Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C89
  Reference Plasmid   CP048872.1
  Reference Plasmid Size   5153
  Reference Plasmid GC Content   0.46
  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
M0143817 LAFFOIBL_00001 866 7 Gut 0.58 protein_coding missense_variant MODERATE 1004C>T Ala335Val
M0143818 LAFFOIBL_00001 1913 7 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -44A>G None
M0143819 LAFFOIBL_00001 4377 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -2508G>A None
M0143820 LAFFOIBL_00001 1428 3 Gut 0.25 protein_coding missense_variant MODERATE 442G>T Ala148Ser
M0143821 LAFFOIBL_00001 3101 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1232T>C None
M0143822 LAFFOIBL_00001 3120 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1251C>T None
M0143823 LAFFOIBL_00001 3132 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1263C>T None
M0143824 LAFFOIBL_00001 3134 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1265G>A None
M0143825 LAFFOIBL_00001 3149 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1280A>C None
M0143826 LAFFOIBL_00001 3154 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1285A>T None
M0143827 LAFFOIBL_00001 3155 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1286T>C None
M0143828 LAFFOIBL_00001 3161 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1292C>T None
M0143829 LAFFOIBL_00001 3199 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1330A>T None
M0143830 LAFFOIBL_00001 3263 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -1394T>A None






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
LAFFOIBL_00001 VFG044066 Colicin E1 94 1.7e-255 1 521 1.0 1 Exotoxin colicin-like pore-forming protein prediction







        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






        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






        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
LAFFOIBL_00001 1.C.1.2.2 86.8 3.5e-235 1 521 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family