Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2728
  Reference Plasmid   1111525849861727_bin.16__k141_70282
  Reference Plasmid Size   4148
  Reference Plasmid GC Content   0.37
  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
M0132139 AOJBEDAH_00005 3429 5 Oral 0.71 protein_coding synonymous_variant LOW 156G>A Lys52Lys
M0132140 AOJBEDAH_00005 3489 5 Oral 0.71 protein_coding synonymous_variant LOW 216G>A Ala72Ala
M0132141 AOJBEDAH_00005 3492 5 Oral 0.71 protein_coding synonymous_variant LOW 219A>G Lys73Lys
M0132142 AOJBEDAH_00001 3686 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -2996G>A None
M0132143 AOJBEDAH_00001 3702 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -3012G>A None
M0132144 AOJBEDAH_00001 3735 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3045T>G None
M0132145 AOJBEDAH_00001 3740 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -3050T>C None
M0132146 AOJBEDAH_00001 3741 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -3051G>A None
M0132147 AOJBEDAH_00001 3754 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3064A>T None
M0132148 AOJBEDAH_00001 3760 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -3070G>A None
M0132149 AOJBEDAH_00001 3762 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3072A>G None
M0132150 AOJBEDAH_00001 3767 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3077T>C None
M0132151 AOJBEDAH_00001 3841 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -3151T>C None
M0132152 AOJBEDAH_00001 3862 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -3172T>A None
M0132153 AOJBEDAH_00001 3948 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3258G>A None
M0132154 AOJBEDAH_00001 4036 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -3346C>G None
M0132155 AOJBEDAH_00003 79 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1970T>C None
M0132156 AOJBEDAH_00003 118 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1931A>G None
M0132157 AOJBEDAH_00003 142 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -1907G>A None
M0132158 AOJBEDAH_00003 178 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1871C>T None
M0132159 AOJBEDAH_00003 204 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1845G>A None
M0132160 AOJBEDAH_00003 222 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1827C>T None
M0132161 AOJBEDAH_00003 250 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -1799G>T None
M0132162 AOJBEDAH_00003 353 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1696C>T None
M0132163 AOJBEDAH_00001 750 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -60A>C None
M0132164 AOJBEDAH_00001 762 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -72C>A None
M0132165 AOJBEDAH_00002 798 3 Oral 0.43 protein_coding synonymous_variant LOW 945A>G Glu315Glu
M0132166 AOJBEDAH_00002 936 4 Oral 0.57 protein_coding synonymous_variant LOW 807T>C Asn269Asn
M0132167 AOJBEDAH_00002 972 5 Oral 0.71 protein_coding synonymous_variant LOW 771A>T Leu257Leu
M0132168 AOJBEDAH_00002 1002 4 Oral 0.57 protein_coding synonymous_variant LOW 741A>G Val247Val
M0132169 AOJBEDAH_00002 1293 5 Oral 0.71 protein_coding synonymous_variant LOW 450T>C Arg150Arg
M0132170 AOJBEDAH_00002 1536 4 Oral 0.57 protein_coding synonymous_variant LOW 207C>G Ala69Ala
M0132171 AOJBEDAH_00002 1563 5 Oral 0.71 protein_coding synonymous_variant LOW 180G>A Leu60Leu
M0132172 AOJBEDAH_00002 1643 4 Oral 0.57 protein_coding synonymous_variant LOW 100T>C Leu34Leu
M0132173 AOJBEDAH_00003 2213 5 Oral 0.71 protein_coding synonymous_variant LOW 165C>T Arg55Arg
M0132174 AOJBEDAH_00003 2256 4 Oral 0.57 protein_coding missense_variant MODERATE 208A>G Ile70Val
M0132175 AOJBEDAH_00003 2367 3 Oral 0.43 protein_coding missense_variant MODERATE 319A>G Ile107Val
M0132176 AOJBEDAH_00003 2438 3 Oral 0.43 protein_coding synonymous_variant LOW 390G>A Leu130Leu
M0132177 AOJBEDAH_00003 2495 3 Oral 0.43 protein_coding synonymous_variant LOW 447C>T Asp149Asp
M0132178 AOJBEDAH_00004 2884 5 Oral 0.71 protein_coding synonymous_variant LOW 207T>C Ser69Ser
M0132179 AOJBEDAH_00004 2981 3 Oral 0.43 protein_coding synonymous_variant LOW 304A>C Arg102Arg
M0132180 AOJBEDAH_00004 2995 3 Oral 0.43 protein_coding synonymous_variant LOW 318C>T Ser106Ser
M0132181 AOJBEDAH_00004 3068 5 Oral 0.71 protein_coding missense_variant MODERATE 391G>T Val131Phe
M0132182 AOJBEDAH_00004 3097 4 Oral 0.57 protein_coding synonymous_variant LOW 420A>T Gly140Gly
M0132183 AOJBEDAH_00004 3146 4 Oral 0.57 protein_coding missense_variant MODERATE 469A>G Thr157Ala
M0132184 AOJBEDAH_00005 3324 3 Oral 0.43 protein_coding synonymous_variant LOW 51T>C Thr17Thr
M0132185 AOJBEDAH_00003 2462 4 Oral 0.57 protein_coding synonymous_variant LOW 414T>A Pro138Pro
M0132186 AOJBEDAH_00004 3226 3 Oral 0.43 protein_coding synonymous_variant LOW 549A>G Gln183Gln
M0132187 AOJBEDAH_00001 1889 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -1199G>A None
M0132188 AOJBEDAH_00001 1896 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -1206A>T None






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