Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1239
  Reference Plasmid   NZ_CP140622.1
  Reference Plasmid Size   83425
  Reference Plasmid GC Content   0.53
  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
M0200564 DHNNAAIM_00061 47707 9 Gut 1.00 protein_coding missense_variant MODERATE 184A>C Asn62His
M0200565 DHNNAAIM_00061 47709 9 Gut 1.00 protein_coding missense_variant MODERATE 186C>G Asn62Lys
M0200566 DHNNAAIM_00061 47712 9 Gut 1.00 protein_coding missense_variant MODERATE 189T>A Asp63Glu
M0200567 DHNNAAIM_00061 47772 9 Gut 1.00 protein_coding synonymous_variant LOW 249G>A Glu83Glu
M0200568 DHNNAAIM_00061 47775 9 Gut 1.00 protein_coding synonymous_variant LOW 252G>T Val84Val
M0200569 DHNNAAIM_00061 47787 9 Gut 1.00 protein_coding synonymous_variant LOW 264G>A Ala88Ala
M0200570 DHNNAAIM_00061 47838 9 Gut 1.00 protein_coding synonymous_variant LOW 315C>A Ile105Ile
M0200571 DHNNAAIM_00061 47839 9 Gut 1.00 protein_coding missense_variant MODERATE 316A>C Ile106Leu
M0200572 DHNNAAIM_00061 47856 9 Gut 1.00 protein_coding synonymous_variant LOW 333T>A Ala111Ala
M0200573 DHNNAAIM_00061 47859 9 Gut 1.00 protein_coding synonymous_variant LOW 336G>A Val112Val
M0200574 DHNNAAIM_00061 47866 9 Gut 1.00 protein_coding missense_variant MODERATE 343A>T Ser115Cys
M0200575 DHNNAAIM_00061 47867 9 Gut 1.00 protein_coding missense_variant MODERATE 344G>C Ser115Thr
M0200576 DHNNAAIM_00061 47868 9 Gut 1.00 protein_coding synonymous_variant LOW 345C>T Ser115Ser
M0200577 DHNNAAIM_00061 47871 9 Gut 1.00 protein_coding synonymous_variant LOW 348C>T Val116Val
M0200578 DHNNAAIM_00061 47873 9 Gut 1.00 protein_coding missense_variant MODERATE 350T>C Val117Ala
M0200579 DHNNAAIM_00061 47874 9 Gut 1.00 protein_coding synonymous_variant LOW 351T>C Val117Val
M0200580 DHNNAAIM_00061 47877 9 Gut 1.00 protein_coding synonymous_variant LOW 354C>A Gly118Gly
M0200581 DHNNAAIM_00061 47878 9 Gut 1.00 protein_coding missense_variant MODERATE 355C>T Leu119Phe
M0200582 DHNNAAIM_00062 47902 9 Gut 1.00 protein_coding missense_variant MODERATE 5C>T Ser2Leu
M0200583 DHNNAAIM_00072 55386 9 Gut 1.00 protein_coding synonymous_variant LOW 1425G>A Gly475Gly
M0200584 DHNNAAIM_00073 56612 9 Gut 1.00 protein_coding synonymous_variant LOW 24G>T Thr8Thr
M0200585 DHNNAAIM_00073 56724 9 Gut 1.00 protein_coding missense_variant MODERATE 136G>A Val46Met
M0200586 DHNNAAIM_00073 56753 9 Gut 1.00 protein_coding synonymous_variant LOW 165C>T Thr55Thr
M0200587 DHNNAAIM_00073 56762 9 Gut 1.00 protein_coding synonymous_variant LOW 174G>A Ala58Ala
M0200588 DHNNAAIM_00073 56885 9 Gut 1.00 protein_coding synonymous_variant LOW 297C>T Ile99Ile
M0200589 DHNNAAIM_00074 57046 9 Gut 1.00 protein_coding synonymous_variant LOW 75C>T Gly25Gly






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
DHNNAAIM_00011 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
DHNNAAIM_00009 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
DHNNAAIM_00010 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
DHNNAAIM_00011 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
DHNNAAIM_00012 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
DHNNAAIM_00018 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
DHNNAAIM_00019 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
DHNNAAIM_00022 ARO:3000375 98 7.97e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
DHNNAAIM_00028 ARO:3001889 100 4.01e-203 1 291 1.0000 1.0000 carbapenem CTX-M beta-lactamase 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
DHNNAAIM_00008 PHI:9804 int 100 2.7e-14 1 37 0.1595 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
DHNNAAIM_00058 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
DHNNAAIM_00014 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