Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1419
  Reference Plasmid   NZ_OX460332.1
  Reference Plasmid Size   88489
  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
M0209612 LBDEEOPI_00046 38009 3 Gut 0.75 protein_coding synonymous_variant LOW 2973A>C Gly991Gly
M0209613 LBDEEOPI_00056 48736 3 Gut 0.75 protein_coding missense_variant MODERATE 2162T>C Leu721Ser






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
LBDEEOPI_00096 VFG044067 Colicin Ia 98.9 0 1 626 1.0 1 Exotoxin colicin-like pore-forming 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






        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
LBDEEOPI_00070 CCE57598.2|GH23 100 2.92e-138 1 186 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
LBDEEOPI_00034 3.A.7.10.1 99.9 0 1 763 1.0000 7.9479 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00035 3.A.7.10.1 99.7 1.2e-207 1 356 1.0000 3.7083 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00036 3.A.7.10.1 100 2.4e-244 1 402 1.0000 4.1875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00037 1.E.53.1.10 88.4 5.4e-16 9 51 0.8431 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
LBDEEOPI_00042 9.B.40.1.2 86.9 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
LBDEEOPI_00053 3.A.7.10.1 99.4 8.8e-184 1 327 1.0000 3.4063 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00054 3.A.7.10.1 99.6 3.3e-129 1 230 1.0000 2.3958 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00055 3.A.7.10.1 100 1.3e-57 1 115 1.0000 1.1979 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00058 3.A.7.10.1 99 4.6e-56 1 96 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00059 3.A.7.10.1 100 3.3e-222 1 382 1.0000 3.9792 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00060 3.A.7.10.1 99.3 4.8e-159 1 272 1.0000 2.8333 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00061 3.A.7.10.1 100 6e-87 1 152 1.0000 1.5833 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
LBDEEOPI_00096 1.C.1.1.1 100 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family