Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C56
  Reference Plasmid   CP006001.1
  Reference Plasmid Size   66341
  Reference Plasmid GC Content   0.51
  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
M0143152 PFMCHKKD_00017 17956 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4619T>C None
M0143153 PFMCHKKD_00025 18258 4 Gut 0.33 protein_coding missense_variant MODERATE 34A>G Ile12Val
M0143154 PFMCHKKD_00026 18781 4 Gut 0.33 protein_coding missense_variant MODERATE 44T>C Leu15Pro
M0143155 PFMCHKKD_00027 19874 4 Gut 0.33 protein_coding missense_variant MODERATE 403G>A Glu135Lys
M0143156 PFMCHKKD_00027 20273 4 Gut 0.33 protein_coding missense_variant MODERATE 4A>G Lys2Glu
M0143157 PFMCHKKD_00021 20402 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4673G>A None
M0143158 PFMCHKKD_00028 20793 4 Gut 0.33 protein_coding synonymous_variant LOW 150G>A Thr50Thr
M0143159 PFMCHKKD_00029 21082 4 Gut 0.33 protein_coding synonymous_variant LOW 240G>A Ala80Ala
M0143160 PFMCHKKD_00029 21113 4 Gut 0.33 protein_coding missense_variant MODERATE 209G>A Cys70Tyr
M0143161 PFMCHKKD_00030 22278 3 Gut 0.25 protein_coding missense_variant MODERATE 521A>G Asp174Gly
M0143162 PFMCHKKD_00030 22384 3 Gut 0.25 protein_coding synonymous_variant LOW 627C>T Asp209Asp
M0143163 PFMCHKKD_00031 22572 3 Gut 0.25 protein_coding synonymous_variant LOW 162T>C Gly54Gly
M0143164 PFMCHKKD_00027 24609 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4333A>G None
M0143165 PFMCHKKD_00034 24672 3 Gut 0.25 protein_coding synonymous_variant LOW 63G>A Lys21Lys
M0143166 PFMCHKKD_00027 24818 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4542T>C None
M0143167 PFMCHKKD_00028 25736 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4794C>T None
M0143168 PFMCHKKD_00038 28353 3 Gut 0.25 protein_coding synonymous_variant LOW 258G>A Lys86Lys
M0143169 PFMCHKKD_00038 28365 3 Gut 0.25 protein_coding synonymous_variant LOW 246A>G Arg82Arg
M0143170 PFMCHKKD_00032 28679 3 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -4647T>C None
M0143171 PFMCHKKD_00039 28833 3 Gut 0.25 protein_coding missense_variant MODERATE 743C>A Pro248Gln
M0143172 PFMCHKKD_00040 29685 3 Gut 0.25 protein_coding missense_variant MODERATE 218T>C Val73Ala






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
PFMCHKKD_00025 VFG002039 Heat-stable toxin (ST) 98.6 9.6e-36 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
PFMCHKKD_00030 VFG036066 Heat-labile toxin (LT) 99.1 4.5e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
PFMCHKKD_00031 VFG036068 Heat-labile toxin (LT) 100 4.8e-67 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
PFMCHKKD_00025 VFG002039 Heat-stable toxin (ST) 98.6 7.2e-35 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
PFMCHKKD_00030 VFG036065 Heat-labile toxin (LT) 99.5 8.9e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
PFMCHKKD_00031 VFG036068 Heat-labile toxin (LT) 100 3.6e-66 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) 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






        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
PFMCHKKD_00020 PHI:3113 stbA 97.9 2.1e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
PFMCHKKD_00030 PHI:698 CtxA 80.7 3.7e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
PFMCHKKD_00031 PHI:699 CtxB 78.2 1.9e-51 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) 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
PFMCHKKD_00007 QAY42704.1|GH23 100 7.04e-124 1 169 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
PFMCHKKD_00030 1.C.72.4.1 99.1 2.7e-128 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family