Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2404
  Reference Plasmid   1111525849768046_bin.37__k141_184812
  Reference Plasmid Size   2261
  Reference Plasmid GC Content   0.33
  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
M0122784 BAKHPDAB_00001 383 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *359G>A None
M0122785 BAKHPDAB_00001 413 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *329G>C None
M0122786 BAKHPDAB_00001 416 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *326A>T None
M0122787 BAKHPDAB_00001 434 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *308A>G None
M0122788 BAKHPDAB_00001 444 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *298C>T None
M0122789 BAKHPDAB_00001 455 4 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *287T>A None
M0122790 BAKHPDAB_00001 467 4 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *275T>C None
M0122791 BAKHPDAB_00001 494 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *248C>A None
M0122792 BAKHPDAB_00001 500 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *242T>G None
M0122793 BAKHPDAB_00001 503 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *239A>G None
M0122794 BAKHPDAB_00001 599 4 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *143C>T None
M0122795 BAKHPDAB_00001 623 4 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *119C>A None
M0122796 BAKHPDAB_00001 638 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *104C>T None
M0122797 BAKHPDAB_00001 734 4 Oral 1.00 protein_coding downstream_gene_variant MODIFIER *8G>A None
M0122798 BAKHPDAB_00001 784 3 Oral 0.75 protein_coding synonymous_variant LOW 1464T>C Gly488Gly
M0122799 BAKHPDAB_00001 853 3 Oral 0.75 protein_coding synonymous_variant LOW 1395C>T His465His
M0122800 BAKHPDAB_00001 860 3 Oral 0.75 protein_coding missense_variant MODERATE 1388C>T Thr463Ile
M0122801 BAKHPDAB_00001 884 4 Oral 1.00 protein_coding missense_variant MODERATE 1364C>A Thr455Asn
M0122802 BAKHPDAB_00001 898 4 Oral 1.00 protein_coding synonymous_variant LOW 1350G>A Val450Val
M0122803 BAKHPDAB_00001 964 3 Oral 0.75 protein_coding synonymous_variant LOW 1284C>T Ala428Ala
M0122804 BAKHPDAB_00001 1008 3 Oral 0.75 protein_coding missense_variant MODERATE 1240G>T Ala414Ser
M0122805 BAKHPDAB_00001 1045 4 Oral 1.00 protein_coding synonymous_variant LOW 1203G>T Val401Val
M0122806 BAKHPDAB_00001 1114 3 Oral 0.75 protein_coding synonymous_variant LOW 1134A>T Thr378Thr
M0122807 BAKHPDAB_00001 1153 3 Oral 0.75 protein_coding synonymous_variant LOW 1095G>T Val365Val
M0122808 BAKHPDAB_00001 1168 4 Oral 1.00 protein_coding synonymous_variant LOW 1080T>C Ser360Ser
M0122809 BAKHPDAB_00001 1570 3 Oral 0.75 protein_coding synonymous_variant LOW 678C>T Asn226Asn
M0122810 BAKHPDAB_00001 1597 3 Oral 0.75 protein_coding synonymous_variant LOW 651T>C Tyr217Tyr
M0122811 BAKHPDAB_00001 1795 3 Oral 0.75 protein_coding synonymous_variant LOW 453A>G Val151Val
M0122812 BAKHPDAB_00001 1992 3 Oral 0.75 protein_coding missense_variant MODERATE 256T>C Ser86Pro
M0122813 BAKHPDAB_00001 2080 3 Oral 0.75 protein_coding synonymous_variant LOW 168T>C Ser56Ser
M0122814 BAKHPDAB_00001 97 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *645T>G None
M0122815 BAKHPDAB_00001 175 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *567A>G None
M0122816 BAKHPDAB_00001 182 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *560T>C None
M0122817 BAKHPDAB_00001 733 3 Oral 0.75 protein_coding downstream_gene_variant MODIFIER *9A>G None
M0122818 BAKHPDAB_00001 1228 3 Oral 0.75 protein_coding synonymous_variant LOW 1020T>C Gly340Gly
M0122819 BAKHPDAB_00001 1346 3 Oral 0.75 protein_coding missense_variant MODERATE 902C>T Ala301Val






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