Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1392
  Reference Plasmid   NZ_MW300275.1
  Reference Plasmid Size   61183
  Reference Plasmid GC Content   0.64
  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
M0208876 JAGOELEP_00030 26231 3 Gut 1.00 protein_coding missense_variant MODERATE 2080G>A Gly694Arg
M0208877 JAGOELEP_00030 26843 3 Gut 1.00 protein_coding synonymous_variant LOW 1468T>C Leu490Leu






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
JAGOELEP_00033 Mercury (Hg) 100 1.3e-41 1 78 1.0000 1.0000 experiment
JAGOELEP_00034 Mercury (Hg) 100 8.4e-64 1 121 1.0000 1.0000 experiment
JAGOELEP_00035 Mercury (Hg) 98.8 5.99999999978328e-314 1 561 1.0000 1.0000 experiment
JAGOELEP_00036 Mercury (Hg) 98.9 8e-43 1 91 1.0000 1.0000 experiment
JAGOELEP_00037 Mercury (Hg) 100 4.4e-62 1 116 1.0000 1.0000 experiment
JAGOELEP_00038 Mercury (Hg) 100 7.1e-78 1 144 1.0000 1.0000 experiment
JAGOELEP_00032 Mercury (Hg) 100 5e-197 1 329 1.0000 0.8044 prediction
JAGOELEP_00033 Mercury (Hg) 100 3e-39 1 78 1.0000 1.0000 prediction
JAGOELEP_00034 Mercury (Hg) 100 1.9e-61 1 121 1.0000 1.0000 prediction
JAGOELEP_00035 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 561 1.0000 1.0000 prediction
JAGOELEP_00036 Mercury (Hg) 100 6.3e-41 1 91 1.0000 1.0000 prediction
JAGOELEP_00037 Mercury (Hg) 100 1e-59 1 116 1.0000 0.8657 prediction
JAGOELEP_00038 Mercury (Hg) 100 1.6e-75 1 144 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
JAGOELEP_00024 ARO:3002281 100 1.57e-192 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
JAGOELEP_00025 ARO:3002601 99.6 1.98e-189 1 263 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
JAGOELEP_00026 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
JAGOELEP_00023 PHI:9804 int 97.3 8.8e-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
JAGOELEP_00013 AFR43800.1|GH23 99.5 6.38e-130 1 196 1 0.9289





        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
JAGOELEP_00001 3.A.7.4.1 93.1 2.3e-168 1 321 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00004 3.A.7.4.1 92.6 0 1 852 1.0000 2.6625 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00005 3.A.7.4.1 82.1 3.1e-123 1 262 1.0000 0.8125 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00006 3.A.7.4.1 84.3 3.6e-144 1 297 1.0000 0.9344 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00008 3.A.7.4.1 75.1 8.3e-188 1 461 1.0000 1.4781 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00009 3.A.7.4.1 73.9 1.4e-96 1 257 1.0000 0.7938 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00011 3.A.7.4.1 78 1.9e-202 1 570 1.0000 1.7875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JAGOELEP_00033 1.A.72.5.1 76 3e-29 1 75 0.9615 0.9615 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JAGOELEP_00036 1.A.72.3.1 98.9 3e-41 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JAGOELEP_00037 1.A.72.3.1 100 1.7e-60 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily