Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C160
  Reference Plasmid   CP091396.1
  Reference Plasmid Size   68189
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   mobilizable





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
M0145867 CCAAGCDP_00048 41650 3 Gut 0.38 protein_coding stop_lost&splice_region_variant HIGH 259T>C Ter87Glnext*?
M0145868 CCAAGCDP_00041 41723 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4146G>A None
M0145869 CCAAGCDP_00041 41872 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4295T>A None
M0145870 CCAAGCDP_00041 41921 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4344T>G None
M0145871 CCAAGCDP_00049 42026 4 Gut 0.50 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0145872 CCAAGCDP_00050 42528 4 Gut 0.50 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0145873 CCAAGCDP_00050 42683 4 Gut 0.50 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0145874 CCAAGCDP_00050 42691 4 Gut 0.50 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0145875 CCAAGCDP_00044 43210 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4321A>G None
M0145876 CCAAGCDP_00044 43292 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4403G>A None
M0145877 CCAAGCDP_00044 43315 4 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4426T>C None






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
CCAAGCDP_00057 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
CCAAGCDP_00010 VFG044066 Colicin E1 94 1.7e-255 1 521 1.0 1 Exotoxin colicin-like pore-forming protein prediction
CCAAGCDP_00057 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB 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






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
CCAAGCDP_00054 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
CCAAGCDP_00055 PHI:10793 cjrB 99.6 8.2e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
CCAAGCDP_00056 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
CCAAGCDP_00057 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)






        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
CCAAGCDP_00010 1.C.1.2.2 86.8 3.5e-235 1 521 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
CCAAGCDP_00055 2.C.1.1.3 99.6 1.8e-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
CCAAGCDP_00056 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
CCAAGCDP_00073 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
CCAAGCDP_00074 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