Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2377
  Reference Plasmid   1111525849768046_bin.37__k141_138827
  Reference Plasmid Size   2095
  Reference Plasmid GC Content   0.35
  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
M0120104 LJOJEMNP_00001 105 4 Oral 0.80 protein_coding downstream_gene_variant MODIFIER *490C>T None
M0120105 LJOJEMNP_00001 116 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *479T>A None
M0120106 LJOJEMNP_00001 245 5 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *350A>G None
M0120107 LJOJEMNP_00001 321 5 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *274T>A None
M0120108 LJOJEMNP_00001 865 4 Oral 0.80 protein_coding synonymous_variant LOW 702A>T Leu234Leu
M0120109 LJOJEMNP_00001 874 3 Oral 0.60 protein_coding synonymous_variant LOW 693T>G Ala231Ala
M0120110 LJOJEMNP_00001 1006 3 Oral 0.60 protein_coding synonymous_variant LOW 561A>T Ser187Ser
M0120111 LJOJEMNP_00001 1111 4 Oral 0.80 protein_coding synonymous_variant LOW 456T>C Ser152Ser
M0120112 LJOJEMNP_00001 1123 5 Oral 1.00 protein_coding synonymous_variant LOW 444T>G Ala148Ala
M0120113 LJOJEMNP_00001 1147 4 Oral 0.80 protein_coding synonymous_variant LOW 420C>T Asn140Asn
M0120114 LJOJEMNP_00001 1327 3 Oral 0.60 protein_coding synonymous_variant LOW 240A>G Arg80Arg
M0120115 LJOJEMNP_00001 1715 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -149C>A None
M0120116 LJOJEMNP_00001 210 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *385T>A None
M0120117 LJOJEMNP_00001 215 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *380C>A None
M0120118 LJOJEMNP_00001 286 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *309C>T None
M0120119 LJOJEMNP_00001 287 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *308C>A None
M0120120 LJOJEMNP_00001 288 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *307C>T None
M0120121 LJOJEMNP_00001 291 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *304A>T None
M0120122 LJOJEMNP_00001 402 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *193T>C None
M0120123 LJOJEMNP_00001 464 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *131A>G None
M0120124 LJOJEMNP_00001 524 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *71A>G None
M0120125 LJOJEMNP_00001 637 3 Oral 0.60 protein_coding synonymous_variant LOW 930C>T Pro310Pro
M0120126 LJOJEMNP_00001 648 3 Oral 0.60 protein_coding missense_variant MODERATE 919T>A Phe307Ile
M0120127 LJOJEMNP_00001 1186 3 Oral 0.60 protein_coding synonymous_variant LOW 381A>T Thr127Thr
M0120128 LJOJEMNP_00001 1216 3 Oral 0.60 protein_coding synonymous_variant LOW 351G>T Ser117Ser
M0120129 LJOJEMNP_00001 1729 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -163A>G None
M0120130 LJOJEMNP_00001 1923 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -357A>G None
M0120131 LJOJEMNP_00001 1961 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -395T>C None
M0120132 LJOJEMNP_00001 1521 3 Oral 0.60 protein_coding missense_variant MODERATE 46G>A Asp16Asn






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