Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3311
  Reference Plasmid   MGYG000298306__MGYG000298306_308
  Reference Plasmid Size   5144
  Reference Plasmid GC Content   0.40
  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
M0134798 JOOMNNMF_00003 1926 3 Oral 0.75 protein_coding synonymous_variant LOW 735C>A Gly245Gly
M0134799 JOOMNNMF_00003 2023 3 Oral 0.75 protein_coding missense_variant MODERATE 832A>C Lys278Gln
M0134800 JOOMNNMF_00003 2118 3 Oral 0.75 protein_coding synonymous_variant LOW 927T>G Val309Val
M0134801 JOOMNNMF_00003 2142 3 Oral 0.75 protein_coding synonymous_variant LOW 951T>C Ser317Ser
M0134802 JOOMNNMF_00003 2256 3 Oral 0.75 protein_coding synonymous_variant LOW 1065G>T Ser355Ser
M0134803 JOOMNNMF_00003 2424 3 Oral 0.75 protein_coding synonymous_variant LOW 1233T>A Thr411Thr
M0134804 JOOMNNMF_00004 2545 3 Oral 0.75 protein_coding upstream_gene_variant MODIFIER -140G>T None
M0134805 JOOMNNMF_00004 3146 3 Oral 0.75 protein_coding synonymous_variant LOW 462T>C Asp154Asp
M0134806 JOOMNNMF_00004 3191 3 Oral 0.75 protein_coding synonymous_variant LOW 507T>C Thr169Thr
M0134807 JOOMNNMF_00004 3203 3 Oral 0.75 protein_coding synonymous_variant LOW 519T>C Tyr173Tyr
M0134808 JOOMNNMF_00004 3689 3 Oral 0.75 protein_coding synonymous_variant LOW 1005C>T Gly335Gly
M0134809 JOOMNNMF_00004 3797 3 Oral 0.75 protein_coding synonymous_variant LOW 1113G>T Ser371Ser
M0134810 JOOMNNMF_00004 3830 3 Oral 0.75 protein_coding synonymous_variant LOW 1146T>C Ile382Ile
M0134811 JOOMNNMF_00004 3860 3 Oral 0.75 protein_coding synonymous_variant LOW 1176C>T Phe392Phe
M0134812 JOOMNNMF_00004 3872 3 Oral 0.75 protein_coding synonymous_variant LOW 1188A>T Ala396Ala
M0134813 JOOMNNMF_00004 4307 3 Oral 0.75 protein_coding synonymous_variant LOW 1623A>C Gly541Gly
M0134814 JOOMNNMF_00004 4457 3 Oral 0.75 protein_coding synonymous_variant LOW 1773G>A Glu591Glu
M0134815 JOOMNNMF_00004 4461 3 Oral 0.75 protein_coding synonymous_variant LOW 1777T>C Leu593Leu






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