Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C391
  Reference Plasmid   NZ_AP027295.1
  Reference Plasmid Size   243853
  Reference Plasmid GC Content   0.36
  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
M0163755 DHBFKIPG_00104 90348 3 Gut 0.60 protein_coding missense_variant MODERATE 157T>G Ser53Ala






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
DHBFKIPG_00147 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 0 1 696 1.0 1 Adherence minor pilin subunit prediction
DHBFKIPG_00148 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.9e-38 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
DHBFKIPG_00149 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 98 2.5e-130 1 253 1.0 1.008 Adherence cell wall-associated LPXTG-like protein prediction
DHBFKIPG_00150 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 6.4e-139 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
DHBFKIPG_00151 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 0 1 658 1.0 1 Adherence PilA prediction
DHBFKIPG_00152 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 1.2e-125 1 223 1.0 1 Adherence putative housekeeping sortase 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
DHBFKIPG_00258 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
DHBFKIPG_00259 Copper (Cu) 100 0 11 821 0.9878 1.0000 experiment
DHBFKIPG_00260 Copper (Cu) 100 1.4e-31 1 68 1.0000 1.0000 experiment
DHBFKIPG_00261 Copper (Cu) 99.9 0 1 710 1.0000 1.0000 experiment
DHBFKIPG_00227 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 99.8 7.5e-307 1 546 1.0000 1.0000 prediction
DHBFKIPG_00228 Mercury (Hg) 100 2.2e-71 1 132 1.0000 1.0000 prediction
DHBFKIPG_00250 Copper (Cu), Cobalt (Co) 99.4 1.2e-309 1 527 1.0000 1.0000 prediction
DHBFKIPG_00258 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
DHBFKIPG_00259 Copper (Cu) 99.8 0 1 821 1.0000 1.0000 prediction
DHBFKIPG_00260 Copper (Cu) 100 3.2e-29 1 68 1.0000 1.0000 prediction
DHBFKIPG_00261 Copper (Cu) 100 0 1 710 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
DHBFKIPG_00006 ARO:3003746 99.7 0 1 637 1.0000 0.9725 oxazolidinone antibiotic Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins antibiotic target protection
DHBFKIPG_00009 ARO:3000347 79.3 2.96e-133 1 242 0.9959 0.9959 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
DHBFKIPG_00059 ARO:3002626 100 9.66e-218 1 287 1.0000 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
DHBFKIPG_00065 ARO:3003206 100 0 1 494 1.0000 1.0000 lincosamide antibiotic lsa-type ABC-F protein antibiotic target protection
DHBFKIPG_00066 ARO:3002836 99.6 4e-191 1 267 1.0000 1.0000 lincosamide antibiotic lincosamide nucleotidyltransferase (LNU) antibiotic inactivation
DHBFKIPG_00072 ARO:3002597 100 0 1 479 1.0000 1.0000 aminoglycoside antibiotic aminoglycoside bifunctional resistance protein antibiotic inactivation
DHBFKIPG_00074 ARO:3002628 98.3 1.65e-174 1 233 1.0000 0.8442 aminoglycoside antibiotic ANT(6) antibiotic inactivation
DHBFKIPG_00075 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
DHBFKIPG_00076 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
DHBFKIPG_00078 ARO:3000375 98.4 2.78e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
DHBFKIPG_00180 ARO:3002868 100 1.88e-125 1 165 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr 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
DHBFKIPG_00094 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DHBFKIPG_00194 PHI:7637 CspA 76.9 7.4e-26 1 65 1.0000 0.9848 bony fishes listeriosis cold shock protein reduced virulence
DHBFKIPG_00199 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.4 5.6e-194 1 338 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DHBFKIPG_00247 PHI:5205 HMPREF0351_10118 (WxL locusC) 90.6 1.6e-82 1 160 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DHBFKIPG_00248 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.1 1.1e-107 1 211 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
DHBFKIPG_00001 CCO10203.2|GH1 86.6 1.66e-239 1 387 0.9923 0.9923
DHBFKIPG_00135 QZY25062.1|GH73 100 1.44e-273 1 401 1 1
DHBFKIPG_00209 CCO11850.2|GH4 98.6 6.39e-149 222 439 0.4966 1
DHBFKIPG_00212 CCO10203.2|GH1 87.6 1.15e-246 1 388 0.9949 0.9949





        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
DHBFKIPG_00006 3.A.1.211.25 100 0 1 637 1.0000 0.9969 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DHBFKIPG_00259 3.A.3.5.15 100 0 11 821 0.9878 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
DHBFKIPG_00261 3.A.3.5.16 99.9 0 1 710 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily