Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C82
  Reference Plasmid   CP042948.1
  Reference Plasmid Size   113164
  Reference Plasmid GC Content   0.50
  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
M0143773 NLMPIOKL_00035 25290 3 Gut 0.05 protein_coding synonymous_variant LOW 279C>T Gly93Gly
M0143774 NLMPIOKL_00128 95303 6 Gut 0.10 protein_coding missense_variant MODERATE 82A>C Met28Leu
M0143775 NLMPIOKL_00082 68247 3 Gut 0.05 protein_coding missense_variant MODERATE 803A>G His268Arg
M0143776 NLMPIOKL_00127 94131 3 Gut 0.05 protein_coding missense_variant MODERATE 496G>A Val166Ile
M0143777 NLMPIOKL_00127 94302 3 Gut 0.05 protein_coding missense_variant MODERATE 325G>A Val109Ile
M0143778 NLMPIOKL_00127 94561 3 Gut 0.05 protein_coding synonymous_variant LOW 66T>C Gly22Gly
M0143779 NLMPIOKL_00127 94573 3 Gut 0.05 protein_coding synonymous_variant LOW 54T>A Ser18Ser






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
NLMPIOKL_00104 VFG000765 Per 100 9.7e-46 1 89 1.0 1 Regulation BfpW experiment
NLMPIOKL_00105 VFG000764 Per 100 5.1e-72 1 129 1.0 1 Regulation BfpV experiment
NLMPIOKL_00130 VFG000762 BFP 100 3.7e-82 1 149 1.0 1 Adherence BFP biogenesis protein BfpL experiment
NLMPIOKL_00131 VFG042796 BFP 100 2.4e-87 1 162 1.0 1 Adherence minor pilin subunit BfpK experiment
NLMPIOKL_00132 VFG000760 BFP 100 8.8e-102 1 183 1.0 1 Adherence minor pilin subunit BfpJ experiment
NLMPIOKL_00133 VFG042794 BFP 99.4 1e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI experiment
NLMPIOKL_00134 VFG042793 BFP 99.3 7.4e-83 1 148 1.0 1 Adherence lipoprotein experiment
NLMPIOKL_00135 VFG000757 BFP 100 2.3e-145 1 249 1.0 1 Adherence prepilin peptidase BfpP experiment
NLMPIOKL_00136 VFG042791 BFP 99.7 9.1e-179 1 318 1.0 0.9607 Adherence retraction ATPase experiment
NLMPIOKL_00137 VFG000755 BFP 100 3.3e-198 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein experiment
NLMPIOKL_00138 VFG042789 BFP 99.8 2.9e-277 1 479 1.0 0.8953 Adherence assembly ATPase experiment
NLMPIOKL_00139 VFG042788 BFP 99.4 1.1e-84 1 164 1.0 1 Adherence periplasmic protein experiment
NLMPIOKL_00140 VFG000752 BFP 100 2.5e-242 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein experiment
NLMPIOKL_00141 VFG000751 BFP 100 5.1e-302 1 552 1.0 1 Adherence BfpB secretin experiment
NLMPIOKL_00142 VFG000750 BFP 95.5 1e-70 1 133 1.0 1 Adherence BFP biogenesis protein BfpG experiment
NLMPIOKL_00143 VFG042784 BFP 85.6 5.4e-81 1 195 1.0 1.0104 Adherence major pilin structural unit bundlin experiment
NLMPIOKL_00104 VFG000765 Per 100 7.2e-45 1 89 1.0 1 Regulation BfpW prediction
NLMPIOKL_00105 VFG000764 Per 100 3.8e-71 1 129 1.0 1 Regulation BfpV prediction
NLMPIOKL_00130 VFG000762 BFP 100 2.8e-81 1 149 1.0 1 Adherence BFP biogenesis protein BfpL prediction
NLMPIOKL_00131 VFG042796 BFP 100 1.8e-86 1 162 1.0 1 Adherence minor pilin subunit BfpK prediction
NLMPIOKL_00132 VFG000760 BFP 100 6.6e-101 1 183 1.0 1 Adherence minor pilin subunit BfpJ prediction
NLMPIOKL_00133 VFG042794 BFP 99.4 7.4e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI prediction
NLMPIOKL_00134 VFG042793 BFP 99.3 5.5e-82 1 148 1.0 1 Adherence lipoprotein prediction
NLMPIOKL_00135 VFG000757 BFP 100 1.7e-144 1 249 1.0 1 Adherence prepilin peptidase BfpP prediction
NLMPIOKL_00136 VFG042791 BFP 99.7 6.8e-178 1 318 1.0 0.9607 Adherence retraction ATPase prediction
NLMPIOKL_00137 VFG000755 BFP 100 2.5e-197 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein prediction
NLMPIOKL_00138 VFG042789 BFP 99.8 2.1e-276 1 479 1.0 0.8953 Adherence assembly ATPase prediction
NLMPIOKL_00139 VFG042788 BFP 99.4 8.6e-84 1 164 1.0 1 Adherence periplasmic protein prediction
NLMPIOKL_00140 VFG000752 BFP 100 1.9e-241 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein prediction
NLMPIOKL_00141 VFG000751 BFP 100 3.8e-301 1 552 1.0 1 Adherence BfpB secretin prediction
NLMPIOKL_00142 VFG000750 BFP 95.5 7.4e-70 1 133 1.0 1 Adherence BFP biogenesis protein BfpG prediction
NLMPIOKL_00143 VFG042784 BFP 85.6 4e-80 1 195 1.0 1.0104 Adherence major pilin structural unit bundlin 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
NLMPIOKL_00019 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
NLMPIOKL_00106 PHI:3803 PerA 100 5e-84 1 158 1.0000 0.9708 nematodes hemorrhagic colitis; hemolytic uremic syndrome LPS O-side chain reduced virulence
NLMPIOKL_00107 PHI:3803 PerA 100 1.5e-56 1 108 0.9153 0.9708 nematodes hemorrhagic colitis; hemolytic uremic syndrome LPS O-side chain 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
NLMPIOKL_00134 BAA84847.1|GH23 100 3.24e-103 1 148 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
NLMPIOKL_00141 1.B.22.7.1 100 3e-301 1 552 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family