Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1345
  Reference Plasmid   NZ_LR132068.1
  Reference Plasmid Size   141895
  Reference Plasmid GC Content   0.36
  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
M0206926 OPKLNLAG_00069 60620 4 Gut 0.57 protein_coding synonymous_variant LOW 612C>T Tyr204Tyr
M0206927 OPKLNLAG_00069 60650 4 Gut 0.57 protein_coding synonymous_variant LOW 642C>T Ser214Ser
M0206928 OPKLNLAG_00069 60826 4 Gut 0.57 protein_coding missense_variant MODERATE 818C>T Pro273Leu
M0206929 OPKLNLAG_00070 60934 4 Gut 0.57 protein_coding upstream_gene_variant MODIFIER -379A>C None
M0206930 OPKLNLAG_00070 60948 4 Gut 0.57 protein_coding upstream_gene_variant MODIFIER -365T>G 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
OPKLNLAG_00007 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 6.7e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
OPKLNLAG_00008 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 97.3 0 1 658 1.0 1 Adherence PilA 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
OPKLNLAG_00091 Copper (Cu) 97.7 0 1 710 1.0000 1.0000 experiment
OPKLNLAG_00092 Copper (Cu) 98.5 5.2e-31 1 67 0.9853 0.9853 experiment
OPKLNLAG_00093 Copper (Cu) 99.5 0 11 821 0.9878 1.0000 experiment
OPKLNLAG_00094 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
OPKLNLAG_00091 Copper (Cu) 100 0 1 710 1.0000 1.0000 prediction
OPKLNLAG_00092 Copper (Cu) 100 2.4e-29 1 68 1.0000 1.0000 prediction
OPKLNLAG_00093 Copper (Cu) 99.9 0 1 821 1.0000 1.0000 prediction
OPKLNLAG_00094 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
OPKLNLAG_00103 Copper (Cu), Cobalt (Co) 99.2 1.6e-309 1 527 1.0000 1.0000 prediction






        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
OPKLNLAG_00057 ARO:3002843 100 1.32e-150 6 209 0.9761 1.0000 streptogramin antibiotic streptogramin vat acetyltransferase antibiotic inactivation
OPKLNLAG_00063 ARO:3000375 98.8 9.7e-175 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
OPKLNLAG_00139 ARO:3002962 100 5.6e-107 1 161 1.0000 1.0000 glycopeptide antibiotic vanZ antibiotic target alteration
OPKLNLAG_00140 ARO:3002955 100 1.88e-223 1 303 1.0000 1.0000 glycopeptide antibiotic vanY antibiotic target alteration
OPKLNLAG_00141 ARO:3002949 99.5 2.46e-155 1 202 1.0000 1.0000 glycopeptide antibiotic vanX antibiotic target alteration
OPKLNLAG_00142 ARO:3000010 100 1.38e-252 1 343 1.0000 1.0000 glycopeptide antibiotic glycopeptide resistance gene cluster antibiotic target alteration
OPKLNLAG_00143 ARO:3002942 100 4.32e-234 1 322 1.0000 1.0000 glycopeptide antibiotic vanH antibiotic target alteration
OPKLNLAG_00144 ARO:3002931 99.7 3.45e-268 1 380 1.0000 0.9896 glycopeptide antibiotic vanS antibiotic target alteration
OPKLNLAG_00145 ARO:3002919 100 7.79e-171 1 231 1.0000 1.0000 glycopeptide antibiotic glycopeptide resistance gene cluster antibiotic target alteration






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
OPKLNLAG_00022 QIV91206.1|GH73 100 2.49e-274 1 401 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
OPKLNLAG_00091 3.A.3.5.16 97.7 0 1 710 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
OPKLNLAG_00093 3.A.3.5.15 99.5 0 11 821 0.9878 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily