Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C461
  Reference Plasmid   NZ_CP018385.1
  Reference Plasmid Size   297875
  Reference Plasmid GC Content   0.61
  Reference Plasmid Mobility Type   non-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
M0088720 GDPNPEJD_00275 230580 3 Skin 0.20 protein_coding synonymous_variant LOW 1026G>A Gln342Gln
M0088721 GDPNPEJD_00275 230769 3 Skin 0.20 protein_coding synonymous_variant LOW 1215T>G Ala405Ala
M0088722 GDPNPEJD_00275 230812 3 Skin 0.20 protein_coding missense_variant MODERATE 1258G>A Gly420Ser






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







        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
GDPNPEJD_00289 Arsenic (As) 73.7 0 1 824 0.9988 0.9976 experiment
GDPNPEJD_00330 Chromium (Cr) 77 5.3e-168 9 391 0.9696 0.9551 experiment
GDPNPEJD_00332 Chromium (Cr) 76.8 6.3e-85 4 193 0.9694 0.9645 experiment
GDPNPEJD_00335 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 78 1.2e-72 1 150 0.9934 1.0000 experiment
GDPNPEJD_00252 Cadmium (Cd), Zinc (Zn) 78 6.1e-196 5 464 0.9725 0.9871 prediction
GDPNPEJD_00256 Cadmium (Cd), Zinc (Zn), Cobalt (Co) 84.6 5.1e-233 1 501 1.0000 1.0503 prediction
GDPNPEJD_00257 Copper (Cu) 71.2 2e-193 3 430 1.0000 0.9131 prediction
GDPNPEJD_00280 Copper (Cu) 84.4 0 59 818 0.9315 0.9974 prediction
GDPNPEJD_00286 Arsenic (As) 99.7 3.8e-214 3 360 0.9944 1.0000 prediction
GDPNPEJD_00289 Arsenic (As) 100 0 1 825 1.0000 1.0000 prediction
GDPNPEJD_00290 Arsenic (As) 100 3e-95 1 177 1.0000 1.0000 prediction
GDPNPEJD_00329 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 84.6 9.4e-156 1 325 1.0000 1.0000 prediction
GDPNPEJD_00330 Chromium (Cr) 78 4.1e-169 10 391 0.9671 0.9526 prediction
GDPNPEJD_00332 Chromium (Cr) 100 9.9e-108 5 196 0.9796 1.0000 prediction
GDPNPEJD_00335 Chromium (Cr) 82 4.6e-73 1 150 0.9934 1.0000 prediction






        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






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






        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
GDPNPEJD_00289 5.A.3.6.1 78.4 0 6 824 0.9927 0.9939 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
GDPNPEJD_00321 2.A.113.1.3 80.8 9.1e-169 1 375 0.9973 0.9920 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.113 The Nickel/cobalt Transporter (NicO) Family
GDPNPEJD_00330 2.A.51.1.1 77 2e-166 9 391 0.9696 0.9551 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family