Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C487
  Reference Plasmid   NZ_CP023350.1
  Reference Plasmid Size   112045
  Reference Plasmid GC Content   0.48
  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
M0167285 PIFFJHGA_00102 86846 3 Gut 0.12 protein_coding synonymous_variant LOW 216T>G Leu72Leu
M0167286 PIFFJHGA_00102 86993 3 Gut 0.12 protein_coding synonymous_variant LOW 363C>T Arg121Arg
M0167287 PIFFJHGA_00102 87163 3 Gut 0.12 protein_coding missense_variant MODERATE 533T>C Leu178Pro
M0167288 PIFFJHGA_00102 87167 3 Gut 0.12 protein_coding synonymous_variant LOW 537A>C Pro179Pro
M0167289 PIFFJHGA_00102 87182 3 Gut 0.12 protein_coding synonymous_variant LOW 552C>T Cys184Cys
M0167290 PIFFJHGA_00102 87280 3 Gut 0.12 protein_coding splice_region_variant&stop_retained_variant LOW 650G>A Ter217Ter
M0167291 PIFFJHGA_00103 87334 3 Gut 0.12 protein_coding synonymous_variant LOW 54T>C Asp18Asp
M0167292 PIFFJHGA_00103 87346 3 Gut 0.12 protein_coding synonymous_variant LOW 66C>T Gly22Gly
M0167293 PIFFJHGA_00103 87361 3 Gut 0.12 protein_coding synonymous_variant LOW 81C>A Ala27Ala
M0167294 PIFFJHGA_00103 87449 3 Gut 0.12 protein_coding synonymous_variant LOW 169C>T Leu57Leu
M0167295 PIFFJHGA_00103 87520 3 Gut 0.12 protein_coding synonymous_variant LOW 240C>T Val80Val
M0167296 PIFFJHGA_00103 87526 3 Gut 0.12 protein_coding synonymous_variant LOW 246C>T Arg82Arg
M0167297 PIFFJHGA_00103 87529 3 Gut 0.12 protein_coding synonymous_variant LOW 249T>C Asp83Asp
M0167298 PIFFJHGA_00103 87532 3 Gut 0.12 protein_coding synonymous_variant LOW 252A>C Gly84Gly
M0167299 PIFFJHGA_00103 87538 3 Gut 0.12 protein_coding synonymous_variant LOW 258T>G Val86Val
M0167300 PIFFJHGA_00103 87562 3 Gut 0.12 protein_coding synonymous_variant LOW 282C>T Ser94Ser
M0167301 PIFFJHGA_00103 87616 3 Gut 0.12 protein_coding synonymous_variant LOW 336A>C Gly112Gly






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
PIFFJHGA_00066 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
PIFFJHGA_00067 VFG036068 Heat-labile toxin (LT) 99.2 1.4e-66 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
PIFFJHGA_00066 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
PIFFJHGA_00067 VFG036068 Heat-labile toxin (LT) 99.2 1e-65 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
PIFFJHGA_00074 VFG042480 Adhesive fimbriae 97.6 3.1e-206 1 372 1.0 0.9973 Adherence CS5 fimbrial minor pilin subunit prediction
PIFFJHGA_00075 VFG042479 Adhesive fimbriae 93.3 3.4e-115 1 225 1.0 1.0045 Adherence hypothetical protein prediction
PIFFJHGA_00076 VFG042478 Adhesive fimbriae 90.6 3.9e-102 1 203 1.0 1 Adherence hypothetical protein prediction
PIFFJHGA_00079 VFG042476 Adhesive fimbriae 94.6 4.8e-122 1 223 1.0 0.9955 Adherence hypothetical protein prediction
PIFFJHGA_00080 VFG001433 Adhesive fimbriae 100 1.3e-105 1 203 1.0 1 Adherence CS7 fimbria major subunit CsvA precursor 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
PIFFJHGA_00066 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
PIFFJHGA_00067 PHI:699 CtxB 79 3e-52 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





        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
PIFFJHGA_00021 8.B.24.2.1 100 1.4e-53 1 105 0.9906 0.8268 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
PIFFJHGA_00066 1.C.72.4.1 99.5 3.1e-129 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
PIFFJHGA_00107 9.B.40.1.2 85.9 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
PIFFJHGA_00114 3.A.7.10.1 99 5.1e-242 1 402 1.0000 4.1875 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
PIFFJHGA_00115 3.A.7.10.1 99.4 2.8e-207 1 356 1.0000 3.7083 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
PIFFJHGA_00116 3.A.7.10.1 99.2 0 1 763 1.0000 7.9479 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