Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2904
  Reference Plasmid   DP1808006749_bin.3__NODE_703_length_4894_cov_0.619604
  Reference Plasmid Size   4894
  Reference Plasmid GC Content   0.70
  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
M0066817 GILGCPCD_00001 1615 3 Skin 0.38 protein_coding synonymous_variant LOW 993C>G Ala331Ala
M0066818 GILGCPCD_00002 1713 4 Skin 0.50 protein_coding synonymous_variant LOW 36T>G Leu12Leu
M0066819 GILGCPCD_00003 2984 6 Skin 0.75 protein_coding synonymous_variant LOW 54A>C Val18Val
M0066820 GILGCPCD_00003 2991 3 Skin 0.38 protein_coding missense_variant MODERATE 61C>A Gln21Lys
M0066821 GILGCPCD_00003 2993 3 Skin 0.38 protein_coding synonymous_variant LOW 63G>A Gln21Gln
M0066822 GILGCPCD_00003 3401 7 Skin 0.88 protein_coding synonymous_variant LOW 471C>T Phe157Phe
M0066823 GILGCPCD_00001 3631 7 Skin 0.88 protein_coding downstream_gene_variant MODIFIER *1947T>C None
M0066824 GILGCPCD_00001 3994 3 Skin 0.38 protein_coding downstream_gene_variant MODIFIER *2310C>T None
M0066825 GILGCPCD_00004 4244 5 Skin 0.63 protein_coding missense_variant MODERATE 353T>C Leu118Pro
M0066826 GILGCPCD_00004 4264 5 Skin 0.63 protein_coding synonymous_variant LOW 333T>C Ala111Ala
M0066827 GILGCPCD_00004 4282 5 Skin 0.63 protein_coding synonymous_variant LOW 315C>G Ser105Ser
M0066828 GILGCPCD_00004 4474 6 Skin 0.75 protein_coding missense_variant MODERATE 123A>C Arg41Ser
M0066829 GILGCPCD_00004 4651 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -55C>T None
M0066830 GILGCPCD_00004 4657 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -61C>G None
M0066831 GILGCPCD_00004 4717 4 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -121G>C None
M0066832 GILGCPCD_00001 1096 3 Skin 0.38 protein_coding synonymous_variant LOW 474A>C Ala158Ala
M0066833 GILGCPCD_00003 3038 5 Skin 0.63 protein_coding synonymous_variant LOW 108T>C Asp36Asp
M0066834 GILGCPCD_00003 3047 5 Skin 0.63 protein_coding synonymous_variant LOW 117G>C Leu39Leu
M0066835 GILGCPCD_00003 3059 5 Skin 0.63 protein_coding synonymous_variant LOW 129A>G Glu43Glu
M0066836 GILGCPCD_00003 3062 5 Skin 0.63 protein_coding synonymous_variant LOW 132C>T Asp44Asp
M0066837 GILGCPCD_00003 3065 4 Skin 0.50 protein_coding synonymous_variant LOW 135C>T Ala45Ala
M0066838 GILGCPCD_00003 3066 4 Skin 0.50 protein_coding missense_variant MODERATE 136G>A Ala46Thr
M0066839 GILGCPCD_00003 3067 5 Skin 0.63 protein_coding missense_variant MODERATE 137C>A Ala46Glu
M0066840 GILGCPCD_00003 3071 5 Skin 0.63 protein_coding synonymous_variant LOW 141A>G Thr47Thr
M0066841 GILGCPCD_00003 3074 5 Skin 0.63 protein_coding synonymous_variant LOW 144T>C Leu48Leu
M0066842 GILGCPCD_00003 3081 5 Skin 0.63 protein_coding missense_variant MODERATE 151C>G Leu51Val
M0066843 GILGCPCD_00003 3089 3 Skin 0.38 protein_coding synonymous_variant LOW 159G>C Ala53Ala
M0066844 GILGCPCD_00001 3706 3 Skin 0.38 protein_coding downstream_gene_variant MODIFIER *2022T>C None
M0066845 GILGCPCD_00004 4117 4 Skin 0.50 protein_coding missense_variant MODERATE 480G>C Met160Ile
M0066846 GILGCPCD_00004 4111 3 Skin 0.38 protein_coding missense_variant MODERATE 486G>T Met162Ile






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