Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C859
  Reference Plasmid   NZ_CP070965.1
  Reference Plasmid Size   43947
  Reference Plasmid GC Content   0.31
  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
M0104439 BNBFJEMJ_00011 10894 9 Skin 0.21 protein_coding synonymous_variant LOW 24A>T Gly8Gly
M0104440 BNBFJEMJ_00011 10921 5 Skin 0.12 protein_coding synonymous_variant LOW 51A>G Val17Val
M0104441 BNBFJEMJ_00011 10945 4 Skin 0.10 protein_coding synonymous_variant LOW 75A>C Ser25Ser
M0104442 BNBFJEMJ_00011 10969 7 Skin 0.17 protein_coding synonymous_variant LOW 99A>C Thr33Thr
M0104443 BNBFJEMJ_00011 10999 8 Skin 0.19 protein_coding synonymous_variant LOW 129C>T His43His
M0104444 BNBFJEMJ_00011 11044 9 Skin 0.21 protein_coding synonymous_variant LOW 174C>T Ile58Ile
M0104445 BNBFJEMJ_00011 11107 4 Skin 0.10 protein_coding synonymous_variant LOW 237G>T Gly79Gly
M0104446 BNBFJEMJ_00011 11173 9 Skin 0.21 protein_coding synonymous_variant LOW 303G>A Glu101Glu
M0104447 BNBFJEMJ_00011 11422 7 Skin 0.17 protein_coding synonymous_variant LOW 552C>T Asp184Asp
M0104448 BNBFJEMJ_00011 11610 5 Skin 0.12 protein_coding missense_variant MODERATE 740A>C Asn247Thr
M0104449 BNBFJEMJ_00011 11635 9 Skin 0.21 protein_coding synonymous_variant LOW 765A>G Val255Val
M0104450 BNBFJEMJ_00011 11807 8 Skin 0.19 protein_coding missense_variant MODERATE 937G>A Val313Ile
M0104451 BNBFJEMJ_00011 11837 9 Skin 0.21 protein_coding missense_variant MODERATE 967A>G Ile323Val
M0104452 BNBFJEMJ_00011 11962 8 Skin 0.19 protein_coding synonymous_variant LOW 1092G>T Ala364Ala
M0104453 BNBFJEMJ_00033 37577 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -2189A>T None
M0104454 BNBFJEMJ_00033 37578 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -2190A>T None
M0104455 BNBFJEMJ_00011 11035 4 Skin 0.10 protein_coding synonymous_variant LOW 165T>C Gly55Gly
M0104456 BNBFJEMJ_00011 11095 4 Skin 0.10 protein_coding synonymous_variant LOW 225T>C Thr75Thr
M0104457 BNBFJEMJ_00011 11260 5 Skin 0.12 protein_coding synonymous_variant LOW 390C>T Asn130Asn
M0104458 BNBFJEMJ_00011 11590 4 Skin 0.10 protein_coding synonymous_variant LOW 720T>C Ile240Ile
M0104459 BNBFJEMJ_00011 11620 4 Skin 0.10 protein_coding synonymous_variant LOW 750C>T Gly250Gly
M0104460 BNBFJEMJ_00011 11686 5 Skin 0.12 protein_coding missense_variant MODERATE 816T>G Ile272Met
M0104461 BNBFJEMJ_00011 11695 4 Skin 0.10 protein_coding synonymous_variant LOW 825C>T Asn275Asn






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
BNBFJEMJ_00034 Cadmium (Cd), Zinc (Zn) 93.2 3.6e-99 1 205 1.0000 1.0000 experiment
BNBFJEMJ_00034 Cadmium (Cd), Zinc (Zn) 99 1.1e-101 1 205 1.0000 1.0000 prediction
BNBFJEMJ_00039 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
BNBFJEMJ_00040 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 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
BNBFJEMJ_00008 ARO:3000251 97.5 0 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection






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
BNBFJEMJ_00009 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
BNBFJEMJ_00017 PHI:6191 Lqo 82.1 2e-248 1 497 0.9960 1.0000 rodents skin infection; food poisoning; respiratory disease L-lactate-quinone oxidoreductases 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
BNBFJEMJ_00008 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
BNBFJEMJ_00019 2.A.21.2.2 73.6 3e-215 1 512 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
BNBFJEMJ_00034 2.A.77.1.1 92.7 3e-97 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
BNBFJEMJ_00040 3.A.3.5.19 73.6 0 4 795 0.9962 0.9888 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily