Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C255
  Reference Plasmid   LR962297.1
  Reference Plasmid Size   66056
  Reference Plasmid GC Content   0.33
  Reference Plasmid Mobility Type   mobilizable





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0149930 DOHEPDCI_00032 37821 6 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3842G>A None






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition
DOHEPDCI_00044 VFG045470 Cytolysin 100 5.9e-32 1 66 1.0 1 Exotoxin cytolysin regulator R2 experiment
DOHEPDCI_00045 VFG045472 Cytolysin 100 1.8e-31 1 68 1.0 1 Exotoxin CylL; cytolysin subunit experiment
DOHEPDCI_00046 VFG045473 Cytolysin 100 8.1e-31 1 63 1.0 1 Exotoxin CylS; cytolysin subunit experiment
DOHEPDCI_00047 VFG045474 Cytolysin 99.4 0 1 993 1.0 1 Exotoxin CylM; cytolysin subunit modifier experiment
DOHEPDCI_00048 VFG002176 Cytolysin 99.9 0 1 714 1.0 1 Exotoxin ABC-type transporter experiment
DOHEPDCI_00049 VFG002177 Cytolysin 99.5 3.1e-232 1 412 1.0 1 Exotoxin cytolysin activator experiment
DOHEPDCI_00050 VFG002178 Cytolysin 96.3 4.5e-173 1 327 1.0 1 Exotoxin cytolysin immunity protein experiment
DOHEPDCI_00044 VFG045470 Cytolysin 100 4.4e-31 1 66 1.0 1 Exotoxin cytolysin regulator R2 prediction
DOHEPDCI_00045 VFG045472 Cytolysin 100 1.3e-30 1 68 1.0 1 Exotoxin CylL; cytolysin subunit prediction
DOHEPDCI_00046 VFG045473 Cytolysin 100 6.1e-30 1 63 1.0 1 Exotoxin CylS; cytolysin subunit prediction
DOHEPDCI_00047 VFG002169 Cytolysin 100 0 1 993 1.0 1 Exotoxin CylM; cytolysin subunit modifier prediction
DOHEPDCI_00048 VFG002176 Cytolysin 99.9 0 1 714 1.0 1 Exotoxin ABC-type transporter prediction
DOHEPDCI_00049 VFG002177 Cytolysin 99.5 2.4e-231 1 412 1.0 1 Exotoxin cytolysin activator prediction
DOHEPDCI_00050 VFG002178 Cytolysin 96.3 3.4e-172 1 327 1.0 1 Exotoxin cytolysin immunity protein prediction







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism
DOHEPDCI_00035 ARO:3000375 98 3.24e-173 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant
DOHEPDCI_00013 PHI:2999 EF0026 98.1 3.3e-91 1 162 1.0000 1.0000 moths nosocomial infection None increased virulence (hypervirulence)






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term
DOHEPDCI_00023 3.A.7.19.1 91.2 2.6e-239 3 447 0.9955 0.7932 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
DOHEPDCI_00045 1.C.60.1.1 100 1e-30 1 68 1.0000 1.0794 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.60 The Two-component <I>Enterococcus faecalis</I> Cytolysin (EFC) Family
DOHEPDCI_00046 1.C.60.1.1 100 4.8e-30 1 63 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.60 The Two-component <I>Enterococcus faecalis</I> Cytolysin (EFC) Family
DOHEPDCI_00048 3.A.1.111.1 99.6 0 1 714 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily