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Conserved domains on  [gi|2258828839|gb|USN53040|]
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MAG: phage holin family protein [Candidatus Nomurabacteria bacterium]

Protein Classification

phage holin family protein( domain architecture ID 10004993)

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 Bacillus subtilis membrane protein YvlD

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
1-115 2.20e-29

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


:

Pssm-ID: 441553  Cd Length: 116  Bit Score: 102.09  E-value: 2.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258828839   1 MKFILRLLLNAVAILLVAKLVSGIVVSGYSTAILAALVLGIINALIRPLMHLLALPITIITFGLFALVINGLMFGLAAGL 80
Cdd:COG1950     2 MRFLIRWLVNALALLIAAYLLPGIEVDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALMLWLAAWL 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2258828839  81 VPGFSVLGFWPAFWGAIVYSVLSYVINGLLMPTRD 115
Cdd:COG1950    82 VPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
 
Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
1-115 2.20e-29

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


Pssm-ID: 441553  Cd Length: 116  Bit Score: 102.09  E-value: 2.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258828839   1 MKFILRLLLNAVAILLVAKLVSGIVVSGYSTAILAALVLGIINALIRPLMHLLALPITIITFGLFALVINGLMFGLAAGL 80
Cdd:COG1950     2 MRFLIRWLVNALALLIAAYLLPGIEVDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALMLWLAAWL 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2258828839  81 VPGFSVLGFWPAFWGAIVYSVLSYVINGLLMPTRD 115
Cdd:COG1950    82 VPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
Phage_holin_4_2 pfam04020
Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane ...
 1-105 4.22e-24

Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organizms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases.


Pssm-ID: 461132 [Multi-domain]  Cd Length: 105  Bit Score: 88.20  E-value: 4.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258828839   1 MKFILRLLLNAVAILLVAKLVSGIVVSGYSTAILAALVLGIINALIRPLMHLLALPITIITFGLFALVINGLMFGLAAGL 80
Cdd:pfam04020   1 MRFLIRWLVNALALLVVAYLLPGIEVDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALMLLLASWL 80

                          90       100
                  ....*....|....*....|....*
gi 2258828839  81 VPGFSVLGFWPAFWGAIVYSVLSYV 105
Cdd:pfam04020  81 VPGFSVDGFWAALLGALVLSIVSSL 105
 
Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
1-115 2.20e-29

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


Pssm-ID: 441553  Cd Length: 116  Bit Score: 102.09  E-value: 2.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258828839   1 MKFILRLLLNAVAILLVAKLVSGIVVSGYSTAILAALVLGIINALIRPLMHLLALPITIITFGLFALVINGLMFGLAAGL 80
Cdd:COG1950     2 MRFLIRWLVNALALLIAAYLLPGIEVDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALMLWLAAWL 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2258828839  81 VPGFSVLGFWPAFWGAIVYSVLSYVINGLLMPTRD 115
Cdd:COG1950    82 VPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
Phage_holin_4_2 pfam04020
Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane ...
 1-105 4.22e-24

Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organizms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases.


Pssm-ID: 461132 [Multi-domain]  Cd Length: 105  Bit Score: 88.20  E-value: 4.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258828839   1 MKFILRLLLNAVAILLVAKLVSGIVVSGYSTAILAALVLGIINALIRPLMHLLALPITIITFGLFALVINGLMFGLAAGL 80
Cdd:pfam04020   1 MRFLIRWLVNALALLVVAYLLPGIEVDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALMLLLASWL 80

                          90       100
                  ....*....|....*....|....*
gi 2258828839  81 VPGFSVLGFWPAFWGAIVYSVLSYV 105
Cdd:pfam04020  81 VPGFSVDGFWAALLGALVLSIVSSL 105
 
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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