Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1298
  Reference Plasmid   NZ_CP148475.1
  Reference Plasmid Size   104495
  Reference Plasmid GC Content   0.49
  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
M0205845 NAOPDHKP_00055 43191 3 Gut 0.43 protein_coding synonymous_variant LOW 300G>A Gly100Gly






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
NAOPDHKP_00091 VFG043568 OmpD 77.3 1.2e-162 8 370 0.9811 1.0028 Adherence phosphoporin PhoE prediction







        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
NAOPDHKP_00078 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
NAOPDHKP_00079 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
NAOPDHKP_00080 Mercury (Hg) 89 1.2e-38 1 91 1.0000 1.0000 experiment
NAOPDHKP_00082 Mercury (Hg) 89.5 1.3e-229 1 455 1.0000 0.8111 experiment
NAOPDHKP_00083 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
NAOPDHKP_00091 Methyl Viologen [class: Paraquat] 77.3 2.6e-164 8 370 1.0000 1.0221 experiment
NAOPDHKP_00078 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 prediction
NAOPDHKP_00079 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
NAOPDHKP_00080 Mercury (Hg) 98.9 1.1e-40 1 91 1.0000 0.8585 prediction
NAOPDHKP_00082 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 1.6e-254 1 455 1.0000 0.8067 prediction
NAOPDHKP_00083 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
NAOPDHKP_00091 Methyl Viologen [class: Paraquat] 100 5.6e-213 1 370 1.0000 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
NAOPDHKP_00091 PHI:123435 ompD 77.3 4.3e-163 8 370 0.9811 0.9890 rodents salmonellosis porin OmpD unaffected pathogenicity
NAOPDHKP_00094 PHI:10179 tnpA 95.4 2.3e-86 1 152 1.0000 1.0000 rodents salmonellosis regulatory RNA/ transposase for IS200 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
NAOPDHKP_00093 QEI69367.1|GH24 100 5.67e-140 1 185 1 1
NAOPDHKP_00097 AYL89119.1|GH24 96.6 0 1753 2255 0.2231 0.9031
NAOPDHKP_00120 BBP41963.1|GH23 98.5 0 1 1246 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
NAOPDHKP_00079 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
NAOPDHKP_00080 1.A.72.3.1 89 4.5e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
NAOPDHKP_00091 1.B.1.1.4 80.3 1.3e-172 1 370 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
NAOPDHKP_00111 1.E.4.1.1 100 1.3e-54 1 109 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.4 The LydA Holin (LydA Holin) Family