Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2671
  Reference Plasmid   1111525849859858_bin.38__k141_398044
  Reference Plasmid Size   24449
  Reference Plasmid GC Content   0.57
  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
M0052710 APDFNAAN_00003 2567 6 Skin 0.38 protein_coding synonymous_variant LOW 309C>T Asn103Asn
M0052711 APDFNAAN_00016 21241 4 Skin 0.25 protein_coding synonymous_variant LOW 480A>C Pro160Pro
M0052712 APDFNAAN_00016 21364 3 Skin 0.19 protein_coding synonymous_variant LOW 357T>C Val119Val
M0052713 APDFNAAN_00016 21376 3 Skin 0.19 protein_coding synonymous_variant LOW 345C>A Gly115Gly
M0052714 APDFNAAN_00016 21418 3 Skin 0.19 protein_coding synonymous_variant LOW 303A>T Pro101Pro
M0052715 APDFNAAN_00016 21640 5 Skin 0.31 protein_coding synonymous_variant LOW 81C>T Ser27Ser
M0052716 APDFNAAN_00016 23448 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -1728C>A None
M0052717 APDFNAAN_00016 23616 5 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -1896A>G None
M0052718 APDFNAAN_00017 22045 3 Skin 0.19 protein_coding synonymous_variant LOW 498T>G Ala166Ala
M0052719 APDFNAAN_00017 22072 3 Skin 0.19 protein_coding synonymous_variant LOW 471A>C Ala157Ala
M0052720 APDFNAAN_00016 24384 5 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2664C>T None
M0052721 APDFNAAN_00017 22477 3 Skin 0.19 protein_coding synonymous_variant LOW 66G>A Pro22Pro
M0052722 APDFNAAN_00017 22501 3 Skin 0.19 protein_coding missense_variant MODERATE 42T>G Phe14Leu
M0052723 APDFNAAN_00017 22504 3 Skin 0.19 protein_coding synonymous_variant LOW 39G>C Gly13Gly
M0052724 APDFNAAN_00017 22506 3 Skin 0.19 protein_coding missense_variant MODERATE 37G>A Gly13Arg
M0052725 APDFNAAN_00017 22508 3 Skin 0.19 protein_coding missense_variant MODERATE 35G>A Arg12His
M0052726 APDFNAAN_00016 24117 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -2397A>G 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






        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
APDFNAAN_00002 PHI:10578 PccS1_002702 82 3.4e-148 1 317 1.0000 1.0000 monocots soft rot transcriptional regulator, LysR family unaffected 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