Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2668
  Reference Plasmid   1111525849859858_bin.38__k141_203122
  Reference Plasmid Size   54236
  Reference Plasmid GC Content   0.54
  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
M0052669 PDFILGNK_00046 47025 11 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -2002G>A None
M0052670 PDFILGNK_00050 47049 11 Skin 0.14 protein_coding synonymous_variant LOW 1047T>G Gly349Gly
M0052671 PDFILGNK_00050 47079 11 Skin 0.14 protein_coding synonymous_variant LOW 1017T>C Ala339Ala
M0052672 PDFILGNK_00050 47085 11 Skin 0.14 protein_coding synonymous_variant LOW 1011C>T Tyr337Tyr
M0052673 PDFILGNK_00050 47088 11 Skin 0.14 protein_coding synonymous_variant LOW 1008G>A Leu336Leu
M0052674 PDFILGNK_00050 47745 7 Skin 0.09 protein_coding synonymous_variant LOW 351A>G Ala117Ala
M0052675 PDFILGNK_00026 24494 12 Skin 0.15 protein_coding synonymous_variant LOW 597T>C Gly199Gly
M0052676 PDFILGNK_00028 26931 4 Skin 0.05 protein_coding synonymous_variant LOW 1122C>T Val374Val
M0052677 PDFILGNK_00028 31956 10 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3904A>C None
M0052678 PDFILGNK_00003 1855 10 Skin 0.12 protein_coding synonymous_variant LOW 549G>A Leu183Leu
M0052679 PDFILGNK_00014 13318 6 Skin 0.07 protein_coding synonymous_variant LOW 738G>C Thr246Thr
M0052680 PDFILGNK_00003 1647 13 Skin 0.16 protein_coding missense_variant MODERATE 341T>A Ile114Asn
M0052681 PDFILGNK_00003 1652 13 Skin 0.16 protein_coding missense_variant MODERATE 346T>C Phe116Leu
M0052682 PDFILGNK_00003 1654 13 Skin 0.16 protein_coding missense_variant MODERATE 348C>G Phe116Leu
M0052683 PDFILGNK_00001 108 8 Skin 0.10 protein_coding missense_variant MODERATE 76G>T Gly26Cys
M0052684 PDFILGNK_00001 124 8 Skin 0.10 protein_coding missense_variant MODERATE 92T>A Leu31His
M0052685 PDFILGNK_00001 139 8 Skin 0.10 protein_coding missense_variant MODERATE 107G>A Gly36Glu
M0052686 PDFILGNK_00050 47310 9 Skin 0.11 protein_coding synonymous_variant LOW 786C>T Asp262Asp
M0052687 PDFILGNK_00051 48932 4 Skin 0.05 protein_coding synonymous_variant LOW 630C>A Ala210Ala
M0052688 PDFILGNK_00051 48944 4 Skin 0.05 protein_coding synonymous_variant LOW 642T>A Ala214Ala
M0052689 PDFILGNK_00051 48962 4 Skin 0.05 protein_coding synonymous_variant LOW 660A>G Thr220Thr
M0052690 PDFILGNK_00052 49496 4 Skin 0.05 protein_coding synonymous_variant LOW 58C>T Leu20Leu
M0052691 PDFILGNK_00052 50599 3 Skin 0.04 protein_coding synonymous_variant LOW 1161C>T Ser387Ser
M0052692 PDFILGNK_00052 51091 3 Skin 0.04 protein_coding synonymous_variant LOW 1653T>C Ala551Ala
M0052693 PDFILGNK_00018 22369 3 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -4759A>C None
M0052694 PDFILGNK_00051 48407 3 Skin 0.04 protein_coding synonymous_variant LOW 105T>G Val35Val
M0052695 PDFILGNK_00029 33441 3 Skin 0.04 protein_coding upstream_gene_variant MODIFIER -4000G>A None
M0052696 PDFILGNK_00048 46129 3 Skin 0.04 protein_coding missense_variant MODERATE 258G>A Met86Ile






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
PDFILGNK_00031 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Rhodamine 6G [class: Xanthene] 83.8 2.1e-222 14 470 0.9462 0.9892 experiment
PDFILGNK_00031 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Rhodamine 6G [class: Xanthene] 88.7 3.3e-237 1 478 0.9896 0.9979 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
PDFILGNK_00031 ARO:3001327 83.9 1.1e-290 1 472 0.9772 0.9958 fluoroquinolone antibiotic multidrug and toxic compound extrusion (MATE) transporter 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






        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
PDFILGNK_00029 SMZ57495.1|GH4 97.9 0 1 435 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
PDFILGNK_00026 9.B.306.4.2 73.7 0 1 789 0.9975 0.9937 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.306 The Putative Calcium Binding Protein with Similarity to the C-termini of Anoctamins (1.A.17.5) (CBP) Family
PDFILGNK_00031 2.A.66.1.22 83.8 7.8e-221 14 470 0.9462 0.9892 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.66 The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily