Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C231
  Reference Plasmid   HG796781.1
  Reference Plasmid Size   5369
  Reference Plasmid GC Content   0.42
  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
M0149264 PALGFMLN_00002 28 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -787T>C None
M0149265 PALGFMLN_00002 57 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -758T>C None
M0149266 PALGFMLN_00001 112 4 Gut 0.67 protein_coding synonymous_variant LOW 252T>C Gly84Gly
M0149267 PALGFMLN_00001 148 4 Gut 0.67 protein_coding synonymous_variant LOW 216T>C Asn72Asn
M0149268 PALGFMLN_00001 151 4 Gut 0.67 protein_coding synonymous_variant LOW 213G>A Lys71Lys
M0149269 PALGFMLN_00001 154 4 Gut 0.67 protein_coding synonymous_variant LOW 210C>T Ala70Ala
M0149270 PALGFMLN_00001 178 4 Gut 0.67 protein_coding synonymous_variant LOW 186G>A Arg62Arg
M0149271 PALGFMLN_00001 540 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -177T>C None
M0149272 PALGFMLN_00001 634 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -271C>T None
M0149273 PALGFMLN_00001 800 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -437C>T None
M0149274 PALGFMLN_00006 3382 4 Gut 0.67 protein_coding missense_variant MODERATE 733A>G Asn245Asp
M0149275 PALGFMLN_00006 3857 5 Gut 0.83 protein_coding synonymous_variant LOW 258A>G Leu86Leu
M0149276 PALGFMLN_00006 3875 5 Gut 0.83 protein_coding synonymous_variant LOW 240T>C Ser80Ser
M0149277 PALGFMLN_00007 4552 3 Gut 0.50 protein_coding synonymous_variant LOW 162G>A Pro54Pro
M0149278 PALGFMLN_00001 4882 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -4519A>G None
M0149279 PALGFMLN_00001 4885 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -4522T>C None
M0149280 PALGFMLN_00001 5117 5 Gut 0.83 protein_coding upstream_gene_variant MODIFIER -4754T>G None
M0149281 PALGFMLN_00001 5122 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -4759C>T None
M0149282 PALGFMLN_00001 5175 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4812T>A None
M0149283 PALGFMLN_00001 5178 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4815A>C None
M0149284 PALGFMLN_00001 5181 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4818T>C None
M0149285 PALGFMLN_00001 5182 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4819T>A None
M0149286 PALGFMLN_00001 5183 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4820T>A None
M0149287 PALGFMLN_00001 5184 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4821T>A None
M0149288 PALGFMLN_00001 5188 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4825G>T None
M0149289 PALGFMLN_00001 5191 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4828T>A None
M0149290 PALGFMLN_00001 5240 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -4877C>T None
M0149291 PALGFMLN_00007 4375 3 Gut 0.50 protein_coding synonymous_variant LOW 339T>C Asp113Asp
M0149292 PALGFMLN_00001 4737 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4374T>C None
M0149293 PALGFMLN_00001 4800 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4437C>T None
M0149294 PALGFMLN_00001 4962 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4599T>C None
M0149295 PALGFMLN_00001 4983 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4620C>T None
M0149296 PALGFMLN_00001 5001 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4638T>A None
M0149297 PALGFMLN_00006 3587 3 Gut 0.50 protein_coding synonymous_variant LOW 528A>G Lys176Lys
M0149298 PALGFMLN_00006 3833 3 Gut 0.50 protein_coding synonymous_variant LOW 282A>G Lys94Lys
M0149299 PALGFMLN_00006 3839 3 Gut 0.50 protein_coding synonymous_variant LOW 276A>C Thr92Thr
M0149300 PALGFMLN_00007 4147 3 Gut 0.50 protein_coding synonymous_variant LOW 567A>G Lys189Lys
M0149301 PALGFMLN_00001 5222 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4859A>G 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