Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2010
  Reference Plasmid   1111525849736936_bin.26__k141_284092
  Reference Plasmid Size   8177
  Reference Plasmid GC Content   0.51
  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
M0022276 LMLPACNF_00004 7246 3 Skin 0.20 protein_coding upstream_gene_variant MODIFIER -2964T>A None
M0022277 LMLPACNF_00007 6571 3 Skin 0.20 protein_coding missense_variant MODERATE 250A>G Thr84Ala
M0022278 LMLPACNF_00007 6600 3 Skin 0.20 protein_coding synonymous_variant LOW 279G>T Thr93Thr






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
LMLPACNF_00001 VFG049144 AcrAB 84.2 0 1 891 1.0 0.8502 Antimicrobial activity/Competitive advantage acriflavine resistance protein B experiment
LMLPACNF_00001 VFG049139 AcrAB 84.4 0 1 891 1.0 0.8502 Antimicrobial activity/Competitive advantage acriflavine resistance protein B 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
LMLPACNF_00001 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Triclosan [class: Phenolic compounds], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Rhodamine 6G [class: Xanthene] 90.7 0 1 889 0.9978 0.8459 experiment
LMLPACNF_00001 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Triclosan [class: Phenolic compounds], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine], Rhodamine 6G [class: Xanthene] 99.4 0 1 891 1.0000 0.8502 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
LMLPACNF_00001 ARO:3000216 83 0 1 891 1.0011 0.8503 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
LMLPACNF_00001 PHI:6451 acrB 84.2 0 1 891 1.0000 0.8502 nematodes pneumonia acriflavine resistance protein reduced virulence
LMLPACNF_00009 PHI:3819 ymoA 91 5.1e-30 1 67 1.0000 1.0000 rodents pneumonic plague represses the transcription and expression of T3SS genes at room temperature 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
LMLPACNF_00001 2.A.6.2.2 83 0 1 891 1.0000 0.8503 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily