Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C366
  Reference Plasmid   NZ_AP022198.1
  Reference Plasmid Size   42961
  Reference Plasmid GC Content   0.60
  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
M0086851 GDLJCKGE_00001 260 3 Skin 0.43 protein_coding synonymous_variant LOW 276A>G Lys92Lys
M0086852 GDLJCKGE_00003 1111 3 Skin 0.43 protein_coding synonymous_variant LOW 141T>C Val47Val
M0086853 GDLJCKGE_00003 1117 3 Skin 0.43 protein_coding synonymous_variant LOW 147C>T Gly49Gly
M0086854 GDLJCKGE_00003 1235 3 Skin 0.43 protein_coding missense_variant MODERATE 265C>G Leu89Val
M0086855 GDLJCKGE_00003 1236 3 Skin 0.43 protein_coding missense_variant MODERATE 266T>C Leu89Pro
M0086856 GDLJCKGE_00001 1260 3 Skin 0.43 protein_coding upstream_gene_variant MODIFIER -725G>A None
M0086857 GDLJCKGE_00004 1299 3 Skin 0.43 protein_coding missense_variant MODERATE 26G>A Gly9Asp
M0086858 GDLJCKGE_00004 1339 3 Skin 0.43 protein_coding synonymous_variant LOW 66C>T Gly22Gly
M0086859 GDLJCKGE_00004 1345 3 Skin 0.43 protein_coding synonymous_variant LOW 72C>G Ala24Ala
M0086860 GDLJCKGE_00004 1372 3 Skin 0.43 protein_coding missense_variant MODERATE 99T>G Phe33Leu
M0086861 GDLJCKGE_00004 1411 3 Skin 0.43 protein_coding synonymous_variant LOW 138G>A Glu46Glu
M0086862 GDLJCKGE_00004 1457 3 Skin 0.43 protein_coding synonymous_variant LOW 184T>C Leu62Leu
M0086863 GDLJCKGE_00004 1483 3 Skin 0.43 protein_coding synonymous_variant LOW 210C>T Leu70Leu
M0086864 GDLJCKGE_00004 1536 3 Skin 0.43 protein_coding missense_variant MODERATE 263T>C Val88Ala
M0086865 GDLJCKGE_00004 1548 3 Skin 0.43 protein_coding missense_variant MODERATE 275C>T Ala92Val
M0086866 GDLJCKGE_00004 1567 3 Skin 0.43 protein_coding synonymous_variant LOW 294C>T Tyr98Tyr
M0086867 GDLJCKGE_00004 1585 3 Skin 0.43 protein_coding synonymous_variant LOW 312A>G Gly104Gly
M0086868 GDLJCKGE_00011 7075 3 Skin 0.43 protein_coding missense_variant MODERATE 137C>T Ser46Leu






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
GDLJCKGE_00001 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 93.1 1.6e-74 1 144 1.0000 1.0000 experiment
GDLJCKGE_00002 Mercury (Hg) 93.1 1.3e-58 1 116 1.0000 1.0000 experiment
GDLJCKGE_00003 Mercury (Hg) 84.6 6.6e-37 1 91 1.0000 1.0000 experiment
GDLJCKGE_00004 Mercury (Hg) 79.4 5.9e-61 1 141 1.0000 1.0000 experiment
GDLJCKGE_00005 Mercury (Hg) 91.4 1.9e-291 1 561 1.0000 1.0000 experiment
GDLJCKGE_00006 Mercury (Hg) 99.2 4.2e-63 1 121 1.0000 1.0000 experiment
GDLJCKGE_00007 Mercury (Hg) 85.7 7.6e-34 1 77 0.9872 0.9872 experiment
GDLJCKGE_00032 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
GDLJCKGE_00001 Mercury (Hg) 100 6.6e-77 1 144 1.0000 1.0000 prediction
GDLJCKGE_00002 Mercury (Hg) 100 2e-60 1 116 1.0000 1.0000 prediction
GDLJCKGE_00003 Mercury (Hg) 98.9 1.3e-41 1 91 1.0000 1.0000 prediction
GDLJCKGE_00004 Mercury (Hg) 80.1 1.2e-59 1 141 1.0000 1.0000 prediction
GDLJCKGE_00005 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 99.8 0 1 561 1.0000 1.0000 prediction
GDLJCKGE_00006 Mercury (Hg) 99.2 5.6e-61 1 121 1.0000 0.9453 prediction
GDLJCKGE_00007 Mercury (Hg) 87 7.8e-32 1 77 0.9872 0.9872 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
GDLJCKGE_00015 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GDLJCKGE_00031 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GDLJCKGE_00032 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
GDLJCKGE_00033 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GDLJCKGE_00034 ARO:3002577 98.9 6.87e-135 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GDLJCKGE_00035 ARO:3001397 100 1.47e-206 1 275 1.0000 1.0000 carbapenem OXA beta-lactamase antibiotic inactivation






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
GDLJCKGE_00035 PHI:123477 Oxa-2 100 5.1e-161 1 275 1.0000 1.0000 moths nosocomial infection beta-lactamase reduced virulence






        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
GDLJCKGE_00002 1.A.72.3.1 88.8 5.1e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GDLJCKGE_00003 1.A.72.3.1 84.6 2.5e-35 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GDLJCKGE_00007 1.A.72.5.1 70.7 2e-25 1 75 0.9615 0.9615 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily