Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3336
  Reference Plasmid   MGYG000298691__MGYG000298691_16
  Reference Plasmid Size   10645
  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
M0135802 HFFNAHIJ_00002 743 3 Oral 0.27 protein_coding missense_variant MODERATE 1027A>G Thr343Ala
M0135803 HFFNAHIJ_00002 956 3 Oral 0.27 protein_coding missense_variant MODERATE 814A>G Ile272Val
M0135804 HFFNAHIJ_00003 2044 5 Oral 0.45 protein_coding missense_variant MODERATE 1316T>C Ile439Thr
M0135805 HFFNAHIJ_00003 2076 3 Oral 0.27 protein_coding synonymous_variant LOW 1284T>A Thr428Thr
M0135806 HFFNAHIJ_00003 2079 3 Oral 0.27 protein_coding synonymous_variant LOW 1281A>C Ile427Ile
M0135807 HFFNAHIJ_00003 2085 3 Oral 0.27 protein_coding synonymous_variant LOW 1275T>C Gly425Gly
M0135808 HFFNAHIJ_00003 2604 5 Oral 0.45 protein_coding synonymous_variant LOW 756A>T Gly252Gly
M0135809 HFFNAHIJ_00003 2616 7 Oral 0.64 protein_coding missense_variant MODERATE 744T>G His248Gln
M0135810 HFFNAHIJ_00003 2723 4 Oral 0.36 protein_coding synonymous_variant LOW 637T>C Leu213Leu
M0135811 HFFNAHIJ_00003 2726 5 Oral 0.45 protein_coding synonymous_variant LOW 634C>T Leu212Leu
M0135812 HFFNAHIJ_00003 2727 5 Oral 0.45 protein_coding synonymous_variant LOW 633C>T Asn211Asn
M0135813 HFFNAHIJ_00003 2730 5 Oral 0.45 protein_coding synonymous_variant LOW 630A>G Gln210Gln
M0135814 HFFNAHIJ_00003 2760 3 Oral 0.27 protein_coding synonymous_variant LOW 600T>C Asp200Asp
M0135815 HFFNAHIJ_00003 2933 4 Oral 0.36 protein_coding synonymous_variant LOW 427T>C Leu143Leu
M0135816 HFFNAHIJ_00003 2970 6 Oral 0.55 protein_coding synonymous_variant LOW 390C>T Tyr130Tyr
M0135817 HFFNAHIJ_00003 3011 6 Oral 0.55 protein_coding missense_variant MODERATE 349A>G Asn117Asp
M0135818 HFFNAHIJ_00003 3245 3 Oral 0.27 protein_coding missense_variant MODERATE 115A>G Ile39Val
M0135819 HFFNAHIJ_00001 3432 5 Oral 0.45 protein_coding upstream_gene_variant MODIFIER -2794T>C None
M0135820 HFFNAHIJ_00001 3510 5 Oral 0.45 protein_coding upstream_gene_variant MODIFIER -2872C>T None
M0135821 HFFNAHIJ_00001 3515 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -2877G>A None
M0135822 HFFNAHIJ_00001 3518 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -2880T>C None
M0135823 HFFNAHIJ_00001 3577 6 Oral 0.55 protein_coding upstream_gene_variant MODIFIER -2939C>T None
M0135824 HFFNAHIJ_00004 3704 6 Oral 0.55 protein_coding missense_variant MODERATE 604A>G Met202Val
M0135825 HFFNAHIJ_00004 3780 6 Oral 0.55 protein_coding synonymous_variant LOW 528T>A Val176Val
M0135826 HFFNAHIJ_00004 3816 6 Oral 0.55 protein_coding synonymous_variant LOW 492T>C Tyr164Tyr
M0135827 HFFNAHIJ_00004 3939 5 Oral 0.45 protein_coding synonymous_variant LOW 369C>A Gly123Gly
M0135828 HFFNAHIJ_00006 4846 4 Oral 0.36 protein_coding synonymous_variant LOW 1023C>A Ile341Ile
M0135829 HFFNAHIJ_00006 4852 4 Oral 0.36 protein_coding synonymous_variant LOW 1017C>T Arg339Arg
M0135830 HFFNAHIJ_00006 4919 4 Oral 0.36 protein_coding missense_variant MODERATE 950C>T Ala317Val
M0135831 HFFNAHIJ_00006 4976 4 Oral 0.36 protein_coding missense_variant MODERATE 893C>A Ser298Tyr
M0135832 HFFNAHIJ_00006 5038 4 Oral 0.36 protein_coding synonymous_variant LOW 831T>C Arg277Arg
M0135833 HFFNAHIJ_00006 5041 4 Oral 0.36 protein_coding synonymous_variant LOW 828T>G Ala276Ala
M0135834 HFFNAHIJ_00006 5052 4 Oral 0.36 protein_coding missense_variant MODERATE 817C>A Leu273Ile
M0135835 HFFNAHIJ_00006 5077 4 Oral 0.36 protein_coding synonymous_variant LOW 792A>T Leu264Leu
M0135836 HFFNAHIJ_00006 5125 3 Oral 0.27 protein_coding synonymous_variant LOW 744T>C Phe248Phe
M0135837 HFFNAHIJ_00006 5134 3 Oral 0.27 protein_coding synonymous_variant LOW 735C>G Gly245Gly
M0135838 HFFNAHIJ_00006 5135 3 Oral 0.27 protein_coding missense_variant MODERATE 734G>C Gly245Ala
M0135839 HFFNAHIJ_00006 5137 3 Oral 0.27 protein_coding missense_variant MODERATE 732T>G Ile244Met
M0135840 HFFNAHIJ_00006 5139 3 Oral 0.27 protein_coding missense_variant MODERATE 730A>G Ile244Val
M0135841 HFFNAHIJ_00006 5269 5 Oral 0.45 protein_coding synonymous_variant LOW 600T>A Ile200Ile
M0135842 HFFNAHIJ_00006 5320 3 Oral 0.27 protein_coding synonymous_variant LOW 549A>G Gly183Gly
M0135843 HFFNAHIJ_00006 5548 5 Oral 0.45 protein_coding synonymous_variant LOW 321C>T His107His
M0135844 HFFNAHIJ_00006 5597 5 Oral 0.45 protein_coding missense_variant MODERATE 272A>G Asn91Ser
M0135845 HFFNAHIJ_00006 5638 5 Oral 0.45 protein_coding synonymous_variant LOW 231T>C Asn77Asn
M0135846 HFFNAHIJ_00002 6594 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -4825A>T None
M0135847 HFFNAHIJ_00002 6599 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4830T>C None
M0135848 HFFNAHIJ_00002 6634 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -4865T>A None
M0135849 HFFNAHIJ_00002 6675 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4906A>T None
M0135850 HFFNAHIJ_00002 6679 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -4910T>C None
M0135851 HFFNAHIJ_00008 7110 5 Oral 0.45 protein_coding synonymous_variant LOW 303A>T Val101Val
M0135852 HFFNAHIJ_00008 7113 5 Oral 0.45 protein_coding synonymous_variant LOW 300G>A Pro100Pro
M0135853 HFFNAHIJ_00008 7203 3 Oral 0.27 protein_coding synonymous_variant LOW 210C>A Thr70Thr
M0135854 HFFNAHIJ_00003 7590 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -4231T>C None
M0135855 HFFNAHIJ_00003 7597 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4238C>T None
M0135856 HFFNAHIJ_00009 8003 6 Oral 0.55 protein_coding missense_variant MODERATE 349T>G Ser117Ala
M0135857 HFFNAHIJ_00009 8353 5 Oral 0.45 protein_coding synonymous_variant LOW 699T>C Ser233Ser
M0135858 HFFNAHIJ_00009 8572 5 Oral 0.45 protein_coding synonymous_variant LOW 918A>G Gln306Gln
M0135859 HFFNAHIJ_00009 8617 3 Oral 0.27 protein_coding synonymous_variant LOW 963C>T Thr321Thr
M0135860 HFFNAHIJ_00009 8626 3 Oral 0.27 protein_coding synonymous_variant LOW 972G>T Ser324Ser
M0135861 HFFNAHIJ_00009 8788 5 Oral 0.45 protein_coding synonymous_variant LOW 1134T>C Asp378Asp
M0135862 HFFNAHIJ_00009 8806 5 Oral 0.45 protein_coding synonymous_variant LOW 1152T>C Tyr384Tyr
M0135863 HFFNAHIJ_00009 8821 5 Oral 0.45 protein_coding synonymous_variant LOW 1167G>A Lys389Lys
M0135864 HFFNAHIJ_00009 8827 5 Oral 0.45 protein_coding synonymous_variant LOW 1173T>A Leu391Leu
M0135865 HFFNAHIJ_00009 8830 5 Oral 0.45 protein_coding missense_variant MODERATE 1176T>A Asp392Glu
M0135866 HFFNAHIJ_00009 8860 4 Oral 0.36 protein_coding synonymous_variant LOW 1206G>T Gly402Gly
M0135867 HFFNAHIJ_00009 8902 5 Oral 0.45 protein_coding synonymous_variant LOW 1248T>C Asn416Asn
M0135868 HFFNAHIJ_00009 8905 6 Oral 0.55 protein_coding synonymous_variant LOW 1251G>A Pro417Pro
M0135869 HFFNAHIJ_00009 8908 6 Oral 0.55 protein_coding synonymous_variant LOW 1254T>A Ile418Ile
M0135870 HFFNAHIJ_00009 8918 6 Oral 0.55 protein_coding missense_variant MODERATE 1264G>C Ala422Pro
M0135871 HFFNAHIJ_00009 8977 5 Oral 0.45 protein_coding synonymous_variant LOW 1323A>T Thr441Thr
M0135872 HFFNAHIJ_00009 9000 6 Oral 0.55 protein_coding missense_variant MODERATE 1346A>C Asn449Thr
M0135873 HFFNAHIJ_00009 9001 6 Oral 0.55 protein_coding missense_variant MODERATE 1347T>A Asn449Lys
M0135874 HFFNAHIJ_00009 9004 6 Oral 0.55 protein_coding synonymous_variant LOW 1350T>A Leu450Leu
M0135875 HFFNAHIJ_00009 9019 6 Oral 0.55 protein_coding synonymous_variant LOW 1365G>A Thr455Thr
M0135876 HFFNAHIJ_00009 9075 6 Oral 0.55 protein_coding missense_variant MODERATE 1421T>C Val474Ala
M0135877 HFFNAHIJ_00009 9119 6 Oral 0.55 protein_coding missense_variant MODERATE 1465C>G Pro489Ala
M0135878 HFFNAHIJ_00004 9256 4 Oral 0.36 protein_coding upstream_gene_variant MODIFIER -4949C>T None
M0135879 HFFNAHIJ_00004 9281 6 Oral 0.55 protein_coding upstream_gene_variant MODIFIER -4974C>T None
M0135880 HFFNAHIJ_00010 9342 3 Oral 0.27 protein_coding missense_variant MODERATE 882C>A Ser294Arg
M0135881 HFFNAHIJ_00010 9362 4 Oral 0.36 protein_coding missense_variant MODERATE 862A>G Lys288Glu
M0135882 HFFNAHIJ_00010 9398 3 Oral 0.27 protein_coding missense_variant MODERATE 826G>A Glu276Lys
M0135883 HFFNAHIJ_00010 9400 3 Oral 0.27 protein_coding missense_variant MODERATE 824A>T Asn275Ile
M0135884 HFFNAHIJ_00010 9425 3 Oral 0.27 protein_coding missense_variant MODERATE 799C>A Gln267Lys
M0135885 HFFNAHIJ_00010 9450 3 Oral 0.27 protein_coding synonymous_variant LOW 774G>A Thr258Thr
M0135886 HFFNAHIJ_00010 9477 4 Oral 0.36 protein_coding synonymous_variant LOW 747T>C Asp249Asp
M0135887 HFFNAHIJ_00010 9510 4 Oral 0.36 protein_coding synonymous_variant LOW 714C>T Ser238Ser
M0135888 HFFNAHIJ_00010 9639 5 Oral 0.45 protein_coding synonymous_variant LOW 585T>C Tyr195Tyr
M0135889 HFFNAHIJ_00010 9663 5 Oral 0.45 protein_coding synonymous_variant LOW 561T>C Asp187Asp
M0135890 HFFNAHIJ_00010 9666 4 Oral 0.36 protein_coding synonymous_variant LOW 558C>A Ile186Ile
M0135891 HFFNAHIJ_00010 9672 4 Oral 0.36 protein_coding synonymous_variant LOW 552G>A Arg184Arg
M0135892 HFFNAHIJ_00010 9684 4 Oral 0.36 protein_coding synonymous_variant LOW 540G>A Val180Val
M0135893 HFFNAHIJ_00010 9692 4 Oral 0.36 protein_coding missense_variant MODERATE 532G>A Asp178Asn
M0135894 HFFNAHIJ_00010 9697 4 Oral 0.36 protein_coding missense_variant MODERATE 527G>C Ser176Thr
M0135895 HFFNAHIJ_00010 9699 4 Oral 0.36 protein_coding synonymous_variant LOW 525A>T Pro175Pro
M0135896 HFFNAHIJ_00010 9707 4 Oral 0.36 protein_coding missense_variant MODERATE 517A>G Arg173Gly
M0135897 HFFNAHIJ_00010 9759 4 Oral 0.36 protein_coding missense_variant MODERATE 465G>T Leu155Phe
M0135898 HFFNAHIJ_00010 9786 4 Oral 0.36 protein_coding synonymous_variant LOW 438A>G Gly146Gly
M0135899 HFFNAHIJ_00009 7822 3 Oral 0.27 protein_coding synonymous_variant LOW 168T>C Asp56Asp
M0135900 HFFNAHIJ_00003 2514 6 Oral 0.55 protein_coding synonymous_variant LOW 846G>A Ala282Ala
M0135901 HFFNAHIJ_00003 2520 4 Oral 0.36 protein_coding synonymous_variant LOW 840A>G Glu280Glu
M0135902 HFFNAHIJ_00003 2562 6 Oral 0.55 protein_coding synonymous_variant LOW 798G>A Lys266Lys
M0135903 HFFNAHIJ_00004 3945 4 Oral 0.36 protein_coding synonymous_variant LOW 363C>T Ala121Ala
M0135904 HFFNAHIJ_00004 3951 4 Oral 0.36 protein_coding synonymous_variant LOW 357C>A Ser119Ser
M0135905 HFFNAHIJ_00004 3956 4 Oral 0.36 protein_coding synonymous_variant LOW 352C>T Leu118Leu
M0135906 HFFNAHIJ_00004 3959 4 Oral 0.36 protein_coding synonymous_variant LOW 349C>T Leu117Leu
M0135907 HFFNAHIJ_00004 3960 4 Oral 0.36 protein_coding synonymous_variant LOW 348C>T Ser116Ser
M0135908 HFFNAHIJ_00004 3963 3 Oral 0.27 protein_coding synonymous_variant LOW 345T>C Asn115Asn
M0135909 HFFNAHIJ_00004 3982 4 Oral 0.36 protein_coding missense_variant MODERATE 326C>T Ser109Leu
M0135910 HFFNAHIJ_00004 4057 4 Oral 0.36 protein_coding missense_variant MODERATE 251G>A Arg84Lys
M0135911 HFFNAHIJ_00008 6942 4 Oral 0.36 protein_coding synonymous_variant LOW 471T>C Asp157Asp
M0135912 HFFNAHIJ_00009 8044 4 Oral 0.36 protein_coding missense_variant MODERATE 390G>T Lys130Asn
M0135913 HFFNAHIJ_00003 2331 4 Oral 0.36 protein_coding synonymous_variant LOW 1029G>A Lys343Lys
M0135914 HFFNAHIJ_00003 2388 4 Oral 0.36 protein_coding synonymous_variant LOW 972C>T Asp324Asp
M0135915 HFFNAHIJ_00003 2396 3 Oral 0.27 protein_coding missense_variant MODERATE 964A>G Ile322Val
M0135916 HFFNAHIJ_00001 3529 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -2891A>G None
M0135917 HFFNAHIJ_00006 5661 3 Oral 0.27 protein_coding missense_variant MODERATE 208A>T Thr70Ser
M0135918 HFFNAHIJ_00006 5662 3 Oral 0.27 protein_coding synonymous_variant LOW 207C>T His69His
M0135919 HFFNAHIJ_00006 5668 3 Oral 0.27 protein_coding synonymous_variant LOW 201T>C Ser67Ser
M0135920 HFFNAHIJ_00006 5675 3 Oral 0.27 protein_coding missense_variant MODERATE 194C>G Pro65Arg
M0135921 HFFNAHIJ_00006 5677 3 Oral 0.27 protein_coding synonymous_variant LOW 192C>T Asn64Asn
M0135922 HFFNAHIJ_00006 5803 3 Oral 0.27 protein_coding synonymous_variant LOW 66A>G Thr22Thr
M0135923 HFFNAHIJ_00006 5844 3 Oral 0.27 protein_coding synonymous_variant LOW 25C>T Leu9Leu
M0135924 HFFNAHIJ_00008 6821 3 Oral 0.27 protein_coding missense_variant MODERATE 592A>T Thr198Ser
M0135925 HFFNAHIJ_00009 8575 3 Oral 0.27 protein_coding synonymous_variant LOW 921A>G Val307Val
M0135926 HFFNAHIJ_00003 1992 3 Oral 0.27 protein_coding synonymous_variant LOW 1368C>T Asp456Asp
M0135927 HFFNAHIJ_00007 6512 3 Oral 0.27 protein_coding missense_variant MODERATE 31C>T His11Tyr
M0135928 HFFNAHIJ_00002 6550 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4781A>G None
M0135929 HFFNAHIJ_00003 7587 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4228A>G None
M0135930 HFFNAHIJ_00003 7591 3 Oral 0.27 protein_coding upstream_gene_variant MODIFIER -4232G>A 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