Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C892
  Reference Plasmid   NZ_CP073083.1
  Reference Plasmid Size   436486
  Reference Plasmid GC Content   0.56
  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
M0104513 LHKACPEE_00186 181837 3 Skin 0.27 protein_coding missense_variant MODERATE 162A>C Leu54Phe
M0104514 LHKACPEE_00187 182128 3 Skin 0.27 protein_coding missense_variant MODERATE 90C>A Asn30Lys
M0104515 LHKACPEE_00187 182129 3 Skin 0.27 protein_coding missense_variant MODERATE 91A>C Met31Leu
M0104516 LHKACPEE_00187 182130 3 Skin 0.27 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
LHKACPEE_00148 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
LHKACPEE_00149 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
LHKACPEE_00150 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
LHKACPEE_00206 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
LHKACPEE_00219 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
LHKACPEE_00239 Mercury (Hg) 75.6 1e-236 1 560 1.0018 1.0000 experiment
LHKACPEE_00240 Mercury (Hg) 73.5 2.6e-56 6 141 0.9444 0.9645 experiment
LHKACPEE_00241 Mercury (Hg) 77.2 3.1e-34 1 92 1.0000 1.0110 experiment
LHKACPEE_00242 Mercury (Hg) 82.8 1.3e-53 1 116 1.0000 1.0000 experiment
LHKACPEE_00243 Mercury (Hg) 77 1.2e-58 1 139 1.0000 0.9653 experiment
LHKACPEE_00148 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
LHKACPEE_00149 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
LHKACPEE_00150 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
LHKACPEE_00187 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
LHKACPEE_00239 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 94.1 5.2e-295 1 560 1.0000 1.0000 prediction
LHKACPEE_00240 Mercury (Hg) 73.9 4.2e-55 6 143 0.9583 0.9787 prediction
LHKACPEE_00241 Mercury (Hg) 98.9 2.2e-41 1 91 0.9891 0.9891 prediction
LHKACPEE_00242 Mercury (Hg) 97.4 9.4e-58 1 116 1.0000 1.0000 prediction
LHKACPEE_00243 Mercury (Hg) 97.1 1.2e-72 1 138 0.9928 0.9928 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
LHKACPEE_00196 ARO:3002243 99.7 4.71e-205 1 288 1.0000 1.0000 penicillin beta-lactam CARB beta-lactamase antibiotic inactivation
LHKACPEE_00197 ARO:3004660 99.5 2.09e-160 1 210 1.0000 1.0000 phenicol antibiotic chloramphenicol acetyltransferase (CAT) antibiotic inactivation
LHKACPEE_00198 ARO:3002799 100 1.34e-79 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
LHKACPEE_00202 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LHKACPEE_00205 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LHKACPEE_00206 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
LHKACPEE_00207 ARO:3002621 99.6 3.29e-186 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LHKACPEE_00209 ARO:3002695 99 3.55e-298 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LHKACPEE_00210 ARO:3004635 100 2.96e-109 1 152 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
LHKACPEE_00213 ARO:3001205 97.5 2.28e-89 1 121 1.0000 1.0000 glycopeptide antibiotic Bleomycin resistant protein antibiotic inactivation
LHKACPEE_00214 ARO:3008070 100 3.57e-194 1 267 1.0000 1.0000 carbapenem AFM beta-lactamase antibiotic inactivation
LHKACPEE_00218 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LHKACPEE_00219 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
LHKACPEE_00220 ARO:3004550 100 9.81e-115 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
LHKACPEE_00221 ARO:3002848 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
LHKACPEE_00223 ARO:3001807 100 7.61e-180 52 301 0.8251 0.9398 cephalosporin OXA beta-lactamase antibiotic inactivation
LHKACPEE_00224 ARO:3004665 100 4.51e-301 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LHKACPEE_00225 ARO:3002594 100 2.6e-139 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
LHKACPEE_00228 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
LHKACPEE_00229 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection






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
LHKACPEE_00029 PHI:10380 RecA 73.2 1.1e-139 1 328 0.9507 0.9398 nematodes nosocomial infection DNA strand exchange and recombination protein reduced virulence
LHKACPEE_00211 PHI:9804 int 100 3.3e-14 1 37 0.1317 1.0000 rodents gastroenteritis integrase reduced virulence
LHKACPEE_00214 PHI:6347 NDM-1 86.6 1.3e-132 7 267 0.9775 0.9667 moths infection carbapenemase unaffected pathogenicity
LHKACPEE_00226 PHI:9804 int 100 3.8e-14 1 37 0.1160 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
LHKACPEE_00328 QFX78706.1|GH23 100 9.1e-168 1 234 1 1
LHKACPEE_00496 UUC21733.1|GT2 97.1 3.17e-192 1 273 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
LHKACPEE_00148 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
LHKACPEE_00209 2.A.1.2.3 98.8 1.2e-230 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
LHKACPEE_00224 2.A.1.2.3 96.4 6.9e-226 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
LHKACPEE_00241 1.A.72.3.1 77.2 1.5e-32 1 92 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
LHKACPEE_00242 1.A.72.3.1 78.4 4.2e-48 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily