Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C240
  Reference Plasmid   LC623931.1
  Reference Plasmid Size   57620
  Reference Plasmid GC Content   0.65
  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
M0071148 JFKGDJKG_00006 9780 5 Skin 0.42 protein_coding upstream_gene_variant MODIFIER -4774G>A None
M0071149 JFKGDJKG_00011 9791 5 Skin 0.42 protein_coding synonymous_variant LOW 2958G>A Leu986Leu
M0071150 JFKGDJKG_00011 9872 5 Skin 0.42 protein_coding synonymous_variant LOW 2877T>C Tyr959Tyr
M0071151 JFKGDJKG_00011 9909 5 Skin 0.42 protein_coding missense_variant MODERATE 2840A>T Gln947Leu
M0071152 JFKGDJKG_00011 9911 5 Skin 0.42 protein_coding synonymous_variant LOW 2838A>C Ala946Ala
M0071153 JFKGDJKG_00011 9916 5 Skin 0.42 protein_coding synonymous_variant LOW 2833C>T Leu945Leu
M0071154 JFKGDJKG_00011 9917 5 Skin 0.42 protein_coding synonymous_variant LOW 2832G>C Val944Val
M0071155 JFKGDJKG_00011 9967 6 Skin 0.50 protein_coding synonymous_variant LOW 2782C>T Leu928Leu
M0071156 JFKGDJKG_00011 10159 6 Skin 0.50 protein_coding synonymous_variant LOW 2590C>T Leu864Leu
M0071157 JFKGDJKG_00011 10229 6 Skin 0.50 protein_coding missense_variant MODERATE 2520A>C Glu840Asp
M0071158 JFKGDJKG_00011 10233 6 Skin 0.50 protein_coding missense_variant MODERATE 2516G>C Gly839Ala
M0071159 JFKGDJKG_00011 10236 6 Skin 0.50 protein_coding missense_variant MODERATE 2513T>C Ile838Thr
M0071160 JFKGDJKG_00011 10256 6 Skin 0.50 protein_coding synonymous_variant LOW 2493C>T Ala831Ala
M0071161 JFKGDJKG_00011 10341 6 Skin 0.50 protein_coding missense_variant MODERATE 2408C>T Ala803Val
M0071162 JFKGDJKG_00011 10814 6 Skin 0.50 protein_coding synonymous_variant LOW 1935C>G Ala645Ala
M0071163 JFKGDJKG_00011 10975 6 Skin 0.50 protein_coding missense_variant MODERATE 1774G>A Ala592Thr
M0071164 JFKGDJKG_00011 11123 5 Skin 0.42 protein_coding synonymous_variant LOW 1626C>T Asn542Asn
M0071165 JFKGDJKG_00011 11397 5 Skin 0.42 protein_coding missense_variant MODERATE 1352G>C Arg451Thr
M0071166 JFKGDJKG_00011 11453 3 Skin 0.25 protein_coding missense_variant MODERATE 1296G>C Met432Ile
M0071167 JFKGDJKG_00011 11462 3 Skin 0.25 protein_coding synonymous_variant LOW 1287G>A Pro429Pro
M0071168 JFKGDJKG_00011 11504 3 Skin 0.25 protein_coding missense_variant MODERATE 1245C>A Asp415Glu
M0071169 JFKGDJKG_00011 11505 3 Skin 0.25 protein_coding missense_variant MODERATE 1244A>C Asp415Ala






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
JFKGDJKG_00059 VFG045767 Lvh (Legionella vir homologs) type IVA secretion system 70.5 4.3e-124 1 315 0.9844 0.9813 Effector delivery system P-type conjugative transfer ATPase TrbB 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
JFKGDJKG_00002 Mercury (Hg) 100 7.1e-78 1 144 1.0000 1.0000 experiment
JFKGDJKG_00003 Mercury (Hg) 100 4.4e-62 1 116 1.0000 1.0000 experiment
JFKGDJKG_00004 Mercury (Hg) 100 2.7e-43 1 91 1.0000 1.0000 experiment
JFKGDJKG_00005 Mercury (Hg) 98.5 1.5e-287 1 517 0.9981 0.9216 experiment
JFKGDJKG_00002 Mercury (Hg) 100 1.6e-75 1 144 1.0000 1.0000 prediction
JFKGDJKG_00003 Mercury (Hg) 100 1e-59 1 116 1.0000 0.8657 prediction
JFKGDJKG_00004 Mercury (Hg) 98.9 1.1e-40 1 91 1.0000 1.0000 prediction
JFKGDJKG_00005 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 6.1e-290 1 517 0.9981 0.9216 prediction
JFKGDJKG_00009 Triclosan [class: Phenolic compounds] 71.6 4.8e-168 14 414 0.9593 1.0025 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
JFKGDJKG_00015 ARO:3004239 100 9.47e-191 1 260 1.0000 1.0000 cephalosporin NPS 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






        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
JFKGDJKG_00047 BCU01165.1|GH23 100 4.7e-145 1 211 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
JFKGDJKG_00003 1.A.72.3.1 100 1.7e-60 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JFKGDJKG_00004 1.A.72.3.1 100 1e-41 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
JFKGDJKG_00049 3.A.7.4.1 97.2 5.9e-276 1 575 1.0000 1.7875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00051 3.A.7.4.1 100 2.5e-130 1 254 1.0000 0.7938 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00052 3.A.7.4.1 99.6 2.5e-264 1 473 1.0000 1.4781 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00054 3.A.7.4.1 99.3 8.9e-167 1 299 1.0000 0.9344 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00055 3.A.7.4.1 99.2 1.1e-147 1 260 1.0000 0.8125 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00056 3.A.7.4.1 99.4 0 1 852 1.0000 2.6625 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
JFKGDJKG_00059 3.A.7.4.1 99.7 3.4e-180 1 320 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family