Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C300
  Reference Plasmid   NC_011603.1
  Reference Plasmid Size   97978
  Reference Plasmid GC Content   0.48
  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
M0151864 ALFCADLJ_00033 27512 3 Gut 0.13 protein_coding missense_variant MODERATE 16A>G Ile6Val
M0151865 ALFCADLJ_00085 77555 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4611G>T None
M0151866 ALFCADLJ_00018 18991 3 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -2635G>A None
M0151867 ALFCADLJ_00024 19762 5 Gut 0.21 protein_coding synonymous_variant LOW 24A>T Ala8Ala






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
ALFCADLJ_00003 VFG042784 BFP 100 3.5e-101 1 193 1.0 1 Adherence major pilin structural unit bundlin experiment
ALFCADLJ_00004 VFG000750 BFP 100 9.6e-74 1 133 1.0 1 Adherence BFP biogenesis protein BfpG experiment
ALFCADLJ_00005 VFG000751 BFP 100 5.1e-302 1 552 1.0 1 Adherence BfpB secretin experiment
ALFCADLJ_00006 VFG000752 BFP 100 2.5e-242 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein experiment
ALFCADLJ_00007 VFG042788 BFP 100 1.4e-85 1 164 1.0 1 Adherence periplasmic protein experiment
ALFCADLJ_00008 VFG042789 BFP 100 3.40000000000022e-311 1 534 1.0 0.9981 Adherence assembly ATPase experiment
ALFCADLJ_00009 VFG000755 BFP 100 3.3e-198 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein experiment
ALFCADLJ_00010 VFG042791 BFP 100 2.5e-187 1 331 1.0 1 Adherence retraction ATPase experiment
ALFCADLJ_00011 VFG000757 BFP 100 2.3e-145 1 249 1.0 1 Adherence prepilin peptidase BfpP experiment
ALFCADLJ_00012 VFG042793 BFP 100 5.7e-83 1 148 1.0 1 Adherence lipoprotein experiment
ALFCADLJ_00013 VFG042794 BFP 100 1e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI experiment
ALFCADLJ_00014 VFG000760 BFP 100 8.8e-102 1 183 1.0 1 Adherence minor pilin subunit BfpJ experiment
ALFCADLJ_00015 VFG042796 BFP 100 2.4e-87 1 162 1.0 1 Adherence minor pilin subunit BfpK experiment
ALFCADLJ_00016 VFG000762 BFP 100 1.5e-71 1 130 1.0 0.8725 Adherence BFP biogenesis protein BfpL experiment
ALFCADLJ_00020 VFG000763 Per 99.3 9e-151 1 274 1.0 1 Regulation BfpT experiment
ALFCADLJ_00021 VFG000764 Per 100 5.1e-72 1 129 1.0 1 Regulation BfpV experiment
ALFCADLJ_00022 VFG000765 Per 100 9.7e-46 1 89 1.0 1 Regulation BfpW experiment
ALFCADLJ_00080 VFG001445 TraJ 98.5 1.2e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
ALFCADLJ_00003 VFG042784 BFP 100 2.6e-100 1 193 1.0 1 Adherence major pilin structural unit bundlin prediction
ALFCADLJ_00004 VFG000750 BFP 100 7.2e-73 1 133 1.0 1 Adherence BFP biogenesis protein BfpG prediction
ALFCADLJ_00005 VFG000751 BFP 100 3.8e-301 1 552 1.0 1 Adherence BfpB secretin prediction
ALFCADLJ_00006 VFG000752 BFP 100 1.9e-241 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein prediction
ALFCADLJ_00007 VFG042788 BFP 100 1e-84 1 164 1.0 1 Adherence periplasmic protein prediction
ALFCADLJ_00008 VFG042789 BFP 100 2.50000000000002e-310 1 534 1.0 0.9981 Adherence assembly ATPase prediction
ALFCADLJ_00009 VFG000755 BFP 100 2.5e-197 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein prediction
ALFCADLJ_00010 VFG042791 BFP 100 1.9e-186 1 331 1.0 1 Adherence retraction ATPase prediction
ALFCADLJ_00011 VFG000757 BFP 100 1.7e-144 1 249 1.0 1 Adherence prepilin peptidase BfpP prediction
ALFCADLJ_00012 VFG042793 BFP 100 4.2e-82 1 148 1.0 1 Adherence lipoprotein prediction
ALFCADLJ_00013 VFG042794 BFP 100 7.4e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI prediction
ALFCADLJ_00014 VFG000760 BFP 100 6.6e-101 1 183 1.0 1 Adherence minor pilin subunit BfpJ prediction
ALFCADLJ_00015 VFG042796 BFP 100 1.8e-86 1 162 1.0 1 Adherence minor pilin subunit BfpK prediction
ALFCADLJ_00016 VFG000762 BFP 100 1.1e-70 1 130 1.0 0.8725 Adherence BFP biogenesis protein BfpL prediction
ALFCADLJ_00020 VFG000763 Per 99.3 6.7e-150 1 274 1.0 1 Regulation BfpT prediction
ALFCADLJ_00021 VFG000764 Per 100 3.8e-71 1 129 1.0 1 Regulation BfpV prediction
ALFCADLJ_00022 VFG000765 Per 100 7.2e-45 1 89 1.0 1 Regulation BfpW prediction
ALFCADLJ_00080 VFG001445 TraJ 98.5 9.3e-113 1 200 0.8772 0.995 Invasion unknown protein 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
ALFCADLJ_00020 PHI:3803 PerA 100 1.6e-151 1 274 1.0000 1.0000 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
ALFCADLJ_00012 CAS07448.1|GH23 100 2.28e-103 1 148 1 1
ALFCADLJ_00082 CAS07513.1|GH23 100 3.49e-124 1 169 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
ALFCADLJ_00005 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