Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1564
  Reference Plasmid   1111525849480213_bin.15__k141_693341
  Reference Plasmid Size   62436
  Reference Plasmid GC Content   0.57
  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
M0007592 LLALEJPI_00047 41034 4 Skin 0.10 protein_coding synonymous_variant LOW 2286A>C Thr762Thr
M0007593 LLALEJPI_00051 46463 3 Skin 0.08 protein_coding synonymous_variant LOW 450G>C Ser150Ser
M0007594 LLALEJPI_00052 47324 3 Skin 0.08 protein_coding missense_variant MODERATE 268T>C Trp90Arg
M0007595 LLALEJPI_00053 49073 3 Skin 0.08 protein_coding synonymous_variant LOW 1035A>G Val345Val
M0007596 LLALEJPI_00056 51950 3 Skin 0.08 protein_coding missense_variant MODERATE 374A>T Glu125Val
M0007597 LLALEJPI_00056 51960 3 Skin 0.08 protein_coding missense_variant MODERATE 384G>T Trp128Cys






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







        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
LLALEJPI_00006 Chromium (Cr) 74.4 1e-194 14 452 0.9736 0.9651 experiment
LLALEJPI_00010 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 92.3 6e-201 1 377 1.0000 1.0000 experiment
LLALEJPI_00011 Nickel (Ni), Zinc (Zn) 96.8 3.5e-49 1 95 1.0000 1.0000 experiment
LLALEJPI_00005 Chromium (Cr), Methyl Viologen [class: Paraquat], Menadione [class: Naphthoquinone] 100 7.2e-177 1 314 1.0000 1.0000 prediction
LLALEJPI_00006 Chromium (Cr) 100 3e-261 1 454 1.0000 1.0000 prediction
LLALEJPI_00010 Nickel (Ni), Cadmium (Cd), Zinc (Zn), Cobalt (Co) 100 5.5e-216 1 377 1.0000 1.0000 prediction
LLALEJPI_00011 Nickel (Ni), Zinc (Zn) 100 1.9e-48 1 95 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






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
LLALEJPI_00054 PHI:7474 PA0336 (RppH) 89.3 6.5e-84 1 159 1.0000 1.0000 nematodes infection nudix-type RNA pyrophosphohydrolase increased virulence (hypervirulence)






        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
LLALEJPI_00006 2.A.51.1.4 75.4 3.2e-200 1 452 0.9956 0.9934 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
LLALEJPI_00053 4.A.2.1.28 82.4 0 1 757 1.0000 8.2283 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.2 The PTS Fructose-Mannitol (Fru) Family