Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C244
  Reference Plasmid   LR735438.1
  Reference Plasmid Size   39876
  Reference Plasmid GC Content   0.30
  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
M0071170 PCIDKJBF_00040 36011 3 Skin 0.19 protein_coding upstream_gene_variant MODIFIER -2538T>G None
M0071171 PCIDKJBF_00045 36602 4 Skin 0.25 protein_coding missense_variant MODERATE 562A>G Ile188Val
M0071172 PCIDKJBF_00046 37916 3 Skin 0.19 protein_coding synonymous_variant LOW 127C>T Leu43Leu






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
PCIDKJBF_00044 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 99.5 4.7e-106 1 188 1.0000 1.0000 experiment
PCIDKJBF_00045 Ethidium Bromide [class: Phenanthridine], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine], Amicarbalide [class: Diamidine], Hexamidine [class: Diamidine], Stilbamidine [class: Diamidine], 1i-39/JC-1-134 [class: Guanylhydrazones], 1a-62/JC-1-127 [class: Guanylhydrazones] 99.4 1e-272 1 514 1.0000 1.0000 experiment
PCIDKJBF_00012 Copper (Cu) 100 1.6e-33 1 69 1.0000 1.0000 prediction
PCIDKJBF_00013 Copper (Cu), Silver (Ag) 75.6 0 1 795 1.0000 1.0013 prediction
PCIDKJBF_00044 Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Pentamidine [class: Diamidine], Propamidine [class: Diamidine], Diaminodiphenylamine [class: Diamidine] 100 5.7e-105 1 188 1.0000 0.9947 prediction
PCIDKJBF_00045 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Crystal Violet [class: Triarylmethane], Pyronin Y [class: Xanthene], Quinaldine red [class: Quinolines], Rhodamine 6G [class: Xanthene], Safranin O [class: Azin], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Alexidine [class: Biguanides], Amicarbalide [class: Diamidine], Pentamidine [class: Diamidine], Hexamidine [class: Diamidine], Propamidine [class: Diamidine], Diamidinodiphenylamine [class: Diamidine], Dibrompropamidine [class: Diamidine], 1a-62/JC-1-127 [class: Guanylhydrazones], 1i-39/JC-1-134 [class: Guanylhydrazones], Stilbamidine [class: Diamidine], Phenamidine [class: Diamidine], Diminazene [class: Diamidine] 100 5.7e-272 1 514 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
PCIDKJBF_00020 ARO:3000250 99.6 9.79e-176 1 244 1.0000 1.0000 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
PCIDKJBF_00024 ARO:3002865 98.1 4.29e-120 1 161 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
PCIDKJBF_00032 ARO:3002597 100 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation
PCIDKJBF_00045 ARO:3003046 98.8 0 1 514 1.0000 1.0000 fluoroquinolone antibiotic major facilitator superfamily (MFS) 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
PCIDKJBF_00009 PHI:6324 StpC 84 1.9e-108 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





        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
PCIDKJBF_00013 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
PCIDKJBF_00027 3.A.7.7.1 100 5.2e-29 1 62 1.0000 1.1273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PCIDKJBF_00028 3.A.7.7.1 100 2.2e-174 1 323 0.9878 5.8727 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PCIDKJBF_00029 3.A.7.7.1 100 1.4e-53 1 104 0.9286 1.8909 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
PCIDKJBF_00045 2.A.1.3.4 99 1.9e-270 1 514 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)