Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C857
  Reference Plasmid   NZ_CP070438.1
  Reference Plasmid Size   112495
  Reference Plasmid GC Content   0.52
  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
M0185159 NENOMJLB_00020 20653 3 Gut 0.75 protein_coding synonymous_variant LOW 1794T>C Thr598Thr
M0185160 NENOMJLB_00020 20713 3 Gut 0.75 protein_coding synonymous_variant LOW 1854G>A Glu618Glu
M0185161 NENOMJLB_00020 21013 3 Gut 0.75 protein_coding synonymous_variant LOW 2154C>T Phe718Phe
M0185162 NENOMJLB_00020 21100 3 Gut 0.75 protein_coding synonymous_variant LOW 2241A>G Pro747Pro
M0185163 NENOMJLB_00020 21154 3 Gut 0.75 protein_coding synonymous_variant LOW 2295C>T Asn765Asn
M0185164 NENOMJLB_00020 21286 3 Gut 0.75 protein_coding synonymous_variant LOW 2427T>C Ser809Ser
M0185165 NENOMJLB_00020 21294 3 Gut 0.75 protein_coding missense_variant MODERATE 2435G>A Ser812Asn
M0185166 NENOMJLB_00020 21313 3 Gut 0.75 protein_coding synonymous_variant LOW 2454A>G Val818Val
M0185167 NENOMJLB_00020 21325 3 Gut 0.75 protein_coding synonymous_variant LOW 2466G>C Thr822Thr






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
LFEHMKPE_00048 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
NENOMJLB_00048 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






        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
LFEHMKPE_00030 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
LFEHMKPE_00032 ARO:3001404 100 3.74e-204 1 274 1.0000 1.0000 penicillin beta-lactam OXA beta-lactamase antibiotic inactivation
LFEHMKPE_00033 ARO:3002601 99.2 2.47e-184 1 258 1.0039 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LFEHMKPE_00034 ARO:3002581 99 2.24e-142 7 201 0.9701 0.9606 aminoglycoside antibiotic AAC(6') antibiotic inactivation
LFEHMKPE_00039 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
LFEHMKPE_00047 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LFEHMKPE_00048 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
LFEHMKPE_00050 ARO:3002854 99.4 2.81e-114 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
LFEHMKPE_00051 ARO:3002848 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
NENOMJLB_00030 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
NENOMJLB_00032 ARO:3001404 100 3.74e-204 1 274 1.0000 1.0000 penicillin beta-lactam OXA beta-lactamase antibiotic inactivation
NENOMJLB_00033 ARO:3002601 99.2 2.47e-184 1 258 1.0039 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
NENOMJLB_00034 ARO:3002581 99 2.24e-142 7 201 0.9701 0.9606 aminoglycoside antibiotic AAC(6') antibiotic inactivation
NENOMJLB_00039 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
NENOMJLB_00047 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
NENOMJLB_00048 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
NENOMJLB_00050 ARO:3002854 99.4 2.81e-114 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
NENOMJLB_00051 ARO:3002848 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) 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
LFEHMKPE_00052 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
NENOMJLB_00052 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
LFEHMKPE_00069 ARX22692.1|GH23 100 9.06e-113 1 159 1 1
NENOMJLB_00069 ARX22692.1|GH23 100 9.06e-113 1 159 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