Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C586
  Reference Plasmid   NZ_CP034948.1
  Reference Plasmid Size   155130
  Reference Plasmid GC Content   0.36
  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
M0168936 LEMNKDED_00179 146530 4 Gut 0.10 protein_coding missense_variant MODERATE 103T>G Ser35Ala
M0168937 LEMNKDED_00181 148146 4 Gut 0.10 protein_coding missense_variant MODERATE 241T>G Ser81Ala
M0168938 LEMNKDED_00046 42991 5 Gut 0.12 protein_coding missense_variant MODERATE 61A>G Ile21Val
M0168939 LEMNKDED_00022 18423 5 Gut 0.12 protein_coding synonymous_variant LOW 57A>G Lys19Lys
M0168940 LEMNKDED_00006 6591 5 Gut 0.12 protein_coding missense_variant MODERATE 95C>G Ala32Gly
M0168941 LEMNKDED_00012 8987 3 Gut 0.07 protein_coding synonymous_variant LOW 402C>T Asn134Asn
M0168942 LEMNKDED_00013 10885 5 Gut 0.12 protein_coding stop_lost&splice_region_variant HIGH 1576T>G Ter526Gluext*?
M0168943 LEMNKDED_00017 13389 5 Gut 0.12 protein_coding missense_variant MODERATE 296C>T Thr99Ile
M0168944 LEMNKDED_00017 14417 5 Gut 0.12 protein_coding missense_variant MODERATE 1324T>G Ser442Ala
M0168945 LEMNKDED_00022 19823 4 Gut 0.10 protein_coding missense_variant MODERATE 1457A>G Glu486Gly
M0168946 LEMNKDED_00028 27111 4 Gut 0.10 protein_coding missense_variant MODERATE 593A>G Gln198Arg
M0168947 LEMNKDED_00028 27367 4 Gut 0.10 protein_coding synonymous_variant LOW 849T>C Phe283Phe
M0168948 LEMNKDED_00033 30016 3 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -179A>T None
M0168949 LEMNKDED_00001 2788 5 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -1924G>A None
M0168950 LEMNKDED_00001 3002 4 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -2138G>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
LEMNKDED_00012 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 1.4e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
LEMNKDED_00013 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99 3.8e-303 1 525 1.0 0.7979 Adherence PilA prediction
LEMNKDED_00014 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 6.4e-139 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
LEMNKDED_00015 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 5.8e-132 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
LEMNKDED_00016 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
LEMNKDED_00017 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.3 0 1 696 1.0 1 Adherence minor pilin subunit 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






        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
LEMNKDED_00028 QCK21891.1|GH73 100 1.18e-272 1 401 1 1
LEMNKDED_00075 QZK92746.1|GH1 100 0 1 468 1 1
LEMNKDED_00187 QCK22010.1|GT2 100 5.55e-285 1 397 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
LEMNKDED_00074 4.A.3.1.1 71.7 4.4e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
LEMNKDED_00110 2.A.7.5.3 96.3 3.8e-154 1 295 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily