Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C439
  Reference Plasmid   NZ_CP013268.1
  Reference Plasmid Size   43676
  Reference Plasmid GC Content   0.63
  Reference Plasmid Mobility Type   conjugative





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
M0087618 JONBCKMJ_00014 17829 3 Skin 0.43 protein_coding synonymous_variant LOW 552A>C Gly184Gly
M0087619 JONBCKMJ_00014 17836 3 Skin 0.43 protein_coding missense_variant MODERATE 559C>T Leu187Phe
M0087620 JONBCKMJ_00014 17838 3 Skin 0.43 protein_coding synonymous_variant LOW 561T>C Leu187Leu
M0087621 JONBCKMJ_00014 17852 3 Skin 0.43 protein_coding missense_variant MODERATE 575A>G Asp192Gly
M0087622 JONBCKMJ_00014 17853 3 Skin 0.43 protein_coding missense_variant MODERATE 576T>A Asp192Glu
M0087623 JONBCKMJ_00014 17875 3 Skin 0.43 protein_coding missense_variant MODERATE 598G>C Ala200Pro
M0087624 JONBCKMJ_00011 17974 3 Skin 0.43 protein_coding upstream_gene_variant MODIFIER -1635T>G None
M0087625 JONBCKMJ_00015 18210 3 Skin 0.43 protein_coding synonymous_variant LOW 216A>G Gln72Gln
M0087626 JONBCKMJ_00015 18230 3 Skin 0.43 protein_coding missense_variant MODERATE 236A>T Glu79Val
M0087627 JONBCKMJ_00015 18485 3 Skin 0.43 protein_coding missense_variant MODERATE 491G>A Arg164His
M0087628 JONBCKMJ_00015 18528 3 Skin 0.43 protein_coding synonymous_variant LOW 534A>G Gly178Gly
M0087629 JONBCKMJ_00015 18543 3 Skin 0.43 protein_coding synonymous_variant LOW 549G>A Glu183Glu
M0087630 JONBCKMJ_00015 18549 3 Skin 0.43 protein_coding synonymous_variant LOW 555A>G Glu185Glu
M0087631 JONBCKMJ_00015 18555 3 Skin 0.43 protein_coding synonymous_variant LOW 561T>C Asn187Asn
M0087632 JONBCKMJ_00015 18579 3 Skin 0.43 protein_coding synonymous_variant LOW 585T>C Arg195Arg
M0087633 JONBCKMJ_00015 18603 3 Skin 0.43 protein_coding synonymous_variant LOW 609A>G Glu203Glu
M0087634 JONBCKMJ_00015 18622 3 Skin 0.43 protein_coding missense_variant MODERATE 628G>T Asp210Tyr
M0087635 JONBCKMJ_00015 18623 3 Skin 0.43 protein_coding missense_variant MODERATE 629A>C Asp210Ala
M0087636 JONBCKMJ_00016 18683 3 Skin 0.43 protein_coding synonymous_variant LOW 39G>C Arg13Arg
M0087637 JONBCKMJ_00016 18714 3 Skin 0.43 protein_coding missense_variant MODERATE 70C>G Pro24Ala
M0087638 JONBCKMJ_00016 18739 3 Skin 0.43 protein_coding missense_variant MODERATE 95G>T Ser32Ile
M0087639 JONBCKMJ_00016 18746 3 Skin 0.43 protein_coding synonymous_variant LOW 102C>T Arg34Arg






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






        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