Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C438
  Reference Plasmid   NZ_CP013265.1
  Reference Plasmid Size   229716
  Reference Plasmid GC Content   0.63
  Reference Plasmid Mobility Type   conjugative





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
M0087603 PFMCADCE_00097 85819 3 Skin 0.20 protein_coding synonymous_variant LOW 438T>G Val146Val
M0087604 PFMCADCE_00097 85820 3 Skin 0.20 protein_coding missense_variant MODERATE 437T>C Val146Ala
M0087605 PFMCADCE_00097 85861 3 Skin 0.20 protein_coding synonymous_variant LOW 396C>T Val132Val
M0087606 PFMCADCE_00097 85882 3 Skin 0.20 protein_coding synonymous_variant LOW 375C>G Ala125Ala
M0087607 PFMCADCE_00097 85921 3 Skin 0.20 protein_coding synonymous_variant LOW 336G>T Thr112Thr
M0087608 PFMCADCE_00097 85960 3 Skin 0.20 protein_coding synonymous_variant LOW 297C>G Ala99Ala
M0087609 PFMCADCE_00097 85978 3 Skin 0.20 protein_coding synonymous_variant LOW 279G>C Ser93Ser
M0087610 PFMCADCE_00097 86002 3 Skin 0.20 protein_coding synonymous_variant LOW 255G>C Thr85Thr
M0087611 PFMCADCE_00097 86119 3 Skin 0.20 protein_coding synonymous_variant LOW 138C>T Thr46Thr
M0087612 PFMCADCE_00098 86286 3 Skin 0.20 protein_coding synonymous_variant LOW 1641C>T Leu547Leu
M0087613 PFMCADCE_00098 86292 3 Skin 0.20 protein_coding synonymous_variant LOW 1635C>G Ala545Ala
M0087614 PFMCADCE_00098 86295 3 Skin 0.20 protein_coding synonymous_variant LOW 1632C>T Val544Val
M0087615 PFMCADCE_00098 86325 3 Skin 0.20 protein_coding synonymous_variant LOW 1602G>A Pro534Pro
M0087616 PFMCADCE_00098 86334 3 Skin 0.20 protein_coding synonymous_variant LOW 1593C>T Gly531Gly
M0087617 PFMCADCE_00098 86361 3 Skin 0.20 protein_coding synonymous_variant LOW 1566G>A Gly522Gly






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
PFMCADCE_00117 Arsenic (As), Antimony (Sb) 70.3 3.3e-54 7 144 0.9452 0.9787 experiment
PFMCADCE_00042 Arsenic (As) 72.5 2.3e-85 12 230 0.8952 0.9328 prediction
PFMCADCE_00045 Arsenic (As) 100 1.8e-208 1 351 1.0000 1.0000 prediction
PFMCADCE_00048 Arsenic (As) 100 2.6e-199 1 359 1.0000 1.0000 prediction
PFMCADCE_00117 Arsenic (As) 72.5 5.2e-53 7 144 0.9452 0.9650 prediction
PFMCADCE_00120 Arsenic (As) 71 6e-86 13 246 0.9675 1.0000 prediction
PFMCADCE_00172 Copper (Cu) 100 1.2e-63 1 125 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






        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
PFMCADCE_00005 QHD70702.1|GH23 92 1.3e-169 36 296 0.8818 1
PFMCADCE_00155 ALR22933.1|GH23 100 7.11e-145 1 221 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
PFMCADCE_00170 3.A.3.5.39 71.8 2.20000000000008e-311 85 857 0.9020 0.9607 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily