Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1225
  Reference Plasmid   NZ_CP137437.1
  Reference Plasmid Size   111591
  Reference Plasmid GC Content   0.51
  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
M0200094 FOIMFDJB_00042 42436 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -4106A>C None
M0200095 FOIMFDJB_00042 42559 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -4229A>C None
M0200096 FOIMFDJB_00042 42584 4 Gut 0.57 protein_coding upstream_gene_variant MODIFIER -4254G>A None
M0200097 FOIMFDJB_00048 43118 4 Gut 0.57 protein_coding synonymous_variant LOW 201A>T Ala67Ala
M0200098 FOIMFDJB_00049 44191 5 Gut 0.71 protein_coding synonymous_variant LOW 531G>T Ala177Ala
M0200099 FOIMFDJB_00051 47507 5 Gut 0.71 protein_coding upstream_gene_variant MODIFIER -10G>A None
M0200100 FOIMFDJB_00052 48229 4 Gut 0.57 protein_coding synonymous_variant LOW 81C>A Thr27Thr
M0200101 FOIMFDJB_00052 48289 4 Gut 0.57 protein_coding missense_variant MODERATE 141G>T Gln47His
M0200102 FOIMFDJB_00053 48985 4 Gut 0.57 protein_coding missense_variant MODERATE 223T>A Ser75Thr
M0200103 FOIMFDJB_00055 50977 4 Gut 0.57 protein_coding missense_variant MODERATE 195G>T Leu65Phe
M0200104 FOIMFDJB_00061 54901 3 Gut 0.43 protein_coding synonymous_variant LOW 702T>C Ser234Ser
M0200105 FOIMFDJB_00061 54967 3 Gut 0.43 protein_coding synonymous_variant LOW 636C>T Pro212Pro






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
FOIMFDJB_00036 VFG034679 Ibes 71.7 2e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
FOIMFDJB_00036 VFG034652 Ibes 71.7 3.9e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC prediction
FOIMFDJB_00051 VFG017870 Icm/dot type IVB locus 77.9 1.6e-90 1 208 0.9905 0.9952 Effector delivery system ParA family protein 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
FOIMFDJB_00021 Copper (Cu), Silver (Ag) 89.6 1e-63 1 144 1.0000 1.0000 experiment
FOIMFDJB_00022 Copper (Cu) 98.9 9.8e-262 1 466 1.0000 1.0000 experiment
FOIMFDJB_00023 Copper (Cu) 100 1.7e-126 1 226 1.0000 1.0000 experiment
FOIMFDJB_00024 Copper (Cu) 99.7 2.5e-165 1 309 1.0000 1.0000 experiment
FOIMFDJB_00025 Copper (Cu) 100 4.9e-67 1 126 1.0000 1.0000 experiment
FOIMFDJB_00026 Copper (Cu) 100 1.5e-175 1 296 1.0000 1.0000 experiment
FOIMFDJB_00027 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
FOIMFDJB_00031 Silver (Ag) 94.6 0 1 815 1.0012 0.9903 experiment
FOIMFDJB_00033 Silver (Ag) 98.9 0 1 1048 1.0000 1.0000 experiment
FOIMFDJB_00034 Silver (Ag) 98.4 3.2e-243 1 430 1.0000 1.0000 experiment
FOIMFDJB_00035 Silver (Ag) 92.5 9.5e-44 28 120 0.7750 0.9688 experiment
FOIMFDJB_00036 Silver (Ag) 99.1 8.8e-255 1 461 1.0000 1.0000 experiment
FOIMFDJB_00037 Silver (Ag) 94.7 3.2e-117 1 226 1.0088 1.0000 experiment
FOIMFDJB_00038 Silver (Ag) 94.1 9e-258 1 491 1.0081 0.9960 experiment
FOIMFDJB_00039 Silver (Ag) 97.2 4.3e-75 1 143 1.0000 1.0000 experiment
FOIMFDJB_00021 Copper (Cu), Silver (Ag) 99.3 6e-70 1 144 1.0000 1.0000 prediction
FOIMFDJB_00022 Copper (Cu) 100 6.3e-262 1 466 1.0000 1.0000 prediction
FOIMFDJB_00023 Copper (Cu) 100 3.9e-124 1 226 1.0000 0.9741 prediction
FOIMFDJB_00024 Copper (Cu) 100 4.4e-163 1 309 1.0000 1.0000 prediction
FOIMFDJB_00025 Copper (Cu) 100 1.1e-64 1 126 1.0000 1.0000 prediction
FOIMFDJB_00026 Copper (Cu) 100 3.5e-173 1 296 1.0000 0.9900 prediction
FOIMFDJB_00027 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
FOIMFDJB_00031 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
FOIMFDJB_00033 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
FOIMFDJB_00034 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
FOIMFDJB_00035 Silver (Ag) 100 1.1e-61 1 120 1.0000 1.0000 prediction
FOIMFDJB_00036 Silver (Ag) 100 6.2e-254 1 461 1.0000 1.0000 prediction
FOIMFDJB_00037 Silver (Ag) 100 3e-124 1 226 1.0000 1.0000 prediction
FOIMFDJB_00038 Silver (Ag) 100 4e-275 1 491 1.0000 1.0000 prediction
FOIMFDJB_00039 Silver (Ag) 100 4.7e-75 1 143 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






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
FOIMFDJB_00089 QJO48544.1|GH23 100 9.06e-113 1 159 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
FOIMFDJB_00024 9.B.62.1.1 99.7 9.5e-164 1 309 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family
FOIMFDJB_00026 1.B.76.1.5 100 5.7e-174 1 296 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.76 The Copper Resistance Putative Porin (CopB) Family
FOIMFDJB_00029 1.A.34.1.3 100 1.1e-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
FOIMFDJB_00031 3.A.3.5.4 94.6 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
FOIMFDJB_00033 2.A.6.1.3 98.9 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
FOIMFDJB_00036 1.B.17.3.4 99.1 3.3e-253 1 461 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
FOIMFDJB_00080 1.E.53.1.7 72 9e-14 1 50 0.9434 0.7042 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family