Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C888
  Reference Plasmid   NZ_CP072260.1
  Reference Plasmid Size   4148
  Reference Plasmid GC Content   0.45
  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
M0188143 CDLHFLHJ_00004 2432 6 Gut 0.27 protein_coding synonymous_variant LOW 84A>T Ala28Ala
M0188144 CDLHFLHJ_00001 1025 9 Gut 0.41 protein_coding splice_region_variant&stop_retained_variant LOW 1025A>G Ter342Ter
M0188145 CDLHFLHJ_00001 1029 9 Gut 0.41 protein_coding downstream_gene_variant MODIFIER *3G>A None
M0188146 CDLHFLHJ_00002 1099 9 Gut 0.41 protein_coding synonymous_variant LOW 195A>G Glu65Glu
M0188147 CDLHFLHJ_00002 1112 9 Gut 0.41 protein_coding missense_variant MODERATE 182A>G Gln61Arg
M0188148 CDLHFLHJ_00002 1114 9 Gut 0.41 protein_coding synonymous_variant LOW 180A>G Gln60Gln
M0188149 CDLHFLHJ_00002 1151 10 Gut 0.45 protein_coding missense_variant MODERATE 143C>T Ala48Val
M0188150 CDLHFLHJ_00002 1210 11 Gut 0.50 protein_coding synonymous_variant LOW 84C>T Ala28Ala
M0188151 CDLHFLHJ_00003 1736 11 Gut 0.50 protein_coding missense_variant MODERATE 29C>T Ala10Val
M0188152 CDLHFLHJ_00004 1747 11 Gut 0.50 protein_coding missense_variant MODERATE 769C>T Pro257Ser
M0188153 CDLHFLHJ_00004 1991 12 Gut 0.55 protein_coding synonymous_variant LOW 525C>A Val175Val
M0188154 CDLHFLHJ_00002 2900 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1607C>T None
M0188155 CDLHFLHJ_00002 2907 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1614C>A None
M0188156 CDLHFLHJ_00002 2920 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1627A>G None
M0188157 CDLHFLHJ_00002 2921 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1628C>T None
M0188158 CDLHFLHJ_00002 2978 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1685A>T None
M0188159 CDLHFLHJ_00002 2979 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -1686A>T None
M0188160 CDLHFLHJ_00007 3249 11 Gut 0.50 protein_coding synonymous_variant LOW 240T>C Tyr80Tyr
M0188161 CDLHFLHJ_00007 3303 11 Gut 0.50 protein_coding synonymous_variant LOW 186C>T Ile62Ile
M0188162 CDLHFLHJ_00008 3506 11 Gut 0.50 protein_coding synonymous_variant LOW 231C>T Asp77Asp
M0188163 CDLHFLHJ_00008 3587 11 Gut 0.50 protein_coding synonymous_variant LOW 150G>A Glu50Glu
M0188164 CDLHFLHJ_00008 3707 11 Gut 0.50 protein_coding synonymous_variant LOW 30A>T Arg10Arg
M0188165 CDLHFLHJ_00002 3759 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2466G>A None
M0188166 CDLHFLHJ_00002 3778 14 Gut 0.64 protein_coding upstream_gene_variant MODIFIER -2485A>G None
M0188167 CDLHFLHJ_00002 3830 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2537G>A None
M0188168 CDLHFLHJ_00002 3869 11 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2576G>A None
M0188169 CDLHFLHJ_00002 3809 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2516A>G None
M0188170 CDLHFLHJ_00004 2153 3 Gut 0.14 protein_coding synonymous_variant LOW 363G>A Leu121Leu
M0188171 CDLHFLHJ_00002 4006 3 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -2713A>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