Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C566
  Reference Plasmid   NZ_CP032258.1
  Reference Plasmid Size   128033
  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
M0168570 ODDAKNGD_00033 24998 7 Gut 0.27 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0168571 ODDAKNGD_00033 25055 7 Gut 0.27 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0168572 ODDAKNGD_00034 25500 7 Gut 0.27 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0168573 ODDAKNGD_00034 25655 7 Gut 0.27 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0168574 ODDAKNGD_00034 25663 7 Gut 0.27 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0168575 ODDAKNGD_00027 26182 7 Gut 0.27 protein_coding upstream_gene_variant MODIFIER -3493A>G None
M0168576 ODDAKNGD_00032 24844 6 Gut 0.23 protein_coding missense_variant MODERATE 400A>T Arg134Trp
M0168577 ODDAKNGD_00032 24893 6 Gut 0.23 protein_coding missense_variant MODERATE 449A>C Gln150Pro






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
ODDAKNGD_00042 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
ODDAKNGD_00114 VFG001445 TraJ 73.7 1.6e-76 2 191 0.8444 0.9453 Invasion unknown protein experiment
ODDAKNGD_00042 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
ODDAKNGD_00114 VFG001445 TraJ 73.7 1.2e-75 2 191 0.8444 0.9453 Invasion unknown 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






        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
ODDAKNGD_00010 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM 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
ODDAKNGD_00039 PHI:10792 cjrA 100 3.6e-162 1 283 1.0000 0.9725 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
ODDAKNGD_00040 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
ODDAKNGD_00041 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
ODDAKNGD_00042 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
ODDAKNGD_00080 PHI:3317 hsdR 73.2 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
ODDAKNGD_00112 QAZ75040.1|GH23 100 4.96e-124 1 169 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
ODDAKNGD_00003 1.E.53.1.11 85.7 1.8e-24 1 63 1.0000 0.9265 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
ODDAKNGD_00017 2.A.108.2.10 99.8 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
ODDAKNGD_00018 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
ODDAKNGD_00040 2.C.1.1.3 100 3.7e-137 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
ODDAKNGD_00041 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ODDAKNGD_00068 2.A.3.1.10 99.8 4.6e-266 9 475 0.9832 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family