Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2600
  Reference Plasmid   1111525849857134_bin.10__k141_178378
  Reference Plasmid Size   31734
  Reference Plasmid GC Content   0.64
  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
M0048750 JBFFEALM_00001 539 3 Skin 0.16 protein_coding upstream_gene_variant MODIFIER -129G>A None
M0048751 JBFFEALM_00005 4069 4 Skin 0.21 protein_coding upstream_gene_variant MODIFIER -1565T>C None
M0048752 JBFFEALM_00004 5029 12 Skin 0.63 protein_coding synonymous_variant LOW 441C>G Gly147Gly
M0048753 JBFFEALM_00004 5038 12 Skin 0.63 protein_coding synonymous_variant LOW 432C>G Gly144Gly
M0048754 JBFFEALM_00006 6535 3 Skin 0.16 protein_coding synonymous_variant LOW 36C>A Leu12Leu






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
JBFFEALM_00007 VFG000162 Pyoverdine 88.1 6.1e-84 1 175 0.9943 0.9358 Nutritional/Metabolic factor extracytoplasmic-function sigma-70 factor experiment
JBFFEALM_00008 VFG016058 Pyoverdine 70.1 0 1 3411 1.0 0.7856 Nutritional/Metabolic factor peptide synthase PvdL experiment
JBFFEALM_00006 VFG015830 Pyoverdine 86 1.7e-179 1 336 0.997 0.997 Nutritional/Metabolic factor acetyltransferase prediction
JBFFEALM_00007 VFG015829 Pyoverdine 98.9 4.9e-93 1 175 0.9943 0.9943 Nutritional/Metabolic factor extracytoplasmic-function sigma-70 factor prediction
JBFFEALM_00008 VFG015827 Pyoverdine 89 0 1 3411 1.0 0.7901 Nutritional/Metabolic factor peptide synthase PvdL 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






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
JBFFEALM_00007 PHI:6939 pvdS 88.1 1.6e-83 1 175 0.9943 0.9412 rodents pneumonia sigma factor reduced virulence
JBFFEALM_00008 PHI:6991 pvdL 70.1 0 1 3411 1.0000 0.9979 rodents opportunistic infection iron siderophore loss of pathogenicity
JBFFEALM_00009 PHI:6991 pvdL 74.3 0 1 893 1.0000 0.9979 rodents opportunistic infection iron siderophore loss of pathogenicity






        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