Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C795
  Reference Plasmid   NZ_CP064407.1
  Reference Plasmid Size   164531
  Reference Plasmid GC Content   0.36
  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
M0183748 NJPFFDMG_00018 16203 3 Gut 0.12 protein_coding synonymous_variant LOW 420G>A Glu140Glu
M0183749 NJPFFDMG_00018 16224 3 Gut 0.12 protein_coding synonymous_variant LOW 399C>A Ala133Ala
M0183750 NJPFFDMG_00018 16298 3 Gut 0.12 protein_coding missense_variant MODERATE 325G>A Val109Ile
M0183751 NJPFFDMG_00018 16367 3 Gut 0.12 protein_coding missense_variant MODERATE 256G>A Val86Ile
M0183752 NJPFFDMG_00013 17350 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -3941C>T None
M0183753 NJPFFDMG_00013 17471 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -4062A>G None
M0183754 NJPFFDMG_00013 17871 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -4462G>A None
M0183755 NJPFFDMG_00142 126497 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1713T>A None
M0183756 NJPFFDMG_00142 126621 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1837A>G None
M0183757 NJPFFDMG_00142 126622 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1838A>T None
M0183758 NJPFFDMG_00142 126623 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1839C>T None
M0183759 NJPFFDMG_00142 129635 3 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -4851A>C None
M0183760 NJPFFDMG_00002 1142 4 Gut 0.15 protein_coding missense_variant MODERATE 38G>A Arg13His
M0183761 NJPFFDMG_00002 1558 4 Gut 0.15 protein_coding missense_variant MODERATE 454A>G Asn152Asp
M0183762 NJPFFDMG_00146 127478 3 Gut 0.12 protein_coding missense_variant MODERATE 478A>G Thr160Ala






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
NJPFFDMG_00051 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.9 0 1 696 1.0 1 Adherence minor pilin subunit prediction
NJPFFDMG_00052 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
NJPFFDMG_00053 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 5.2e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
NJPFFDMG_00054 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.4 2.7e-137 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
NJPFFDMG_00055 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 98.5 0 1 658 1.0 1 Adherence PilA prediction
NJPFFDMG_00056 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 4.7e-125 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
NJPFFDMG_00008 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NJPFFDMG_00064 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NJPFFDMG_00168 PHI:5205 HMPREF0351_10118 (WxL locusC) 79.4 6.8e-99 1 214 0.8359 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
NJPFFDMG_00040 QUM65579.1|GH73 100 4.31e-275 1 401 1 1
NJPFFDMG_00161 QCJ65091.1|GH65 100 0 1 764 1 1
NJPFFDMG_00179 QUM65688.1|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
NJPFFDMG_00069 1.C.24.1.12 90.1 7.3e-35 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family