Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C48
  Reference Plasmid   AP031268.1
  Reference Plasmid Size   183248
  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
M0143084 ILLMGIOB_00114 109686 3 Gut 0.38 protein_coding missense_variant MODERATE 878C>T Thr293Ile
M0143085 ILLMGIOB_00114 109770 3 Gut 0.38 protein_coding missense_variant MODERATE 794G>A Gly265Asp
M0143086 ILLMGIOB_00114 109870 3 Gut 0.38 protein_coding missense_variant MODERATE 694T>G Cys232Gly
M0143087 ILLMGIOB_00114 110311 3 Gut 0.38 protein_coding missense_variant MODERATE 253T>C Phe85Leu
M0143088 ILLMGIOB_00114 110419 3 Gut 0.38 protein_coding stop_gained HIGH 145C>T Arg49*
M0143089 ILLMGIOB_00111 110726 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -3914T>G None
M0143090 ILLMGIOB_00111 110737 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -3925T>C 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
ILLMGIOB_00015 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.7 0 1 696 1.0 1 Adherence minor pilin subunit prediction
ILLMGIOB_00016 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 96.5 2.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
ILLMGIOB_00017 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
ILLMGIOB_00018 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 1.3e-136 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
ILLMGIOB_00019 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.5 0 1 658 1.0 1 Adherence PilA prediction
ILLMGIOB_00020 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 3.6e-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
ILLMGIOB_00081 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
ILLMGIOB_00086 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 8.9e-30 28 90 0.7000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
ILLMGIOB_00093 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
ILLMGIOB_00114 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
ILLMGIOB_00121 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
ILLMGIOB_00158 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
ILLMGIOB_00169 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






        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
ILLMGIOB_00004 AOM35786.1|GH73 100 8.69e-275 1 401 1 1
ILLMGIOB_00063 AMQ98678.1|GH1 100 0 1 488 1 1
ILLMGIOB_00067 CCO10203.2|GH1 86.4 8.63e-242 1 390 1 1
ILLMGIOB_00151 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
ILLMGIOB_00171 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