Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C10
  Reference Plasmid   NZ_OP927727.1
  Reference Plasmid Size   226067
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   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
M0116779 NLCNCCDM_00096 72506 3 Skin 0.43 protein_coding missense_variant MODERATE 838A>G Ile280Val
M0209455 OCKDFMAH_00121 94447 3 Gut 0.60 protein_coding missense_variant MODERATE 80C>T Ala27Val
M0209456 OCKDFMAH_00121 94496 3 Gut 0.60 protein_coding synonymous_variant LOW 129G>A Ser43Ser
M0209457 OCKDFMAH_00121 94719 3 Gut 0.60 protein_coding missense_variant MODERATE 352C>T Leu118Phe
M0209458 OCKDFMAH_00121 94908 3 Gut 0.60 protein_coding missense_variant MODERATE 541G>A Glu181Lys
M0209459 OCKDFMAH_00121 94984 3 Gut 0.60 protein_coding missense_variant MODERATE 617G>A Ser206Asn
M0209460 OCKDFMAH_00118 95001 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3121T>G None
M0209461 OCKDFMAH_00229 173275 3 Gut 0.60 protein_coding missense_variant MODERATE 302C>T Ser101Leu






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
NLCNCCDM_00034 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 80.6 9.9e-126 1 267 1.0037 0.9537 experiment
NLCNCCDM_00090 Tellurium (Te) 100 8.9e-85 1 156 0.9512 0.8125 experiment
NLCNCCDM_00091 Tellurium (Te) 99.7 2.1e-161 1 293 1.0000 0.8468 experiment
NLCNCCDM_00107 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
OCKDFMAH_00034 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 80.6 9.9e-126 1 267 1.0037 0.9537 experiment
OCKDFMAH_00090 Tellurium (Te) 100 8.9e-85 1 156 0.9512 0.8125 experiment
OCKDFMAH_00091 Tellurium (Te) 99.7 2.1e-161 1 293 1.0000 0.8468 experiment
OCKDFMAH_00107 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
NLCNCCDM_00034 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 81 2.7e-124 1 267 1.0037 0.9537 prediction
NLCNCCDM_00052 Iron (Fe), Nickel (Ni) 75.8 1.8e-117 1 256 1.0000 1.0000 prediction
NLCNCCDM_00090 Tellurium (Te) 100 2e-82 1 156 0.9512 0.8125 prediction
NLCNCCDM_00091 Tellurium (Te) 100 7.4e-160 1 293 1.0000 0.9071 prediction
OCKDFMAH_00034 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 81 2.7e-124 1 267 1.0037 0.9537 prediction
OCKDFMAH_00052 Iron (Fe), Nickel (Ni) 75.8 1.8e-117 1 256 1.0000 1.0000 prediction
OCKDFMAH_00090 Tellurium (Te) 100 2e-82 1 156 0.9512 0.8125 prediction
OCKDFMAH_00091 Tellurium (Te) 100 7.4e-160 1 293 1.0000 0.9071 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
NLCNCCDM_00105 ARO:3004498 98.7 1.18e-53 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NLCNCCDM_00107 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
NLCNCCDM_00108 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
OCKDFMAH_00105 ARO:3004498 98.7 1.18e-53 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
OCKDFMAH_00107 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
OCKDFMAH_00108 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
NLCNCCDM_00103 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
OCKDFMAH_00103 PHI:9804 int 100 4e-14 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
NLCNCCDM_00237 QJN57824.1|GH23 100 6.61e-135 1 186 1 1
OCKDFMAH_00237 QJN57824.1|GH23 100 6.61e-135 1 186 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
NLCNCCDM_00034 1.A.8.1.1 80.6 3.7e-124 1 267 1.0000 0.9537 1 Channels/Pores 1.A α-Type Channels 1.A.8 The Major Intrinsic Protein (MIP) Family
NLCNCCDM_00091 2.A.109.1.1 90.8 1.5e-147 1 293 1.0000 0.8468 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family
OCKDFMAH_00034 1.A.8.1.1 80.6 3.7e-124 1 267 1.0000 0.9537 1 Channels/Pores 1.A α-Type Channels 1.A.8 The Major Intrinsic Protein (MIP) Family
OCKDFMAH_00091 2.A.109.1.1 90.8 1.5e-147 1 293 1.0000 0.8468 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family