Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1296
  Reference Plasmid   NZ_CP148424.1
  Reference Plasmid Size   91103
  Reference Plasmid GC Content   0.44
  Reference Plasmid Mobility Type   non-mobilizable





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
M0205838 GKIBKPGJ_00103 84000 3 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -2180T>G None
M0205839 GKIBKPGJ_00106 88352 5 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -1054C>T None
M0205840 GKIBKPGJ_00106 88496 5 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -1198A>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
GKIBKPGJ_00008 VFG000764 Per 95.3 4.1e-69 1 129 1.0 1 Regulation BfpV experiment
GKIBKPGJ_00009 VFG000765 Per 97.8 8.2e-45 1 89 1.0 1 Regulation BfpW experiment
GKIBKPGJ_00063 VFG042784 BFP 86.1 8.2e-82 62 254 0.7598 1 Adherence major pilin structural unit bundlin experiment
GKIBKPGJ_00064 VFG000750 BFP 96.2 1.3e-70 1 133 1.0 1 Adherence BFP biogenesis protein BfpG experiment
GKIBKPGJ_00065 VFG000751 BFP 99.6 5.6e-301 1 552 1.0 1 Adherence BfpB secretin experiment
GKIBKPGJ_00066 VFG000752 BFP 97.8 3.2e-237 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein experiment
GKIBKPGJ_00067 VFG042788 BFP 98.8 2e-84 1 164 1.0 1 Adherence periplasmic protein experiment
GKIBKPGJ_00070 VFG042789 BFP 99.1 7.7e-242 1 422 1.0 0.7888 Adherence assembly ATPase experiment
GKIBKPGJ_00071 VFG000755 BFP 99.4 2.8e-197 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein experiment
GKIBKPGJ_00072 VFG042791 BFP 98.9 1.5e-150 1 274 1.0 0.8278 Adherence retraction ATPase experiment
GKIBKPGJ_00073 VFG000757 BFP 98.4 4.8e-143 1 249 1.0 1 Adherence prepilin peptidase BfpP experiment
GKIBKPGJ_00074 VFG042793 BFP 93.3 6.3e-52 1 105 0.9906 0.7095 Adherence lipoprotein experiment
GKIBKPGJ_00076 VFG042796 BFP 98.8 1.6e-86 1 162 1.0 1 Adherence minor pilin subunit BfpK experiment
GKIBKPGJ_00077 VFG000762 BFP 99.2 9.7e-71 1 130 1.0 0.8725 Adherence BFP biogenesis protein BfpL experiment
GKIBKPGJ_00095 VFG042219 TTSS secreted effectors 83.3 6.2e-63 1 132 0.9429 0.7213 Effector delivery system Type III secretion system effector EspT, Rho guanine exchange factor experiment
GKIBKPGJ_00008 VFG000764 Per 95.3 3e-68 1 129 1.0 1 Regulation BfpV prediction
GKIBKPGJ_00009 VFG000765 Per 97.8 6.1e-44 1 89 1.0 1 Regulation BfpW prediction
GKIBKPGJ_00063 VFG042784 BFP 86.1 6.2e-81 62 254 0.7598 1 Adherence major pilin structural unit bundlin prediction
GKIBKPGJ_00064 VFG000750 BFP 96.2 9.7e-70 1 133 1.0 1 Adherence BFP biogenesis protein BfpG prediction
GKIBKPGJ_00065 VFG000751 BFP 99.6 4.2e-300 1 552 1.0 1 Adherence BfpB secretin prediction
GKIBKPGJ_00066 VFG000752 BFP 97.8 2.4e-236 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein prediction
GKIBKPGJ_00067 VFG042788 BFP 98.8 1.5e-83 1 164 1.0 1 Adherence periplasmic protein prediction
GKIBKPGJ_00070 VFG042789 BFP 99.1 5.7e-241 1 422 1.0 0.7888 Adherence assembly ATPase prediction
GKIBKPGJ_00071 VFG000755 BFP 99.4 2.1e-196 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein prediction
GKIBKPGJ_00072 VFG042791 BFP 98.9 1.1e-149 1 274 1.0 0.8278 Adherence retraction ATPase prediction
GKIBKPGJ_00073 VFG000757 BFP 98.4 3.6e-142 1 249 1.0 1 Adherence prepilin peptidase BfpP prediction
GKIBKPGJ_00074 VFG042793 BFP 93.3 4.7e-51 1 105 0.9906 0.7095 Adherence lipoprotein prediction
GKIBKPGJ_00076 VFG042796 BFP 98.8 1.2e-85 1 162 1.0 1 Adherence minor pilin subunit BfpK prediction
GKIBKPGJ_00077 VFG000762 BFP 99.2 7.3e-70 1 130 1.0 0.8725 Adherence BFP biogenesis protein BfpL prediction
GKIBKPGJ_00084 VFG041523 T3SS 79.8 2.7e-98 1 213 1.0 1 Effector delivery system T3SS effector NleG family protein prediction
GKIBKPGJ_00089 VFG033809 Vat 89.7 0 1 957 0.9938 0.7016 Effector delivery system vacuolating autotransporter toxin prediction
GKIBKPGJ_00095 VFG042219 TTSS secreted effectors 83.3 4.6e-62 1 132 0.9429 0.7213 Effector delivery system Type III secretion system effector EspT, Rho guanine exchange factor 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
GKIBKPGJ_00006 PHI:3803 PerA 93.4 3.1e-26 1 61 1.0000 0.7993 nematodes hemorrhagic colitis; hemolytic uremic syndrome LPS O-side chain reduced virulence
GKIBKPGJ_00007 PHI:3803 PerA 96.8 1.5e-80 1 158 1.0000 0.7993 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





        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
GKIBKPGJ_00065 1.B.22.7.1 99.6 3.3e-300 1 552 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family