Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C716
  Reference Plasmid   NZ_CP050649.1
  Reference Plasmid Size   141022
  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
M0173505 HCKDDKPC_00076 66171 3 Gut 0.27 protein_coding missense_variant MODERATE 143A>G Asp48Gly
M0173506 HCKDDKPC_00078 67622 3 Gut 0.27 protein_coding missense_variant MODERATE 176T>C Val59Ala
M0173507 HCKDDKPC_00079 67849 3 Gut 0.27 protein_coding synonymous_variant LOW 1170T>C Ile390Ile
M0173508 HCKDDKPC_00079 68161 3 Gut 0.27 protein_coding synonymous_variant LOW 858A>C Gly286Gly
M0173509 HCKDDKPC_00079 68173 3 Gut 0.27 protein_coding synonymous_variant LOW 846T>C Gly282Gly
M0173510 HCKDDKPC_00079 68284 3 Gut 0.27 protein_coding synonymous_variant LOW 735G>A Thr245Thr
M0173511 HCKDDKPC_00079 68290 3 Gut 0.27 protein_coding synonymous_variant LOW 729C>T Asn243Asn
M0173512 HCKDDKPC_00079 68293 3 Gut 0.27 protein_coding synonymous_variant LOW 726C>T Asn242Asn
M0173513 HCKDDKPC_00079 68295 3 Gut 0.27 protein_coding missense_variant MODERATE 724A>G Asn242Asp
M0173514 HCKDDKPC_00079 68299 3 Gut 0.27 protein_coding synonymous_variant LOW 720C>T Gly240Gly
M0173515 HCKDDKPC_00142 127880 3 Gut 0.27 protein_coding synonymous_variant LOW 237C>T Asp79Asp
M0173516 HCKDDKPC_00142 127914 3 Gut 0.27 protein_coding missense_variant MODERATE 271T>G Ser91Ala
M0173517 HCKDDKPC_00089 80293 3 Gut 0.27 protein_coding missense_variant MODERATE 22A>G Ile8Val






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
HCKDDKPC_00090 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 0 1 696 1.0 1 Adherence minor pilin subunit prediction
HCKDDKPC_00091 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.9e-38 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
HCKDDKPC_00092 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 8.9e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
HCKDDKPC_00093 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 100 1.3e-139 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
HCKDDKPC_00094 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 0 1 658 1.0 1 Adherence PilA prediction
HCKDDKPC_00095 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
HCKDDKPC_00001 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.5 1.6e-168 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
HCKDDKPC_00013 PHI:5205 HMPREF0351_10118 (WxL locusC) 71 8.3e-165 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
HCKDDKPC_00021 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.6 4.4e-206 1 394 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
HCKDDKPC_00108 PHI:5205 HMPREF0351_10118 (WxL locusC) 96.9 1.9e-49 1 98 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
HCKDDKPC_00109 PHI:5205 HMPREF0351_10118 (WxL locusC) 91.2 5.5e-83 1 160 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
HCKDDKPC_00112 PHI:5205 HMPREF0351_10118 (WxL locusC) 88.2 7.9e-141 1 279 0.9859 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
HCKDDKPC_00079 QIT62351.1|GH73 100 3.54e-274 1 401 1 1
HCKDDKPC_00119 QIT59863.1|GT2 100 0 1 440 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