Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2475
  Reference Plasmid   1111525849768046_bin.37__k141_922
  Reference Plasmid Size   3306
  Reference Plasmid GC Content   0.41
  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
M0128925 LOPOECDC_00001 82 5 Oral 0.83 protein_coding downstream_gene_variant MODIFIER *359A>G None
M0128926 LOPOECDC_00001 85 5 Oral 0.83 protein_coding downstream_gene_variant MODIFIER *356G>A None
M0128927 LOPOECDC_00001 151 4 Oral 0.67 protein_coding downstream_gene_variant MODIFIER *290G>T None
M0128928 LOPOECDC_00001 217 5 Oral 0.83 protein_coding downstream_gene_variant MODIFIER *224T>C None
M0128929 LOPOECDC_00001 220 5 Oral 0.83 protein_coding downstream_gene_variant MODIFIER *221C>T None
M0128930 LOPOECDC_00001 246 5 Oral 0.83 protein_coding downstream_gene_variant MODIFIER *195A>G None
M0128931 LOPOECDC_00001 382 3 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *59G>A None
M0128932 LOPOECDC_00001 400 3 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *41C>T None
M0128933 LOPOECDC_00001 415 3 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *26A>C None
M0128934 LOPOECDC_00001 416 3 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *25A>G None
M0128935 LOPOECDC_00001 471 5 Oral 0.83 protein_coding synonymous_variant LOW 912T>C Gly304Gly
M0128936 LOPOECDC_00001 477 5 Oral 0.83 protein_coding missense_variant MODERATE 906A>T Glu302Asp
M0128937 LOPOECDC_00001 519 3 Oral 0.50 protein_coding synonymous_variant LOW 864T>A Ser288Ser
M0128938 LOPOECDC_00001 591 5 Oral 0.83 protein_coding synonymous_variant LOW 792C>T Thr264Thr
M0128939 LOPOECDC_00001 669 5 Oral 0.83 protein_coding synonymous_variant LOW 714C>T Thr238Thr
M0128940 LOPOECDC_00001 676 5 Oral 0.83 protein_coding missense_variant MODERATE 707C>T Ala236Val
M0128941 LOPOECDC_00001 711 5 Oral 0.83 protein_coding synonymous_variant LOW 672G>A Arg224Arg
M0128942 LOPOECDC_00001 972 4 Oral 0.67 protein_coding missense_variant MODERATE 411G>A Met137Ile
M0128943 LOPOECDC_00001 1026 5 Oral 0.83 protein_coding synonymous_variant LOW 357T>C Ile119Ile
M0128944 LOPOECDC_00001 1074 4 Oral 0.67 protein_coding synonymous_variant LOW 309G>A Pro103Pro
M0128945 LOPOECDC_00001 1119 4 Oral 0.67 protein_coding synonymous_variant LOW 264T>C Leu88Leu
M0128946 LOPOECDC_00001 1488 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -106C>A None
M0128947 LOPOECDC_00002 1766 5 Oral 0.83 protein_coding synonymous_variant LOW 189T>C Ile63Ile
M0128948 LOPOECDC_00001 2001 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -619T>G None
M0128949 LOPOECDC_00003 2034 5 Oral 0.83 protein_coding missense_variant MODERATE 410A>G Asp137Gly
M0128950 LOPOECDC_00003 2057 5 Oral 0.83 protein_coding synonymous_variant LOW 387C>T Ile129Ile
M0128951 LOPOECDC_00003 2117 4 Oral 0.67 protein_coding synonymous_variant LOW 327A>C Gly109Gly
M0128952 LOPOECDC_00003 2180 5 Oral 0.83 protein_coding synonymous_variant LOW 264T>C Gly88Gly
M0128953 LOPOECDC_00003 2225 3 Oral 0.50 protein_coding synonymous_variant LOW 219C>G Thr73Thr
M0128954 LOPOECDC_00001 2466 4 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -1084C>A None
M0128955 LOPOECDC_00001 2645 3 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -1263A>G None
M0128956 LOPOECDC_00004 2778 4 Oral 0.67 protein_coding synonymous_variant LOW 522A>C Pro174Pro
M0128957 LOPOECDC_00004 2817 4 Oral 0.67 protein_coding synonymous_variant LOW 483A>C Ile161Ile
M0128958 LOPOECDC_00004 2829 3 Oral 0.50 protein_coding synonymous_variant LOW 471C>T Ile157Ile
M0128959 LOPOECDC_00001 97 3 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *344C>T None
M0128960 LOPOECDC_00002 1634 3 Oral 0.50 protein_coding synonymous_variant LOW 321G>A Gly107Gly
M0128961 LOPOECDC_00003 2126 3 Oral 0.50 protein_coding synonymous_variant LOW 318G>A Lys106Lys
M0128962 LOPOECDC_00004 2985 3 Oral 0.50 protein_coding synonymous_variant LOW 315T>A Ala105Ala






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