Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1346
  Reference Plasmid   NZ_LR134106.1
  Reference Plasmid Size   164095
  Reference Plasmid GC Content   0.35
  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
M0206931 PPBOJNLG_00114 102581 3 Gut 0.23 protein_coding missense_variant MODERATE 91A>G Asn31Asp
M0206932 PPBOJNLG_00114 102631 3 Gut 0.23 protein_coding missense_variant MODERATE 41C>A Thr14Lys
M0206933 PPBOJNLG_00115 102873 3 Gut 0.23 protein_coding synonymous_variant LOW 657C>T Asp219Asp
M0206934 PPBOJNLG_00115 102894 3 Gut 0.23 protein_coding synonymous_variant LOW 636T>C Ala212Ala






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






        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
PPBOJNLG_00122 ARO:3002597 99.8 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation
PPBOJNLG_00124 ARO:3002597 100 1.59e-282 1 378 1.0000 0.7891 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation






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
PPBOJNLG_00053 PHI:5205 HMPREF0351_10118 (WxL locusC) 76.9 3.7e-107 1 242 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
PPBOJNLG_00098 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.1 1.4e-207 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
PPBOJNLG_00110 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 5e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
PPBOJNLG_00118 PHI:5205 HMPREF0351_10118 (WxL locusC) 70.7 2.9e-162 1 388 0.9974 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
PPBOJNLG_00042 QZK92746.1|GH1 100 0 1 468 1 1
PPBOJNLG_00072 QEN53531.1|GH4 100 0 1 436 1 1
PPBOJNLG_00078 QAA21152.1|GH36 100 0 1 727 1 1
PPBOJNLG_00079 AQT58537.1|GH13_31 100 5.12e-306 1 406 1 1
PPBOJNLG_00080 AVJ46693.1|GH13_18 100 0 1 486 1 1
PPBOJNLG_00121 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
PPBOJNLG_00178 QOJ75557.1|GH36 100 0 1 749 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
PPBOJNLG_00041 4.A.3.1.1 72.2 7.9e-241 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
PPBOJNLG_00061 4.A.2.1.8 70.2 4.4e-176 1 465 0.9667 0.9936 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.2 The PTS Fructose-Mannitol (Fru) Family
PPBOJNLG_00076 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
PPBOJNLG_00077 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