Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2396
  Reference Plasmid   1111525849768046_bin.37__k141_174254
  Reference Plasmid Size   5528
  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
M0121807 GPJKGBKF_00001 115 6 Oral 0.86 protein_coding downstream_gene_variant MODIFIER *393C>G None
M0121808 GPJKGBKF_00001 174 5 Oral 0.71 protein_coding downstream_gene_variant MODIFIER *334T>C None
M0121809 GPJKGBKF_00001 183 3 Oral 0.43 protein_coding downstream_gene_variant MODIFIER *325A>C None
M0121810 GPJKGBKF_00001 216 3 Oral 0.43 protein_coding downstream_gene_variant MODIFIER *292G>T None
M0121811 GPJKGBKF_00001 229 3 Oral 0.43 protein_coding downstream_gene_variant MODIFIER *279A>G None
M0121812 GPJKGBKF_00001 282 5 Oral 0.71 protein_coding downstream_gene_variant MODIFIER *226C>A None
M0121813 GPJKGBKF_00001 388 3 Oral 0.43 protein_coding downstream_gene_variant MODIFIER *120G>A None
M0121814 GPJKGBKF_00001 398 5 Oral 0.71 protein_coding downstream_gene_variant MODIFIER *110C>A None
M0121815 GPJKGBKF_00001 399 4 Oral 0.57 protein_coding downstream_gene_variant MODIFIER *109A>C None
M0121816 GPJKGBKF_00001 403 4 Oral 0.57 protein_coding downstream_gene_variant MODIFIER *105C>T None
M0121817 GPJKGBKF_00001 406 5 Oral 0.71 protein_coding downstream_gene_variant MODIFIER *102T>C None
M0121818 GPJKGBKF_00001 453 3 Oral 0.43 protein_coding downstream_gene_variant MODIFIER *55A>T None
M0121819 GPJKGBKF_00001 576 5 Oral 0.71 protein_coding synonymous_variant LOW 1168T>C Leu390Leu
M0121820 GPJKGBKF_00001 604 3 Oral 0.43 protein_coding synonymous_variant LOW 1140C>T Asp380Asp
M0121821 GPJKGBKF_00001 622 3 Oral 0.43 protein_coding synonymous_variant LOW 1122C>T Leu374Leu
M0121822 GPJKGBKF_00001 727 4 Oral 0.57 protein_coding synonymous_variant LOW 1017T>C Asn339Asn
M0121823 GPJKGBKF_00001 811 5 Oral 0.71 protein_coding synonymous_variant LOW 933G>T Leu311Leu
M0121824 GPJKGBKF_00001 814 5 Oral 0.71 protein_coding synonymous_variant LOW 930T>C Phe310Phe
M0121825 GPJKGBKF_00001 898 5 Oral 0.71 protein_coding synonymous_variant LOW 846G>A Leu282Leu
M0121826 GPJKGBKF_00001 919 4 Oral 0.57 protein_coding synonymous_variant LOW 825C>T Gly275Gly
M0121827 GPJKGBKF_00001 931 5 Oral 0.71 protein_coding synonymous_variant LOW 813T>G Ser271Ser
M0121828 GPJKGBKF_00001 1092 3 Oral 0.43 protein_coding missense_variant MODERATE 652A>C Ile218Leu
M0121829 GPJKGBKF_00001 1240 4 Oral 0.57 protein_coding synonymous_variant LOW 504A>T Thr168Thr
M0121830 GPJKGBKF_00001 1309 3 Oral 0.43 protein_coding synonymous_variant LOW 435T>A Thr145Thr
M0121831 GPJKGBKF_00001 1331 5 Oral 0.71 protein_coding missense_variant MODERATE 413A>T His138Leu
M0121832 GPJKGBKF_00002 1820 4 Oral 0.57 protein_coding synonymous_variant LOW 1146T>C Arg382Arg
M0121833 GPJKGBKF_00002 1835 5 Oral 0.71 protein_coding synonymous_variant LOW 1131A>G Pro377Pro
M0121834 GPJKGBKF_00002 1877 5 Oral 0.71 protein_coding synonymous_variant LOW 1089A>C Gly363Gly
M0121835 GPJKGBKF_00002 1919 3 Oral 0.43 protein_coding synonymous_variant LOW 1047C>T Asp349Asp
M0121836 GPJKGBKF_00002 1943 4 Oral 0.57 protein_coding synonymous_variant LOW 1023T>C Asp341Asp
M0121837 GPJKGBKF_00002 1964 3 Oral 0.43 protein_coding synonymous_variant LOW 1002A>G Glu334Glu
M0121838 GPJKGBKF_00002 1997 3 Oral 0.43 protein_coding synonymous_variant LOW 969C>T Ala323Ala
M0121839 GPJKGBKF_00002 2005 3 Oral 0.43 protein_coding synonymous_variant LOW 961C>T Leu321Leu
M0121840 GPJKGBKF_00002 2006 3 Oral 0.43 protein_coding synonymous_variant LOW 960G>C Thr320Thr
M0121841 GPJKGBKF_00002 2105 4 Oral 0.57 protein_coding synonymous_variant LOW 861T>C Gly287Gly
M0121842 GPJKGBKF_00002 2252 5 Oral 0.71 protein_coding synonymous_variant LOW 714T>C Gly238Gly
M0121843 GPJKGBKF_00002 2390 4 Oral 0.57 protein_coding synonymous_variant LOW 576G>A Glu192Glu
M0121844 GPJKGBKF_00002 2426 3 Oral 0.43 protein_coding synonymous_variant LOW 540C>T Thr180Thr
M0121845 GPJKGBKF_00002 2516 4 Oral 0.57 protein_coding synonymous_variant LOW 450A>G Leu150Leu
M0121846 GPJKGBKF_00002 2657 3 Oral 0.43 protein_coding synonymous_variant LOW 309T>C Arg103Arg
M0121847 GPJKGBKF_00002 2759 4 Oral 0.57 protein_coding synonymous_variant LOW 207T>C Cys69Cys
M0121848 GPJKGBKF_00002 2792 5 Oral 0.71 protein_coding synonymous_variant LOW 174G>A Ser58Ser
M0121849 GPJKGBKF_00002 2819 5 Oral 0.71 protein_coding synonymous_variant LOW 147T>C Asp49Asp
M0121850 GPJKGBKF_00001 3020 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1277T>C None
M0121851 GPJKGBKF_00001 3128 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -1385A>G None
M0121852 GPJKGBKF_00001 3197 5 Oral 0.71 protein_coding upstream_gene_variant MODIFIER -1454T>C None
M0121853 GPJKGBKF_00001 3203 4 Oral 0.57 protein_coding upstream_gene_variant MODIFIER -1460C>T None
M0121854 GPJKGBKF_00003 3258 3 Oral 0.43 protein_coding synonymous_variant LOW 867A>G Leu289Leu
M0121855 GPJKGBKF_00003 3372 5 Oral 0.71 protein_coding synonymous_variant LOW 753T>C Cys251Cys
M0121856 GPJKGBKF_00003 3465 4 Oral 0.57 protein_coding synonymous_variant LOW 660C>T Cys220Cys
M0121857 GPJKGBKF_00003 3495 3 Oral 0.43 protein_coding synonymous_variant LOW 630T>A Ile210Ile
M0121858 GPJKGBKF_00003 3600 4 Oral 0.57 protein_coding synonymous_variant LOW 525A>G Glu175Glu
M0121859 GPJKGBKF_00003 3690 5 Oral 0.71 protein_coding synonymous_variant LOW 435A>C Ala145Ala
M0121860 GPJKGBKF_00003 3858 3 Oral 0.43 protein_coding synonymous_variant LOW 267C>A Arg89Arg
M0121861 GPJKGBKF_00001 4235 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -2492A>G None
M0121862 GPJKGBKF_00001 1258 3 Oral 0.43 protein_coding synonymous_variant LOW 486T>C Ala162Ala
M0121863 GPJKGBKF_00001 1273 3 Oral 0.43 protein_coding synonymous_variant LOW 471T>C Gly157Gly
M0121864 GPJKGBKF_00001 1576 3 Oral 0.43 protein_coding synonymous_variant LOW 168T>A Ala56Ala
M0121865 GPJKGBKF_00001 1720 3 Oral 0.43 protein_coding synonymous_variant LOW 24C>T Ile8Ile
M0121866 GPJKGBKF_00001 1721 3 Oral 0.43 protein_coding missense_variant MODERATE 23T>A Ile8Asn
M0121867 GPJKGBKF_00001 1722 3 Oral 0.43 protein_coding missense_variant MODERATE 22A>T Ile8Phe
M0121868 GPJKGBKF_00001 1751 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -8C>A None
M0121869 GPJKGBKF_00001 1757 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -14A>G None
M0121870 GPJKGBKF_00002 1847 3 Oral 0.43 protein_coding synonymous_variant LOW 1119C>T Ile373Ile
M0121871 GPJKGBKF_00002 2338 3 Oral 0.43 protein_coding synonymous_variant LOW 628C>T Leu210Leu
M0121872 GPJKGBKF_00002 2339 3 Oral 0.43 protein_coding synonymous_variant LOW 627C>A Thr209Thr
M0121873 GPJKGBKF_00002 2455 3 Oral 0.43 protein_coding missense_variant MODERATE 511G>A Asp171Asn
M0121874 GPJKGBKF_00002 2642 4 Oral 0.57 protein_coding synonymous_variant LOW 324A>G Val108Val
M0121875 GPJKGBKF_00001 3174 3 Oral 0.43 protein_coding upstream_gene_variant MODIFIER -1431A>G None
M0121876 GPJKGBKF_00003 3339 4 Oral 0.57 protein_coding synonymous_variant LOW 786C>T Arg262Arg
M0121877 GPJKGBKF_00003 3453 3 Oral 0.43 protein_coding synonymous_variant LOW 672C>T Ile224Ile
M0121878 GPJKGBKF_00003 3525 3 Oral 0.43 protein_coding synonymous_variant LOW 600C>T Cys200Cys
M0121879 GPJKGBKF_00003 3549 4 Oral 0.57 protein_coding synonymous_variant LOW 576C>A Gly192Gly
M0121880 GPJKGBKF_00003 3612 3 Oral 0.43 protein_coding synonymous_variant LOW 513A>G Glu171Glu
M0121881 GPJKGBKF_00002 1931 3 Oral 0.43 protein_coding synonymous_variant LOW 1035C>A Ala345Ala






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