Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2469
  Reference Plasmid   1111525849768046_bin.37__k141_76520
  Reference Plasmid Size   5118
  Reference Plasmid GC Content   0.37
  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
M0128447 CIMDOOFJ_00001 674 3 Oral 0.38 protein_coding synonymous_variant LOW 798A>G Gly266Gly
M0128448 CIMDOOFJ_00001 677 6 Oral 0.75 protein_coding synonymous_variant LOW 795C>T Ile265Ile
M0128449 CIMDOOFJ_00001 806 6 Oral 0.75 protein_coding synonymous_variant LOW 666A>G Glu222Glu
M0128450 CIMDOOFJ_00001 866 3 Oral 0.38 protein_coding synonymous_variant LOW 606T>C Asn202Asn
M0128451 CIMDOOFJ_00001 875 3 Oral 0.38 protein_coding synonymous_variant LOW 597T>C Arg199Arg
M0128452 CIMDOOFJ_00001 950 4 Oral 0.50 protein_coding synonymous_variant LOW 522T>G Ser174Ser
M0128453 CIMDOOFJ_00001 1343 3 Oral 0.38 protein_coding synonymous_variant LOW 129A>T Val43Val
M0128454 CIMDOOFJ_00001 1409 5 Oral 0.63 protein_coding synonymous_variant LOW 63A>C Thr21Thr
M0128455 CIMDOOFJ_00001 1445 6 Oral 0.75 protein_coding synonymous_variant LOW 27A>G Leu9Leu
M0128456 CIMDOOFJ_00001 1450 6 Oral 0.75 protein_coding missense_variant MODERATE 22T>A Phe8Ile
M0128457 CIMDOOFJ_00001 1453 4 Oral 0.50 protein_coding missense_variant MODERATE 19C>T Leu7Phe
M0128458 CIMDOOFJ_00001 1472 3 Oral 0.38 protein_coding upstream_gene_variant MODIFIER -1T>C None
M0128459 CIMDOOFJ_00001 1689 3 Oral 0.38 protein_coding upstream_gene_variant MODIFIER -218G>A None
M0128460 CIMDOOFJ_00002 1763 3 Oral 0.38 protein_coding synonymous_variant LOW 723T>C Leu241Leu
M0128461 CIMDOOFJ_00002 1778 3 Oral 0.38 protein_coding missense_variant MODERATE 708A>T Lys236Asn
M0128462 CIMDOOFJ_00002 1931 5 Oral 0.63 protein_coding synonymous_variant LOW 555C>T Pro185Pro
M0128463 CIMDOOFJ_00002 2021 3 Oral 0.38 protein_coding synonymous_variant LOW 465T>C Leu155Leu
M0128464 CIMDOOFJ_00002 2081 4 Oral 0.50 protein_coding synonymous_variant LOW 405A>G Glu135Glu
M0128465 CIMDOOFJ_00002 2090 4 Oral 0.50 protein_coding missense_variant MODERATE 396C>G Asp132Glu
M0128466 CIMDOOFJ_00002 2470 4 Oral 0.50 protein_coding missense_variant MODERATE 16A>G Lys6Glu
M0128467 CIMDOOFJ_00003 2544 3 Oral 0.38 protein_coding synonymous_variant LOW 2469C>T Cys823Cys
M0128468 CIMDOOFJ_00003 2655 4 Oral 0.50 protein_coding synonymous_variant LOW 2358C>T Tyr786Tyr
M0128469 CIMDOOFJ_00003 2673 4 Oral 0.50 protein_coding missense_variant MODERATE 2340T>G His780Gln
M0128470 CIMDOOFJ_00003 2693 6 Oral 0.75 protein_coding missense_variant MODERATE 2320T>G Tyr774Asp
M0128471 CIMDOOFJ_00003 2913 3 Oral 0.38 protein_coding synonymous_variant LOW 2100C>T Asp700Asp
M0128472 CIMDOOFJ_00003 2922 3 Oral 0.38 protein_coding synonymous_variant LOW 2091C>T Arg697Arg
M0128473 CIMDOOFJ_00003 2997 3 Oral 0.38 protein_coding synonymous_variant LOW 2016A>T Ala672Ala
M0128474 CIMDOOFJ_00003 3024 7 Oral 0.88 protein_coding synonymous_variant LOW 1989C>T Asn663Asn
M0128475 CIMDOOFJ_00003 3075 4 Oral 0.50 protein_coding synonymous_variant LOW 1938T>C Arg646Arg
M0128476 CIMDOOFJ_00003 3111 4 Oral 0.50 protein_coding synonymous_variant LOW 1902G>A Lys634Lys
M0128477 CIMDOOFJ_00003 3285 4 Oral 0.50 protein_coding synonymous_variant LOW 1728C>T Phe576Phe
M0128478 CIMDOOFJ_00003 3330 5 Oral 0.63 protein_coding synonymous_variant LOW 1683T>C Asn561Asn
M0128479 CIMDOOFJ_00003 3435 7 Oral 0.88 protein_coding synonymous_variant LOW 1578G>A Lys526Lys
M0128480 CIMDOOFJ_00003 3507 5 Oral 0.63 protein_coding synonymous_variant LOW 1506A>G Glu502Glu
M0128481 CIMDOOFJ_00003 3651 5 Oral 0.63 protein_coding synonymous_variant LOW 1362G>A Leu454Leu
M0128482 CIMDOOFJ_00003 3975 3 Oral 0.38 protein_coding synonymous_variant LOW 1038G>T Val346Val
M0128483 CIMDOOFJ_00003 4017 6 Oral 0.75 protein_coding synonymous_variant LOW 996C>T Asp332Asp
M0128484 CIMDOOFJ_00003 4041 3 Oral 0.38 protein_coding synonymous_variant LOW 972A>G Lys324Lys
M0128485 CIMDOOFJ_00003 4071 3 Oral 0.38 protein_coding synonymous_variant LOW 942A>G Lys314Lys
M0128486 CIMDOOFJ_00003 4491 6 Oral 0.75 protein_coding synonymous_variant LOW 522T>C Phe174Phe
M0128487 CIMDOOFJ_00003 4497 6 Oral 0.75 protein_coding synonymous_variant LOW 516G>A Glu172Glu
M0128488 CIMDOOFJ_00003 4530 6 Oral 0.75 protein_coding synonymous_variant LOW 483A>C Thr161Thr
M0128489 CIMDOOFJ_00003 4662 6 Oral 0.75 protein_coding synonymous_variant LOW 351A>C Ile117Ile
M0128490 CIMDOOFJ_00003 4971 7 Oral 0.88 protein_coding synonymous_variant LOW 42T>C Asn14Asn
M0128491 CIMDOOFJ_00001 5049 5 Oral 0.63 protein_coding upstream_gene_variant MODIFIER -3578A>T None
M0128492 CIMDOOFJ_00001 440 3 Oral 0.38 protein_coding synonymous_variant LOW 1032T>C Asp344Asp
M0128493 CIMDOOFJ_00001 1010 3 Oral 0.38 protein_coding synonymous_variant LOW 462C>T Asp154Asp
M0128494 CIMDOOFJ_00001 1088 3 Oral 0.38 protein_coding synonymous_variant LOW 384A>G Glu128Glu
M0128495 CIMDOOFJ_00001 1100 3 Oral 0.38 protein_coding synonymous_variant LOW 372C>T Arg124Arg
M0128496 CIMDOOFJ_00001 1195 3 Oral 0.38 protein_coding missense_variant MODERATE 277A>G Ile93Val
M0128497 CIMDOOFJ_00001 1226 3 Oral 0.38 protein_coding synonymous_variant LOW 246G>A Glu82Glu
M0128498 CIMDOOFJ_00002 2228 3 Oral 0.38 protein_coding synonymous_variant LOW 258G>A Gln86Gln
M0128499 CIMDOOFJ_00002 2231 3 Oral 0.38 protein_coding synonymous_variant LOW 255A>G Glu85Glu
M0128500 CIMDOOFJ_00003 3201 4 Oral 0.50 protein_coding missense_variant MODERATE 1812G>A Met604Ile
M0128501 CIMDOOFJ_00003 3207 4 Oral 0.50 protein_coding synonymous_variant LOW 1806T>C Asn602Asn
M0128502 CIMDOOFJ_00003 3276 4 Oral 0.50 protein_coding synonymous_variant LOW 1737T>C Cys579Cys
M0128503 CIMDOOFJ_00003 3291 4 Oral 0.50 protein_coding synonymous_variant LOW 1722T>C Asn574Asn
M0128504 CIMDOOFJ_00003 4266 4 Oral 0.50 protein_coding synonymous_variant LOW 747C>T Gly249Gly
M0128505 CIMDOOFJ_00003 4317 3 Oral 0.38 protein_coding synonymous_variant LOW 696T>C Asp232Asp
M0128506 CIMDOOFJ_00003 4635 3 Oral 0.38 protein_coding synonymous_variant LOW 378G>A Glu126Glu
M0128507 CIMDOOFJ_00001 61 3 Oral 0.38 protein_coding downstream_gene_variant MODIFIER *187A>T None
M0128508 CIMDOOFJ_00001 70 3 Oral 0.38 protein_coding downstream_gene_variant MODIFIER *178A>G None
M0128509 CIMDOOFJ_00003 3639 3 Oral 0.38 protein_coding synonymous_variant LOW 1374A>T Ala458Ala
M0128510 CIMDOOFJ_00001 398 3 Oral 0.38 protein_coding synonymous_variant LOW 1074A>C Thr358Thr






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
CIMDOOFJ_00001 EFC70822.1|GH33 94.6 7.13e-293 1 407 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