Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C417
  Reference Plasmid   NZ_CP010179.1
  Reference Plasmid Size   116417
  Reference Plasmid GC Content   0.51
  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
M0164226 BICAFMKF_00054 48233 7 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -3512C>A None
M0164227 BICAFMKF_00030 23558 3 Gut 0.08 protein_coding synonymous_variant LOW 111T>C Phe37Phe






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
BICAFMKF_00061 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
BICAFMKF_00062 Arsenic (As), Antimony (Sb) 98.3 1.6e-67 1 120 1.0000 1.0000 experiment
BICAFMKF_00063 Arsenic (As), Antimony (Sb) 99.1 0 1 583 1.0000 1.0000 experiment
BICAFMKF_00064 Arsenic (As), Antimony (Sb) 99.3 1.7e-231 1 429 1.0000 1.0000 experiment
BICAFMKF_00065 Arsenic (As), Antimony (Sb) 99.3 3.5e-77 1 141 1.0000 1.0000 experiment
BICAFMKF_00061 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
BICAFMKF_00062 Arsenic (As) 100 4.4e-66 1 120 1.0000 1.0000 prediction
BICAFMKF_00063 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
BICAFMKF_00064 Arsenic (As), Antimony (Sb) 100 6.9e-231 1 429 1.0000 1.0000 prediction
BICAFMKF_00065 Arsenic (As) 100 1.6e-75 1 141 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






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
BICAFMKF_00034 PHI:10113 STM14_RS07770 (ttrA) 83.3 0 1 1021 1.0000 1.0000 eudicots infection tetrathionate reductase subunit A reduced virulence
BICAFMKF_00035 PHI:10114 STM14_RS07775 (ttrC) 76.8 4.4e-154 1 340 1.0000 1.0000 eudicots infection tetrathionate reductase subunit C reduced virulence
BICAFMKF_00036 PHI:10115 STM14_RS07780 (ttrB) 91.8 2.7e-137 1 244 1.0000 0.9760 eudicots infection tetrathionate reductase subunit B reduced virulence
BICAFMKF_00037 PHI:10116 STM14_RS07785 (ttrS) 76.9 1.8e-264 1 593 1.0000 1.0000 eudicots infection two-component system sensor histidine kinase reduced virulence
BICAFMKF_00038 PHI:10117 STM14_RS07790 (ttrR) 80.3 4.4e-82 1 193 0.9948 0.9369 eudicots infection two-component system response regulator reduced virulence
BICAFMKF_00039 PHI:10118 STM14_RS07795 (orf70) 84.2 3.3e-21 1 57 0.8507 0.8143 eudicots infection hypothetical protein reduced virulence
BICAFMKF_00089 PHI:3531 pld1 87.7 3e-24 1 63 1.0000 1.0000 rodents urinary tract infection; nosocomial pneumonia; abdominal infection lipid metabolism loss of pathogenicity
BICAFMKF_00130 PHI:3317 hsdR 73.1 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
BICAFMKF_00024 AYL89119.1|GH24 96.8 5.75e-309 1 462 1 0.8294





        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
BICAFMKF_00020 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family
BICAFMKF_00063 3.A.4.1.1 85.7 5e-283 1 581 0.9966 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
BICAFMKF_00064 3.A.4.1.1 93.7 1.3e-219 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family