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Conserved domains on  [gi|1168748013|ref|WP_080319997|]
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3TM-type holin [Croceivirga radicis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GTA_holin_3TM super family cl12888
Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In ...
 21-109 3.64e-12

Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In Rhodobacter capsulatus the protein is expressed just overlapping and downstream of a putative N-acetylmuramidase lysozyme (an endolysin) thought to be responsible for lysing a phage particle, RcGTA - a gene-transfer agent. A holin would be necessary for such an endolysin to access the peptidoglycan. Gene-transfer agents are bacteriophage-like genetic elements with the sole known function of horizontal gene transfer, serving an important role in microbial evolution. In order to be released from the cell these require the combined action of an endolysin and this holin.


The actual alignment was detected with superfamily member pfam11351:

Pssm-ID: 402795  Cd Length: 123  Bit Score: 58.66  E-value: 3.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168748013  21 QAFRIELIKELQKMDVAQIELNKVEASHKNIFVSGWRPFIGWVCGSALAYHFIFRDLAQWGLnALGLQLNPLPvielgqL 100
Cdd:pfam11351  35 QYGAAGWFDRELALLEAQMEIMKAEAASADGLNRRPRPAIGYVTLALFAWAFMLDPEGFAAR-ALGLALVPEP------L 107


                  ....*....
gi 1168748013 101 ISILLAMLG 109
Cdd:pfam11351 108 WWLLGGVVG 116
 
Name Accession Description Interval E-value
GTA_holin_3TM pfam11351
Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In ...
 21-109 3.64e-12

Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In Rhodobacter capsulatus the protein is expressed just overlapping and downstream of a putative N-acetylmuramidase lysozyme (an endolysin) thought to be responsible for lysing a phage particle, RcGTA - a gene-transfer agent. A holin would be necessary for such an endolysin to access the peptidoglycan. Gene-transfer agents are bacteriophage-like genetic elements with the sole known function of horizontal gene transfer, serving an important role in microbial evolution. In order to be released from the cell these require the combined action of an endolysin and this holin.


Pssm-ID: 402795  Cd Length: 123  Bit Score: 58.66  E-value: 3.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168748013  21 QAFRIELIKELQKMDVAQIELNKVEASHKNIFVSGWRPFIGWVCGSALAYHFIFRDLAQWGLnALGLQLNPLPvielgqL 100
Cdd:pfam11351  35 QYGAAGWFDRELALLEAQMEIMKAEAASADGLNRRPRPAIGYVTLALFAWAFMLDPEGFAAR-ALGLALVPEP------L 107


                  ....*....
gi 1168748013 101 ISILLAMLG 109
Cdd:pfam11351 108 WWLLGGVVG 116
 
Name Accession Description Interval E-value
GTA_holin_3TM pfam11351
Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In ...
 21-109 3.64e-12

Holin of 3TMs, for gene-transfer release; This is a family of bacterial 3TM holins. In Rhodobacter capsulatus the protein is expressed just overlapping and downstream of a putative N-acetylmuramidase lysozyme (an endolysin) thought to be responsible for lysing a phage particle, RcGTA - a gene-transfer agent. A holin would be necessary for such an endolysin to access the peptidoglycan. Gene-transfer agents are bacteriophage-like genetic elements with the sole known function of horizontal gene transfer, serving an important role in microbial evolution. In order to be released from the cell these require the combined action of an endolysin and this holin.


Pssm-ID: 402795  Cd Length: 123  Bit Score: 58.66  E-value: 3.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168748013  21 QAFRIELIKELQKMDVAQIELNKVEASHKNIFVSGWRPFIGWVCGSALAYHFIFRDLAQWGLnALGLQLNPLPvielgqL 100
Cdd:pfam11351  35 QYGAAGWFDRELALLEAQMEIMKAEAASADGLNRRPRPAIGYVTLALFAWAFMLDPEGFAAR-ALGLALVPEP------L 107


                  ....*....
gi 1168748013 101 ISILLAMLG 109
Cdd:pfam11351 108 WWLLGGVVG 116
 
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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