Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1195
  Reference Plasmid   NZ_CP131786.1
  Reference Plasmid Size   461212
  Reference Plasmid GC Content   0.57
  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
M0112861 DEOCPECH_00338 296432 6 Skin 0.08 protein_coding missense_variant MODERATE 137G>A Ser46Asn
M0112862 DEOCPECH_00283 233243 3 Skin 0.04 protein_coding synonymous_variant LOW 654C>T Pro218Pro
M0112863 DEOCPECH_00284 234353 5 Skin 0.06 protein_coding missense_variant MODERATE 347T>C Leu116Ser
M0112864 DEOCPECH_00286 236066 4 Skin 0.05 protein_coding missense_variant MODERATE 562C>T Pro188Ser
M0112865 DEOCPECH_00279 233033 3 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -2592C>G None
M0112866 DEOCPECH_00285 235026 4 Skin 0.05 protein_coding synonymous_variant LOW 354A>G Leu118Leu
M0112867 DEOCPECH_00285 240290 5 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -4911C>T None
M0112868 DEOCPECH_00294 244538 4 Skin 0.05 protein_coding synonymous_variant LOW 90T>C Ser30Ser
M0112869 DEOCPECH_00294 244543 4 Skin 0.05 protein_coding missense_variant MODERATE 95G>C Arg32Pro






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
DEOCPECH_00214 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
DEOCPECH_00215 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
DEOCPECH_00216 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
DEOCPECH_00292 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
DEOCPECH_00300 Cobalt (Co), Nickel (Ni) 72.4 2.3e-173 14 467 0.9560 0.9520 experiment
DEOCPECH_00300 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 72.4 2.3e-173 14 467 0.9560 0.9520 experiment
DEOCPECH_00301 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 76.7 0 1 1032 0.9981 0.9990 experiment
DEOCPECH_00314 Mercury (Hg) 75.2 8.5e-236 5 564 0.9947 1.0000 experiment
DEOCPECH_00315 Mercury (Hg) 71.7 1e-55 6 143 0.9583 0.9787 experiment
DEOCPECH_00316 Mercury (Hg) 76.9 8.9e-34 1 91 1.0000 1.0000 experiment
DEOCPECH_00317 Mercury (Hg) 83.6 7e-52 1 116 1.0000 1.0000 experiment
DEOCPECH_00318 Mercury (Hg) 77.9 3.2e-56 1 136 1.0000 0.9444 experiment
DEOCPECH_00214 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
DEOCPECH_00215 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
DEOCPECH_00216 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
DEOCPECH_00300 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 100 5.8e-255 1 477 1.0000 1.0000 prediction
DEOCPECH_00301 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 100 0 1 1044 1.0000 1.0000 prediction
DEOCPECH_00302 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 98.4 4.5e-205 1 387 1.0000 1.0000 prediction
DEOCPECH_00314 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 3.60000000001819e-313 5 564 0.9929 1.0000 prediction
DEOCPECH_00315 Mercury (Hg) 71.7 2.3e-53 6 143 0.9583 0.9787 prediction
DEOCPECH_00316 Mercury (Hg) 100 4.1e-40 1 91 1.0000 1.0000 prediction
DEOCPECH_00317 Mercury (Hg) 100 3.2e-58 1 116 1.0000 0.8406 prediction
DEOCPECH_00318 Mercury (Hg) 100 8.7e-71 1 136 1.0000 1.0000 prediction
DEOCPECH_00336 Mercury (Hg) 96.7 9.7e-42 1 91 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
DEOCPECH_00283 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
DEOCPECH_00284 ARO:3002639 100 3.6e-203 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
DEOCPECH_00291 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
DEOCPECH_00292 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
DEOCPECH_00293 ARO:3002594 100 2.6e-139 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
DEOCPECH_00300 ARO:3000802 72.8 3.75e-211 19 465 0.9413 0.9374 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
DEOCPECH_00301 ARO:3000801 76.6 0 1 1032 0.9981 0.9990 macrolide antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
DEOCPECH_00370 ARO:3002272 100 1.91e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
DEOCPECH_00371 ARO:3002578 99.5 2.85e-154 1 210 1.0000 0.8046 aminoglycoside antibiotic AAC(6') 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
DEOCPECH_00107 PHI:10380 RecA 72.9 2.4e-139 1 328 0.9507 0.9398 nematodes nosocomial infection DNA strand exchange and recombination protein reduced virulence
DEOCPECH_00294 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
DEOCPECH_00372 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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
DEOCPECH_00026 UUC21733.1|GT2 96.7 1.29e-191 1 273 1 1
DEOCPECH_00416 QGQ00737.1|GH23 100 1.29e-167 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
DEOCPECH_00214 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
DEOCPECH_00287 2.A.53.3.1 74.5 1e-204 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
DEOCPECH_00300 2.A.6.2.15 72.4 8.6e-172 14 467 0.9518 1.1692 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
DEOCPECH_00301 2.A.6.2.15 76.7 0 1 1032 0.9885 2.6462 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
DEOCPECH_00302 2.A.6.2.15 86.4 3.4e-179 1 387 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
DEOCPECH_00316 1.A.72.3.1 76.9 4.3e-32 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
DEOCPECH_00317 1.A.72.3.1 77.6 1.5e-45 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily