Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C551
  Reference Plasmid   NZ_CP030003.1
  Reference Plasmid Size   119613
  Reference Plasmid GC Content   0.49
  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
M0168168 LBEGDONK_00078 70286 4 Gut 1.00 protein_coding missense_variant MODERATE 250A>G Lys84Glu
M0168169 LBEGDONK_00078 70334 3 Gut 0.75 protein_coding missense_variant MODERATE 202A>T Arg68Trp






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
LBEGDONK_00029 VFG034679 Ibes 71.9 1.1e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
LBEGDONK_00029 VFG034652 Ibes 71.9 2.3e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC 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
LBEGDONK_00008 Copper (Cu), Silver (Ag) 100 2.4e-70 1 144 1.0000 1.0000 experiment
LBEGDONK_00009 Copper (Cu) 99.8 1e-263 1 466 1.0000 1.0000 experiment
LBEGDONK_00010 Copper (Cu) 100 1.7e-126 1 226 1.0000 1.0000 experiment
LBEGDONK_00024 Silver (Ag) 93.9 0 1 815 1.0012 0.9903 experiment
LBEGDONK_00026 Silver (Ag) 96.9 0 1 1048 1.0000 1.0000 experiment
LBEGDONK_00027 Silver (Ag) 96.3 2.8e-239 1 430 1.0000 1.0000 experiment
LBEGDONK_00028 Silver (Ag) 96.7 2e-46 28 117 0.7692 0.9375 experiment
LBEGDONK_00029 Silver (Ag) 97.2 6.5e-250 1 461 1.0000 1.0000 experiment
LBEGDONK_00030 Silver (Ag) 93 3.5e-116 1 226 1.0088 1.0000 experiment
LBEGDONK_00031 Silver (Ag) 92.7 1.6e-254 1 491 1.0081 0.9960 experiment
LBEGDONK_00032 Silver (Ag) 92.3 1.8e-70 40 182 0.7857 1.0000 experiment
LBEGDONK_00008 Copper (Cu), Silver (Ag) 100 5.6e-68 1 144 1.0000 1.0000 prediction
LBEGDONK_00009 Copper (Cu) 100 3.7e-262 1 466 1.0000 1.0000 prediction
LBEGDONK_00010 Copper (Cu) 100 3.9e-124 1 226 1.0000 0.9741 prediction
LBEGDONK_00024 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
LBEGDONK_00026 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
LBEGDONK_00027 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
LBEGDONK_00028 Silver (Ag) 99.1 2.7e-60 1 117 1.0000 1.0000 prediction
LBEGDONK_00029 Silver (Ag) 100 1.4e-253 1 461 1.0000 1.0000 prediction
LBEGDONK_00030 Silver (Ag) 100 7.8e-125 1 226 1.0000 1.0000 prediction
LBEGDONK_00031 Silver (Ag) 100 4.7e-276 1 491 1.0000 1.0000 prediction
LBEGDONK_00032 Silver (Ag) 100 1e-74 40 182 0.7857 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
LBEGDONK_00016 ARO:3000166 99.3 3.06e-283 1 401 1.0000 1.0000 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LBEGDONK_00017 ARO:3003479 100 1.46e-152 1 207 1.0000 0.9952 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic target alteration






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
LBEGDONK_00007 PHI:11470 STM14_3563 74 8.8e-27 5 81 0.8953 0.8462 rodents salmonellosis putative transcriptional regulator 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
LBEGDONK_00114 CCE57598.2|GH23 100 2.92e-138 1 186 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
LBEGDONK_00016 2.A.1.2.68 99.8 6.4e-221 1 401 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
LBEGDONK_00022 1.A.34.1.3 99.2 7.4e-135 1 245 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.34 The <i>Bacillus</i> Gap Junction-like Channel-forming Complex (GJ-CC) Family
LBEGDONK_00024 3.A.3.5.4 93.9 0 1 815 1.0000 0.9879 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
LBEGDONK_00026 2.A.6.1.3 96.9 0 1 1048 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
LBEGDONK_00029 1.B.17.3.4 97.2 2.4e-248 1 461 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
LBEGDONK_00074 3.A.7.10.1 99.7 0 1 763 1.0000 7.9479 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
LBEGDONK_00075 3.A.7.10.1 99.2 6.1e-207 1 356 1.0000 3.7083 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
LBEGDONK_00076 3.A.7.10.1 100 2.4e-244 1 402 1.0000 4.1875 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
LBEGDONK_00086 9.B.40.1.2 92.5 0 1 723 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
LBEGDONK_00097 3.A.7.10.1 100 6.1e-185 1 327 1.0000 3.4063 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
LBEGDONK_00098 3.A.7.10.1 100 6.7e-130 1 230 1.0000 2.3958 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
LBEGDONK_00099 3.A.7.10.1 100 1.3e-57 1 115 1.0000 1.1979 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
LBEGDONK_00104 3.A.7.10.1 97.9 1.3e-55 1 96 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
LBEGDONK_00105 3.A.7.10.1 100 3.3e-222 1 382 1.0000 3.9792 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
LBEGDONK_00106 3.A.7.10.1 99.6 1.3e-159 1 272 1.0000 2.8333 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
LBEGDONK_00107 3.A.7.10.1 100 6e-87 1 152 1.0000 1.5833 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