Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C346
  Reference Plasmid   NC_022598.1
  Reference Plasmid Size   60563
  Reference Plasmid GC Content   0.28
  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
M0086060 BCJLPABG_00021 23508 3 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3418T>G None
M0086061 BCJLPABG_00021 23521 3 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3431C>T None
M0086062 BCJLPABG_00035 32692 3 Skin 0.15 protein_coding missense_variant MODERATE 548A>G His183Arg
M0086063 BCJLPABG_00035 32913 3 Skin 0.15 protein_coding missense_variant MODERATE 769A>G Asn257Asp
M0086064 BCJLPABG_00035 32958 3 Skin 0.15 protein_coding missense_variant MODERATE 814A>G Ile272Val
M0086065 BCJLPABG_00030 32979 3 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3877A>C None
M0086066 BCJLPABG_00030 32991 3 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -3889A>G None






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
BCJLPABG_00056 VFG001801 Exfoliative toxin 100 4.5e-158 1 277 1.0 1 Exoenzyme exfoliative toxin B experiment
NLHLHJFM_00056 VFG001801 Exfoliative toxin 100 4.5e-158 1 277 1.0 1 Exoenzyme exfoliative toxin B experiment
BCJLPABG_00052 VFG043670 Epidermal cell differentiation inhibitor (EDIN-C, C3stau3) 100 2.7e-134 1 247 1.0 1 Exotoxin ADP-ribosyltransferase prediction
BCJLPABG_00056 VFG001801 Exfoliative toxin 100 3.4e-157 1 277 1.0 1 Exoenzyme exfoliative toxin B prediction
NLHLHJFM_00052 VFG043670 Epidermal cell differentiation inhibitor (EDIN-C, C3stau3) 100 2.7e-134 1 247 1.0 1 Exotoxin ADP-ribosyltransferase prediction
NLHLHJFM_00056 VFG001801 Exfoliative toxin 100 3.4e-157 1 277 1.0 1 Exoenzyme exfoliative toxin B 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
BCJLPABG_00009 Cadmium (Cd), Zinc (Zn) 93.7 2.9e-101 1 205 1.0000 1.0000 experiment
NLHLHJFM_00009 Cadmium (Cd), Zinc (Zn) 93.7 2.9e-101 1 205 1.0000 1.0000 experiment
BCJLPABG_00009 Cadmium (Cd), Zinc (Zn) 100 1e-102 1 205 1.0000 1.0000 prediction
NLHLHJFM_00009 Cadmium (Cd), Zinc (Zn) 100 1e-102 1 205 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
BCJLPABG_00017 ARO:3000251 97.5 0 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
BCJLPABG_00022 ARO:3008823 100 1.9e-196 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
BCJLPABG_00028 ARO:3002597 100 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation
NLHLHJFM_00017 ARO:3000251 97.5 0 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
NLHLHJFM_00022 ARO:3008823 100 1.9e-196 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
NLHLHJFM_00028 ARO:3002597 100 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation






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
BCJLPABG_00016 PHI:6324 StpC 85.7 2.9e-109 1 231 1.0000 1.0000 birds skin infection; food poisoning; respiratory disease cysteine protease unaffected pathogenicity
NLHLHJFM_00016 PHI:6324 StpC 85.7 2.9e-109 1 231 1.0000 1.0000 birds skin infection; food poisoning; respiratory disease cysteine protease unaffected pathogenicity






        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
BCJLPABG_00027 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
BCJLPABG_00030 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
NLHLHJFM_00027 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
NLHLHJFM_00030 CCO10203.2|GH1 86.9 1.56e-244 1 390 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
BCJLPABG_00009 2.A.77.1.1 93.2 2.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
BCJLPABG_00017 3.A.1.121.1 99.8 2.5e-275 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
BCJLPABG_00040 1.C.21.2.4 75.4 1.1e-21 7 62 0.9032 0.8769 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.21 The Lacticin 481 (Lacticin 481) Family
NLHLHJFM_00009 2.A.77.1.1 93.2 2.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
NLHLHJFM_00017 3.A.1.121.1 99.8 2.5e-275 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NLHLHJFM_00040 1.C.21.2.4 75.4 1.1e-21 7 62 0.9032 0.8769 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.21 The Lacticin 481 (Lacticin 481) Family