Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1992
  Reference Plasmid   1111525849736738_bin.5__k141_21047
  Reference Plasmid Size   4252
  Reference Plasmid GC Content   0.37
  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
M0118118 LCAPCDLJ_00001 1907 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -964G>A None
M0118119 LCAPCDLJ_00001 1921 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -978A>C None
M0118120 LCAPCDLJ_00001 1937 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -994A>G None
M0118121 LCAPCDLJ_00004 3155 3 Oral 1.00 protein_coding synonymous_variant LOW 462T>C Ala154Ala
M0118122 LCAPCDLJ_00004 3159 3 Oral 1.00 protein_coding missense_variant MODERATE 466G>A Val156Ile
M0118123 LCAPCDLJ_00004 3161 3 Oral 1.00 protein_coding synonymous_variant LOW 468T>C Val156Val
M0118124 LCAPCDLJ_00004 3170 3 Oral 1.00 protein_coding synonymous_variant LOW 477C>T Ala159Ala
M0118125 LCAPCDLJ_00004 3200 3 Oral 1.00 protein_coding synonymous_variant LOW 507A>G Gln169Gln
M0118126 LCAPCDLJ_00004 3203 3 Oral 1.00 protein_coding synonymous_variant LOW 510G>A Ala170Ala
M0118127 LCAPCDLJ_00004 3209 3 Oral 1.00 protein_coding synonymous_variant LOW 516G>A Ala172Ala
M0118128 LCAPCDLJ_00004 3233 3 Oral 1.00 protein_coding synonymous_variant LOW 540A>C Ala180Ala
M0118129 LCAPCDLJ_00004 3236 3 Oral 1.00 protein_coding missense_variant MODERATE 543T>A Asp181Glu
M0118130 LCAPCDLJ_00004 3245 3 Oral 1.00 protein_coding synonymous_variant LOW 552C>T Ala184Ala
M0118131 LCAPCDLJ_00004 3257 3 Oral 1.00 protein_coding synonymous_variant LOW 564G>A Glu188Glu
M0118132 LCAPCDLJ_00004 3269 3 Oral 1.00 protein_coding synonymous_variant LOW 576C>T Asn192Asn
M0118133 LCAPCDLJ_00004 3270 3 Oral 1.00 protein_coding missense_variant MODERATE 577A>G Ile193Val
M0118134 LCAPCDLJ_00004 3276 3 Oral 1.00 protein_coding missense_variant MODERATE 583T>G Ser195Ala
M0118135 LCAPCDLJ_00004 3287 3 Oral 1.00 protein_coding synonymous_variant LOW 594T>C Asp198Asp
M0118136 LCAPCDLJ_00001 3396 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -2453A>C None
M0118137 LCAPCDLJ_00001 3430 3 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -2487C>T None
M0118138 LCAPCDLJ_00005 3640 3 Oral 1.00 protein_coding missense_variant MODERATE 94A>G Ile32Val
M0118139 LCAPCDLJ_00005 3651 3 Oral 1.00 protein_coding synonymous_variant LOW 105G>A Glu35Glu
M0118140 LCAPCDLJ_00005 3655 3 Oral 1.00 protein_coding missense_variant MODERATE 109A>T Ile37Phe
M0118141 LCAPCDLJ_00005 3657 3 Oral 1.00 protein_coding synonymous_variant LOW 111T>C Ile37Ile
M0118142 LCAPCDLJ_00005 3687 3 Oral 1.00 protein_coding synonymous_variant LOW 141A>G Glu47Glu
M0118143 LCAPCDLJ_00005 3710 3 Oral 1.00 protein_coding missense_variant MODERATE 164C>T Thr55Ile
M0118144 LCAPCDLJ_00005 3747 3 Oral 1.00 protein_coding synonymous_variant LOW 201A>T Ala67Ala






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