Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1291
  Reference Plasmid   NZ_CP148358.1
  Reference Plasmid Size   91121
  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
M0205793 DFDKDPDD_00030 30866 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -2716C>G None
M0205794 DFDKDPDD_00030 30894 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -2744T>C None
M0205795 DFDKDPDD_00030 30908 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -2758A>G None
M0205796 DFDKDPDD_00030 30926 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -2776T>C None
M0205797 DFDKDPDD_00030 31137 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -2987A>G None
M0205798 DFDKDPDD_00030 31283 3 Gut 0.17 protein_coding upstream_gene_variant MODIFIER -3133C>T None
M0205799 DFDKDPDD_00030 27153 3 Gut 0.17 protein_coding missense_variant MODERATE 998A>G Glu333Gly






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
DFDKDPDD_00024 VFG000862 Pet 99.2 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter experiment
DFDKDPDD_00057 VFG001827 ShET2 99.5 3e-224 1 391 1.0 1 Exotoxin enterotoxin experiment
DFDKDPDD_00067 VFG000905 Alpha-Hemolysin 95.3 1.9e-98 1 170 1.0 1 Exotoxin Hemolysin C experiment
DFDKDPDD_00068 VFG000906 Alpha-Hemolysin 96.5 0 1 1024 1.0 1 Exotoxin Hemolysin A experiment
DFDKDPDD_00069 VFG000907 Alpha-Hemolysin 98.9 0 1 707 1.0 1 Exotoxin Hemolysin B experiment
DFDKDPDD_00070 VFG000908 Alpha-Hemolysin 95.8 8.1e-248 1 478 1.0 1 Exotoxin Hemolysin D experiment
DFDKDPDD_00024 VFG000862 Pet 99.2 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter prediction
DFDKDPDD_00057 VFG036084 Enterotoxin SenB/TieB 99.7 4.5e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
DFDKDPDD_00067 VFG033901 Hemolysin 99.4 1.4e-100 1 170 1.0 1 Exotoxin Hemolysin C prediction
DFDKDPDD_00068 VFG033893 Hemolysin 98.6 0 1 1024 1.0 1 Exotoxin Hemolysin A prediction
DFDKDPDD_00069 VFG033885 Hemolysin 99.4 0 1 707 1.0 1 Exotoxin Hemolysin B prediction
DFDKDPDD_00070 VFG033877 Hemolysin 98.5 5.1e-254 1 478 1.0 1 Exotoxin Hemolysin D 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
DFDKDPDD_00019 Cadmium (Cd), Mercury (Hg), Tributyltin (TBT) [class: Organo-tin], Hydrogen Peroxide (H2O2) [class: Peroxides], Hydrochloric acid (HCl) [class: Acid] 96.9 3e-65 1 127 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
DFDKDPDD_00054 PHI:10792 cjrA 98.9 1.2e-160 1 283 1.0000 0.9725 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
DFDKDPDD_00055 PHI:10793 cjrB 99.6 1.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
DFDKDPDD_00056 PHI:10794 cjrC 99.5 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
DFDKDPDD_00057 PHI:10795 senB 99.7 1.6e-224 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
DFDKDPDD_00068 PHI:4522 HlyA 98.6 0 1 1024 1.0000 1.0000 rodents urinary tract infection induces caspase-1/caspase-4-dependent inflammatory cell death in human urothelial cells unaffected pathogenicity






        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





        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
DFDKDPDD_00024 1.B.12.4.4 99.2 0 1 1295 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
DFDKDPDD_00055 2.C.1.1.3 99.6 2.4e-136 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
DFDKDPDD_00056 1.B.14.7.1 99.5 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
DFDKDPDD_00068 1.C.11.1.3 96.7 0 1 1024 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
DFDKDPDD_00069 3.A.1.109.1 99 0 1 707 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
DFDKDPDD_00070 8.A.1.3.1 98.3 9.9e-253 1 478 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.1 The Membrane Fusion Protein (MFP) Family