Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1687
  Reference Plasmid   1111525849486576_bin.33__k141_708227
  Reference Plasmid Size   38603
  Reference Plasmid GC Content   0.71
  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
M0010881 GEOJDPLP_00024 24129 7 Skin 0.23 protein_coding missense_variant MODERATE 913A>G Thr305Ala
M0010882 GEOJDPLP_00024 24134 7 Skin 0.23 protein_coding missense_variant MODERATE 918G>T Glu306Asp
M0010883 GEOJDPLP_00025 24469 7 Skin 0.23 protein_coding synonymous_variant LOW 159C>T Asp53Asp
M0010884 GEOJDPLP_00025 24748 5 Skin 0.16 protein_coding synonymous_variant LOW 438C>T Val146Val
M0010885 GEOJDPLP_00025 24751 5 Skin 0.16 protein_coding synonymous_variant LOW 441T>C Tyr147Tyr
M0010886 GEOJDPLP_00025 24877 6 Skin 0.19 protein_coding synonymous_variant LOW 567G>C Ala189Ala
M0010887 GEOJDPLP_00025 24878 6 Skin 0.19 protein_coding missense_variant MODERATE 568C>G His190Asp
M0010888 GEOJDPLP_00025 24879 6 Skin 0.19 protein_coding missense_variant MODERATE 569A>G His190Arg
M0010889 GEOJDPLP_00025 24928 6 Skin 0.19 protein_coding synonymous_variant LOW 618G>A Gln206Gln
M0010890 GEOJDPLP_00025 24946 6 Skin 0.19 protein_coding synonymous_variant LOW 636G>C Gly212Gly
M0010891 GEOJDPLP_00026 25501 4 Skin 0.13 protein_coding missense_variant MODERATE 590A>C Gln197Pro
M0010892 GEOJDPLP_00027 26412 5 Skin 0.16 protein_coding synonymous_variant LOW 924G>C Ala308Ala
M0010893 GEOJDPLP_00027 26493 5 Skin 0.16 protein_coding synonymous_variant LOW 843A>C Arg281Arg
M0010894 GEOJDPLP_00027 26520 5 Skin 0.16 protein_coding synonymous_variant LOW 816G>C Leu272Leu
M0010895 GEOJDPLP_00027 26755 5 Skin 0.16 protein_coding missense_variant MODERATE 581C>A Ala194Glu
M0010896 GEOJDPLP_00027 26774 5 Skin 0.16 protein_coding missense_variant MODERATE 562T>A Ser188Thr
M0010897 GEOJDPLP_00026 27338 5 Skin 0.16 protein_coding upstream_gene_variant MODIFIER -1248C>T None
M0010898 GEOJDPLP_00030 29120 3 Skin 0.10 protein_coding synonymous_variant LOW 165A>G Ser55Ser
M0010899 GEOJDPLP_00030 29123 3 Skin 0.10 protein_coding synonymous_variant LOW 168C>G Ser56Ser
M0010900 GEOJDPLP_00030 29156 3 Skin 0.10 protein_coding synonymous_variant LOW 201G>T Leu67Leu
M0010901 GEOJDPLP_00030 29162 3 Skin 0.10 protein_coding synonymous_variant LOW 207G>C Leu69Leu
M0010902 GEOJDPLP_00030 29164 3 Skin 0.10 protein_coding missense_variant MODERATE 209G>A Arg70Lys
M0010903 GEOJDPLP_00030 29171 3 Skin 0.10 protein_coding synonymous_variant LOW 216A>G Ala72Ala
M0010904 GEOJDPLP_00016 15270 4 Skin 0.13 protein_coding synonymous_variant LOW 900G>T Thr300Thr
M0010905 GEOJDPLP_00016 15278 5 Skin 0.16 protein_coding missense_variant MODERATE 892A>G Thr298Ala
M0010906 GEOJDPLP_00016 15354 5 Skin 0.16 protein_coding synonymous_variant LOW 816T>C His272His
M0010907 GEOJDPLP_00016 15453 5 Skin 0.16 protein_coding synonymous_variant LOW 717C>G Ala239Ala
M0010908 GEOJDPLP_00016 15483 5 Skin 0.16 protein_coding synonymous_variant LOW 687C>G Leu229Leu
M0010909 GEOJDPLP_00016 15492 5 Skin 0.16 protein_coding synonymous_variant LOW 678C>G Arg226Arg
M0010910 GEOJDPLP_00016 15495 5 Skin 0.16 protein_coding synonymous_variant LOW 675T>G Leu225Leu
M0010911 GEOJDPLP_00016 15503 5 Skin 0.16 protein_coding synonymous_variant LOW 667C>A Arg223Arg
M0010912 GEOJDPLP_00016 15786 5 Skin 0.16 protein_coding synonymous_variant LOW 384G>A Val128Val
M0010913 GEOJDPLP_00016 15810 5 Skin 0.16 protein_coding synonymous_variant LOW 360G>T Ala120Ala
M0010914 GEOJDPLP_00016 15939 5 Skin 0.16 protein_coding synonymous_variant LOW 231A>G Ala77Ala
M0010915 GEOJDPLP_00021 20191 4 Skin 0.13 protein_coding missense_variant MODERATE 242G>T Gly81Val
M0010916 GEOJDPLP_00008 8191 13 Skin 0.42 protein_coding missense_variant MODERATE 677G>A Gly226Glu
M0010917 GEOJDPLP_00002 1108 4 Skin 0.13 protein_coding synonymous_variant LOW 681G>T Gly227Gly
M0010918 GEOJDPLP_00002 1112 4 Skin 0.13 protein_coding missense_variant MODERATE 685G>A Gly229Ser
M0010919 GEOJDPLP_00002 1113 4 Skin 0.13 protein_coding missense_variant MODERATE 686G>A Gly229Asp
M0010920 GEOJDPLP_00002 1165 4 Skin 0.13 protein_coding synonymous_variant LOW 738T>C His246His
M0010921 GEOJDPLP_00002 1183 4 Skin 0.13 protein_coding synonymous_variant LOW 756A>G Ala252Ala
M0010922 GEOJDPLP_00002 1189 5 Skin 0.16 protein_coding synonymous_variant LOW 762C>G Ala254Ala
M0010923 GEOJDPLP_00002 1228 6 Skin 0.19 protein_coding synonymous_variant LOW 801G>C Gly267Gly
M0010924 GEOJDPLP_00002 1306 6 Skin 0.19 protein_coding synonymous_variant LOW 879A>C Ala293Ala
M0010925 GEOJDPLP_00002 1321 5 Skin 0.16 protein_coding synonymous_variant LOW 894G>C Ala298Ala
M0010926 GEOJDPLP_00002 1342 5 Skin 0.16 protein_coding synonymous_variant LOW 915C>T Ala305Ala
M0010927 GEOJDPLP_00002 1352 6 Skin 0.19 protein_coding missense_variant MODERATE 925C>G Arg309Gly
M0010928 GEOJDPLP_00002 1383 6 Skin 0.19 protein_coding missense_variant MODERATE 956C>T Pro319Leu
M0010929 GEOJDPLP_00002 1403 5 Skin 0.16 protein_coding missense_variant MODERATE 976G>A Gly326Arg
M0010930 GEOJDPLP_00002 1408 5 Skin 0.16 protein_coding synonymous_variant LOW 981C>T Phe327Phe
M0010931 GEOJDPLP_00001 44 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -37G>C None
M0010932 GEOJDPLP_00001 61 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -20C>T None
M0010933 GEOJDPLP_00001 74 3 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -7T>C None
M0010934 GEOJDPLP_00001 122 3 Skin 0.10 protein_coding synonymous_variant LOW 42A>C Ala14Ala
M0010935 GEOJDPLP_00001 149 3 Skin 0.10 protein_coding synonymous_variant LOW 69T>C Leu23Leu
M0010936 GEOJDPLP_00001 398 3 Skin 0.10 protein_coding synonymous_variant LOW 318C>T Asp106Asp
M0010937 GEOJDPLP_00002 484 3 Skin 0.10 protein_coding synonymous_variant LOW 57T>C Gly19Gly
M0010938 GEOJDPLP_00002 518 3 Skin 0.10 protein_coding missense_variant MODERATE 91G>A Val31Ile
M0010939 GEOJDPLP_00002 673 3 Skin 0.10 protein_coding synonymous_variant LOW 246G>T Pro82Pro
M0010940 GEOJDPLP_00002 679 3 Skin 0.10 protein_coding synonymous_variant LOW 252A>G Gln84Gln
M0010941 GEOJDPLP_00002 685 4 Skin 0.13 protein_coding synonymous_variant LOW 258C>G Val86Val
M0010942 GEOJDPLP_00002 700 4 Skin 0.13 protein_coding synonymous_variant LOW 273T>C Phe91Phe
M0010943 GEOJDPLP_00002 733 4 Skin 0.13 protein_coding synonymous_variant LOW 306T>C Leu102Leu
M0010944 GEOJDPLP_00002 742 4 Skin 0.13 protein_coding synonymous_variant LOW 315A>G Gln105Gln
M0010945 GEOJDPLP_00002 833 4 Skin 0.13 protein_coding missense_variant MODERATE 406C>G His136Asp
M0010946 GEOJDPLP_00002 817 3 Skin 0.10 protein_coding synonymous_variant LOW 390G>C Ala130Ala
M0010947 GEOJDPLP_00002 822 3 Skin 0.10 protein_coding missense_variant MODERATE 395C>T Ala132Val
M0010948 GEOJDPLP_00002 831 3 Skin 0.10 protein_coding missense_variant MODERATE 404A>G Gln135Arg






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
GEOJDPLP_00021 ARJ70932.1|GT4 78.8 4.06e-179 9 352 0.9529 0.9772
GEOJDPLP_00022 WAJ29215.1|GT0 75.3 2.89e-204 1 360 0.9756 0.9756





        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