Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C67
  Reference Plasmid   CP025890.1
  Reference Plasmid Size   80572
  Reference Plasmid GC Content   0.46
  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
M0143581 LBDLAJGH_00039 36234 3 Gut 0.20 protein_coding upstream_gene_variant MODIFIER -4060A>G None
M0143582 LBDLAJGH_00047 37419 3 Gut 0.20 protein_coding missense_variant MODERATE 534C>A Ser178Arg






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
LBDLAJGH_00005 VFG035903 Dispersin 95.7 1.9e-187 4 379 0.9921 1 Others permease AatP prediction
LBDLAJGH_00006 VFG035910 Dispersin 96.8 6.7e-215 1 400 1.0 1 Others outer membrane protein AatA prediction
LBDLAJGH_00007 VFG035917 Dispersin 98 1.5e-140 1 255 1.0 1 Others AatB prediction
LBDLAJGH_00008 VFG035924 Dispersin 77.3 1e-89 1 207 0.9952 0.9952 Others ATP-binding protein AatC prediction
LBDLAJGH_00020 VFG035931 Dispersin 98.6 4.9e-232 11 424 0.9764 1 Others AatD prediction
LBDLAJGH_00049 VFG020186 VirK 97.2 1.1e-185 1 316 1.0 1 Others virulence factor VirK prediction
LBDLAJGH_00050 VFG013087 MsbB2 97.5 4.1e-183 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
LBDLAJGH_00058 VFG033834 Pic 97.1 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
LBDLAJGH_00067 VFG001432 Adhesive fimbriae 92.9 1.6e-79 1 154 1.0 1 Adherence CS6 structural subunit A prediction
LBDLAJGH_00068 VFG042483 Adhesive fimbriae 96.4 2.5e-86 1 167 1.0 1 Adherence CS6 fimbrial subunit CssB prediction
LBDLAJGH_00069 VFG042482 Adhesive fimbriae 98.3 9.5e-129 1 232 1.0 1 Adherence CS6 fimbrial biogenesis chaperone CssC prediction
LBDLAJGH_00070 VFG042481 Adhesive fimbriae 96.9 0 1 811 1.0 0.9902 Adherence CS6 fimbrial usher CssD 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
LBDLAJGH_00048 PHI:10400 Sfgtr4 (ORF186) 95.9 9.6e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
LBDLAJGH_00048 QJB53856.1|GT4 99.7 8.93e-271 1 362 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
LBDLAJGH_00061 9.A.18.1.1 98.3 4.8e-199 1 360 0.9972 0.8867 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.18 The Peptide Uptake Permease (PUP) Family
LBDLAJGH_00070 1.B.11.3.4 100 0 10 811 0.9889 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family