Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1405
  Reference Plasmid   NZ_ON833286.1
  Reference Plasmid Size   217441
  Reference Plasmid GC Content   0.45
  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
M0116777 LMMNEFOO_00181 178210 4 Skin 0.50 protein_coding synonymous_variant LOW 531C>A Thr177Thr
M0116778 LMMNEFOO_00181 178593 3 Skin 0.38 protein_coding missense_variant MODERATE 148G>A Ala50Thr






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
LMMNEFOO_00014 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 78.2 9e-45 104 213 0.5164 1.0000 experiment
LMMNEFOO_00015 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
LMMNEFOO_00053 Tellurium (Te) 75.4 8.3e-82 1 191 0.9948 1.0000 experiment
LMMNEFOO_00054 Tellurium (Te) 77 1.2e-85 3 193 0.9896 0.9948 experiment
LMMNEFOO_00055 Tellurium (Te) 80.5 2.2e-154 1 344 1.0000 0.9942 experiment
LMMNEFOO_00186 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
LMMNEFOO_00195 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)] 98.9 3.8e-48 2 93 0.9892 0.8000 experiment
LMMNEFOO_00210 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
LMMNEFOO_00014 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 79.1 5.4e-43 104 213 0.5164 1.0000 prediction
LMMNEFOO_00046 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 74 0 1 1045 1.0000 1.0010 prediction
LMMNEFOO_00053 Tellurium (Te) 75.9 8.5e-80 1 191 0.9948 1.0000 prediction
LMMNEFOO_00054 Tellurium (Te) 79.6 1.8e-85 3 193 0.9896 0.9948 prediction
LMMNEFOO_00055 Tellurium (Te) 82.3 5.9e-156 1 344 1.0000 0.9942 prediction
LMMNEFOO_00195 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], 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)] 98.9 8.7e-46 2 93 0.9892 0.8000 prediction
LMMNEFOO_00225 Triclosan [class: Phenolic compounds], n-hexane [class: Alkane], p-xylene [class: Aromatic hydrocarbons] 73.7 0 1 1045 1.0000 1.0010 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
LMMNEFOO_00014 ARO:3005098 78.2 3.23e-57 104 213 0.5164 1.0000 disinfecting agents and antiseptics small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
LMMNEFOO_00015 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
LMMNEFOO_00016 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LMMNEFOO_00185 ARO:3002602 99.6 1.78e-185 43 301 0.8605 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LMMNEFOO_00186 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
LMMNEFOO_00187 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LMMNEFOO_00195 ARO:3005010 98.9 1.39e-61 2 93 0.9892 0.8000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LMMNEFOO_00196 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LMMNEFOO_00201 ARO:3001205 100 1.67e-91 1 121 1.0000 1.0000 glycopeptide antibiotic Bleomycin resistant protein antibiotic inactivation
LMMNEFOO_00202 ARO:3000589 100 4.69e-196 1 270 1.0000 1.0000 carbapenem NDM beta-lactamase antibiotic inactivation
LMMNEFOO_00207 ARO:3003014 100 8.07e-114 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
LMMNEFOO_00208 ARO:3002242 99.7 1.26e-217 1 304 1.0000 1.0000 penicillin beta-lactam CARB beta-lactamase antibiotic inactivation
LMMNEFOO_00209 ARO:3002602 100 2.01e-185 12 269 0.9591 0.9961 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LMMNEFOO_00210 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
LMMNEFOO_00211 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LMMNEFOO_00217 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
LMMNEFOO_00218 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) 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
LMMNEFOO_00202 PHI:6347 NDM-1 100 4.1e-155 1 270 1.0000 1.0000 moths infection carbapenemase unaffected pathogenicity






        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
LMMNEFOO_00032 2.A.53.3.1 74.4 4e-202 35 530 0.9358 0.9980 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
LMMNEFOO_00055 2.A.109.1.1 82 3.6e-156 1 344 1.0000 0.9942 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family