Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C408
  Reference Plasmid   NZ_CP007792.1
  Reference Plasmid Size   96094
  Reference Plasmid GC Content   0.63
  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
M0087146 DNEPLAKI_00054 49915 6 Skin 0.75 protein_coding missense_variant MODERATE 1459G>C Val487Leu
M0087147 DNEPLAKI_00054 50235 4 Skin 0.50 protein_coding missense_variant MODERATE 1139G>A Gly380Asp
M0087148 DNEPLAKI_00054 50322 6 Skin 0.75 protein_coding missense_variant MODERATE 1052G>A Arg351His
M0087149 DNEPLAKI_00054 50372 4 Skin 0.50 protein_coding synonymous_variant LOW 1002G>A Lys334Lys
M0087150 DNEPLAKI_00054 50473 5 Skin 0.63 protein_coding missense_variant MODERATE 901T>C Trp301Arg
M0087151 DNEPLAKI_00054 50664 6 Skin 0.75 protein_coding missense_variant MODERATE 710T>C Val237Ala
M0087152 DNEPLAKI_00054 50723 4 Skin 0.50 protein_coding synonymous_variant LOW 651A>G Gly217Gly
M0087153 DNEPLAKI_00054 50727 4 Skin 0.50 protein_coding missense_variant MODERATE 647T>A Met216Lys
M0087154 DNEPLAKI_00054 50730 4 Skin 0.50 protein_coding missense_variant MODERATE 644G>A Arg215Lys
M0087155 DNEPLAKI_00054 50869 4 Skin 0.50 protein_coding missense_variant MODERATE 505A>G Ile169Val
M0087156 DNEPLAKI_00054 50911 5 Skin 0.63 protein_coding missense_variant MODERATE 463A>T Thr155Ser
M0087157 DNEPLAKI_00054 51164 3 Skin 0.38 protein_coding synonymous_variant LOW 210C>T Gly70Gly
M0087158 DNEPLAKI_00054 51179 6 Skin 0.75 protein_coding synonymous_variant LOW 195C>T Ser65Ser
M0087159 DNEPLAKI_00054 51254 5 Skin 0.63 protein_coding synonymous_variant LOW 120C>T Ser40Ser
M0087160 DNEPLAKI_00054 51259 5 Skin 0.63 protein_coding missense_variant MODERATE 115C>T Pro39Ser
M0087161 DNEPLAKI_00055 51488 4 Skin 0.50 protein_coding missense_variant MODERATE 532A>G Thr178Ala
M0087162 DNEPLAKI_00055 51503 3 Skin 0.38 protein_coding missense_variant MODERATE 517A>G Thr173Ala
M0087163 DNEPLAKI_00055 51719 5 Skin 0.63 protein_coding missense_variant MODERATE 301A>C Ile101Leu
M0087164 DNEPLAKI_00055 51723 5 Skin 0.63 protein_coding synonymous_variant LOW 297G>C Pro99Pro
M0087165 DNEPLAKI_00055 51726 5 Skin 0.63 protein_coding synonymous_variant LOW 294T>A Ala98Ala
M0087166 DNEPLAKI_00055 51729 5 Skin 0.63 protein_coding synonymous_variant LOW 291T>C Val97Val
M0087167 DNEPLAKI_00055 51731 5 Skin 0.63 protein_coding missense_variant MODERATE 289G>A Val97Ile
M0087168 DNEPLAKI_00055 51813 5 Skin 0.63 protein_coding synonymous_variant LOW 207C>A Ser69Ser
M0087169 DNEPLAKI_00055 51889 5 Skin 0.63 protein_coding missense_variant MODERATE 131C>A Ala44Asp
M0087170 DNEPLAKI_00055 51917 3 Skin 0.38 protein_coding missense_variant MODERATE 103A>G Thr35Ala
M0087171 DNEPLAKI_00051 52108 5 Skin 0.63 protein_coding upstream_gene_variant MODIFIER -3891G>T None
M0087172 DNEPLAKI_00051 52110 5 Skin 0.63 protein_coding upstream_gene_variant MODIFIER -3893G>A None
M0087173 DNEPLAKI_00051 52162 5 Skin 0.63 protein_coding upstream_gene_variant MODIFIER -3945G>T None
M0087174 DNEPLAKI_00051 52164 5 Skin 0.63 protein_coding upstream_gene_variant MODIFIER -3947G>A None
M0087175 DNEPLAKI_00051 52187 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -3970C>T None
M0087176 DNEPLAKI_00051 52276 5 Skin 0.63 protein_coding upstream_gene_variant MODIFIER -4059A>G None
M0087177 DNEPLAKI_00054 51323 3 Skin 0.38 protein_coding synonymous_variant LOW 51G>C Leu17Leu
M0087178 DNEPLAKI_00055 51673 3 Skin 0.38 protein_coding missense_variant MODERATE 347T>A Leu116Gln






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
DNEPLAKI_00021 Cobalt (Co), Nickel (Ni) 74.5 6e-40 1 102 1.0000 0.7083 prediction
DNEPLAKI_00034 Cobalt (Co), Nickel (Ni) 100 1.4e-62 13 131 0.9084 1.0000 prediction






        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
DNEPLAKI_00063 AJK70165.1|GH65 100 0 1 1073 1 1





        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
DNEPLAKI_00036 9.B.62.3.10 84.2 0 1 658 0.9564 0.9747 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family