Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2908
  Reference Plasmid   DP1808006750_bin.4__NODE_560_length_5825_cov_0.800733
  Reference Plasmid Size   5825
  Reference Plasmid GC Content   0.70
  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
M0066885 ALPPDFEN_00002 1328 3 Skin 0.60 protein_coding synonymous_variant LOW 399G>C Ala133Ala
M0066886 ALPPDFEN_00001 1814 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -662A>G None
M0066887 ALPPDFEN_00001 1826 3 Skin 0.60 protein_coding upstream_gene_variant MODIFIER -674G>T None
M0066888 ALPPDFEN_00003 2206 3 Skin 0.60 protein_coding synonymous_variant LOW 279G>A Glu93Glu
M0066889 ALPPDFEN_00003 2323 3 Skin 0.60 protein_coding synonymous_variant LOW 162G>C Ala54Ala
M0066890 ALPPDFEN_00003 2403 3 Skin 0.60 protein_coding missense_variant MODERATE 82G>A Gly28Ser
M0066891 ALPPDFEN_00004 3239 4 Skin 0.80 protein_coding synonymous_variant LOW 552C>T Tyr184Tyr
M0066892 ALPPDFEN_00004 3830 3 Skin 0.60 protein_coding synonymous_variant LOW 1143G>T Pro381Pro
M0066893 ALPPDFEN_00004 3873 3 Skin 0.60 protein_coding synonymous_variant LOW 1186T>C Leu396Leu
M0066894 ALPPDFEN_00005 4600 4 Skin 0.80 protein_coding synonymous_variant LOW 474C>G Ala158Ala
M0066895 ALPPDFEN_00004 3293 3 Skin 0.60 protein_coding synonymous_variant LOW 606C>T Phe202Phe
M0066896 ALPPDFEN_00004 3314 3 Skin 0.60 protein_coding synonymous_variant LOW 627C>G Thr209Thr
M0066897 ALPPDFEN_00004 3330 3 Skin 0.60 protein_coding synonymous_variant LOW 643A>C Arg215Arg
M0066898 ALPPDFEN_00004 3347 3 Skin 0.60 protein_coding synonymous_variant LOW 660C>G Arg220Arg
M0066899 ALPPDFEN_00004 3356 3 Skin 0.60 protein_coding synonymous_variant LOW 669C>G Leu223Leu
M0066900 ALPPDFEN_00004 3362 3 Skin 0.60 protein_coding synonymous_variant LOW 675C>G Pro225Pro
M0066901 ALPPDFEN_00004 3366 3 Skin 0.60 protein_coding missense_variant MODERATE 679G>T Asp227Tyr
M0066902 ALPPDFEN_00004 3372 3 Skin 0.60 protein_coding missense_variant MODERATE 685G>A Ala229Thr
M0066903 ALPPDFEN_00004 3374 3 Skin 0.60 protein_coding synonymous_variant LOW 687G>C Ala229Ala






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






        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





        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