Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3055
  Reference Plasmid   DSKIN0147-1_bin.9__k141_47801
  Reference Plasmid Size   36758
  Reference Plasmid GC Content   0.69
  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
M0070401 PAADNEFM_00018 17034 3 Skin 0.38 protein_coding synonymous_variant LOW 588T>C Thr196Thr
M0070402 PAADNEFM_00018 17151 3 Skin 0.38 protein_coding synonymous_variant LOW 705T>A Arg235Arg
M0070403 PAADNEFM_00018 17160 3 Skin 0.38 protein_coding synonymous_variant LOW 714T>C Ala238Ala
M0070404 PAADNEFM_00019 17992 4 Skin 0.50 protein_coding missense_variant MODERATE 139C>T Pro47Ser
M0070405 PAADNEFM_00019 18402 3 Skin 0.38 protein_coding synonymous_variant LOW 549G>A Glu183Glu
M0070406 PAADNEFM_00019 19005 4 Skin 0.50 protein_coding synonymous_variant LOW 1152T>C Pro384Pro
M0070407 PAADNEFM_00019 19041 4 Skin 0.50 protein_coding synonymous_variant LOW 1188C>A Arg396Arg
M0070408 PAADNEFM_00019 19237 6 Skin 0.75 protein_coding synonymous_variant LOW 1384C>T Leu462Leu
M0070409 PAADNEFM_00019 19254 6 Skin 0.75 protein_coding missense_variant MODERATE 1401C>A His467Gln
M0070410 PAADNEFM_00019 19266 6 Skin 0.75 protein_coding synonymous_variant LOW 1413A>C Arg471Arg
M0070411 PAADNEFM_00019 19288 6 Skin 0.75 protein_coding missense_variant MODERATE 1435A>C Met479Leu
M0070412 PAADNEFM_00019 19319 6 Skin 0.75 protein_coding missense_variant MODERATE 1466G>A Arg489Lys
M0070413 PAADNEFM_00019 19344 6 Skin 0.75 protein_coding synonymous_variant LOW 1491T>C Gly497Gly
M0070414 PAADNEFM_00019 19377 6 Skin 0.75 protein_coding synonymous_variant LOW 1524C>T Pro508Pro
M0070415 PAADNEFM_00019 19428 5 Skin 0.63 protein_coding synonymous_variant LOW 1575C>T Asp525Asp
M0070416 PAADNEFM_00020 20278 4 Skin 0.50 protein_coding missense_variant MODERATE 925C>A Pro309Thr
M0070417 PAADNEFM_00020 20279 4 Skin 0.50 protein_coding synonymous_variant LOW 924A>C Pro308Pro
M0070418 PAADNEFM_00020 20942 4 Skin 0.50 protein_coding synonymous_variant LOW 261G>A Leu87Leu
M0070419 PAADNEFM_00020 20951 4 Skin 0.50 protein_coding synonymous_variant LOW 252G>C Thr84Thr
M0070420 PAADNEFM_00019 18549 5 Skin 0.63 protein_coding synonymous_variant LOW 696C>G Gly232Gly
M0070421 PAADNEFM_00015 14420 3 Skin 0.38 protein_coding synonymous_variant LOW 207A>G Val69Val
M0070422 PAADNEFM_00016 15396 3 Skin 0.38 protein_coding synonymous_variant LOW 486A>G Glu162Glu
M0070423 PAADNEFM_00016 15546 3 Skin 0.38 protein_coding synonymous_variant LOW 636T>C Gly212Gly
M0070424 PAADNEFM_00019 18582 4 Skin 0.50 protein_coding synonymous_variant LOW 729T>G Ser243Ser
M0070425 PAADNEFM_00019 18720 4 Skin 0.50 protein_coding synonymous_variant LOW 867G>A Val289Val
M0070426 PAADNEFM_00019 18768 3 Skin 0.38 protein_coding synonymous_variant LOW 915C>G Leu305Leu
M0070427 PAADNEFM_00020 20606 3 Skin 0.38 protein_coding synonymous_variant LOW 597G>C Val199Val
M0070428 PAADNEFM_00021 21778 3 Skin 0.38 protein_coding missense_variant MODERATE 499G>A Ala167Thr
M0070429 PAADNEFM_00021 21788 3 Skin 0.38 protein_coding missense_variant MODERATE 509G>A Gly170Asp
M0070430 PAADNEFM_00021 21842 3 Skin 0.38 protein_coding missense_variant MODERATE 563C>G Ala188Gly
M0070431 PAADNEFM_00021 21973 3 Skin 0.38 protein_coding synonymous_variant LOW 694T>C Leu232Leu
M0070432 PAADNEFM_00021 21366 3 Skin 0.38 protein_coding synonymous_variant LOW 87C>T Asp29Asp






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
PAADNEFM_00016 3.A.1.3.19 79.6 2.5e-111 1 245 1.0000 0.9531 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily