Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2405
  Reference Plasmid   1111525849768046_bin.37__k141_18535
  Reference Plasmid Size   8655
  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
M0122820 JFANFOPB_00002 2636 4 Oral 0.33 protein_coding synonymous_variant LOW 822C>T Pro274Pro
M0122821 JFANFOPB_00002 2651 4 Oral 0.33 protein_coding synonymous_variant LOW 807A>G Val269Val
M0122822 JFANFOPB_00002 2999 4 Oral 0.33 protein_coding synonymous_variant LOW 459T>C Ala153Ala
M0122823 JFANFOPB_00002 3007 4 Oral 0.33 protein_coding missense_variant MODERATE 451G>A Ala151Thr
M0122824 JFANFOPB_00002 3033 4 Oral 0.33 protein_coding missense_variant MODERATE 425A>G His142Arg
M0122825 JFANFOPB_00002 3053 4 Oral 0.33 protein_coding synonymous_variant LOW 405A>G Glu135Glu
M0122826 JFANFOPB_00002 3176 4 Oral 0.33 protein_coding synonymous_variant LOW 282T>C Asn94Asn
M0122827 JFANFOPB_00001 3583 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -1703T>C None
M0122828 JFANFOPB_00001 3586 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -1706C>T None
M0122829 JFANFOPB_00001 3587 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -1707G>A None
M0122830 JFANFOPB_00003 3987 4 Oral 0.33 protein_coding synonymous_variant LOW 1536T>A Gly512Gly
M0122831 JFANFOPB_00003 4035 3 Oral 0.25 protein_coding synonymous_variant LOW 1488T>C Thr496Thr
M0122832 JFANFOPB_00003 4454 3 Oral 0.25 protein_coding synonymous_variant LOW 1069T>C Leu357Leu
M0122833 JFANFOPB_00003 4601 3 Oral 0.25 protein_coding missense_variant MODERATE 922G>A Ala308Thr
M0122834 JFANFOPB_00003 4608 3 Oral 0.25 protein_coding synonymous_variant LOW 915T>A Ala305Ala
M0122835 JFANFOPB_00003 4852 3 Oral 0.25 protein_coding missense_variant MODERATE 671A>G Asn224Ser
M0122836 JFANFOPB_00003 4866 4 Oral 0.33 protein_coding synonymous_variant LOW 657A>G Ala219Ala
M0122837 JFANFOPB_00003 4890 3 Oral 0.25 protein_coding synonymous_variant LOW 633T>C Gly211Gly
M0122838 JFANFOPB_00003 4903 4 Oral 0.33 protein_coding missense_variant MODERATE 620T>C Val207Ala
M0122839 JFANFOPB_00003 4918 3 Oral 0.25 protein_coding missense_variant MODERATE 605C>G Thr202Ser
M0122840 JFANFOPB_00003 4926 3 Oral 0.25 protein_coding synonymous_variant LOW 597T>C Asp199Asp
M0122841 JFANFOPB_00003 4935 3 Oral 0.25 protein_coding synonymous_variant LOW 588G>A Lys196Lys
M0122842 JFANFOPB_00003 5361 4 Oral 0.33 protein_coding synonymous_variant LOW 162A>G Val54Val
M0122843 JFANFOPB_00003 5393 4 Oral 0.33 protein_coding missense_variant MODERATE 130G>A Ala44Thr
M0122844 JFANFOPB_00004 5855 3 Oral 0.25 protein_coding synonymous_variant LOW 651A>T Ala217Ala
M0122845 JFANFOPB_00004 6098 4 Oral 0.33 protein_coding synonymous_variant LOW 408G>A Gly136Gly
M0122846 JFANFOPB_00004 6308 4 Oral 0.33 protein_coding synonymous_variant LOW 198C>A Ala66Ala
M0122847 JFANFOPB_00004 6323 4 Oral 0.33 protein_coding synonymous_variant LOW 183T>C Tyr61Tyr
M0122848 JFANFOPB_00004 6332 6 Oral 0.50 protein_coding synonymous_variant LOW 174G>A Thr58Thr
M0122849 JFANFOPB_00004 6344 6 Oral 0.50 protein_coding synonymous_variant LOW 162T>C Leu54Leu
M0122850 JFANFOPB_00004 6440 4 Oral 0.33 protein_coding missense_variant MODERATE 66C>A Asp22Glu
M0122851 JFANFOPB_00004 6468 3 Oral 0.25 protein_coding missense_variant MODERATE 38G>T Cys13Phe
M0122852 JFANFOPB_00004 6490 3 Oral 0.25 protein_coding missense_variant MODERATE 16A>G Ile6Val
M0122853 JFANFOPB_00005 6663 3 Oral 0.25 protein_coding synonymous_variant LOW 1011C>T Ala337Ala
M0122854 JFANFOPB_00005 6708 4 Oral 0.33 protein_coding synonymous_variant LOW 966C>T Pro322Pro
M0122855 JFANFOPB_00005 6717 3 Oral 0.25 protein_coding synonymous_variant LOW 957C>T Gly319Gly
M0122856 JFANFOPB_00005 6806 5 Oral 0.42 protein_coding missense_variant MODERATE 868A>G Thr290Ala
M0122857 JFANFOPB_00005 6828 4 Oral 0.33 protein_coding synonymous_variant LOW 846C>A Gly282Gly
M0122858 JFANFOPB_00005 6882 3 Oral 0.25 protein_coding synonymous_variant LOW 792C>T Val264Val
M0122859 JFANFOPB_00005 6914 4 Oral 0.33 protein_coding missense_variant MODERATE 760G>A Val254Ile
M0122860 JFANFOPB_00005 6993 5 Oral 0.42 protein_coding synonymous_variant LOW 681G>A Gln227Gln
M0122861 JFANFOPB_00005 7039 3 Oral 0.25 protein_coding missense_variant MODERATE 635C>T Ala212Val
M0122862 JFANFOPB_00005 7071 4 Oral 0.33 protein_coding synonymous_variant LOW 603T>C Asp201Asp
M0122863 JFANFOPB_00005 7083 3 Oral 0.25 protein_coding synonymous_variant LOW 591T>C Ile197Ile
M0122864 JFANFOPB_00005 7170 4 Oral 0.33 protein_coding synonymous_variant LOW 504A>G Thr168Thr
M0122865 JFANFOPB_00005 7248 3 Oral 0.25 protein_coding synonymous_variant LOW 426G>A Leu142Leu
M0122866 JFANFOPB_00005 7280 4 Oral 0.33 protein_coding missense_variant MODERATE 394G>A Val132Ile
M0122867 JFANFOPB_00005 7345 5 Oral 0.42 protein_coding missense_variant MODERATE 329T>C Val110Ala
M0122868 JFANFOPB_00005 7350 3 Oral 0.25 protein_coding synonymous_variant LOW 324C>T His108His
M0122869 JFANFOPB_00005 7413 5 Oral 0.42 protein_coding synonymous_variant LOW 261A>T Ala87Ala
M0122870 JFANFOPB_00005 7464 4 Oral 0.33 protein_coding synonymous_variant LOW 210T>C Asn70Asn
M0122871 JFANFOPB_00005 7482 3 Oral 0.25 protein_coding synonymous_variant LOW 192C>T Pro64Pro
M0122872 JFANFOPB_00005 7539 3 Oral 0.25 protein_coding synonymous_variant LOW 135T>C Asp45Asp
M0122873 JFANFOPB_00005 7564 5 Oral 0.42 protein_coding missense_variant MODERATE 110T>C Val37Ala
M0122874 JFANFOPB_00005 7572 5 Oral 0.42 protein_coding synonymous_variant LOW 102T>C Asp34Asp
M0122875 JFANFOPB_00005 7638 5 Oral 0.42 protein_coding synonymous_variant LOW 36A>G Leu12Leu
M0122876 JFANFOPB_00005 7651 5 Oral 0.42 protein_coding missense_variant MODERATE 23C>T Ala8Val
M0122877 JFANFOPB_00006 7720 4 Oral 0.33 protein_coding synonymous_variant LOW 930A>C Leu310Leu
M0122878 JFANFOPB_00006 7747 4 Oral 0.33 protein_coding synonymous_variant LOW 903T>A Ala301Ala
M0122879 JFANFOPB_00006 7782 3 Oral 0.25 protein_coding missense_variant MODERATE 868T>C Ser290Pro
M0122880 JFANFOPB_00006 7792 3 Oral 0.25 protein_coding synonymous_variant LOW 858T>C Arg286Arg
M0122881 JFANFOPB_00006 7810 5 Oral 0.42 protein_coding synonymous_variant LOW 840T>A Gly280Gly
M0122882 JFANFOPB_00006 8196 3 Oral 0.25 protein_coding synonymous_variant LOW 454C>T Leu152Leu
M0122883 JFANFOPB_00006 8263 6 Oral 0.50 protein_coding synonymous_variant LOW 387C>T Arg129Arg
M0122884 JFANFOPB_00006 8308 6 Oral 0.50 protein_coding synonymous_variant LOW 342T>C Leu114Leu
M0122885 JFANFOPB_00006 8323 5 Oral 0.42 protein_coding synonymous_variant LOW 327T>C Tyr109Tyr
M0122886 JFANFOPB_00006 8493 5 Oral 0.42 protein_coding missense_variant MODERATE 157A>T Met53Leu
M0122887 JFANFOPB_00006 8503 3 Oral 0.25 protein_coding synonymous_variant LOW 147C>T Thr49Thr
M0122888 JFANFOPB_00006 8545 3 Oral 0.25 protein_coding synonymous_variant LOW 105T>C Asp35Asp
M0122889 JFANFOPB_00006 8554 3 Oral 0.25 protein_coding synonymous_variant LOW 96T>C His32His
M0122890 JFANFOPB_00006 8575 5 Oral 0.42 protein_coding synonymous_variant LOW 75G>A Glu25Glu
M0122891 JFANFOPB_00006 8614 5 Oral 0.42 protein_coding synonymous_variant LOW 36T>C Tyr12Tyr
M0122892 JFANFOPB_00006 8626 5 Oral 0.42 protein_coding missense_variant MODERATE 24T>G Asn8Lys
M0122893 JFANFOPB_00006 8145 3 Oral 0.25 protein_coding synonymous_variant LOW 505T>C Leu169Leu
M0122894 JFANFOPB_00006 8245 4 Oral 0.33 protein_coding synonymous_variant LOW 405T>C Thr135Thr
M0122895 JFANFOPB_00006 8443 3 Oral 0.25 protein_coding synonymous_variant LOW 207A>T Ala69Ala
M0122896 JFANFOPB_00006 7966 3 Oral 0.25 protein_coding synonymous_variant LOW 684C>A Ala228Ala
M0122897 JFANFOPB_00006 7967 3 Oral 0.25 protein_coding missense_variant MODERATE 683C>T Ala228Val
M0122898 JFANFOPB_00006 8005 3 Oral 0.25 protein_coding synonymous_variant LOW 645T>G Val215Val
M0122899 JFANFOPB_00002 2813 3 Oral 0.25 protein_coding synonymous_variant LOW 645C>T Asp215Asp
M0122900 JFANFOPB_00002 2921 4 Oral 0.33 protein_coding synonymous_variant LOW 537G>A Thr179Thr
M0122901 JFANFOPB_00002 2923 3 Oral 0.25 protein_coding missense_variant MODERATE 535A>G Thr179Ala
M0122902 JFANFOPB_00002 2924 3 Oral 0.25 protein_coding synonymous_variant LOW 534A>G Ala178Ala
M0122903 JFANFOPB_00002 3080 3 Oral 0.25 protein_coding synonymous_variant LOW 378A>G Leu126Leu
M0122904 JFANFOPB_00002 3092 3 Oral 0.25 protein_coding synonymous_variant LOW 366C>T Asp122Asp
M0122905 JFANFOPB_00002 3254 3 Oral 0.25 protein_coding synonymous_variant LOW 204T>A Leu68Leu
M0122906 JFANFOPB_00003 5421 3 Oral 0.25 protein_coding synonymous_variant LOW 102A>T Ala34Ala
M0122907 JFANFOPB_00005 6936 3 Oral 0.25 protein_coding synonymous_variant LOW 738G>A Glu246Glu
M0122908 JFANFOPB_00001 152 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *1090G>A None
M0122909 JFANFOPB_00001 197 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *1045T>C None
M0122910 JFANFOPB_00001 203 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *1039T>C None
M0122911 JFANFOPB_00001 239 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *1003A>G None
M0122912 JFANFOPB_00001 379 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *863A>G None
M0122913 JFANFOPB_00001 452 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *790G>A None
M0122914 JFANFOPB_00001 1072 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *170T>G None
M0122915 JFANFOPB_00001 1142 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *100C>T None
M0122916 JFANFOPB_00001 1147 3 Oral 0.25 protein_coding downstream_gene_variant MODIFIER *95T>C None
M0122917 JFANFOPB_00001 1238 4 Oral 0.33 protein_coding downstream_gene_variant MODIFIER *4G>A None
M0122918 JFANFOPB_00001 1251 3 Oral 0.25 protein_coding synonymous_variant LOW 630T>C His210His
M0122919 JFANFOPB_00001 1269 4 Oral 0.33 protein_coding synonymous_variant LOW 612C>A Ala204Ala
M0122920 JFANFOPB_00002 3143 3 Oral 0.25 protein_coding synonymous_variant LOW 315G>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