Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C126
  Reference Plasmid   CP077275.1
  Reference Plasmid Size   12821
  Reference Plasmid GC Content   0.48
  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
M0144797 LKNFMPKN_00002 2827 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -403T>G None
M0144798 LKNFMPKN_00002 3063 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -167G>C None
M0144799 LKNFMPKN_00002 3067 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -163C>A None
M0144800 LKNFMPKN_00002 3081 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -149G>A None
M0144801 LKNFMPKN_00003 3684 3 Gut 1.00 protein_coding synonymous_variant LOW 217A>C Arg73Arg
M0144802 LKNFMPKN_00004 4170 3 Gut 1.00 protein_coding synonymous_variant LOW 366C>T Pro122Pro
M0144803 LKNFMPKN_00004 4429 3 Gut 1.00 protein_coding synonymous_variant LOW 625C>A Arg209Arg
M0144804 LKNFMPKN_00005 7027 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -828T>C None
M0144805 LKNFMPKN_00009 9116 3 Gut 1.00 protein_coding missense_variant MODERATE 68C>T Ala23Val






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
LKNFMPKN_00008 VFG043983 Colicin S4 99.2 1.2e-282 1 499 1.0 1 Exotoxin colicin S4 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






        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
LKNFMPKN_00008 1.C.1.3.4 99.2 9.6e-283 1 499 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
LKNFMPKN_00009 8.B.24.1.1 77.5 1.1e-71 1 178 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family