Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1168
  Reference Plasmid   NZ_CP127033.1
  Reference Plasmid Size   129491
  Reference Plasmid GC Content   0.48
  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
M0199119 LEEBIELI_00025 20124 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -776C>T None
M0199120 LEEBIELI_00027 20699 3 Gut 0.43 protein_coding synonymous_variant LOW 27T>C Val9Val
M0199121 LEEBIELI_00025 20847 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -1499A>G None
M0199122 LEEBIELI_00028 20978 3 Gut 0.43 protein_coding missense_variant MODERATE 514A>G Lys172Glu
M0199123 LEEBIELI_00028 21466 3 Gut 0.43 protein_coding missense_variant MODERATE 26T>C Val9Ala
M0199124 LEEBIELI_00025 21512 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -2164A>G None
M0199125 LEEBIELI_00025 21515 3 Gut 0.43 protein_coding upstream_gene_variant MODIFIER -2167G>A 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
LEEBIELI_00077 VFG035923 Dispersin 78.4 4.8e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC experiment
LEEBIELI_00097 VFG042382 EtpA 99.5 0 1 598 1.0 0.9917 Adherence two-partner secretion transporter EtpB experiment
LEEBIELI_00006 VFG020186 VirK 98.6 8.1e-167 1 282 1.0 0.8924 Others virulence factor VirK prediction
LEEBIELI_00007 VFG013087 MsbB2 96.8 6.5e-164 1 285 1.0 0.9076 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
LEEBIELI_00062 VFG033834 Pic 99 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
LEEBIELI_00077 VFG035919 Dispersin 79.3 5.6e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC prediction
LEEBIELI_00084 VFG043747 Heat-stable toxin (ST) 97.2 1e-33 1 72 1.0 1 Exotoxin unknown protein prediction
LEEBIELI_00097 VFG042382 EtpA 99.5 0 1 598 1.0 0.9917 Adherence two-partner secretion transporter EtpB prediction
LEEBIELI_00108 VFG017870 Icm/dot type IVB locus 77.9 9.3e-91 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






        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
LEEBIELI_00005 PHI:10400 Sfgtr4 (ORF186) 96.1 8.7e-209 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
LEEBIELI_00005 QJB53856.1|GT4 99.7 1.27e-270 1 362 1 1
LEEBIELI_00091 CBJ04457.1|GT41 99.2 0 1 636 1 0.9984





        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
LEEBIELI_00090 9.B.127.1.3 95.1 3.1e-89 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
LEEBIELI_00097 1.B.20.3.3 99.5 0 1 598 1.0000 0.9917 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family