Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C509
  Reference Plasmid   NZ_CP024425.1
  Reference Plasmid Size   167927
  Reference Plasmid GC Content   0.65
  Reference Plasmid Mobility Type   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
M0091581 LMFEBFPD_00099 101858 3 Skin 0.08 protein_coding synonymous_variant LOW 7T>C Leu3Leu
M0091582 LMFEBFPD_00099 101979 4 Skin 0.10 protein_coding missense_variant MODERATE 128G>A Gly43Asp
M0091583 LMFEBFPD_00099 102110 4 Skin 0.10 protein_coding missense_variant MODERATE 259A>G Thr87Ala
M0091584 LMFEBFPD_00099 102118 4 Skin 0.10 protein_coding missense_variant MODERATE 267A>C Leu89Phe
M0091585 LMFEBFPD_00100 102324 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -256A>G None
M0091586 LMFEBFPD_00100 102405 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -175A>G None
M0091587 LMFEBFPD_00100 102406 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -174T>C None
M0091588 LMFEBFPD_00100 102523 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -57T>C None
M0091589 LMFEBFPD_00100 102553 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -27T>C None
M0091590 LMFEBFPD_00100 102693 5 Skin 0.13 protein_coding synonymous_variant LOW 114T>G Leu38Leu
M0091591 LMFEBFPD_00100 102742 3 Skin 0.08 protein_coding missense_variant MODERATE 163A>G Met55Val
M0091592 LMFEBFPD_00100 102939 4 Skin 0.10 protein_coding synonymous_variant LOW 360A>G Val120Val
M0091593 LMFEBFPD_00100 103008 4 Skin 0.10 protein_coding synonymous_variant LOW 429G>C Gly143Gly
M0091594 LMFEBFPD_00100 103029 4 Skin 0.10 protein_coding synonymous_variant LOW 450T>C Ile150Ile
M0091595 LMFEBFPD_00110 117599 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -4395T>C None
M0091596 LMFEBFPD_00114 117637 3 Skin 0.08 protein_coding splice_region_variant&stop_retained_variant LOW 867G>A Ter289Ter
M0091597 LMFEBFPD_00114 117709 3 Skin 0.08 protein_coding synonymous_variant LOW 795C>A Ala265Ala
M0091598 LMFEBFPD_00092 93247 3 Skin 0.08 protein_coding synonymous_variant LOW 2013T>G Gly671Gly
M0091599 LMFEBFPD_00092 93661 3 Skin 0.08 protein_coding synonymous_variant LOW 2427G>A Glu809Glu
M0091600 LMFEBFPD_00094 95629 3 Skin 0.08 protein_coding missense_variant MODERATE 418A>G Thr140Ala
M0091601 LMFEBFPD_00094 95631 3 Skin 0.08 protein_coding synonymous_variant LOW 420G>C Thr140Thr
M0091602 LMFEBFPD_00094 95637 3 Skin 0.08 protein_coding synonymous_variant LOW 426T>C Asp142Asp
M0091603 LMFEBFPD_00094 95768 3 Skin 0.08 protein_coding missense_variant MODERATE 557A>G Asp186Gly
M0091604 LMFEBFPD_00094 95784 3 Skin 0.08 protein_coding synonymous_variant LOW 573T>C Phe191Phe
M0091605 LMFEBFPD_00094 95913 3 Skin 0.08 protein_coding synonymous_variant LOW 702T>C Phe234Phe
M0091606 LMFEBFPD_00094 95921 3 Skin 0.08 protein_coding missense_variant MODERATE 710T>C Leu237Pro
M0091607 LMFEBFPD_00094 96150 3 Skin 0.08 protein_coding synonymous_variant LOW 939T>C Gly313Gly
M0091608 LMFEBFPD_00094 96341 3 Skin 0.08 protein_coding missense_variant MODERATE 1130T>C Ile377Thr
M0091609 LMFEBFPD_00094 96387 3 Skin 0.08 protein_coding synonymous_variant LOW 1176T>C Asn392Asn
M0091610 LMFEBFPD_00094 96423 3 Skin 0.08 protein_coding synonymous_variant LOW 1212A>G Ala404Ala
M0091611 LMFEBFPD_00094 96468 3 Skin 0.08 protein_coding synonymous_variant LOW 1257G>C Thr419Thr
M0091612 LMFEBFPD_00094 96652 3 Skin 0.08 protein_coding missense_variant MODERATE 1441C>G Pro481Ala
M0091613 LMFEBFPD_00094 96654 3 Skin 0.08 protein_coding synonymous_variant LOW 1443C>A Pro481Pro
M0091614 LMFEBFPD_00094 96655 3 Skin 0.08 protein_coding missense_variant MODERATE 1444T>C Ser482Pro
M0091615 LMFEBFPD_00094 96656 3 Skin 0.08 protein_coding missense_variant MODERATE 1445C>A Ser482Tyr
M0091616 LMFEBFPD_00094 96657 3 Skin 0.08 protein_coding synonymous_variant LOW 1446C>G Ser482Ser
M0091617 LMFEBFPD_00094 96666 3 Skin 0.08 protein_coding synonymous_variant LOW 1455G>C Ala485Ala
M0091618 LMFEBFPD_00094 96714 3 Skin 0.08 protein_coding synonymous_variant LOW 1503C>G Gly501Gly
M0091619 LMFEBFPD_00094 96836 3 Skin 0.08 protein_coding missense_variant MODERATE 1625T>C Val542Ala
M0091620 LMFEBFPD_00094 96927 3 Skin 0.08 protein_coding synonymous_variant LOW 1716G>C Ala572Ala
M0091621 LMFEBFPD_00095 97202 3 Skin 0.08 protein_coding synonymous_variant LOW 111T>G Leu37Leu
M0091622 LMFEBFPD_00095 97751 4 Skin 0.10 protein_coding synonymous_variant LOW 660A>C Arg220Arg
M0091623 LMFEBFPD_00095 97352 3 Skin 0.08 protein_coding synonymous_variant LOW 261G>C Gly87Gly
M0091624 LMFEBFPD_00095 97358 3 Skin 0.08 protein_coding synonymous_variant LOW 267A>G Arg89Arg
M0091625 LMFEBFPD_00095 97369 3 Skin 0.08 protein_coding missense_variant MODERATE 278G>A Ser93Asn
M0091626 LMFEBFPD_00095 97454 3 Skin 0.08 protein_coding synonymous_variant LOW 363C>G Ser121Ser
M0091627 LMFEBFPD_00095 97460 3 Skin 0.08 protein_coding synonymous_variant LOW 369T>C Phe123Phe
M0091628 LMFEBFPD_00095 97547 3 Skin 0.08 protein_coding synonymous_variant LOW 456G>A Gln152Gln
M0091629 LMFEBFPD_00095 98241 3 Skin 0.08 protein_coding missense_variant MODERATE 1150A>G Thr384Ala
M0091630 LMFEBFPD_00095 98255 3 Skin 0.08 protein_coding synonymous_variant LOW 1164T>C His388His
M0091631 LMFEBFPD_00095 98421 3 Skin 0.08 protein_coding missense_variant MODERATE 1330T>G Ser444Ala
M0091632 LMFEBFPD_00095 98423 3 Skin 0.08 protein_coding synonymous_variant LOW 1332C>G Ser444Ser
M0091633 LMFEBFPD_00095 98432 3 Skin 0.08 protein_coding synonymous_variant LOW 1341C>T Gly447Gly
M0091634 LMFEBFPD_00095 98438 3 Skin 0.08 protein_coding synonymous_variant LOW 1347C>A Ala449Ala
M0091635 LMFEBFPD_00095 98466 3 Skin 0.08 protein_coding missense_variant MODERATE 1375T>G Ser459Ala
M0091636 LMFEBFPD_00095 98499 3 Skin 0.08 protein_coding missense_variant MODERATE 1408G>A Val470Ile
M0091637 LMFEBFPD_00095 98639 3 Skin 0.08 protein_coding synonymous_variant LOW 1548C>G Val516Val
M0091638 LMFEBFPD_00095 98813 3 Skin 0.08 protein_coding synonymous_variant LOW 1722T>G Leu574Leu
M0091639 LMFEBFPD_00095 98814 3 Skin 0.08 protein_coding missense_variant MODERATE 1723G>T Val575Phe
M0091640 LMFEBFPD_00096 98881 3 Skin 0.08 protein_coding missense_variant MODERATE 4C>T Pro2Ser
M0091641 LMFEBFPD_00096 99135 3 Skin 0.08 protein_coding synonymous_variant LOW 258G>C Ala86Ala
M0091642 LMFEBFPD_00096 99141 3 Skin 0.08 protein_coding synonymous_variant LOW 264C>G Thr88Thr
M0091643 LMFEBFPD_00100 103336 4 Skin 0.10 protein_coding missense_variant MODERATE 757C>T Leu253Phe
M0091644 LMFEBFPD_00100 103348 4 Skin 0.10 protein_coding missense_variant MODERATE 769A>G Asn257Asp
M0091645 LMFEBFPD_00102 103449 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1392T>C None
M0091646 LMFEBFPD_00102 103450 5 Skin 0.13 protein_coding upstream_gene_variant MODIFIER -1391G>T None
M0091647 LMFEBFPD_00102 103451 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1390C>T None
M0091648 LMFEBFPD_00100 102275 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -305C>T None
M0091649 LMFEBFPD_00100 102347 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -233C>T None
M0091650 LMFEBFPD_00100 102409 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -171A>G None
M0091651 LMFEBFPD_00102 103495 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1346C>T None
M0091652 LMFEBFPD_00102 103501 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1340T>G None
M0091653 LMFEBFPD_00102 103525 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1316G>C None
M0091654 LMFEBFPD_00102 103537 3 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -1304G>T None
M0091655 LMFEBFPD_00102 103549 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1292T>C None
M0091656 LMFEBFPD_00102 103596 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1245T>C None
M0091657 LMFEBFPD_00084 84055 3 Skin 0.08 protein_coding synonymous_variant LOW 747A>G Arg249Arg






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
LMFEBFPD_00079 Arsenic (As) 70.1 2.7e-82 27 230 0.8681 0.8793 experiment
LMFEBFPD_00079 Arsenic (As) 77.8 3.7e-101 1 231 0.9957 0.9750 prediction
LMFEBFPD_00080 Arsenic (As) 85.1 1e-163 1 348 0.9721 0.9803 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






        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
LMFEBFPD_00007 AYF03124.1|GT2 99.5 0 1 777 1 1
LMFEBFPD_00009 ATQ58209.1|GH8 100 2.85e-262 1 361 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