Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C488
  Reference Plasmid   NZ_CP023424.1
  Reference Plasmid Size   195692
  Reference Plasmid GC Content   0.35
  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
M0167302 KENEFKND_00100 91781 3 Gut 0.15 protein_coding missense_variant MODERATE 905A>G Asp302Gly
M0167303 KENEFKND_00100 92026 3 Gut 0.15 protein_coding missense_variant MODERATE 660G>A Met220Ile
M0167304 KENEFKND_00100 92281 3 Gut 0.15 protein_coding synonymous_variant LOW 405T>C Ile135Ile
M0167305 KENEFKND_00096 92774 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4632A>G None
M0167306 KENEFKND_00096 92819 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4677G>T None






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
KENEFKND_00007 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 1e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
KENEFKND_00008 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 0 1 658 1.0 1 Adherence PilA prediction
KENEFKND_00009 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 1.2e-137 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
KENEFKND_00010 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 98.4 1.1e-130 1 253 1.0 1.008 Adherence cell wall-associated LPXTG-like protein prediction
KENEFKND_00011 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 96.5 2.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
KENEFKND_00012 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.7 0 1 696 1.0 1 Adherence minor pilin subunit 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
KENEFKND_00120 ARO:3002597 99.8 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation
KENEFKND_00122 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
KENEFKND_00057 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
KENEFKND_00068 PHI:5205 HMPREF0351_10118 (WxL locusC) 77.9 2e-23 13 80 0.8095 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
KENEFKND_00102 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
KENEFKND_00109 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.1 2.2e-66 1 162 0.9759 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
KENEFKND_00028 ATD79686.1|GH73 100 9.24e-286 1 401 1 1
KENEFKND_00075 QMV94891.1|GH32 100 0 1 479 1 1
KENEFKND_00119 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
KENEFKND_00147 AUH46335.1|GH32 100 0 1 494 1 1
KENEFKND_00150 CCO12977.2|GH3 70.4 8.46e-116 101 330 0.697 0.9957
KENEFKND_00160 AAN34803.1|GH84 100 0 1 553 1 1
KENEFKND_00161 QEW99892.1|GH2 100 0 1 993 1 1
KENEFKND_00162 QSQ01358.1|GH20 100 0 1 637 1 1
KENEFKND_00203 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
KENEFKND_00055 1.C.90.3.3 100 2.3e-38 1 87 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.90 The Carnocyclin A (Carnocyclin) Family