Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1112
  Reference Plasmid   NZ_CP116550.1
  Reference Plasmid Size   160122
  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
M0196212 CPFEDIAP_00106 96197 3 Gut 0.43 protein_coding missense_variant MODERATE 91A>G Asn31Asp
M0196213 CPFEDIAP_00106 96247 3 Gut 0.43 protein_coding missense_variant MODERATE 41C>A Thr14Lys
M0196214 CPFEDIAP_00107 96510 3 Gut 0.43 protein_coding synonymous_variant LOW 636T>C Ala212Ala
M0196215 CPFEDIAP_00107 97125 3 Gut 0.43 protein_coding synonymous_variant LOW 21G>A Val7Val
M0196216 CPFEDIAP_00104 97992 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -2628A>G None
M0196217 CPFEDIAP_00109 98167 3 Gut 0.43 protein_coding synonymous_variant LOW 678G>A Gly226Gly
M0196218 CPFEDIAP_00104 98923 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -3559A>G None
M0196219 CPFEDIAP_00104 98934 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -3570A>C None
M0196220 CPFEDIAP_00110 99241 3 Gut 0.43 protein_coding stop_gained HIGH 145C>T Arg49*
M0196221 CPFEDIAP_00110 99349 3 Gut 0.43 protein_coding missense_variant MODERATE 253T>C Phe85Leu
M0196222 CPFEDIAP_00110 99790 3 Gut 0.43 protein_coding missense_variant MODERATE 694T>G Cys232Gly
M0196223 CPFEDIAP_00110 99890 3 Gut 0.43 protein_coding missense_variant MODERATE 794G>A Gly265Asp
M0196224 CPFEDIAP_00110 99974 3 Gut 0.43 protein_coding missense_variant MODERATE 878C>T Thr293Ile






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
CPFEDIAP_00009 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 2.7e-125 1 223 1.0 1 Adherence putative housekeeping sortase prediction
CPFEDIAP_00010 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 0 1 658 1.0 1 Adherence PilA prediction
CPFEDIAP_00011 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 1.2e-137 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
CPFEDIAP_00012 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 6.8e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
CPFEDIAP_00013 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 96.5 4.1e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
CPFEDIAP_00014 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 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






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
CPFEDIAP_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
CPFEDIAP_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
CPFEDIAP_00103 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
CPFEDIAP_00110 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
CPFEDIAP_00134 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1.1e-29 44 106 0.5943 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
CPFEDIAP_00141 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.3 2.7e-208 1 392 1.0000 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
CPFEDIAP_00025 QUM65579.1|GH73 99.8 1.23e-274 1 401 1 1
CPFEDIAP_00075 QMV94891.1|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
CPFEDIAP_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