Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C643
  Reference Plasmid   NZ_CP040877.1
  Reference Plasmid Size   154417
  Reference Plasmid GC Content   0.34
  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
M0170137 ABFDBPPH_00075 69068 3 Gut 0.13 protein_coding missense_variant MODERATE 5C>T Ala2Val
M0170138 ABFDBPPH_00073 70458 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -1778T>G None
M0170139 ABFDBPPH_00073 70506 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -1826G>T None
M0170140 ABFDBPPH_00081 72234 3 Gut 0.13 protein_coding start_lost HIGH 1A>G Met1?






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
ABFDBPPH_00052 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 0 1 696 1.0 1 Adherence minor pilin subunit prediction
ABFDBPPH_00053 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.9e-38 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
ABFDBPPH_00054 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 3.4e-132 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
ABFDBPPH_00055 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 1.4e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
ABFDBPPH_00056 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.5 0 1 658 1.0 1 Adherence PilA prediction
ABFDBPPH_00057 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 6.7e-124 1 223 1.0 1 Adherence putative housekeeping sortase 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
ABFDBPPH_00002 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.5 2.6e-166 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
ABFDBPPH_00030 PHI:5205 HMPREF0351_10118 (WxL locusC) 87 4.7e-200 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
ABFDBPPH_00101 PHI:5205 HMPREF0351_10118 (WxL locusC) 70.7 2.6e-35 1 98 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
ABFDBPPH_00130 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.5 4.4e-166 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
ABFDBPPH_00162 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.5 4.9e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
ABFDBPPH_00035 QAR74517.1|GH65 100 0 1 764 1 1
ABFDBPPH_00071 QAT24339.1|GH36 100 0 1 749 1 1
ABFDBPPH_00146 AOM14759.1|GH13_18 100 0 1 486 1 1
ABFDBPPH_00147 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
ABFDBPPH_00148 QAA21152.1|GH36 99.9 0 1 727 1 1
ABFDBPPH_00152 QEN53531.1|GH4 100 0 1 436 1 1
ABFDBPPH_00172 VEF84274.1|GH32 100 0 1 479 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
ABFDBPPH_00084 1.C.24.1.10 100 7.8e-37 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family
ABFDBPPH_00110 9.A.59.1.1 100 4.9e-21 1 44 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.59 The Bacteriocin: Enterocin/Pediocin (BEP) Family
ABFDBPPH_00116 3.A.1.122.3 75.8 4.7e-163 3 405 0.9951 1.7797 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ABFDBPPH_00117 3.A.1.122.3 92.5 3.1e-119 1 227 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
ABFDBPPH_00118 3.A.1.122.3 89.2 1.6e-192 1 399 1.0000 1.7577 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ABFDBPPH_00149 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
ABFDBPPH_00150 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily