Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2385
  Reference Plasmid   1111525849768046_bin.37__k141_150563
  Reference Plasmid Size   5268
  Reference Plasmid GC Content   0.35
  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
M0120729 JDENOBIK_00003 3093 6 Oral 0.50 protein_coding synonymous_variant LOW 162C>T Asn54Asn
M0120730 JDENOBIK_00003 3111 6 Oral 0.50 protein_coding synonymous_variant LOW 180A>G Glu60Glu
M0120731 JDENOBIK_00003 3309 8 Oral 0.67 protein_coding synonymous_variant LOW 378C>T Arg126Arg
M0120732 JDENOBIK_00003 3342 6 Oral 0.50 protein_coding synonymous_variant LOW 411T>C Tyr137Tyr
M0120733 JDENOBIK_00003 3456 6 Oral 0.50 protein_coding synonymous_variant LOW 525T>C His175His
M0120734 JDENOBIK_00003 3516 10 Oral 0.83 protein_coding synonymous_variant LOW 585T>C His195His
M0120735 JDENOBIK_00003 3594 5 Oral 0.42 protein_coding synonymous_variant LOW 663T>C Gly221Gly
M0120736 JDENOBIK_00003 3714 9 Oral 0.75 protein_coding synonymous_variant LOW 783T>A Ala261Ala
M0120737 JDENOBIK_00003 3717 10 Oral 0.83 protein_coding synonymous_variant LOW 786T>C Ile262Ile
M0120738 JDENOBIK_00003 3747 6 Oral 0.50 protein_coding synonymous_variant LOW 816G>A Glu272Glu
M0120739 JDENOBIK_00003 3792 6 Oral 0.50 protein_coding synonymous_variant LOW 861T>C Asn287Asn
M0120740 JDENOBIK_00003 3796 6 Oral 0.50 protein_coding missense_variant MODERATE 865G>T Ala289Ser
M0120741 JDENOBIK_00003 3879 4 Oral 0.33 protein_coding synonymous_variant LOW 948A>G Gln316Gln
M0120742 JDENOBIK_00003 3909 4 Oral 0.33 protein_coding synonymous_variant LOW 978T>C Ile326Ile
M0120743 JDENOBIK_00003 3918 8 Oral 0.67 protein_coding synonymous_variant LOW 987T>C Phe329Phe
M0120744 JDENOBIK_00003 3933 8 Oral 0.67 protein_coding synonymous_variant LOW 1002A>G Glu334Glu
M0120745 JDENOBIK_00003 3934 8 Oral 0.67 protein_coding synonymous_variant LOW 1003C>T Leu335Leu
M0120746 JDENOBIK_00003 4011 4 Oral 0.33 protein_coding synonymous_variant LOW 1080T>C Gly360Gly
M0120747 JDENOBIK_00003 4128 5 Oral 0.42 protein_coding synonymous_variant LOW 1197T>C Tyr399Tyr
M0120748 JDENOBIK_00003 4131 5 Oral 0.42 protein_coding synonymous_variant LOW 1200A>T Ser400Ser
M0120749 JDENOBIK_00003 4143 5 Oral 0.42 protein_coding synonymous_variant LOW 1212T>C Ser404Ser
M0120750 JDENOBIK_00003 4242 5 Oral 0.42 protein_coding synonymous_variant LOW 1311T>C Tyr437Tyr
M0120751 JDENOBIK_00003 4314 5 Oral 0.42 protein_coding synonymous_variant LOW 1383T>C Arg461Arg
M0120752 JDENOBIK_00003 4353 9 Oral 0.75 protein_coding synonymous_variant LOW 1422T>C Tyr474Tyr
M0120753 JDENOBIK_00003 4365 7 Oral 0.58 protein_coding synonymous_variant LOW 1434C>T Gly478Gly
M0120754 JDENOBIK_00003 4374 5 Oral 0.42 protein_coding synonymous_variant LOW 1443C>T Cys481Cys
M0120755 JDENOBIK_00003 4377 7 Oral 0.58 protein_coding synonymous_variant LOW 1446T>C Ser482Ser
M0120756 JDENOBIK_00003 4497 5 Oral 0.42 protein_coding synonymous_variant LOW 1566T>C Phe522Phe
M0120757 JDENOBIK_00003 4503 5 Oral 0.42 protein_coding synonymous_variant LOW 1572T>C Asp524Asp
M0120758 JDENOBIK_00003 4530 4 Oral 0.33 protein_coding missense_variant MODERATE 1599A>C Lys533Asn
M0120759 JDENOBIK_00001 4595 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -3164G>A None
M0120760 JDENOBIK_00001 4768 8 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -3337A>G None
M0120761 JDENOBIK_00001 4883 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -3452G>A None
M0120762 JDENOBIK_00001 4916 7 Oral 0.58 protein_coding upstream_gene_variant MODIFIER -3485A>G None
M0120763 JDENOBIK_00001 5000 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -3569A>T None
M0120764 JDENOBIK_00001 5012 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3581C>T None
M0120765 JDENOBIK_00001 5015 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3584A>G None
M0120766 JDENOBIK_00001 5021 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -3590A>T None
M0120767 JDENOBIK_00001 5051 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3620A>T None
M0120768 JDENOBIK_00001 5081 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -3650A>T None
M0120769 JDENOBIK_00001 5126 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -3695C>A None
M0120770 JDENOBIK_00001 5150 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3719G>A None
M0120771 JDENOBIK_00003 52 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -2880G>T None
M0120772 JDENOBIK_00003 55 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -2877C>T None
M0120773 JDENOBIK_00003 58 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -2874A>G None
M0120774 JDENOBIK_00003 67 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2865A>G None
M0120775 JDENOBIK_00003 94 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2838A>G None
M0120776 JDENOBIK_00003 142 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2790G>A None
M0120777 JDENOBIK_00003 169 8 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -2763C>T None
M0120778 JDENOBIK_00003 175 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2757A>G None
M0120779 JDENOBIK_00003 188 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2744G>C None
M0120780 JDENOBIK_00003 232 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2700C>T None
M0120781 JDENOBIK_00003 244 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2688C>T None
M0120782 JDENOBIK_00003 262 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2670T>A None
M0120783 JDENOBIK_00003 334 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2598T>A None
M0120784 JDENOBIK_00003 370 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2562T>A None
M0120785 JDENOBIK_00003 373 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2559G>A None
M0120786 JDENOBIK_00003 391 8 Oral 0.67 protein_coding upstream_gene_variant MODIFIER -2541G>T None
M0120787 JDENOBIK_00003 430 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2502T>A None
M0120788 JDENOBIK_00003 520 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2412A>G None
M0120789 JDENOBIK_00001 690 6 Oral 0.50 protein_coding stop_gained HIGH 742C>T Gln248*
M0120790 JDENOBIK_00001 718 6 Oral 0.50 protein_coding synonymous_variant LOW 714A>G Glu238Glu
M0120791 JDENOBIK_00001 760 6 Oral 0.50 protein_coding synonymous_variant LOW 672A>G Gln224Gln
M0120792 JDENOBIK_00001 763 6 Oral 0.50 protein_coding synonymous_variant LOW 669A>G Leu223Leu
M0120793 JDENOBIK_00001 775 6 Oral 0.50 protein_coding synonymous_variant LOW 657C>T Ile219Ile
M0120794 JDENOBIK_00001 777 6 Oral 0.50 protein_coding missense_variant MODERATE 655A>G Ile219Val
M0120795 JDENOBIK_00001 796 6 Oral 0.50 protein_coding synonymous_variant LOW 636G>A Lys212Lys
M0120796 JDENOBIK_00001 835 5 Oral 0.42 protein_coding synonymous_variant LOW 597A>G Glu199Glu
M0120797 JDENOBIK_00001 852 8 Oral 0.67 protein_coding missense_variant MODERATE 580G>A Asp194Asn
M0120798 JDENOBIK_00001 862 7 Oral 0.58 protein_coding synonymous_variant LOW 570C>T Phe190Phe
M0120799 JDENOBIK_00001 1082 7 Oral 0.58 protein_coding missense_variant MODERATE 350G>A Arg117Lys
M0120800 JDENOBIK_00001 1138 9 Oral 0.75 protein_coding synonymous_variant LOW 294C>T Asn98Asn
M0120801 JDENOBIK_00001 1225 4 Oral 0.33 protein_coding synonymous_variant LOW 207C>T Asn69Asn
M0120802 JDENOBIK_00001 1438 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -7A>G None
M0120803 JDENOBIK_00002 1594 6 Oral 0.50 protein_coding synonymous_variant LOW 1209T>A Ile403Ile
M0120804 JDENOBIK_00002 1780 6 Oral 0.50 protein_coding synonymous_variant LOW 1023C>T Gly341Gly
M0120805 JDENOBIK_00002 1804 6 Oral 0.50 protein_coding synonymous_variant LOW 999T>C Arg333Arg
M0120806 JDENOBIK_00002 1813 7 Oral 0.58 protein_coding synonymous_variant LOW 990C>T Tyr330Tyr
M0120807 JDENOBIK_00002 2358 4 Oral 0.33 protein_coding missense_variant MODERATE 445T>G Ser149Ala
M0120808 JDENOBIK_00002 2407 5 Oral 0.42 protein_coding synonymous_variant LOW 396T>A Ala132Ala
M0120809 JDENOBIK_00002 2422 5 Oral 0.42 protein_coding synonymous_variant LOW 381T>C Asp127Asp
M0120810 JDENOBIK_00002 2443 6 Oral 0.50 protein_coding synonymous_variant LOW 360T>C Pro120Pro
M0120811 JDENOBIK_00002 2449 7 Oral 0.58 protein_coding synonymous_variant LOW 354T>C Asn118Asn
M0120812 JDENOBIK_00002 2467 7 Oral 0.58 protein_coding synonymous_variant LOW 336T>G Leu112Leu
M0120813 JDENOBIK_00002 2497 7 Oral 0.58 protein_coding synonymous_variant LOW 306C>T Asn102Asn
M0120814 JDENOBIK_00002 2500 7 Oral 0.58 protein_coding synonymous_variant LOW 303T>C Asp101Asp
M0120815 JDENOBIK_00002 2503 7 Oral 0.58 protein_coding synonymous_variant LOW 300T>A Thr100Thr
M0120816 JDENOBIK_00002 2629 5 Oral 0.42 protein_coding synonymous_variant LOW 174C>T Tyr58Tyr
M0120817 JDENOBIK_00002 2644 4 Oral 0.33 protein_coding synonymous_variant LOW 159G>A Lys53Lys
M0120818 JDENOBIK_00002 2648 6 Oral 0.50 protein_coding missense_variant MODERATE 155G>T Ser52Ile
M0120819 JDENOBIK_00003 4395 4 Oral 0.33 protein_coding synonymous_variant LOW 1464T>C Ser488Ser
M0120820 JDENOBIK_00003 4404 4 Oral 0.33 protein_coding synonymous_variant LOW 1473T>A Val491Val
M0120821 JDENOBIK_00001 4715 6 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -3284C>G None
M0120822 JDENOBIK_00001 4734 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -3303T>C None
M0120823 JDENOBIK_00001 4802 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -3371C>T None
M0120824 JDENOBIK_00001 5120 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -3689A>C None
M0120825 JDENOBIK_00003 340 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2592A>T None
M0120826 JDENOBIK_00003 580 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -2352G>A None
M0120827 JDENOBIK_00001 727 3 Oral 0.25 protein_coding synonymous_variant LOW 705C>T Asp235Asp
M0120828 JDENOBIK_00001 889 4 Oral 0.33 protein_coding synonymous_variant LOW 543A>T Gly181Gly
M0120829 JDENOBIK_00002 1999 3 Oral 0.25 protein_coding synonymous_variant LOW 804C>T Thr268Thr
M0120830 JDENOBIK_00002 2368 5 Oral 0.42 protein_coding synonymous_variant LOW 435G>A Lys145Lys
M0120831 JDENOBIK_00002 2482 3 Oral 0.25 protein_coding synonymous_variant LOW 321A>T Ser107Ser
M0120832 JDENOBIK_00002 2566 4 Oral 0.33 protein_coding synonymous_variant LOW 237A>T Ile79Ile
M0120833 JDENOBIK_00002 2592 4 Oral 0.33 protein_coding synonymous_variant LOW 211T>C Leu71Leu
M0120834 JDENOBIK_00003 100 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2832G>A None
M0120835 JDENOBIK_00003 138 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2794G>A None
M0120836 JDENOBIK_00003 139 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2793T>A None
M0120837 JDENOBIK_00003 151 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2781T>C None
M0120838 JDENOBIK_00003 157 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -2775G>A None
M0120839 JDENOBIK_00003 181 5 Oral 0.42 protein_coding upstream_gene_variant MODIFIER -2751C>T None
M0120840 JDENOBIK_00001 901 3 Oral 0.25 protein_coding synonymous_variant LOW 531G>A Leu177Leu
M0120841 JDENOBIK_00001 1381 3 Oral 0.25 protein_coding synonymous_variant LOW 51T>C Ile17Ile
M0120842 JDENOBIK_00001 1390 3 Oral 0.25 protein_coding synonymous_variant LOW 42A>G Leu14Leu
M0120843 JDENOBIK_00001 1417 4 Oral 0.33 protein_coding synonymous_variant LOW 15C>T Ile5Ile
M0120844 JDENOBIK_00001 1440 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -9C>T None
M0120845 JDENOBIK_00001 1476 4 Oral 0.33 protein_coding upstream_gene_variant MODIFIER -45A>G None
M0120846 JDENOBIK_00002 2047 3 Oral 0.25 protein_coding synonymous_variant LOW 756T>C Arg252Arg
M0120847 JDENOBIK_00002 2068 3 Oral 0.25 protein_coding synonymous_variant LOW 735A>G Lys245Lys
M0120848 JDENOBIK_00002 2647 4 Oral 0.33 protein_coding synonymous_variant LOW 156T>C Ser52Ser
M0120849 JDENOBIK_00001 2870 3 Oral 0.25 protein_coding upstream_gene_variant MODIFIER -1439A>T None
M0120850 JDENOBIK_00003 3210 3 Oral 0.25 protein_coding synonymous_variant LOW 279C>T Thr93Thr
M0120851 JDENOBIK_00003 3408 6 Oral 0.50 protein_coding synonymous_variant LOW 477T>C Ala159Ala
M0120852 JDENOBIK_00003 3444 3 Oral 0.25 protein_coding synonymous_variant LOW 513G>T Ala171Ala
M0120853 JDENOBIK_00003 4273 6 Oral 0.50 protein_coding synonymous_variant LOW 1342C>T Leu448Leu
M0120854 JDENOBIK_00002 2752 4 Oral 0.33 protein_coding missense_variant MODERATE 51G>A Met17Ile
M0120855 JDENOBIK_00003 3591 3 Oral 0.25 protein_coding missense_variant MODERATE 660T>A Asp220Glu
M0120856 JDENOBIK_00003 3015 3 Oral 0.25 protein_coding synonymous_variant LOW 84A>G Lys28Lys






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