Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1355
  Reference Plasmid   NZ_LR883005.1
  Reference Plasmid Size   83375
  Reference Plasmid GC Content   0.54
  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
M0207091 HOICGFFI_00062 48714 3 Gut 0.60 protein_coding synonymous_variant LOW 687T>G Ala229Ala
M0207092 HOICGFFI_00063 48770 3 Gut 0.60 protein_coding synonymous_variant LOW 15T>C Asn5Asn
M0207093 HOICGFFI_00063 49223 3 Gut 0.60 protein_coding synonymous_variant LOW 468C>A Val156Val
M0207094 HOICGFFI_00064 50364 3 Gut 0.60 protein_coding synonymous_variant LOW 168T>C Asn56Asn
M0207095 HOICGFFI_00068 51848 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -327T>A None
M0207096 HOICGFFI_00068 52309 3 Gut 0.60 protein_coding synonymous_variant LOW 135C>A Thr45Thr
M0207097 HOICGFFI_00070 52897 3 Gut 0.60 protein_coding missense_variant MODERATE 305T>A Met102Lys
M0207098 HOICGFFI_00070 53063 3 Gut 0.60 protein_coding synonymous_variant LOW 471G>C Arg157Arg






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







        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
HOICGFFI_00016 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
HOICGFFI_00017 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
HOICGFFI_00018 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
HOICGFFI_00020 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
HOICGFFI_00021 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
HOICGFFI_00022 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
HOICGFFI_00016 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 prediction
HOICGFFI_00017 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
HOICGFFI_00018 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
HOICGFFI_00020 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
HOICGFFI_00021 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
HOICGFFI_00022 Mercury (Hg) 83.3 2.7e-32 1 78 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
HOICGFFI_00008 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
HOICGFFI_00013 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
HOICGFFI_00027 PHI:3113 stbA 98.8 2.5e-183 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid 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
HOICGFFI_00055 QJS03103.1|GH23 100 1e-123 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
HOICGFFI_00012 2.A.7.3.67 100 2.7e-123 1 232 1.0000 0.7891 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
HOICGFFI_00013 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
HOICGFFI_00017 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
HOICGFFI_00018 1.A.72.3.1 90.1 2.6e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
HOICGFFI_00022 1.A.72.5.1 100 1.8e-39 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily