Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C388
  Reference Plasmid   NZ_AP026405.1
  Reference Plasmid Size   36687
  Reference Plasmid GC Content   0.61
  Reference Plasmid Mobility Type   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
M0087005 KJIMDIMC_00022 18852 5 Skin 0.71 protein_coding upstream_gene_variant MODIFIER -2690G>A None
M0087006 KJIMDIMC_00027 18863 5 Skin 0.71 protein_coding synonymous_variant LOW 2958G>A Leu986Leu
M0087007 KJIMDIMC_00027 18944 5 Skin 0.71 protein_coding synonymous_variant LOW 2877T>C Tyr959Tyr
M0087008 KJIMDIMC_00027 18981 5 Skin 0.71 protein_coding missense_variant MODERATE 2840A>T Gln947Leu
M0087009 KJIMDIMC_00027 18983 5 Skin 0.71 protein_coding synonymous_variant LOW 2838A>C Ala946Ala
M0087010 KJIMDIMC_00027 18988 5 Skin 0.71 protein_coding synonymous_variant LOW 2833C>T Leu945Leu
M0087011 KJIMDIMC_00027 18989 5 Skin 0.71 protein_coding synonymous_variant LOW 2832G>C Val944Val
M0087012 KJIMDIMC_00027 19039 5 Skin 0.71 protein_coding synonymous_variant LOW 2782C>T Leu928Leu
M0087013 KJIMDIMC_00027 19231 5 Skin 0.71 protein_coding synonymous_variant LOW 2590C>T Leu864Leu
M0087014 KJIMDIMC_00027 19301 5 Skin 0.71 protein_coding missense_variant MODERATE 2520A>C Glu840Asp
M0087015 KJIMDIMC_00027 19305 5 Skin 0.71 protein_coding missense_variant MODERATE 2516G>C Gly839Ala
M0087016 KJIMDIMC_00027 19308 5 Skin 0.71 protein_coding missense_variant MODERATE 2513T>C Ile838Thr
M0087017 KJIMDIMC_00027 19328 5 Skin 0.71 protein_coding synonymous_variant LOW 2493C>T Ala831Ala
M0087018 KJIMDIMC_00027 19413 5 Skin 0.71 protein_coding missense_variant MODERATE 2408C>T Ala803Val
M0087019 KJIMDIMC_00027 19886 5 Skin 0.71 protein_coding synonymous_variant LOW 1935C>G Ala645Ala
M0087020 KJIMDIMC_00027 20047 5 Skin 0.71 protein_coding missense_variant MODERATE 1774G>A Ala592Thr
M0087021 KJIMDIMC_00027 20195 5 Skin 0.71 protein_coding synonymous_variant LOW 1626C>T Asn542Asn
M0087022 KJIMDIMC_00027 20469 4 Skin 0.57 protein_coding missense_variant MODERATE 1352G>C Arg451Thr
M0087023 KJIMDIMC_00027 20525 4 Skin 0.57 protein_coding missense_variant MODERATE 1296G>C Met432Ile
M0087024 KJIMDIMC_00027 20534 4 Skin 0.57 protein_coding synonymous_variant LOW 1287G>A Pro429Pro
M0087025 KJIMDIMC_00027 20576 4 Skin 0.57 protein_coding missense_variant MODERATE 1245C>A Asp415Glu
M0087026 KJIMDIMC_00027 20577 4 Skin 0.57 protein_coding missense_variant MODERATE 1244A>C Asp415Ala
M0087027 KJIMDIMC_00027 20625 4 Skin 0.57 protein_coding missense_variant MODERATE 1196A>T Glu399Val
M0087028 KJIMDIMC_00027 20651 4 Skin 0.57 protein_coding missense_variant MODERATE 1170G>A Met390Ile
M0087029 KJIMDIMC_00027 20675 4 Skin 0.57 protein_coding synonymous_variant LOW 1146C>G Pro382Pro
M0087030 KJIMDIMC_00027 20677 4 Skin 0.57 protein_coding missense_variant MODERATE 1144C>T Pro382Ser
M0087031 KJIMDIMC_00027 20699 4 Skin 0.57 protein_coding synonymous_variant LOW 1122C>G Thr374Thr
M0087032 KJIMDIMC_00027 20714 4 Skin 0.57 protein_coding synonymous_variant LOW 1107A>G Pro369Pro
M0087033 KJIMDIMC_00027 20849 4 Skin 0.57 protein_coding synonymous_variant LOW 972A>C Gly324Gly
M0087034 KJIMDIMC_00027 20977 3 Skin 0.43 protein_coding missense_variant MODERATE 844T>C Tyr282His
M0087035 KJIMDIMC_00027 20984 3 Skin 0.43 protein_coding synonymous_variant LOW 837A>T Ala279Ala
M0087036 KJIMDIMC_00027 21009 3 Skin 0.43 protein_coding missense_variant MODERATE 812G>C Gly271Ala
M0087037 KJIMDIMC_00027 21425 3 Skin 0.43 protein_coding synonymous_variant LOW 396C>T Arg132Arg
M0087038 KJIMDIMC_00027 21428 3 Skin 0.43 protein_coding synonymous_variant LOW 393G>A Ala131Ala
M0087039 KJIMDIMC_00027 21429 3 Skin 0.43 protein_coding missense_variant MODERATE 392C>G Ala131Gly
M0087040 KJIMDIMC_00027 21521 3 Skin 0.43 protein_coding synonymous_variant LOW 300G>A Val100Val
M0087041 KJIMDIMC_00027 21551 3 Skin 0.43 protein_coding synonymous_variant LOW 270T>C Arg90Arg
M0087042 KJIMDIMC_00027 21605 3 Skin 0.43 protein_coding synonymous_variant LOW 216C>T Asp72Asp
M0087043 KJIMDIMC_00027 21610 3 Skin 0.43 protein_coding missense_variant MODERATE 211C>A Leu71Ile
M0087044 KJIMDIMC_00027 21626 3 Skin 0.43 protein_coding synonymous_variant LOW 195T>C Leu65Leu
M0087045 KJIMDIMC_00027 21683 3 Skin 0.43 protein_coding synonymous_variant LOW 138C>T Phe46Phe
M0087046 KJIMDIMC_00027 21798 3 Skin 0.43 protein_coding missense_variant MODERATE 23C>A Thr8Lys
M0087047 KJIMDIMC_00028 21918 3 Skin 0.43 protein_coding synonymous_variant LOW 651G>A Ala217Ala
M0087048 KJIMDIMC_00028 21990 3 Skin 0.43 protein_coding synonymous_variant LOW 579C>G Gly193Gly
M0087049 KJIMDIMC_00028 21993 3 Skin 0.43 protein_coding synonymous_variant LOW 576C>T Gly192Gly
M0087050 KJIMDIMC_00028 22068 3 Skin 0.43 protein_coding synonymous_variant LOW 501T>G Ala167Ala
M0087051 KJIMDIMC_00028 22092 3 Skin 0.43 protein_coding synonymous_variant LOW 477G>A Leu159Leu
M0087052 KJIMDIMC_00028 22125 3 Skin 0.43 protein_coding synonymous_variant LOW 444C>T Asn148Asn
M0087053 KJIMDIMC_00028 22137 3 Skin 0.43 protein_coding synonymous_variant LOW 432A>G Ser144Ser






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
KJIMDIMC_00002 Mercury (Hg) 88.7 5.5e-73 1 151 1.0000 1.0000 experiment
KJIMDIMC_00003 Mercury (Hg) 99.1 1.2e-61 32 146 0.7877 0.9914 experiment
KJIMDIMC_00004 Mercury (Hg) 85.7 4.5e-38 1 91 1.0000 1.0000 experiment
KJIMDIMC_00005 Mercury (Hg) 80.1 1.6e-61 1 141 1.0000 1.0000 experiment
KJIMDIMC_00006 Mercury (Hg) 92.5 8.4e-292 1 561 1.0000 1.0000 experiment
KJIMDIMC_00007 Mercury (Hg) 90.1 1.6e-54 1 121 1.0000 1.0000 experiment
KJIMDIMC_00008 Mercury (Hg) 96.2 2.7e-39 1 78 1.0000 1.0000 experiment
KJIMDIMC_00035 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
KJIMDIMC_00002 Mercury (Hg) 99.3 7.9e-81 1 151 1.0000 1.0000 prediction
KJIMDIMC_00003 Mercury (Hg) 100 8.8e-69 12 146 0.9247 0.9926 prediction
KJIMDIMC_00004 Mercury (Hg) 94.5 9.1e-40 1 91 1.0000 1.0000 prediction
KJIMDIMC_00005 Mercury (Hg) 80.9 3.2e-60 1 141 1.0000 1.0000 prediction
KJIMDIMC_00006 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 99.8 0 1 561 1.0000 1.0000 prediction
KJIMDIMC_00007 Mercury (Hg) 100 3.1e-59 1 121 1.0000 1.0000 prediction
KJIMDIMC_00008 Mercury (Hg) 98.7 5.1e-39 1 78 1.0000 1.0000 prediction






        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
KJIMDIMC_00031 ARO:3004239 98.8 4.5e-189 1 260 1.0000 1.0000 cephalosporin NPS beta-lactamase antibiotic inactivation
KJIMDIMC_00033 ARO:3002578 99 3.33e-153 1 210 1.0000 0.8046 aminoglycoside antibiotic AAC(6') antibiotic inactivation
KJIMDIMC_00035 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
KJIMDIMC_00036 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
KJIMDIMC_00003 1.A.72.3.1 93 9e-56 32 146 0.7877 1.2637 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
KJIMDIMC_00004 1.A.72.3.1 85.7 1.7e-36 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
KJIMDIMC_00008 1.A.72.5.1 80.8 7.5e-33 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily