Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2397
  Reference Plasmid   1111525849768046_bin.37__k141_175464
  Reference Plasmid Size   9468
  Reference Plasmid GC Content   0.39
  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
M0121882 PHFKDFCL_00004 5681 3 Oral 0.60 protein_coding missense_variant MODERATE 19A>G Thr7Ala
M0121883 PHFKDFCL_00004 5698 3 Oral 0.60 protein_coding start_lost HIGH 2T>C Met1?
M0121884 PHFKDFCL_00004 5942 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -243G>T None
M0121885 PHFKDFCL_00005 6380 3 Oral 0.60 protein_coding synonymous_variant LOW 429G>A Thr143Thr
M0121886 PHFKDFCL_00006 6702 4 Oral 0.80 protein_coding synonymous_variant LOW 238T>C Leu80Leu
M0121887 PHFKDFCL_00006 6791 3 Oral 0.60 protein_coding synonymous_variant LOW 327C>T Ile109Ile
M0121888 PHFKDFCL_00006 7059 3 Oral 0.60 protein_coding missense_variant MODERATE 595A>T Met199Leu
M0121889 PHFKDFCL_00006 7121 4 Oral 0.80 protein_coding synonymous_variant LOW 657A>C Gly219Gly
M0121890 PHFKDFCL_00006 7166 4 Oral 0.80 protein_coding synonymous_variant LOW 702T>C Asn234Asn
M0121891 PHFKDFCL_00006 7181 3 Oral 0.60 protein_coding missense_variant MODERATE 717T>A Asp239Glu
M0121892 PHFKDFCL_00006 7589 4 Oral 0.80 protein_coding synonymous_variant LOW 1125T>C Asp375Asp
M0121893 PHFKDFCL_00006 7655 4 Oral 0.80 protein_coding synonymous_variant LOW 1191A>G Leu397Leu
M0121894 PHFKDFCL_00006 7701 4 Oral 0.80 protein_coding missense_variant MODERATE 1237T>C Ser413Pro
M0121895 PHFKDFCL_00006 7796 4 Oral 0.80 protein_coding synonymous_variant LOW 1332T>C Gly444Gly
M0121896 PHFKDFCL_00006 7799 3 Oral 0.60 protein_coding synonymous_variant LOW 1335T>C Asp445Asp
M0121897 PHFKDFCL_00006 8087 3 Oral 0.60 protein_coding synonymous_variant LOW 1623T>C Ile541Ile
M0121898 PHFKDFCL_00006 8156 3 Oral 0.60 protein_coding synonymous_variant LOW 1692A>T Gly564Gly
M0121899 PHFKDFCL_00004 8275 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -2576T>C None
M0121900 PHFKDFCL_00004 8288 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -2589A>G None
M0121901 PHFKDFCL_00007 8378 3 Oral 0.60 protein_coding synonymous_variant LOW 42A>G Leu14Leu
M0121902 PHFKDFCL_00007 8390 3 Oral 0.60 protein_coding synonymous_variant LOW 54A>G Thr18Thr
M0121903 PHFKDFCL_00007 8402 3 Oral 0.60 protein_coding synonymous_variant LOW 66G>A Ala22Ala
M0121904 PHFKDFCL_00007 8585 3 Oral 0.60 protein_coding synonymous_variant LOW 249T>A Thr83Thr
M0121905 PHFKDFCL_00007 8611 4 Oral 0.80 protein_coding missense_variant MODERATE 275G>C Ser92Thr
M0121906 PHFKDFCL_00007 8622 4 Oral 0.80 protein_coding missense_variant MODERATE 286T>A Ser96Thr
M0121907 PHFKDFCL_00007 8805 3 Oral 0.60 protein_coding missense_variant MODERATE 469G>A Ala157Thr
M0121908 PHFKDFCL_00007 8829 3 Oral 0.60 protein_coding synonymous_variant LOW 493T>C Leu165Leu
M0121909 PHFKDFCL_00007 9015 3 Oral 0.60 protein_coding missense_variant MODERATE 679A>G Thr227Ala
M0121910 PHFKDFCL_00004 9290 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3591C>T None
M0121911 PHFKDFCL_00004 9321 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -3622A>G None
M0121912 PHFKDFCL_00004 9322 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3623C>T None
M0121913 PHFKDFCL_00004 9326 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3627A>G None
M0121914 PHFKDFCL_00004 9341 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3642G>T None
M0121915 PHFKDFCL_00004 9342 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -3643C>T None
M0121916 PHFKDFCL_00004 9412 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -3713C>T None
M0121917 PHFKDFCL_00006 6794 3 Oral 0.60 protein_coding synonymous_variant LOW 330G>A Lys110Lys
M0121918 PHFKDFCL_00006 7386 3 Oral 0.60 protein_coding missense_variant MODERATE 922C>G Leu308Val






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