Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1107
  Reference Plasmid   NZ_CP116024.1
  Reference Plasmid Size   137763
  Reference Plasmid GC Content   0.36
  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
M0195998 DHMCIOPI_00087 92472 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3587A>G None
M0195999 DHMCIOPI_00087 92541 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3656G>A None
M0196000 DHMCIOPI_00093 93712 6 Gut 0.50 protein_coding synonymous_variant LOW 280T>C Leu94Leu
M0196001 DHMCIOPI_00094 93944 6 Gut 0.50 protein_coding missense_variant MODERATE 53A>C Asp18Ala
M0196002 DHMCIOPI_00094 94004 6 Gut 0.50 protein_coding missense_variant MODERATE 113A>C His38Pro
M0196003 DHMCIOPI_00094 94100 6 Gut 0.50 protein_coding missense_variant MODERATE 209G>A Gly70Asp
M0196004 DHMCIOPI_00088 94374 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4651T>A None
M0196005 DHMCIOPI_00089 95306 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4780T>C None
M0196006 DHMCIOPI_00089 95334 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4808T>G None
M0196007 DHMCIOPI_00089 95346 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4820G>A None
M0196008 DHMCIOPI_00089 95361 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4835T>A None
M0196009 DHMCIOPI_00089 95384 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4858A>G None
M0196010 DHMCIOPI_00089 95396 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4870A>T None
M0196011 DHMCIOPI_00089 95430 7 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -4904C>A None
M0196012 DHMCIOPI_00089 95461 7 Gut 0.58 protein_coding upstream_gene_variant MODIFIER -4935C>T None
M0196013 DHMCIOPI_00090 95800 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4444C>A None
M0196014 DHMCIOPI_00090 95854 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4498A>C None
M0196015 DHMCIOPI_00090 95861 8 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -4505A>G None
M0196016 DHMCIOPI_00083 87754 6 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3966G>T None
M0196017 DHMCIOPI_00088 88934 6 Gut 0.50 protein_coding missense_variant MODERATE 790A>G Lys264Glu
M0196018 DHMCIOPI_00089 89726 6 Gut 0.50 protein_coding splice_region_variant&stop_retained_variant LOW 801A>G Ter267Ter
M0196019 DHMCIOPI_00089 89728 6 Gut 0.50 protein_coding stop_lost&splice_region_variant HIGH 799T>C Ter267Glnext*?
M0196020 DHMCIOPI_00089 90179 6 Gut 0.50 protein_coding synonymous_variant LOW 348A>G Gly116Gly






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
DHMCIOPI_00055 PHI:7637 CspA 76.9 7.4e-26 1 65 1.0000 0.9848 bony fishes listeriosis cold shock protein reduced virulence
DHMCIOPI_00081 PHI:5205 HMPREF0351_10118 (WxL locusC) 91.5 1.8e-156 1 295 1.0000 0.9770 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DHMCIOPI_00103 PHI:5205 HMPREF0351_10118 (WxL locusC) 74 2e-158 1 364 0.9239 0.9770 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence






        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
DHMCIOPI_00002 CCO10203.2|GH1 86.4 2.59e-243 1 390 1 1
DHMCIOPI_00029 CCO10203.2|GH1 86.7 3.15e-244 1 390 1 1
DHMCIOPI_00034 QPQ17866.1|GH16_21 97.6 9.91e-217 1 490 1 1
DHMCIOPI_00039 QMV94891.1|GH32 100 0 1 479 1 1
DHMCIOPI_00044 AUJ66534.1|GH1 100 0 1 479 1 1
DHMCIOPI_00067 CCO10203.2|GH1 86.2 6.08e-242 1 390 1 1
DHMCIOPI_00084 CCO11850.2|GH4 98.6 6.39e-149 222 439 0.4966 1
DHMCIOPI_00124 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949





        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