Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1080
  Reference Plasmid   NZ_CP104587.1
  Reference Plasmid Size   426499
  Reference Plasmid GC Content   0.57
  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
M0106984 HPPNAFDN_00478 385490 5 Skin 0.25 protein_coding missense_variant MODERATE 257T>A Val86Glu
M0106985 HPPNAFDN_00478 385505 5 Skin 0.25 protein_coding missense_variant MODERATE 242C>T Ala81Val
M0106986 HPPNAFDN_00474 386435 5 Skin 0.25 protein_coding upstream_gene_variant MODIFIER -3327C>T None
M0106987 HPPNAFDN_00484 388939 5 Skin 0.25 protein_coding synonymous_variant LOW 1026T>C Tyr342Tyr
M0106988 HPPNAFDN_00401 315957 6 Skin 0.30 protein_coding synonymous_variant LOW 822A>G Val274Val
M0106989 HPPNAFDN_00401 316238 6 Skin 0.30 protein_coding missense_variant MODERATE 1103A>G Glu368Gly
M0106990 HPPNAFDN_00401 316257 6 Skin 0.30 protein_coding synonymous_variant LOW 1122A>G Gln374Gln
M0106991 HPPNAFDN_00401 316312 6 Skin 0.30 protein_coding missense_variant MODERATE 1177C>T Pro393Ser
M0106992 HPPNAFDN_00401 316586 6 Skin 0.30 protein_coding missense_variant MODERATE 1451A>G His484Arg
M0106993 HPPNAFDN_00401 316591 6 Skin 0.30 protein_coding missense_variant MODERATE 1456C>T Pro486Ser
M0106994 HPPNAFDN_00401 316594 6 Skin 0.30 protein_coding missense_variant MODERATE 1459G>T Ala487Ser
M0106995 HPPNAFDN_00484 388022 3 Skin 0.15 protein_coding missense_variant MODERATE 109A>G Thr37Ala
M0106996 HPPNAFDN_00401 315790 3 Skin 0.15 protein_coding missense_variant MODERATE 655A>G Ser219Gly
M0106997 HPPNAFDN_00401 315817 3 Skin 0.15 protein_coding synonymous_variant LOW 682C>T Leu228Leu
M0106998 HPPNAFDN_00401 315835 3 Skin 0.15 protein_coding synonymous_variant LOW 700C>T Leu234Leu
M0106999 HPPNAFDN_00401 315837 3 Skin 0.15 protein_coding synonymous_variant LOW 702G>C Leu234Leu
M0107000 HPPNAFDN_00401 315840 3 Skin 0.15 protein_coding missense_variant MODERATE 705C>A Asp235Glu
M0107001 HPPNAFDN_00401 315870 3 Skin 0.15 protein_coding synonymous_variant LOW 735C>T Arg245Arg
M0107002 HPPNAFDN_00401 315871 3 Skin 0.15 protein_coding synonymous_variant LOW 736T>C Leu246Leu
M0107003 HPPNAFDN_00401 315888 3 Skin 0.15 protein_coding synonymous_variant LOW 753A>G Glu251Glu






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
HPPNAFDN_00349 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
HPPNAFDN_00350 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
HPPNAFDN_00351 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
HPPNAFDN_00406 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
HPPNAFDN_00407 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 93.6 4.2e-54 1 110 1.0000 1.0000 experiment
HPPNAFDN_00453 Mercury (Hg) 75.2 8.5e-236 5 564 0.9947 1.0000 experiment
HPPNAFDN_00454 Mercury (Hg) 71.7 1e-55 6 143 0.9583 0.9787 experiment
HPPNAFDN_00455 Mercury (Hg) 76.9 8.9e-34 1 91 1.0000 1.0000 experiment
HPPNAFDN_00456 Mercury (Hg) 83.6 7e-52 1 116 1.0000 1.0000 experiment
HPPNAFDN_00457 Mercury (Hg) 77.9 3.2e-56 1 136 1.0000 0.9444 experiment
HPPNAFDN_00349 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
HPPNAFDN_00350 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
HPPNAFDN_00351 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
HPPNAFDN_00407 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 100 1.7e-53 1 110 1.0000 1.0000 prediction
HPPNAFDN_00453 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 3.60000000001819e-313 5 564 0.9929 1.0000 prediction
HPPNAFDN_00454 Mercury (Hg) 71.7 2.3e-53 6 143 0.9583 0.9787 prediction
HPPNAFDN_00455 Mercury (Hg) 100 4.1e-40 1 91 1.0000 1.0000 prediction
HPPNAFDN_00456 Mercury (Hg) 100 3.2e-58 1 116 1.0000 0.8406 prediction
HPPNAFDN_00457 Mercury (Hg) 100 8.7e-71 1 136 1.0000 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
HPPNAFDN_00396 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
HPPNAFDN_00397 ARO:3002639 100 3.6e-203 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
HPPNAFDN_00405 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
HPPNAFDN_00406 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
HPPNAFDN_00407 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
HPPNAFDN_00408 ARO:3002601 99.6 1.33e-186 1 259 1.0000 0.9848 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
HPPNAFDN_00409 ARO:3001439 100 1.83e-191 1 266 1.0000 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
HPPNAFDN_00410 ARO:3002577 100 7.15e-137 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
HPPNAFDN_00411 ARO:3007822 100 5.48e-193 1 266 1.0000 1.0000 carbapenem VIM beta-lactamase antibiotic inactivation
HPPNAFDN_00471 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
HPPNAFDN_00242 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
HPPNAFDN_00412 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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





        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
HPPNAFDN_00349 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
HPPNAFDN_00455 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
HPPNAFDN_00456 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
HPPNAFDN_00471 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)