Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C839
  Reference Plasmid   NZ_CP069561.1
  Reference Plasmid Size   144098
  Reference Plasmid GC Content   0.52
  Reference Plasmid Mobility Type   conjugative





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
M0184527 JHNCPHAJ_00043 42368 7 Gut 0.78 protein_coding upstream_gene_variant MODIFIER -4276A>C None
M0184528 JHNCPHAJ_00051 44156 7 Gut 0.78 protein_coding synonymous_variant LOW 2109G>A Leu703Leu
M0184529 JHNCPHAJ_00051 44375 7 Gut 0.78 protein_coding missense_variant MODERATE 1890A>G Ile630Met
M0184530 JHNCPHAJ_00051 44395 7 Gut 0.78 protein_coding missense_variant MODERATE 1870C>T His624Tyr
M0184531 JHNCPHAJ_00051 44571 7 Gut 0.78 protein_coding missense_variant MODERATE 1694G>A Gly565Asp
M0184532 JHNCPHAJ_00051 44593 7 Gut 0.78 protein_coding missense_variant MODERATE 1672C>A Leu558Met
M0184533 JHNCPHAJ_00048 46347 7 Gut 0.78 protein_coding upstream_gene_variant MODIFIER -4442A>G None
M0184534 JHNCPHAJ_00052 46561 7 Gut 0.78 protein_coding missense_variant MODERATE 649T>C Phe217Leu
M0184535 JHNCPHAJ_00053 47592 7 Gut 0.78 protein_coding missense_variant MODERATE 477A>G Ile159Met
M0184536 JHNCPHAJ_00053 47902 7 Gut 0.78 protein_coding missense_variant MODERATE 167A>G Gln56Arg
M0184537 JHNCPHAJ_00050 48343 7 Gut 0.78 protein_coding upstream_gene_variant MODIFIER -4409A>G None
M0184538 JHNCPHAJ_00054 48588 4 Gut 0.44 protein_coding missense_variant MODERATE 403G>T Ala135Ser






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
JHNCPHAJ_00050 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
JHNCPHAJ_00050 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction







        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
JHNCPHAJ_00082 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
JHNCPHAJ_00093 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
JHNCPHAJ_00094 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
JHNCPHAJ_00095 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
JHNCPHAJ_00097 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
JHNCPHAJ_00098 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
JHNCPHAJ_00099 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
JHNCPHAJ_00093 Mercury (Hg) 83.3 2.7e-32 1 78 1.0000 1.0000 prediction
JHNCPHAJ_00094 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
JHNCPHAJ_00095 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
JHNCPHAJ_00097 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
JHNCPHAJ_00098 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
JHNCPHAJ_00099 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 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
JHNCPHAJ_00080 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
JHNCPHAJ_00081 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
JHNCPHAJ_00082 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
JHNCPHAJ_00083 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JHNCPHAJ_00088 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JHNCPHAJ_00089 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation






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
JHNCPHAJ_00050 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
JHNCPHAJ_00051 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
JHNCPHAJ_00052 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
JHNCPHAJ_00053 PHI:10792 cjrA 100 3.6e-162 1 283 1.0000 0.9725 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
JHNCPHAJ_00079 PHI:9804 int 100 4e-14 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
JHNCPHAJ_00154 AXI38019.1|GH23 100 2.02e-123 1 169 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
JHNCPHAJ_00051 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
JHNCPHAJ_00052 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
JHNCPHAJ_00074 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JHNCPHAJ_00075 2.A.108.2.10 99.8 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JHNCPHAJ_00084 2.A.51.1.7 99.5 5.1e-210 1 376 0.9377 0.9666 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
JHNCPHAJ_00093 1.A.72.5.1 100 1.8e-39 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JHNCPHAJ_00097 1.A.72.3.1 90.1 2.6e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JHNCPHAJ_00098 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JHNCPHAJ_00107 1.E.53.1.11 98 3.2e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family