Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1129
  Reference Plasmid   NZ_CP118956.1
  Reference Plasmid Size   142622
  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
M0197051 EMHDODPA_00116 100062 3 Gut 0.15 protein_coding synonymous_variant LOW 897T>G Thr299Thr
M0197052 EMHDODPA_00119 102666 3 Gut 0.15 protein_coding missense_variant MODERATE 375G>T Glu125Asp
M0197053 EMHDODPA_00120 103450 3 Gut 0.15 protein_coding missense_variant MODERATE 146C>T Ala49Val
M0197054 EMHDODPA_00114 103637 3 Gut 0.15 protein_coding upstream_gene_variant MODIFIER -4804A>C None
M0197055 EMHDODPA_00125 106877 3 Gut 0.15 protein_coding synonymous_variant LOW 714T>C Phe238Phe
M0197056 EMHDODPA_00120 107907 4 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -4312G>T None
M0197057 EMHDODPA_00120 107911 4 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -4316C>T None
M0197058 EMHDODPA_00128 111826 3 Gut 0.15 protein_coding missense_variant MODERATE 2618T>C Leu873Pro
M0197059 EMHDODPA_00128 111852 3 Gut 0.15 protein_coding synonymous_variant LOW 2592A>G Val864Val






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
EMHDODPA_00010 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 1.2e-125 1 223 1.0 1 Adherence putative housekeeping sortase prediction
EMHDODPA_00011 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.7 0 1 658 1.0 1 Adherence PilA prediction
EMHDODPA_00012 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 100 1.3e-139 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
EMHDODPA_00013 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 100 2.4e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
EMHDODPA_00014 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
EMHDODPA_00015 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 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
EMHDODPA_00059 PHI:8586 mntH1 80.2 1.2e-112 15 277 0.9038 0.9436 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity
EMHDODPA_00060 PHI:8586 mntH1 74.1 1.3e-96 1 239 0.9795 0.9436 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity
EMHDODPA_00070 PHI:5205 HMPREF0351_10118 (WxL locusC) 91.1 3.3e-49 1 101 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EMHDODPA_00071 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.2 8.7e-128 1 246 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EMHDODPA_00082 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.2 1.9e-161 1 381 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
EMHDODPA_00026 QUM65579.1|GH73 99.5 2.49e-274 1 401 1 1
EMHDODPA_00063 AWJ95641.1|GT2 99.7 2.26e-284 1 397 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