Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3406
  Reference Plasmid   MGYG000304073__MGYG000304073_97
  Reference Plasmid Size   7056
  Reference Plasmid GC Content   0.51
  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
M0142282 KEHADGNN_00001 56 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -132T>A None
M0142283 KEHADGNN_00001 107 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -81A>G None
M0142284 KEHADGNN_00001 140 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -48T>G None
M0142285 KEHADGNN_00001 182 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -6A>G None
M0142286 KEHADGNN_00001 209 4 Vaginal 0.67 protein_coding synonymous_variant LOW 22C>T Leu8Leu
M0142287 KEHADGNN_00001 218 4 Vaginal 0.67 protein_coding missense_variant MODERATE 31C>T Arg11Cys
M0142288 KEHADGNN_00001 245 4 Vaginal 0.67 protein_coding missense_variant MODERATE 58A>G Asn20Asp
M0142289 KEHADGNN_00001 263 4 Vaginal 0.67 protein_coding missense_variant MODERATE 76C>T Leu26Phe
M0142290 KEHADGNN_00001 272 4 Vaginal 0.67 protein_coding missense_variant MODERATE 85G>A Glu29Lys
M0142291 KEHADGNN_00001 275 4 Vaginal 0.67 protein_coding missense_variant MODERATE 88A>G Thr30Ala
M0142292 KEHADGNN_00001 278 4 Vaginal 0.67 protein_coding missense_variant MODERATE 91A>G Ile31Val
M0142293 KEHADGNN_00001 626 4 Vaginal 0.67 protein_coding missense_variant MODERATE 439A>G Lys147Glu
M0142294 KEHADGNN_00001 638 4 Vaginal 0.67 protein_coding missense_variant MODERATE 451A>G Ser151Gly
M0142295 KEHADGNN_00002 1039 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -368G>T None
M0142296 KEHADGNN_00002 1044 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -363C>T None
M0142297 KEHADGNN_00002 1056 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -351T>C None
M0142298 KEHADGNN_00002 1058 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -349C>A None
M0142299 KEHADGNN_00002 1059 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -348G>A None
M0142300 KEHADGNN_00002 1073 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -334C>T None
M0142301 KEHADGNN_00002 1091 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -316T>C None
M0142302 KEHADGNN_00002 1097 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -310A>G None
M0142303 KEHADGNN_00002 1108 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -299C>T None
M0142304 KEHADGNN_00002 1115 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -292C>T None
M0142305 KEHADGNN_00002 1118 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -289A>T None
M0142306 KEHADGNN_00002 1131 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -276G>A None
M0142307 KEHADGNN_00002 1152 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -255A>G None
M0142308 KEHADGNN_00002 1169 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -238A>G None
M0142309 KEHADGNN_00002 1356 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -51T>C None
M0142310 KEHADGNN_00002 1359 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -48A>G None
M0142311 KEHADGNN_00002 1361 4 Vaginal 0.67 protein_coding upstream_gene_variant MODIFIER -46T>C None
M0142312 KEHADGNN_00002 1608 4 Vaginal 0.67 protein_coding synonymous_variant LOW 202C>T Leu68Leu
M0142313 KEHADGNN_00002 1631 5 Vaginal 0.83 protein_coding synonymous_variant LOW 225A>G Leu75Leu
M0142314 KEHADGNN_00002 1661 4 Vaginal 0.67 protein_coding synonymous_variant LOW 255G>A Val85Val
M0142315 KEHADGNN_00003 2146 3 Vaginal 0.50 protein_coding synonymous_variant LOW 258T>C Asp86Asp
M0142316 KEHADGNN_00003 2149 3 Vaginal 0.50 protein_coding synonymous_variant LOW 261A>C Ile87Ile
M0142317 KEHADGNN_00003 2170 3 Vaginal 0.50 protein_coding synonymous_variant LOW 282A>G Lys94Lys
M0142318 KEHADGNN_00003 2179 3 Vaginal 0.50 protein_coding synonymous_variant LOW 291C>T Phe97Phe
M0142319 KEHADGNN_00003 2200 3 Vaginal 0.50 protein_coding synonymous_variant LOW 312T>A Val104Val
M0142320 KEHADGNN_00003 2224 3 Vaginal 0.50 protein_coding synonymous_variant LOW 336C>T Arg112Arg
M0142321 KEHADGNN_00003 2230 3 Vaginal 0.50 protein_coding synonymous_variant LOW 342C>T His114His
M0142322 KEHADGNN_00003 2239 3 Vaginal 0.50 protein_coding synonymous_variant LOW 351C>T Ile117Ile
M0142323 KEHADGNN_00003 2248 3 Vaginal 0.50 protein_coding synonymous_variant LOW 360T>G Val120Val
M0142324 KEHADGNN_00003 2257 3 Vaginal 0.50 protein_coding synonymous_variant LOW 369C>T Asp123Asp
M0142325 KEHADGNN_00003 2296 4 Vaginal 0.67 protein_coding synonymous_variant LOW 408T>C Tyr136Tyr
M0142326 KEHADGNN_00003 2299 4 Vaginal 0.67 protein_coding synonymous_variant LOW 411T>C Arg137Arg
M0142327 KEHADGNN_00003 2305 4 Vaginal 0.67 protein_coding synonymous_variant LOW 417A>G Lys139Lys
M0142328 KEHADGNN_00003 2308 4 Vaginal 0.67 protein_coding synonymous_variant LOW 420A>G Gln140Gln
M0142329 KEHADGNN_00003 2311 4 Vaginal 0.67 protein_coding synonymous_variant LOW 423C>T Ile141Ile
M0142330 KEHADGNN_00003 2314 4 Vaginal 0.67 protein_coding synonymous_variant LOW 426C>T Thr142Thr
M0142331 KEHADGNN_00003 2323 4 Vaginal 0.67 protein_coding synonymous_variant LOW 435G>T Leu145Leu
M0142332 KEHADGNN_00003 2326 4 Vaginal 0.67 protein_coding synonymous_variant LOW 438G>A Glu146Glu
M0142333 KEHADGNN_00003 2328 4 Vaginal 0.67 protein_coding missense_variant MODERATE 440A>G Lys147Arg
M0142334 KEHADGNN_00003 2384 4 Vaginal 0.67 protein_coding missense_variant MODERATE 496A>T Ser166Cys
M0142335 KEHADGNN_00003 2386 4 Vaginal 0.67 protein_coding synonymous_variant LOW 498C>T Ser166Ser
M0142336 KEHADGNN_00003 2389 4 Vaginal 0.67 protein_coding synonymous_variant LOW 501G>A Lys167Lys
M0142337 KEHADGNN_00003 2397 4 Vaginal 0.67 protein_coding missense_variant MODERATE 509C>T Ala170Val
M0142338 KEHADGNN_00003 2419 4 Vaginal 0.67 protein_coding synonymous_variant LOW 531A>G Lys177Lys
M0142339 KEHADGNN_00003 2431 4 Vaginal 0.67 protein_coding synonymous_variant LOW 543C>T Asn181Asn
M0142340 KEHADGNN_00003 2435 4 Vaginal 0.67 protein_coding missense_variant MODERATE 547G>C Val183Leu
M0142341 KEHADGNN_00003 2440 5 Vaginal 0.83 protein_coding synonymous_variant LOW 552A>G Lys184Lys
M0142342 KEHADGNN_00003 2596 4 Vaginal 0.67 protein_coding synonymous_variant LOW 708G>C Val236Val
M0142343 KEHADGNN_00003 2656 4 Vaginal 0.67 protein_coding missense_variant MODERATE 768G>T Lys256Asn
M0142344 KEHADGNN_00003 2917 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1029C>T His343His
M0142345 KEHADGNN_00003 2920 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1032C>T Phe344Phe
M0142346 KEHADGNN_00003 2935 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1047C>A Ala349Ala
M0142347 KEHADGNN_00003 2941 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1053A>G Gln351Gln
M0142348 KEHADGNN_00003 2954 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1066T>C Leu356Leu
M0142349 KEHADGNN_00003 2966 4 Vaginal 0.67 protein_coding missense_variant MODERATE 1078A>G Met360Val
M0142350 KEHADGNN_00003 2986 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1098A>G Ala366Ala
M0142351 KEHADGNN_00003 2992 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1104A>G Gly368Gly
M0142352 KEHADGNN_00003 3131 4 Vaginal 0.67 protein_coding missense_variant MODERATE 1243T>A Leu415Met
M0142353 KEHADGNN_00004 3304 5 Vaginal 0.83 protein_coding synonymous_variant LOW 138C>T Gly46Gly
M0142354 KEHADGNN_00004 3808 4 Vaginal 0.67 protein_coding synonymous_variant LOW 642G>A Lys214Lys
M0142355 KEHADGNN_00004 3811 4 Vaginal 0.67 protein_coding synonymous_variant LOW 645A>C Ser215Ser
M0142356 KEHADGNN_00004 3817 4 Vaginal 0.67 protein_coding synonymous_variant LOW 651C>A Ala217Ala
M0142357 KEHADGNN_00004 3823 4 Vaginal 0.67 protein_coding synonymous_variant LOW 657A>G Val219Val
M0142358 KEHADGNN_00004 3828 4 Vaginal 0.67 protein_coding missense_variant MODERATE 662A>G Asn221Ser
M0142359 KEHADGNN_00004 3829 4 Vaginal 0.67 protein_coding synonymous_variant LOW 663T>C Asn221Asn
M0142360 KEHADGNN_00004 3861 4 Vaginal 0.67 protein_coding missense_variant MODERATE 695T>C Leu232Ser
M0142361 KEHADGNN_00004 3862 4 Vaginal 0.67 protein_coding synonymous_variant LOW 696G>A Leu232Leu
M0142362 KEHADGNN_00004 3868 4 Vaginal 0.67 protein_coding synonymous_variant LOW 702C>T Tyr234Tyr
M0142363 KEHADGNN_00004 3874 4 Vaginal 0.67 protein_coding synonymous_variant LOW 708T>C Tyr236Tyr
M0142364 KEHADGNN_00004 3889 4 Vaginal 0.67 protein_coding synonymous_variant LOW 723C>T Ser241Ser
M0142365 KEHADGNN_00004 4366 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1200A>C Ser400Ser
M0142366 KEHADGNN_00004 4378 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1212T>C Tyr404Tyr
M0142367 KEHADGNN_00004 4399 4 Vaginal 0.67 protein_coding synonymous_variant LOW 1233G>A Glu411Glu






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