Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C176
  Reference Plasmid   CP103111.1
  Reference Plasmid Size   8606
  Reference Plasmid GC Content   0.43
  Reference Plasmid Mobility Type   non-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
M0146419 PHFNJPCB_00004 2123 8 Gut 0.47 protein_coding synonymous_variant LOW 781T>C Leu261Leu
M0146420 PHFNJPCB_00003 1564 9 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -149C>T None
M0146421 PHFNJPCB_00002 562 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -21G>T None
M0146422 PHFNJPCB_00003 1485 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -70G>A None
M0146423 PHFNJPCB_00004 1822 8 Gut 0.47 protein_coding missense_variant MODERATE 1082G>A Arg361Lys
M0146424 PHFNJPCB_00003 1517 4 Gut 0.24 protein_coding upstream_gene_variant MODIFIER -102G>A None
M0146425 PHFNJPCB_00003 5692 7 Gut 0.41 protein_coding upstream_gene_variant MODIFIER -4277A>C None
M0146426 PHFNJPCB_00004 6740 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -3837G>T None
M0146427 PHFNJPCB_00002 836 3 Gut 0.18 protein_coding missense_variant MODERATE 254C>T Ala85Val
M0146428 PHFNJPCB_00005 3188 4 Gut 0.24 protein_coding synonymous_variant LOW 483C>T Ser161Ser
M0146429 PHFNJPCB_00003 5739 4 Gut 0.24 protein_coding upstream_gene_variant MODIFIER -4324G>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







        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