Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3346
  Reference Plasmid   MGYG000298800__MGYG000298800_44
  Reference Plasmid Size   7381
  Reference Plasmid GC Content   0.58
  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
M0136349 JMCIJMCJ_00001 909 3 Oral 0.60 protein_coding missense_variant MODERATE 764A>G Glu255Gly
M0136350 JMCIJMCJ_00001 925 3 Oral 0.60 protein_coding synonymous_variant LOW 780G>A Ala260Ala
M0136351 JMCIJMCJ_00001 949 3 Oral 0.60 protein_coding synonymous_variant LOW 804G>T Ala268Ala
M0136352 JMCIJMCJ_00002 1204 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -41G>C None
M0136353 JMCIJMCJ_00002 1319 4 Oral 0.80 protein_coding synonymous_variant LOW 75A>G Pro25Pro
M0136354 JMCIJMCJ_00002 1550 3 Oral 0.60 protein_coding synonymous_variant LOW 306G>A Lys102Lys
M0136355 JMCIJMCJ_00002 1563 4 Oral 0.80 protein_coding missense_variant MODERATE 319A>C Met107Leu
M0136356 JMCIJMCJ_00002 1806 4 Oral 0.80 protein_coding missense_variant MODERATE 562A>G Asn188Asp
M0136357 JMCIJMCJ_00002 1889 4 Oral 0.80 protein_coding synonymous_variant LOW 645T>C Asp215Asp
M0136358 JMCIJMCJ_00002 1901 4 Oral 0.80 protein_coding synonymous_variant LOW 657T>C Gly219Gly
M0136359 JMCIJMCJ_00002 2045 4 Oral 0.80 protein_coding synonymous_variant LOW 801C>G Pro267Pro
M0136360 JMCIJMCJ_00002 2057 4 Oral 0.80 protein_coding synonymous_variant LOW 813C>T Thr271Thr
M0136361 JMCIJMCJ_00002 2168 4 Oral 0.80 protein_coding synonymous_variant LOW 924T>C Ser308Ser
M0136362 JMCIJMCJ_00002 2173 3 Oral 0.60 protein_coding missense_variant MODERATE 929A>C Gln310Pro
M0136363 JMCIJMCJ_00002 2375 3 Oral 0.60 protein_coding synonymous_variant LOW 1131T>C Leu377Leu
M0136364 JMCIJMCJ_00002 2378 3 Oral 0.60 protein_coding synonymous_variant LOW 1134C>T Gly378Gly
M0136365 JMCIJMCJ_00002 2399 4 Oral 0.80 protein_coding synonymous_variant LOW 1155T>C Cys385Cys
M0136366 JMCIJMCJ_00003 2503 4 Oral 0.80 protein_coding missense_variant MODERATE 40T>G Ser14Ala
M0136367 JMCIJMCJ_00003 2571 4 Oral 0.80 protein_coding synonymous_variant LOW 108A>G Ala36Ala
M0136368 JMCIJMCJ_00003 2583 3 Oral 0.60 protein_coding synonymous_variant LOW 120G>A Ala40Ala
M0136369 JMCIJMCJ_00003 2664 3 Oral 0.60 protein_coding synonymous_variant LOW 201T>C Ile67Ile
M0136370 JMCIJMCJ_00003 2824 3 Oral 0.60 protein_coding missense_variant MODERATE 361A>G Thr121Ala
M0136371 JMCIJMCJ_00003 2844 4 Oral 0.80 protein_coding synonymous_variant LOW 381T>C Arg127Arg
M0136372 JMCIJMCJ_00003 2994 4 Oral 0.80 protein_coding synonymous_variant LOW 531C>T Arg177Arg
M0136373 JMCIJMCJ_00003 3003 4 Oral 0.80 protein_coding synonymous_variant LOW 540C>G Leu180Leu
M0136374 JMCIJMCJ_00003 3021 4 Oral 0.80 protein_coding synonymous_variant LOW 558C>A Gly186Gly
M0136375 JMCIJMCJ_00003 3195 3 Oral 0.60 protein_coding synonymous_variant LOW 732G>A Glu244Glu
M0136376 JMCIJMCJ_00003 3198 3 Oral 0.60 protein_coding synonymous_variant LOW 735T>G Pro245Pro
M0136377 JMCIJMCJ_00003 3213 3 Oral 0.60 protein_coding synonymous_variant LOW 750T>C Leu250Leu
M0136378 JMCIJMCJ_00004 3324 3 Oral 0.60 protein_coding synonymous_variant LOW 84T>C Leu28Leu
M0136379 JMCIJMCJ_00004 3327 3 Oral 0.60 protein_coding synonymous_variant LOW 87A>G Ala29Ala
M0136380 JMCIJMCJ_00004 3372 3 Oral 0.60 protein_coding synonymous_variant LOW 132C>G Ser44Ser
M0136381 JMCIJMCJ_00004 3633 3 Oral 0.60 protein_coding synonymous_variant LOW 393T>C Val131Val
M0136382 JMCIJMCJ_00004 3636 3 Oral 0.60 protein_coding synonymous_variant LOW 396G>A Glu132Glu
M0136383 JMCIJMCJ_00004 3639 3 Oral 0.60 protein_coding synonymous_variant LOW 399A>G Gly133Gly
M0136384 JMCIJMCJ_00004 3642 3 Oral 0.60 protein_coding synonymous_variant LOW 402T>C His134His
M0136385 JMCIJMCJ_00004 3645 3 Oral 0.60 protein_coding synonymous_variant LOW 405C>T Phe135Phe
M0136386 JMCIJMCJ_00004 3807 3 Oral 0.60 protein_coding synonymous_variant LOW 567G>T Ala189Ala
M0136387 JMCIJMCJ_00004 4026 3 Oral 0.60 protein_coding synonymous_variant LOW 786C>T Ser262Ser
M0136388 JMCIJMCJ_00005 4805 3 Oral 0.60 protein_coding synonymous_variant LOW 567A>G Thr189Thr
M0136389 JMCIJMCJ_00005 4913 3 Oral 0.60 protein_coding synonymous_variant LOW 459A>G Val153Val
M0136390 JMCIJMCJ_00005 4994 3 Oral 0.60 protein_coding synonymous_variant LOW 378A>G Leu126Leu
M0136391 JMCIJMCJ_00005 5000 3 Oral 0.60 protein_coding synonymous_variant LOW 372T>G Arg124Arg
M0136392 JMCIJMCJ_00005 5111 3 Oral 0.60 protein_coding synonymous_variant LOW 261G>C Gly87Gly
M0136393 JMCIJMCJ_00005 5120 3 Oral 0.60 protein_coding synonymous_variant LOW 252C>G Thr84Thr
M0136394 JMCIJMCJ_00005 5162 3 Oral 0.60 protein_coding synonymous_variant LOW 210G>C Gly70Gly
M0136395 JMCIJMCJ_00005 5264 4 Oral 0.80 protein_coding synonymous_variant LOW 108A>G Glu36Glu
M0136396 JMCIJMCJ_00005 5447 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -76C>G None
M0136397 JMCIJMCJ_00006 5993 3 Oral 0.60 protein_coding synonymous_variant LOW 1275T>C Ser425Ser
M0136398 JMCIJMCJ_00006 6140 3 Oral 0.60 protein_coding synonymous_variant LOW 1128G>C Val376Val
M0136399 JMCIJMCJ_00006 6269 3 Oral 0.60 protein_coding synonymous_variant LOW 999C>T Ile333Ile
M0136400 JMCIJMCJ_00006 6277 3 Oral 0.60 protein_coding missense_variant MODERATE 991C>A Leu331Ile
M0136401 JMCIJMCJ_00006 6556 3 Oral 0.60 protein_coding missense_variant MODERATE 712A>G Thr238Ala
M0136402 JMCIJMCJ_00006 6608 3 Oral 0.60 protein_coding synonymous_variant LOW 660C>T Gly220Gly
M0136403 JMCIJMCJ_00006 6716 3 Oral 0.60 protein_coding synonymous_variant LOW 552C>T Val184Val
M0136404 JMCIJMCJ_00002 1481 3 Oral 0.60 protein_coding synonymous_variant LOW 237C>T Val79Val
M0136405 JMCIJMCJ_00003 2574 3 Oral 0.60 protein_coding synonymous_variant LOW 111A>T Leu37Leu






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