Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3409
  Reference Plasmid   MGYG000304292__MGYG000304292_22
  Reference Plasmid Size   12542
  Reference Plasmid GC Content   0.38
  Reference Plasmid Mobility Type   non-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
M0142613 LODIJFBI_00007 6859 4 Vaginal 0.80 protein_coding synonymous_variant LOW 97C>T Leu33Leu
M0142614 LODIJFBI_00007 6919 3 Vaginal 0.60 protein_coding missense_variant MODERATE 157G>A Asp53Asn
M0142615 LODIJFBI_00008 7151 5 Vaginal 1.00 protein_coding synonymous_variant LOW 189A>C Thr63Thr
M0142616 LODIJFBI_00008 7265 3 Vaginal 0.60 protein_coding synonymous_variant LOW 303C>A Ile101Ile
M0142617 LODIJFBI_00008 7287 5 Vaginal 1.00 protein_coding missense_variant MODERATE 325A>G Thr109Ala
M0142618 LODIJFBI_00008 7313 5 Vaginal 1.00 protein_coding synonymous_variant LOW 351C>T Phe117Phe
M0142619 LODIJFBI_00009 7718 4 Vaginal 0.80 protein_coding synonymous_variant LOW 315C>T Val105Val
M0142620 LODIJFBI_00009 7753 3 Vaginal 0.60 protein_coding missense_variant MODERATE 280G>A Gly94Ser
M0142621 LODIJFBI_00009 7857 5 Vaginal 1.00 protein_coding missense_variant MODERATE 176A>G Asn59Ser
M0142622 LODIJFBI_00009 7861 5 Vaginal 1.00 protein_coding synonymous_variant LOW 172T>C Leu58Leu
M0142623 LODIJFBI_00002 8033 3 Vaginal 0.60 protein_coding upstream_gene_variant MODIFIER -3959T>C None
M0142624 LODIJFBI_00002 8122 4 Vaginal 0.80 protein_coding upstream_gene_variant MODIFIER -4048A>G None
M0142625 LODIJFBI_00008 7069 3 Vaginal 0.60 protein_coding missense_variant MODERATE 107T>C Val36Ala
M0142626 LODIJFBI_00008 7150 4 Vaginal 0.80 protein_coding missense_variant MODERATE 188C>A Thr63Lys
M0142627 LODIJFBI_00008 7164 3 Vaginal 0.60 protein_coding missense_variant MODERATE 202A>G Met68Val
M0142628 LODIJFBI_00009 7403 3 Vaginal 0.60 protein_coding missense_variant MODERATE 630T>G Phe210Leu
M0142629 LODIJFBI_00009 7424 3 Vaginal 0.60 protein_coding synonymous_variant LOW 609A>G Lys203Lys
M0142630 LODIJFBI_00009 7717 3 Vaginal 0.60 protein_coding synonymous_variant LOW 316C>T Leu106Leu
M0142631 LODIJFBI_00009 7889 3 Vaginal 0.60 protein_coding synonymous_variant LOW 144C>A Ile48Ile
M0142632 LODIJFBI_00007 6810 3 Vaginal 0.60 protein_coding synonymous_variant LOW 48G>A Gln16Gln






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






        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





        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
LODIJFBI_00001 2.A.1.87.1 95.3 3.5e-220 1 430 0.9931 0.9885 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)