Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1081
  Reference Plasmid   NZ_CP104591.1
  Reference Plasmid Size   462066
  Reference Plasmid GC Content   0.56
  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
M0107004 GBEAOFDI_00035 27387 11 Skin 0.39 protein_coding missense_variant MODERATE 1459G>T Ala487Ser
M0107005 GBEAOFDI_00035 27390 11 Skin 0.39 protein_coding missense_variant MODERATE 1456C>T Pro486Ser
M0107006 GBEAOFDI_00035 27395 11 Skin 0.39 protein_coding missense_variant MODERATE 1451A>G His484Arg
M0107007 GBEAOFDI_00035 27669 11 Skin 0.39 protein_coding missense_variant MODERATE 1177C>T Pro393Ser
M0107008 GBEAOFDI_00035 27724 11 Skin 0.39 protein_coding synonymous_variant LOW 1122A>G Gln374Gln
M0107009 GBEAOFDI_00035 27743 11 Skin 0.39 protein_coding missense_variant MODERATE 1103A>G Glu368Gly
M0107010 GBEAOFDI_00035 28024 11 Skin 0.39 protein_coding synonymous_variant LOW 822A>G Val274Val
M0107011 GBEAOFDI_00348 282575 3 Skin 0.11 protein_coding synonymous_variant LOW 954C>T Arg318Arg
M0107012 GBEAOFDI_00348 282617 3 Skin 0.11 protein_coding synonymous_variant LOW 912G>C Thr304Thr
M0107013 GBEAOFDI_00348 282752 3 Skin 0.11 protein_coding synonymous_variant LOW 777T>C Asp259Asp
M0107014 GBEAOFDI_00348 282823 3 Skin 0.11 protein_coding synonymous_variant LOW 706T>C Leu236Leu
M0107015 GBEAOFDI_00348 282824 3 Skin 0.11 protein_coding synonymous_variant LOW 705T>G Ser235Ser
M0107016 GBEAOFDI_00348 282830 3 Skin 0.11 protein_coding synonymous_variant LOW 699A>C Thr233Thr
M0107017 GBEAOFDI_00348 282896 3 Skin 0.11 protein_coding synonymous_variant LOW 633G>T Thr211Thr
M0107018 GBEAOFDI_00348 282962 3 Skin 0.11 protein_coding synonymous_variant LOW 567A>G Ser189Ser
M0107019 GBEAOFDI_00348 283025 3 Skin 0.11 protein_coding synonymous_variant LOW 504G>A Glu168Glu
M0107020 GBEAOFDI_00348 283133 3 Skin 0.11 protein_coding synonymous_variant LOW 396T>G Leu132Leu
M0107021 GBEAOFDI_00348 283220 3 Skin 0.11 protein_coding synonymous_variant LOW 309T>C Tyr103Tyr
M0107022 GBEAOFDI_00348 283253 3 Skin 0.11 protein_coding synonymous_variant LOW 276C>G Ser92Ser
M0107023 GBEAOFDI_00348 283265 3 Skin 0.11 protein_coding synonymous_variant LOW 264G>C Leu88Leu
M0107024 GBEAOFDI_00348 283280 3 Skin 0.11 protein_coding synonymous_variant LOW 249C>T Ala83Ala
M0107025 GBEAOFDI_00348 283304 3 Skin 0.11 protein_coding synonymous_variant LOW 225T>G Ala75Ala
M0107026 GBEAOFDI_00348 283310 3 Skin 0.11 protein_coding synonymous_variant LOW 219G>A Leu73Leu
M0107027 GBEAOFDI_00348 283319 3 Skin 0.11 protein_coding synonymous_variant LOW 210C>G Arg70Arg
M0107028 GBEAOFDI_00348 283325 3 Skin 0.11 protein_coding synonymous_variant LOW 204T>C Arg68Arg
M0107029 GBEAOFDI_00348 283334 3 Skin 0.11 protein_coding synonymous_variant LOW 195C>T Asp65Asp
M0107030 GBEAOFDI_00348 283367 3 Skin 0.11 protein_coding synonymous_variant LOW 162C>T Ile54Ile
M0107031 GBEAOFDI_00348 283400 3 Skin 0.11 protein_coding synonymous_variant LOW 129A>G Glu43Glu
M0107032 GBEAOFDI_00348 283406 3 Skin 0.11 protein_coding synonymous_variant LOW 123G>T Arg41Arg
M0107033 GBEAOFDI_00348 283439 3 Skin 0.11 protein_coding synonymous_variant LOW 90C>T Gly30Gly
M0107034 GBEAOFDI_00348 283496 3 Skin 0.11 protein_coding synonymous_variant LOW 33C>A Ala11Ala
M0107035 GBEAOFDI_00348 283502 3 Skin 0.11 protein_coding synonymous_variant LOW 27A>G Thr9Thr
M0107036 GBEAOFDI_00035 28093 7 Skin 0.25 protein_coding synonymous_variant LOW 753A>G Glu251Glu
M0107037 GBEAOFDI_00035 28110 7 Skin 0.25 protein_coding synonymous_variant LOW 736T>C Leu246Leu
M0107038 GBEAOFDI_00035 28111 7 Skin 0.25 protein_coding synonymous_variant LOW 735C>T Arg245Arg
M0107039 GBEAOFDI_00035 28141 7 Skin 0.25 protein_coding missense_variant MODERATE 705C>A Asp235Glu
M0107040 GBEAOFDI_00035 28144 7 Skin 0.25 protein_coding synonymous_variant LOW 702G>C Leu234Leu
M0107041 GBEAOFDI_00035 28146 7 Skin 0.25 protein_coding synonymous_variant LOW 700C>T Leu234Leu
M0107042 GBEAOFDI_00035 28164 7 Skin 0.25 protein_coding synonymous_variant LOW 682C>T Leu228Leu
M0107043 GBEAOFDI_00035 28191 7 Skin 0.25 protein_coding missense_variant MODERATE 655A>G Ser219Gly






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
GBEAOFDI_00029 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 93.6 4.2e-54 1 110 1.0000 1.0000 experiment
GBEAOFDI_00030 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
GBEAOFDI_00085 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
GBEAOFDI_00086 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
GBEAOFDI_00087 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
GBEAOFDI_00555 Mercury (Hg) 77.9 3.2e-56 1 136 1.0000 0.9444 experiment
GBEAOFDI_00556 Mercury (Hg) 83.6 7e-52 1 116 1.0000 1.0000 experiment
GBEAOFDI_00557 Mercury (Hg) 76.9 8.9e-34 1 91 1.0000 1.0000 experiment
GBEAOFDI_00558 Mercury (Hg) 71.7 1e-55 6 143 0.9583 0.9787 experiment
GBEAOFDI_00559 Mercury (Hg) 75.2 8.5e-236 5 564 0.9947 1.0000 experiment
GBEAOFDI_00029 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 100 1.7e-53 1 110 1.0000 1.0000 prediction
GBEAOFDI_00085 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
GBEAOFDI_00086 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
GBEAOFDI_00087 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
GBEAOFDI_00555 Mercury (Hg) 100 8.7e-71 1 136 1.0000 1.0000 prediction
GBEAOFDI_00556 Mercury (Hg) 100 3.2e-58 1 116 1.0000 0.8406 prediction
GBEAOFDI_00557 Mercury (Hg) 100 4.1e-40 1 91 1.0000 1.0000 prediction
GBEAOFDI_00558 Mercury (Hg) 71.7 2.3e-53 6 143 0.9583 0.9787 prediction
GBEAOFDI_00559 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 3.60000000001819e-313 5 564 0.9929 1.0000 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
GBEAOFDI_00025 ARO:3007822 100 5.48e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
GBEAOFDI_00026 ARO:3002577 100 7.15e-137 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GBEAOFDI_00027 ARO:3001439 100 1.83e-191 1 266 1.0000 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
GBEAOFDI_00028 ARO:3002601 99.6 1.33e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GBEAOFDI_00029 ARO:3005098 93.6 1.69e-70 1 110 1.0000 1.0000 disinfecting agents and antiseptics small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
GBEAOFDI_00030 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
GBEAOFDI_00031 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GBEAOFDI_00039 ARO:3002639 100 3.6e-203 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
GBEAOFDI_00040 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
GBEAOFDI_00541 ARO:3002699 82.3 1.28e-238 1 406 0.9951 0.9644 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump 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
GBEAOFDI_00024 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
GBEAOFDI_00194 PHI:10380 RecA 73.2 1.1e-139 1 328 0.9507 0.9398 nematodes nosocomial infection DNA strand exchange and recombination protein reduced virulence






        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
GBEAOFDI_00268 UUC21733.1|GT2 97.1 3.17e-192 1 273 1 1
GBEAOFDI_00482 QFX78706.1|GH23 100 9.1e-168 1 234 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
GBEAOFDI_00087 2.A.109.1.1 71.9 1.8e-139 1 340 0.9884 0.9884 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family
GBEAOFDI_00541 2.A.1.2.3 74.1 1.9e-167 1 406 0.9951 0.9690 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GBEAOFDI_00556 1.A.72.3.1 77.6 1.5e-45 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GBEAOFDI_00557 1.A.72.3.1 76.9 4.3e-32 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily