Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3404
  Reference Plasmid   MGYG000304055__MGYG000304055_7
  Reference Plasmid Size   55249
  Reference Plasmid GC Content   0.46
  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
M0142236 LKPPMFBA_00016 16452 4 Vaginal 0.57 protein_coding missense_variant MODERATE 151A>G Met51Val
M0142237 LKPPMFBA_00017 16661 3 Vaginal 0.43 protein_coding missense_variant MODERATE 16G>A Asp6Asn
M0142238 LKPPMFBA_00017 16740 3 Vaginal 0.43 protein_coding missense_variant MODERATE 95G>A Arg32Lys
M0142239 LKPPMFBA_00017 17095 3 Vaginal 0.43 protein_coding synonymous_variant LOW 450T>C Ile150Ile
M0142240 LKPPMFBA_00018 17424 3 Vaginal 0.43 protein_coding synonymous_variant LOW 159C>T Arg53Arg
M0142241 LKPPMFBA_00018 18014 3 Vaginal 0.43 protein_coding missense_variant MODERATE 749A>G His250Arg
M0142242 LKPPMFBA_00030 33726 3 Vaginal 0.43 protein_coding missense_variant MODERATE 38A>T Asn13Ile
M0142243 LKPPMFBA_00030 33738 3 Vaginal 0.43 protein_coding missense_variant MODERATE 50C>T Ala17Val
M0142244 LKPPMFBA_00030 33740 3 Vaginal 0.43 protein_coding missense_variant MODERATE 52C>T Arg18Trp
M0142245 LKPPMFBA_00030 33744 3 Vaginal 0.43 protein_coding missense_variant MODERATE 56T>A Ile19Lys
M0142246 LKPPMFBA_00030 33755 3 Vaginal 0.43 protein_coding missense_variant MODERATE 67A>G Met23Val
M0142247 LKPPMFBA_00030 33767 3 Vaginal 0.43 protein_coding missense_variant MODERATE 79C>T Arg27Cys
M0142248 LKPPMFBA_00030 33792 3 Vaginal 0.43 protein_coding missense_variant MODERATE 104T>C Ile35Thr
M0142249 LKPPMFBA_00030 33812 3 Vaginal 0.43 protein_coding missense_variant MODERATE 124C>T Leu42Phe
M0142250 LKPPMFBA_00030 33841 3 Vaginal 0.43 protein_coding synonymous_variant LOW 153A>G Ala51Ala
M0142251 LKPPMFBA_00030 33842 3 Vaginal 0.43 protein_coding missense_variant MODERATE 154G>A Asp52Asn
M0142252 LKPPMFBA_00030 33848 3 Vaginal 0.43 protein_coding missense_variant MODERATE 160T>C Cys54Arg
M0142253 LKPPMFBA_00030 33859 3 Vaginal 0.43 protein_coding stop_gained HIGH 171T>A Cys57*
M0142254 LKPPMFBA_00030 33880 3 Vaginal 0.43 protein_coding synonymous_variant LOW 192C>T Arg64Arg
M0142255 LKPPMFBA_00030 33882 3 Vaginal 0.43 protein_coding missense_variant MODERATE 194C>T Pro65Leu
M0142256 LKPPMFBA_00030 33902 3 Vaginal 0.43 protein_coding missense_variant MODERATE 214G>A Ala72Thr
M0142257 LKPPMFBA_00030 33928 3 Vaginal 0.43 protein_coding synonymous_variant LOW 240T>A Ala80Ala
M0142258 LKPPMFBA_00031 33976 3 Vaginal 0.43 protein_coding missense_variant MODERATE 10A>G Thr4Ala
M0142259 LKPPMFBA_00031 33979 3 Vaginal 0.43 protein_coding synonymous_variant LOW 13C>T Leu5Leu
M0142260 LKPPMFBA_00031 34006 3 Vaginal 0.43 protein_coding missense_variant MODERATE 40A>G Asn14Asp
M0142261 LKPPMFBA_00031 34127 3 Vaginal 0.43 protein_coding missense_variant MODERATE 161A>T Glu54Val
M0142262 LKPPMFBA_00031 34147 3 Vaginal 0.43 protein_coding missense_variant MODERATE 181G>A Ala61Thr
M0142263 LKPPMFBA_00027 34246 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2720G>C None
M0142264 LKPPMFBA_00027 34265 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2739T>A None
M0142265 LKPPMFBA_00027 34285 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2759G>A None
M0142266 LKPPMFBA_00027 34290 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2764A>G None
M0142267 LKPPMFBA_00027 34363 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2837A>G None
M0142268 LKPPMFBA_00027 34379 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2853G>A None
M0142269 LKPPMFBA_00027 34392 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2866G>A None
M0142270 LKPPMFBA_00027 34408 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2882C>T None
M0142271 LKPPMFBA_00027 34416 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2890A>G None
M0142272 LKPPMFBA_00027 34417 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2891T>C None
M0142273 LKPPMFBA_00027 34456 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2930G>A None
M0142274 LKPPMFBA_00027 34461 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2935A>G None
M0142275 LKPPMFBA_00027 34485 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2959A>T None
M0142276 LKPPMFBA_00027 34525 3 Vaginal 0.43 protein_coding upstream_gene_variant MODIFIER -2999A>G None
M0142277 LKPPMFBA_00016 16518 3 Vaginal 0.43 protein_coding missense_variant MODERATE 85G>A Glu29Lys






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