Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C416
  Reference Plasmid   NZ_CP009975.1
  Reference Plasmid Size   583900
  Reference Plasmid GC Content   0.58
  Reference Plasmid Mobility Type   conjugative





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
M0087194 IBBBJDNE_00398 363527 12 Skin 0.26 protein_coding missense_variant MODERATE 818C>A Ala273Glu
M0087195 IBBBJDNE_00396 360932 4 Skin 0.09 protein_coding missense_variant MODERATE 90C>A Asn30Lys
M0087196 IBBBJDNE_00396 360933 4 Skin 0.09 protein_coding missense_variant MODERATE 91A>C Met31Leu
M0087197 IBBBJDNE_00396 360934 4 Skin 0.09 protein_coding missense_variant MODERATE 92T>C Met31Thr






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
IBBBJDNE_00100 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
IBBBJDNE_00101 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
IBBBJDNE_00102 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
IBBBJDNE_00339 Mercury (Hg) 100 2.9e-41 1 78 1.0000 1.0000 experiment
IBBBJDNE_00340 Mercury (Hg) 98.3 1.6e-62 1 121 1.0000 1.0000 experiment
IBBBJDNE_00341 Mercury (Hg) 85.4 1.6e-266 1 548 1.0237 1.0000 experiment
IBBBJDNE_00342 Mercury (Hg) 100 3.3e-40 1 81 1.0000 1.0000 experiment
IBBBJDNE_00343 Mercury (Hg) 93.3 4.9e-40 1 90 0.9890 0.9890 experiment
IBBBJDNE_00344 Mercury (Hg) 94 4.1e-60 1 116 1.0000 1.0000 experiment
IBBBJDNE_00345 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 94.4 1.5e-75 1 144 1.0000 1.0000 experiment
IBBBJDNE_00440 Toluene [class: Aromatic hydrocarbons], Styrene [class: Polystyrenes], m-xylene [class: Aromatic hydrocarbons], Ethylbenzene [class: Aromatic hydrocarbons], Propylbenzene [class: Aromatic hydrocarbons] 100 5.8e-262 1 470 1.0000 1.0000 experiment
IBBBJDNE_00441 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 100 0 1 1049 1.0000 1.0000 experiment
IBBBJDNE_00445 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 99.1 1.2e-171 1 315 0.9162 0.8298 experiment
IBBBJDNE_00446 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 100 8.4e-138 1 259 1.0000 1.0000 experiment
IBBBJDNE_00447 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 100 7.2e-119 1 213 1.0000 1.0000 experiment
IBBBJDNE_00654 Nickel (Ni), Zinc (Zn) 74.5 6.8e-38 12 105 0.8952 0.9895 experiment
IBBBJDNE_00662 Chromium (Cr) 71.1 1.2e-190 12 454 0.9781 0.9738 experiment
IBBBJDNE_00663 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 73.3 1.7e-66 1 150 1.0000 1.0000 experiment
IBBBJDNE_00100 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
IBBBJDNE_00101 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
IBBBJDNE_00102 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
IBBBJDNE_00332 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
IBBBJDNE_00339 Mercury (Hg) 100 6.6e-39 1 78 1.0000 1.0000 prediction
IBBBJDNE_00340 Mercury (Hg) 100 7.3e-61 1 121 1.0000 1.0000 prediction
IBBBJDNE_00341 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 1.7e-306 1 548 1.0000 1.0000 prediction
IBBBJDNE_00342 Mercury (Hg) 100 7.6e-38 1 81 1.0000 1.0000 prediction
IBBBJDNE_00343 Mercury (Hg) 100 8.2e-41 1 91 1.0000 0.9785 prediction
IBBBJDNE_00344 Mercury (Hg) 100 7e-61 1 116 1.0000 1.0000 prediction
IBBBJDNE_00345 Mercury (Hg) 100 6.6e-77 1 144 1.0000 1.0000 prediction
IBBBJDNE_00355 Copper (Cu), Sodium acetate [class: Acetate] 84.7 1.9e-249 13 548 0.9781 0.9781 prediction
IBBBJDNE_00396 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
IBBBJDNE_00440 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 100 1.3e-259 1 470 1.0000 1.0000 prediction
IBBBJDNE_00441 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 100 0 1 1049 1.0000 1.0000 prediction
IBBBJDNE_00445 n-hexane [class: Alkane], Toluene [class: Aromatic hydrocarbons], Dimethylphthalate [class: Pthalate] 99.1 2.7e-169 1 315 0.9162 0.8298 prediction
IBBBJDNE_00446 Toluene [class: Aromatic hydrocarbons], Styrene [class: Polystyrenes] 100 1.9e-135 1 259 1.0000 1.0000 prediction
IBBBJDNE_00447 Toluene [class: Aromatic hydrocarbons], Styrene [class: Polystyrenes] 100 1.6e-116 1 213 1.0000 1.0000 prediction
IBBBJDNE_00654 Nickel (Ni), Zinc (Zn) 100 7.5e-54 1 105 1.0000 1.0000 prediction
IBBBJDNE_00660 Nickel (Ni), Cobalt (Co) 100 9.8e-233 1 434 1.0000 1.0000 prediction
IBBBJDNE_00661 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 100 7.2e-177 1 313 1.0000 1.0000 prediction
IBBBJDNE_00662 Chromium (Cr) 100 2.7e-265 1 456 1.0000 1.0000 prediction
IBBBJDNE_00663 Chromium (Cr) 80.7 9.6e-71 1 150 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






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
IBBBJDNE_00217 PHI:10380 RecA 72.3 2.5e-68 1 173 0.9943 0.9857 nematodes nosocomial infection DNA strand exchange and recombination protein reduced virulence
IBBBJDNE_00363 PHI:9583 paaK1 71.3 1.9e-178 10 434 0.9725 0.9838 nematodes cystic fibrosis-like disease phenylacetate-coenzyme A ligase increased virulence (hypervirulence)
IBBBJDNE_00372 PHI:9583 paaK1 70.4 1.2e-175 10 435 0.9748 0.9838 nematodes cystic fibrosis-like disease phenylacetate-coenzyme A ligase increased virulence (hypervirulence)






        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
IBBBJDNE_00303 UUC21733.1|GT2 97.1 3.17e-192 1 273 1 1
IBBBJDNE_00569 QFX78706.1|GH23 100 9.1e-168 1 234 1 1





        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
IBBBJDNE_00026 2.A.53.3.1 74.5 4.4e-203 1 494 0.9980 0.9939 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
IBBBJDNE_00102 2.A.109.1.1 71.9 1.8e-139 1 340 0.9884 0.9884 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family
IBBBJDNE_00339 1.A.72.5.1 78.2 1.1e-31 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBBBJDNE_00342 1.A.72.1.1 100 1.2e-38 1 81 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBBBJDNE_00343 1.A.72.3.1 93.3 3.1e-38 1 90 0.9890 0.9890 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBBBJDNE_00344 1.A.72.3.1 93.1 1.1e-56 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IBBBJDNE_00355 2.A.21.7.1 83.5 1e-240 29 548 0.9489 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
IBBBJDNE_00440 2.A.6.2.11 99.6 4.1e-259 1 470 1.0000 1.2020 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IBBBJDNE_00441 2.A.6.2.11 99.5 0 1 1049 1.0000 2.6829 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IBBBJDNE_00445 2.A.6.2.11 98.1 1.9e-168 1 315 0.9104 0.8107 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
IBBBJDNE_00662 2.A.51.1.4 73.5 6.7e-198 1 456 1.0000 0.9978 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family