Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C923
  Reference Plasmid   NZ_CP079125.1
  Reference Plasmid Size   37333
  Reference Plasmid GC Content   0.59
  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
M0104835 GGPBGPLD_00024 22011 3 Skin 0.75 protein_coding synonymous_variant LOW 198T>C Gly66Gly
M0104836 GGPBGPLD_00024 22089 3 Skin 0.75 protein_coding synonymous_variant LOW 120A>G Val40Val
M0104837 GGPBGPLD_00025 22264 3 Skin 0.75 protein_coding synonymous_variant LOW 1527T>C Asn509Asn
M0104838 GGPBGPLD_00025 22486 3 Skin 0.75 protein_coding synonymous_variant LOW 1305C>T Arg435Arg
M0104839 GGPBGPLD_00025 22525 3 Skin 0.75 protein_coding synonymous_variant LOW 1266A>G Lys422Lys
M0104840 GGPBGPLD_00025 22792 3 Skin 0.75 protein_coding synonymous_variant LOW 999T>C Arg333Arg
M0104841 GGPBGPLD_00025 22840 3 Skin 0.75 protein_coding synonymous_variant LOW 951T>C Thr317Thr
M0104842 GGPBGPLD_00025 22867 3 Skin 0.75 protein_coding synonymous_variant LOW 924T>C Arg308Arg
M0104843 GGPBGPLD_00025 22885 3 Skin 0.75 protein_coding synonymous_variant LOW 906C>G Pro302Pro
M0104844 GGPBGPLD_00025 22900 3 Skin 0.75 protein_coding synonymous_variant LOW 891T>C Phe297Phe
M0104845 GGPBGPLD_00025 22967 3 Skin 0.75 protein_coding missense_variant MODERATE 824A>C His275Pro
M0104846 GGPBGPLD_00025 23044 3 Skin 0.75 protein_coding synonymous_variant LOW 747C>G Gly249Gly
M0104847 GGPBGPLD_00025 23053 3 Skin 0.75 protein_coding synonymous_variant LOW 738T>C Gly246Gly
M0104848 GGPBGPLD_00025 23116 3 Skin 0.75 protein_coding synonymous_variant LOW 675T>C Val225Val
M0104849 GGPBGPLD_00025 23239 3 Skin 0.75 protein_coding synonymous_variant LOW 552G>C Ala184Ala
M0104850 GGPBGPLD_00025 23290 3 Skin 0.75 protein_coding synonymous_variant LOW 501A>G Pro167Pro
M0104851 GGPBGPLD_00025 23446 3 Skin 0.75 protein_coding synonymous_variant LOW 345A>G Pro115Pro
M0104852 GGPBGPLD_00025 23548 3 Skin 0.75 protein_coding synonymous_variant LOW 243C>T His81His
M0104853 GGPBGPLD_00021 23871 3 Skin 0.75 protein_coding upstream_gene_variant MODIFIER -4095T>C None
M0104854 GGPBGPLD_00032 30117 3 Skin 0.75 protein_coding synonymous_variant LOW 615T>C Ala205Ala






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
GGPBGPLD_00012 Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Tetraphenylarsonium (TPA) [class: Quaternary Ammonium Compounds (QACs)] 76.1 2.3e-177 7 408 0.9854 0.9902 experiment
GGPBGPLD_00012 Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Tetraphenylarsonium (TPA) [class: Quaternary Ammonium Compounds (QACs)] 78.9 3.5e-179 1 402 0.9757 0.9734 prediction
GGPBGPLD_00035 Palmitic acid [class: Free Fatty Acids] 100 1.5e-76 1 146 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
GGPBGPLD_00002 ARO:3004111 99.3 1.35e-101 1 139 1.0000 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase antibiotic inactivation
GGPBGPLD_00012 ARO:3001214 76.1 1.66e-223 7 408 0.9854 0.9902 fluoroquinolone antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
GGPBGPLD_00021 PHI:7575 yjiY 94.1 0 1 716 1.0000 1.0000 rodents salmonellosis peptide-utilizing carbon starvation protein 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





        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
GGPBGPLD_00012 2.A.1.2.52 76.1 8.5e-176 7 408 0.9757 0.9902 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GGPBGPLD_00021 2.A.114.1.10 94.1 0 1 716 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.114 The Putative Peptide Transporter Carbon Starvation CstA (CstA) Family
GGPBGPLD_00027 2.A.1.14.9 71.5 7.4e-173 17 434 0.9248 0.9279 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)