Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C305
  Reference Plasmid   NC_012642.1
  Reference Plasmid Size   7078
  Reference Plasmid GC Content   0.35
  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
M0151888 CCKNJGJF_00001 517 4 Gut 0.67 protein_coding missense_variant MODERATE 16A>G Ile6Val
M0151889 CCKNJGJF_00001 762 5 Gut 0.83 protein_coding missense_variant MODERATE 261T>G Ile87Met
M0151890 CCKNJGJF_00001 793 5 Gut 0.83 protein_coding missense_variant MODERATE 292G>A Ala98Thr
M0151891 CCKNJGJF_00002 1169 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1383A>T None
M0151892 CCKNJGJF_00002 1209 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1343C>T None
M0151893 CCKNJGJF_00002 1225 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1327A>G None
M0151894 CCKNJGJF_00002 2041 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -511T>A None
M0151895 CCKNJGJF_00002 2075 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -477A>T None
M0151896 CCKNJGJF_00002 2081 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -471T>C None
M0151897 CCKNJGJF_00002 2090 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -462T>A None
M0151898 CCKNJGJF_00002 2363 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -189T>A None
M0151899 CCKNJGJF_00002 2367 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -185G>A None
M0151900 CCKNJGJF_00002 2373 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -179T>C None
M0151901 CCKNJGJF_00002 2378 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -174T>C None
M0151902 CCKNJGJF_00002 2388 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -164A>G None
M0151903 CCKNJGJF_00002 2410 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -142A>T None
M0151904 CCKNJGJF_00002 2415 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -137C>T None
M0151905 CCKNJGJF_00002 2420 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -132T>A None
M0151906 CCKNJGJF_00002 2421 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -131T>A None
M0151907 CCKNJGJF_00002 2432 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -120G>A None
M0151908 CCKNJGJF_00002 2452 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -100C>T None
M0151909 CCKNJGJF_00002 2473 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -79C>A None
M0151910 CCKNJGJF_00002 2489 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -63C>A None
M0151911 CCKNJGJF_00002 2536 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -16T>C None
M0151912 CCKNJGJF_00002 2538 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -14A>T None
M0151913 CCKNJGJF_00002 2566 3 Gut 0.50 protein_coding synonymous_variant LOW 15T>C Phe5Phe
M0151914 CCKNJGJF_00002 2653 3 Gut 0.50 protein_coding synonymous_variant LOW 102A>T Ile34Ile
M0151915 CCKNJGJF_00002 2680 3 Gut 0.50 protein_coding synonymous_variant LOW 129A>C Ile43Ile
M0151916 CCKNJGJF_00002 2703 4 Gut 0.67 protein_coding missense_variant MODERATE 152G>A Arg51Lys
M0151917 CCKNJGJF_00002 2737 6 Gut 1.00 protein_coding synonymous_variant LOW 186G>A Leu62Leu
M0151918 CCKNJGJF_00002 2755 3 Gut 0.50 protein_coding synonymous_variant LOW 204A>G Lys68Lys
M0151919 CCKNJGJF_00002 2818 5 Gut 0.83 protein_coding synonymous_variant LOW 267G>A Leu89Leu
M0151920 CCKNJGJF_00002 2860 3 Gut 0.50 protein_coding synonymous_variant LOW 309C>T Ser103Ser
M0151921 CCKNJGJF_00002 2872 3 Gut 0.50 protein_coding synonymous_variant LOW 321G>A Lys107Lys
M0151922 CCKNJGJF_00002 2899 3 Gut 0.50 protein_coding synonymous_variant LOW 348A>G Val116Val
M0151923 CCKNJGJF_00002 2941 5 Gut 0.83 protein_coding synonymous_variant LOW 390A>G Arg130Arg
M0151924 CCKNJGJF_00002 3052 5 Gut 0.83 protein_coding synonymous_variant LOW 501A>G Ser167Ser
M0151925 CCKNJGJF_00002 3079 5 Gut 0.83 protein_coding synonymous_variant LOW 528C>T Leu176Leu
M0151926 CCKNJGJF_00002 3118 3 Gut 0.50 protein_coding synonymous_variant LOW 567G>T Leu189Leu
M0151927 CCKNJGJF_00002 3175 3 Gut 0.50 protein_coding synonymous_variant LOW 624T>C Asn208Asn
M0151928 CCKNJGJF_00002 3194 3 Gut 0.50 protein_coding missense_variant MODERATE 643C>A Gln215Lys
M0151929 CCKNJGJF_00002 3273 5 Gut 0.83 protein_coding missense_variant MODERATE 722G>A Arg241Lys
M0151930 CCKNJGJF_00002 2647 3 Gut 0.50 protein_coding synonymous_variant LOW 96G>A Lys32Lys
M0151931 CCKNJGJF_00002 3358 3 Gut 0.50 protein_coding synonymous_variant LOW 807A>T Ala269Ala
M0151932 CCKNJGJF_00002 3388 3 Gut 0.50 protein_coding synonymous_variant LOW 837C>T Thr279Thr
M0151933 CCKNJGJF_00002 3466 3 Gut 0.50 protein_coding synonymous_variant LOW 915G>A Glu305Glu
M0151934 CCKNJGJF_00002 3467 3 Gut 0.50 protein_coding missense_variant MODERATE 916A>G Asn306Asp
M0151935 CCKNJGJF_00002 3496 3 Gut 0.50 protein_coding synonymous_variant LOW 945T>G Ala315Ala
M0151936 CCKNJGJF_00002 3715 3 Gut 0.50 protein_coding synonymous_variant LOW 1164C>T Arg388Arg
M0151937 CCKNJGJF_00003 5659 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -922A>G None
M0151938 CCKNJGJF_00003 5755 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1018T>C None
M0151939 CCKNJGJF_00001 43 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -459G>A None
M0151940 CCKNJGJF_00001 207 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -295A>C 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






        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