Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C392
  Reference Plasmid   NZ_AP027301.1
  Reference Plasmid Size   122510
  Reference Plasmid GC Content   0.37
  Reference Plasmid Mobility Type   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
M0087054 CHDFHLNK_00087 77096 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -4812A>C None
M0087055 CHDFHLNK_00096 77294 3 Skin 0.38 protein_coding missense_variant MODERATE 22T>A Tyr8Asn






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
CHDFHLNK_00046 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
CHDFHLNK_00047 Copper (Cu) 99.4 0 11 821 0.9878 1.0000 experiment
CHDFHLNK_00048 Copper (Cu) 98.5 5.2e-31 1 67 0.9853 0.9853 experiment
CHDFHLNK_00049 Copper (Cu) 95.3 0 1 730 1.0000 1.0282 experiment
NBCOPMAM_00046 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
NBCOPMAM_00047 Copper (Cu) 99.4 0 11 821 0.9878 1.0000 experiment
NBCOPMAM_00048 Copper (Cu) 98.5 5.2e-31 1 67 0.9853 0.9853 experiment
NBCOPMAM_00049 Copper (Cu) 95.3 0 1 730 1.0000 1.0282 experiment
DGDEPGLK_00046 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
DGDEPGLK_00047 Copper (Cu) 99.4 0 11 821 0.9878 1.0000 experiment
DGDEPGLK_00048 Copper (Cu) 98.5 5.2e-31 1 67 0.9853 0.9853 experiment
DGDEPGLK_00049 Copper (Cu) 95.3 0 1 730 1.0000 1.0282 experiment
CHDFHLNK_00037 Copper (Cu), Cobalt (Co) 99.2 1.6e-309 1 527 1.0000 1.0000 prediction
CHDFHLNK_00046 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
CHDFHLNK_00047 Copper (Cu) 99.9 0 1 821 1.0000 1.0000 prediction
CHDFHLNK_00048 Copper (Cu) 100 2.4e-29 1 68 1.0000 1.0000 prediction
CHDFHLNK_00049 Copper (Cu) 100 0 1 730 1.0000 1.0000 prediction
NBCOPMAM_00037 Copper (Cu), Cobalt (Co) 99.2 1.6e-309 1 527 1.0000 1.0000 prediction
NBCOPMAM_00046 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
NBCOPMAM_00047 Copper (Cu) 99.9 0 1 821 1.0000 1.0000 prediction
NBCOPMAM_00048 Copper (Cu) 100 2.4e-29 1 68 1.0000 1.0000 prediction
NBCOPMAM_00049 Copper (Cu) 100 0 1 730 1.0000 1.0000 prediction
DGDEPGLK_00037 Copper (Cu), Cobalt (Co) 99.2 1.6e-309 1 527 1.0000 1.0000 prediction
DGDEPGLK_00046 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
DGDEPGLK_00047 Copper (Cu) 99.9 0 1 821 1.0000 1.0000 prediction
DGDEPGLK_00048 Copper (Cu) 100 2.4e-29 1 68 1.0000 1.0000 prediction
DGDEPGLK_00049 Copper (Cu) 100 0 1 730 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
CHDFHLNK_00095 ARO:3000375 98.4 2.78e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
CHDFHLNK_00097 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
CHDFHLNK_00098 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
CHDFHLNK_00099 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
NBCOPMAM_00095 ARO:3000375 98.4 2.78e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
NBCOPMAM_00097 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
NBCOPMAM_00098 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
NBCOPMAM_00099 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
DGDEPGLK_00095 ARO:3000375 98.4 2.78e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
DGDEPGLK_00097 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
DGDEPGLK_00098 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
DGDEPGLK_00099 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) 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
CHDFHLNK_00116 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 9e-72 14 146 0.9110 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
CHDFHLNK_00118 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.5 7.1e-107 1 190 0.9223 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
CHDFHLNK_00119 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 3.9e-17 1 41 1.0000 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NBCOPMAM_00116 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 9e-72 14 146 0.9110 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NBCOPMAM_00118 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.5 7.1e-107 1 190 0.9223 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NBCOPMAM_00119 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 3.9e-17 1 41 1.0000 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DGDEPGLK_00116 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 9e-72 14 146 0.9110 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DGDEPGLK_00118 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.5 7.1e-107 1 190 0.9223 0.9158 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
DGDEPGLK_00119 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 3.9e-17 1 41 1.0000 0.9158 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
CHDFHLNK_00008 CCO10203.2|GH1 87.6 4.68e-246 1 388 0.9949 0.9949
CHDFHLNK_00017 CCO10203.2|GH1 86.5 3.16e-213 1 340 0.9942 0.8718
CHDFHLNK_00071 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
CHDFHLNK_00117 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
CHDFHLNK_00152 QZY25062.1|GH73 100 1.44e-273 1 401 1 1
NBCOPMAM_00008 CCO10203.2|GH1 87.6 4.68e-246 1 388 0.9949 0.9949
NBCOPMAM_00017 CCO10203.2|GH1 86.5 3.16e-213 1 340 0.9942 0.8718
NBCOPMAM_00071 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
NBCOPMAM_00117 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
NBCOPMAM_00152 QZY25062.1|GH73 100 1.44e-273 1 401 1 1
DGDEPGLK_00008 CCO10203.2|GH1 87.6 4.68e-246 1 388 0.9949 0.9949
DGDEPGLK_00017 CCO10203.2|GH1 86.5 3.16e-213 1 340 0.9942 0.8718
DGDEPGLK_00071 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
DGDEPGLK_00117 CCO10203.2|GH1 87.9 8.11e-247 1 388 0.9949 0.9949
DGDEPGLK_00152 QZY25062.1|GH73 100 1.44e-273 1 401 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
CHDFHLNK_00047 3.A.3.5.15 99.4 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
CHDFHLNK_00049 3.A.3.5.16 95.3 0 1 730 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
NBCOPMAM_00047 3.A.3.5.15 99.4 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
NBCOPMAM_00049 3.A.3.5.16 95.3 0 1 730 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
DGDEPGLK_00047 3.A.3.5.15 99.4 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
DGDEPGLK_00049 3.A.3.5.16 95.3 0 1 730 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