Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C562
  Reference Plasmid   NZ_CP031272.1
  Reference Plasmid Size   28583
  Reference Plasmid GC Content   0.29
  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
M0095077 GKCLPBJD_00011 10305 3 Skin 0.12 protein_coding synonymous_variant LOW 462C>T Ser154Ser
M0095078 GKCLPBJD_00014 12506 3 Skin 0.12 protein_coding missense_variant MODERATE 652G>T Asp218Tyr
M0095079 GKCLPBJD_00014 12550 5 Skin 0.20 protein_coding missense_variant MODERATE 608G>A Gly203Glu
M0095080 GKCLPBJD_00015 13305 5 Skin 0.20 protein_coding missense_variant MODERATE 211T>C Tyr71His
M0095081 GKCLPBJD_00016 13564 5 Skin 0.20 protein_coding synonymous_variant LOW 240A>C Thr80Thr
M0095082 GKCLPBJD_00010 13812 5 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -4409A>C None
M0095083 GKCLPBJD_00017 14065 4 Skin 0.16 protein_coding synonymous_variant LOW 597T>C Asn199Asn
M0095084 GKCLPBJD_00002 7260 5 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -4725T>C None
M0095085 GKCLPBJD_00004 7887 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3504A>G None
M0095086 GKCLPBJD_00004 7891 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3508A>C None
M0095087 GKCLPBJD_00004 7903 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3520C>T None
M0095088 GKCLPBJD_00004 7905 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3522C>T None
M0095089 GKCLPBJD_00004 7909 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3526T>A None
M0095090 GKCLPBJD_00004 7913 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3530T>G None
M0095091 GKCLPBJD_00004 7920 3 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3537A>T 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







        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
GKCLPBJD_00024 Cadmium (Cd), Zinc (Zn) 93.7 3.2e-100 1 205 1.0000 1.0000 experiment
GKCLPBJD_00024 Cadmium (Cd), Zinc (Zn) 99.5 1e-102 1 205 1.0000 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
GKCLPBJD_00021 ARO:3008823 97.5 1.43e-191 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation






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
GKCLPBJD_00004 PHI:6191 Lqo 81.5 1.2e-245 1 497 0.9980 1.0000 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases reduced virulence






        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
GKCLPBJD_00024 2.A.77.1.1 93.2 2.7e-98 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family