Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1625
  Reference Plasmid   1111525849481828_bin.7__k141_638260
  Reference Plasmid Size   50511
  Reference Plasmid GC Content   0.63
  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
M0008908 JPGDOPCJ_00001 6523 36 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4917G>C None
M0008909 JPGDOPCJ_00001 6525 34 Skin 0.18 protein_coding upstream_gene_variant MODIFIER -4919T>C None
M0008910 JPGDOPCJ_00001 6541 36 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -4935T>A None
M0008911 JPGDOPCJ_00007 8204 34 Skin 0.18 protein_coding missense_variant MODERATE 272T>G Ile91Ser
M0008912 JPGDOPCJ_00032 35037 35 Skin 0.18 protein_coding synonymous_variant LOW 711T>C Gly237Gly
M0008913 JPGDOPCJ_00032 35608 27 Skin 0.14 protein_coding missense_variant MODERATE 140C>G Ala47Gly
M0008914 JPGDOPCJ_00020 23627 23 Skin 0.12 protein_coding missense_variant MODERATE 821G>A Arg274Lys
M0008915 JPGDOPCJ_00010 12215 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -1215G>T None
M0008916 JPGDOPCJ_00010 12218 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -1218G>A None
M0008917 JPGDOPCJ_00020 28824 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -4377G>A None
M0008918 JPGDOPCJ_00001 6459 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -4853G>A None
M0008919 JPGDOPCJ_00001 6515 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -4909C>A None
M0008920 JPGDOPCJ_00001 6531 4 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -4925C>G None
M0008921 JPGDOPCJ_00010 13838 3 Skin 0.02 protein_coding upstream_gene_variant MODIFIER -2838C>A None
M0008922 JPGDOPCJ_00014 18460 3 Skin 0.02 protein_coding synonymous_variant LOW 49T>C Leu17Leu
M0008923 JPGDOPCJ_00023 26577 7 Skin 0.04 protein_coding missense_variant MODERATE 455G>T Arg152Leu
M0008924 JPGDOPCJ_00010 10714 3 Skin 0.02 protein_coding missense_variant MODERATE 287C>G Ala96Gly
M0008925 JPGDOPCJ_00010 10782 7 Skin 0.04 protein_coding synonymous_variant LOW 219C>T Gly73Gly






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
JPGDOPCJ_00013 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 97.7 3.4e-265 1 484 1.0000 1.0000 experiment
JPGDOPCJ_00014 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 98.2 0 1 1050 1.0000 1.0000 experiment
JPGDOPCJ_00015 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 95.6 3.9e-200 1 384 1.0000 1.0000 experiment
JPGDOPCJ_00016 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 93.3 1.3e-109 1 210 1.0000 1.0000 experiment
JPGDOPCJ_00013 Toluene [class: Aromatic hydrocarbons] [class: Aromatic hydrocarbons], n-hexane [class: Alkane] 100 3e-267 1 484 1.0000 1.0000 prediction
JPGDOPCJ_00014 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 100 0 1 1050 1.0000 1.0000 prediction
JPGDOPCJ_00015 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 97.4 1.3e-201 1 384 1.0000 1.0000 prediction
JPGDOPCJ_00016 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 98.6 5.8e-114 1 210 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
JPGDOPCJ_00014 ARO:3000378 78.4 0 1 1042 0.9933 0.9971 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
JPGDOPCJ_00014 PHI:10531 mexB 82.8 0 1 1034 0.9848 0.9904 eudicots infection efflux pump membrane transporter 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
JPGDOPCJ_00034 AXQ49514.1|GH3 100 0 1 762 1 0.9987





        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
JPGDOPCJ_00004 2.A.1.15.1 95.8 2.2e-238 1 447 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
JPGDOPCJ_00006 2.A.1.6.3 94.6 1.2e-228 1 429 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
JPGDOPCJ_00012 1.B.25.1.14 71.4 2.6e-172 15 418 0.9665 0.9691 1 Channels/Pores 1.B β-Barrel Porins 1.B.25 The Outer Membrane Porin (Opr) Family
JPGDOPCJ_00013 2.A.6.2.9 97.7 1.3e-263 1 484 1.0000 1.2604 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
JPGDOPCJ_00014 2.A.6.2.9 98.2 0 1 1050 1.0000 2.7344 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
JPGDOPCJ_00015 2.A.6.2.9 95.6 1.5e-198 1 384 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily