Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1198
  Reference Plasmid   NZ_CP132305.1
  Reference Plasmid Size   172303
  Reference Plasmid GC Content   0.61
  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
M0112912 CCHALLCI_00072 62778 9 Skin 0.69 protein_coding missense_variant MODERATE 465G>T Gln155His
M0112913 CCHALLCI_00072 62976 4 Skin 0.31 protein_coding synonymous_variant LOW 663C>T Phe221Phe
M0112914 CCHALLCI_00072 63155 10 Skin 0.77 protein_coding missense_variant MODERATE 842T>A Val281Asp
M0112915 CCHALLCI_00073 63480 4 Skin 0.31 protein_coding missense_variant MODERATE 38C>T Thr13Ile
M0112916 CCHALLCI_00074 64133 4 Skin 0.31 protein_coding missense_variant MODERATE 76C>A Leu26Met
M0112917 CCHALLCI_00074 64165 4 Skin 0.31 protein_coding synonymous_variant LOW 108C>T Val36Val
M0112918 CCHALLCI_00074 64564 11 Skin 0.85 protein_coding synonymous_variant LOW 507C>T His169His
M0112919 CCHALLCI_00074 64773 4 Skin 0.31 protein_coding missense_variant MODERATE 716T>C Val239Ala
M0112920 CCHALLCI_00074 64828 4 Skin 0.31 protein_coding synonymous_variant LOW 771A>C Ala257Ala
M0112921 CCHALLCI_00074 64960 3 Skin 0.23 protein_coding synonymous_variant LOW 903C>T Asn301Asn
M0112922 CCHALLCI_00074 64993 3 Skin 0.23 protein_coding synonymous_variant LOW 936C>A Arg312Arg
M0112923 CCHALLCI_00069 65495 11 Skin 0.85 protein_coding upstream_gene_variant MODIFIER -4451A>G None
M0112924 CCHALLCI_00068 58429 3 Skin 0.23 protein_coding synonymous_variant LOW 1722G>A Thr574Thr
M0112925 CCHALLCI_00070 61141 5 Skin 0.38 protein_coding missense_variant MODERATE 398T>G Leu133Trp
M0112926 CCHALLCI_00070 61284 5 Skin 0.38 protein_coding synonymous_variant LOW 255G>C Val85Val
M0112927 CCHALLCI_00070 61524 5 Skin 0.38 protein_coding synonymous_variant LOW 15T>G Val5Val
M0112928 CCHALLCI_00071 61699 5 Skin 0.38 protein_coding missense_variant MODERATE 460G>A Ala154Thr
M0112929 CCHALLCI_00067 62165 6 Skin 0.46 protein_coding upstream_gene_variant MODIFIER -3823C>T None
M0112930 CCHALLCI_00067 62247 8 Skin 0.62 protein_coding upstream_gene_variant MODIFIER -3905A>C None
M0112931 CCHALLCI_00067 62266 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -3924T>A None
M0112932 CCHALLCI_00067 62268 7 Skin 0.54 protein_coding upstream_gene_variant MODIFIER -3926A>G None
M0112933 CCHALLCI_00072 62370 3 Skin 0.23 protein_coding synonymous_variant LOW 57G>A Glu19Glu
M0112934 CCHALLCI_00072 62502 8 Skin 0.62 protein_coding synonymous_variant LOW 189T>C His63His
M0112935 CCHALLCI_00072 62668 8 Skin 0.62 protein_coding missense_variant MODERATE 355A>G Lys119Glu
M0112936 CCHALLCI_00067 62217 5 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -3875G>A None
M0112937 CCHALLCI_00068 63414 4 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -3264A>G None
M0112938 CCHALLCI_00073 63478 5 Skin 0.38 protein_coding missense_variant MODERATE 36A>T Glu12Asp
M0112939 CCHALLCI_00073 63598 5 Skin 0.38 protein_coding synonymous_variant LOW 156C>A Ala52Ala
M0112940 CCHALLCI_00074 64434 5 Skin 0.38 protein_coding missense_variant MODERATE 377T>C Val126Ala
M0112941 CCHALLCI_00072 63018 3 Skin 0.23 protein_coding synonymous_variant LOW 705G>C Ala235Ala
M0112942 CCHALLCI_00072 63024 3 Skin 0.23 protein_coding missense_variant MODERATE 711G>C Glu237Asp






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
CCHALLCI_00178 Arsenic (As) 91.1 1.2e-123 1 236 1.0000 0.9752 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






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
CCHALLCI_00139 3.A.1.3.5 72.2 1.2e-98 8 255 0.9538 1.0122 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily