKKALEQLKDKKDE 131
Phage_holin_4_1 pfam05105
Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial ...
 48-154 1.58e-33

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: 114.51  E-value: 1.58e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  48 IYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLL-MVTIFFYIAN 126
Cdd:pfam05105   1 LFGGWDYLLYALLLLMVIDYITGLLAAIKEGKLSSKKGFKGIAKKVGILLLVLVAHLLDVLLGTNGGYIrTAVIIFYIAN 80

                          90       100
                  ....*....|....*....|....*...
gi 1842001649 127 EGLSIVENCAEMGVLIPEEIGEKLKVIR 154
Cdd:pfam05105  81 EGISILENAGLMGVPVPEKLKKALEQLK 108
holin_tox_secr TIGR01593
toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar ...
 42-158 1.37e-19

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: 79.27  E-value: 1.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  42 DAFHTFIYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLLMVTIF 121
Cdd:TIGR01593   5 GSVMGTEFGKVDYSLTLLLVLIIIDFITGVLKAWKNKKLSSKKGIKGLVKKLATLILVILAHPFDVLLPTNGFMLLLVIY 84

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1842001649 122 -FYIANEGLSIVENCAEMGVLIPEEIGEKLKVIRSRDN 158
Cdd:TIGR01593  85 nFYILNESLSILENLALLGVKVPEMLVDILETLKNKTK 122
 
Name Accession Description Interval E-value
COG4824 COG4824
Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];
43-159 8.33e-37

Phage-related holin (Lysis protein) [Mobilome: prophages, transposons];


Pssm-ID: 443852  Cd Length: 135  Bit Score: 123.79  E-value: 8.33e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  43 AFHTFIYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLLMVTIFF 122
Cdd:COG4824    15 GVLGYLLGGWDGLLYALVILMVIDYITGVLAAIKEKKLSSKKGFKGIAKKVLIFLLVAVAHLLDQVLGTGGFIRTAVIFF 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1842001649 123 YIANEGLSIVENCAEMGVLIPEEIGEKLKVIRSRDNK 159
Cdd:COG4824    95 YIANEGISILENAGRLGLPIPEKLKKALEQLKDKKDE 131
Phage_holin_4_1 pfam05105
Bacteriophage holin family; Phage holins and lytic enzymes are both necessary for bacterial ...
 48-154 1.58e-33

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: 114.51  E-value: 1.58e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  48 IYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLL-MVTIFFYIAN 126
Cdd:pfam05105   1 LFGGWDYLLYALLLLMVIDYITGLLAAIKEGKLSSKKGFKGIAKKVGILLLVLVAHLLDVLLGTNGGYIrTAVIIFYIAN 80

                          90       100
                  ....*....|....*....|....*...
gi 1842001649 127 EGLSIVENCAEMGVLIPEEIGEKLKVIR 154
Cdd:pfam05105  81 EGISILENAGLMGVPVPEKLKKALEQLK 108
holin_tox_secr TIGR01593
toxin secretion/phage lysis holin; This model describes one of the many mutally dissimilar ...
 42-158 1.37e-19

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: 79.27  E-value: 1.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842001649  42 DAFHTFIYAGDIKLLYFLMVLMLIDIITGLAKAFKNKNLWSRKSMYGFGRKILIFCIIILANIIDQILNLNNGLLMVTIF 121
Cdd:TIGR01593   5 GSVMGTEFGKVDYSLTLLLVLIIIDFITGVLKAWKNKKLSSKKGIKGLVKKLATLILVILAHPFDVLLPTNGFMLLLVIY 84

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1842001649 122 -FYIANEGLSIVENCAEMGVLIPEEIGEKLKVIRSRDN 158
Cdd:TIGR01593  85 nFYILNESLSILENLALLGVKVPEMLVDILETLKNKTK 122
 
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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