Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C53
  Reference Plasmid   AP031567.1
  Reference Plasmid Size   134012
  Reference Plasmid GC Content   0.44
  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
M0058671 OKMDKOCF_00021 15977 3 Skin 0.09 protein_coding missense_variant MODERATE 266C>T Ala89Val
M0058672 OKMDKOCF_00035 27448 3 Skin 0.09 protein_coding missense_variant MODERATE 1111C>G Leu371Val
M0058673 OKMDKOCF_00035 27461 3 Skin 0.09 protein_coding synonymous_variant LOW 1098A>G Gly366Gly
M0058674 OKMDKOCF_00035 27572 3 Skin 0.09 protein_coding synonymous_variant LOW 987G>A Glu329Glu
M0058675 OKMDKOCF_00035 27652 3 Skin 0.09 protein_coding missense_variant MODERATE 907A>G Thr303Ala
M0058676 OKMDKOCF_00035 27654 3 Skin 0.09 protein_coding missense_variant MODERATE 905T>C Val302Ala
M0058677 OKMDKOCF_00035 27655 3 Skin 0.09 protein_coding missense_variant MODERATE 904G>T Val302Phe
M0058678 OKMDKOCF_00035 27671 3 Skin 0.09 protein_coding synonymous_variant LOW 888T>C Gly296Gly
M0058679 OKMDKOCF_00035 27718 3 Skin 0.09 protein_coding missense_variant MODERATE 841G>T Ala281Ser
M0058680 OKMDKOCF_00035 27725 3 Skin 0.09 protein_coding synonymous_variant LOW 834A>G Gln278Gln
M0058681 OKMDKOCF_00035 27855 4 Skin 0.13 protein_coding missense_variant MODERATE 704T>C Val235Ala
M0058682 OKMDKOCF_00035 27872 4 Skin 0.13 protein_coding synonymous_variant LOW 687T>C Phe229Phe
M0058683 OKMDKOCF_00035 28058 4 Skin 0.13 protein_coding synonymous_variant LOW 501T>C Ser167Ser






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
OKMDKOCF_00121 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment






        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
OKMDKOCF_00060 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
OKMDKOCF_00061 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
OKMDKOCF_00065 ARO:3000566 100 1.19e-277 1 395 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
OKMDKOCF_00108 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
OKMDKOCF_00109 ARO:3005056 96.6 5.13e-268 1 378 1.0000 1.0000 tetracycline antibiotic tetracycline inactivation enzyme antibiotic inactivation
OKMDKOCF_00117 ARO:3003015 97.9 4.79e-133 1 189 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
OKMDKOCF_00119 ARO:3002848 100 1.22e-113 59 208 0.7212 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
OKMDKOCF_00120 ARO:3002580 100 5.54e-142 15 206 0.9320 0.9458 aminoglycoside antibiotic AAC(6') antibiotic inactivation
OKMDKOCF_00121 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
OKMDKOCF_00122 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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
OKMDKOCF_00065 2.A.1.2.38 100 1.4e-215 1 395 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)