Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1643
  Reference Plasmid   1111525849483863_bin.32__k141_164755
  Reference Plasmid Size   39069
  Reference Plasmid GC Content   0.55
  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
M0009781 HCOBGIIM_00001 608 21 Skin 0.28 protein_coding missense_variant MODERATE 499T>G Leu167Val






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
HCOBGIIM_00002 VFG002304 MisL 87.2 0 1 932 1.0 0.9759 Adherence putative autotransporter experiment
HCOBGIIM_00002 VFG018394 MisL 87.8 0 1 932 1.0 0.9811 Adherence putative autotransporter 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
HCOBGIIM_00031 Selenium (Se), Hydrogen Peroxide (H2O2) [class: Peroxides] 95.1 7.2e-116 1 206 1.0000 1.0000 experiment
HCOBGIIM_00035 Hydrogen Peroxide (H2O2) [class: Peroxides], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides] 95.4 3.1e-252 1 456 0.9978 0.9978 experiment
HCOBGIIM_00036 Hydrogen Peroxide (H2O2) [class: Peroxides], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides] 97.4 8.3e-129 1 232 1.0000 1.0000 experiment
HCOBGIIM_00038 Chlorhexidine [class: Biguanides] 88.6 5.9e-151 1 299 0.9934 0.9967 experiment
HCOBGIIM_00031 Selenium (Se), Hydrogen Peroxide (H2O2) [class: Peroxides] 100 2.2e-118 1 206 1.0000 1.0000 prediction
HCOBGIIM_00035 Hydrogen Peroxide (H2O2) [class: Peroxides], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides] 100 3.7e-259 1 457 1.0000 1.0000 prediction
HCOBGIIM_00036 Hydrogen Peroxide (H2O2) [class: Peroxides], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides] 100 1.8e-129 1 232 1.0000 1.0000 prediction
HCOBGIIM_00038 Iron (Fe), Zinc (Zn), Cobalt (Co), Cadmium (Cd), Nickel (Ni) 100 4.6e-165 1 301 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
HCOBGIIM_00035 ARO:3000830 95.4 4.33000001570805e-316 1 456 0.9978 0.9978 aminoglycoside antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux






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
HCOBGIIM_00016 PHI:10994 fdoG 90.5 0 1 804 1.0000 0.9833 rodents infection formate dehydrogenase-O major subunit unaffected pathogenicity
HCOBGIIM_00017 PHI:10994 fdoG 93.8 3e-107 1 195 1.0000 0.9833 rodents infection formate dehydrogenase-O major subunit unaffected pathogenicity
HCOBGIIM_00031 PHI:11376 sodA 94.2 7.8e-114 1 206 1.0000 1.0000 moths salmonellosis cytoplasmic superoxide dismutase reduced virulence
HCOBGIIM_00035 PHI:8513 cpxA 95.6 1.2e-250 1 456 0.9978 0.9978 rodents colitis two-component sensor kinase loss of pathogenicity
HCOBGIIM_00036 PHI:8512 cpxR 97 1.2e-126 1 232 1.0000 1.0000 rodents colitis two-component response regulator loss of pathogenicity
HCOBGIIM_00037 PHI:8515 cpxP 77 1.4e-60 1 164 0.9880 0.9940 rodents colitis periplasmic protein unaffected pathogenicity
HCOBGIIM_00039 PHI:9309 pfkA 89.4 4.1e-170 1 320 1.0000 1.0000 eudicots fire blight ATP-dependent 6-phosphofructokinase 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





        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
HCOBGIIM_00001 2.A.1.52.1 89.9 1.8e-199 1 388 1.0000 0.9216 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
HCOBGIIM_00002 1.B.12.1.3 87.2 0 1 932 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
HCOBGIIM_00007 9.B.126.2.1 86.7 5.7e-139 1 285 0.9965 0.9828 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.126 The Putative Lipid IV Exporter (YhjD) Family
HCOBGIIM_00016 5.A.3.2.1 76.5 0 1 803 0.9988 0.7901 5 Transmembrane Electron Carriers 5.A Transmembrane 2-electron transfer carriers 5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
HCOBGIIM_00030 2.A.7.6.1 91.3 3.3e-181 1 344 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
HCOBGIIM_00032 2.A.10.1.2 93.9 1.2e-164 1 327 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.10 The 2-Keto-3-Deoxygluconate Transporter (KdgT) Family
HCOBGIIM_00038 2.A.4.7.1 88.9 9.3e-148 1 297 0.9867 0.9833 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.4 The Cation Diffusion Facilitator (CDF) Family