Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2446
  Reference Plasmid   1111525849768046_bin.37__k141_40216
  Reference Plasmid Size   3607
  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
M0126502 PJNFMGDJ_00001 214 4 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -448T>C None
M0126503 PJNFMGDJ_00001 270 4 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -392T>C None
M0126504 PJNFMGDJ_00001 281 4 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -381A>G None
M0126505 PJNFMGDJ_00001 544 4 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -118T>C None
M0126506 PJNFMGDJ_00001 564 3 Oral 0.38 protein_coding upstream_gene_variant MODIFIER -98G>A None
M0126507 PJNFMGDJ_00001 599 4 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -63T>C None
M0126508 PJNFMGDJ_00001 687 3 Oral 0.38 protein_coding missense_variant MODERATE 26T>C Val9Ala
M0126509 PJNFMGDJ_00001 766 3 Oral 0.38 protein_coding synonymous_variant LOW 105T>C Ala35Ala
M0126510 PJNFMGDJ_00001 823 3 Oral 0.38 protein_coding synonymous_variant LOW 162A>G Val54Val
M0126511 PJNFMGDJ_00001 946 4 Oral 0.50 protein_coding synonymous_variant LOW 285A>G Ser95Ser
M0126512 PJNFMGDJ_00001 1192 4 Oral 0.50 protein_coding synonymous_variant LOW 531T>A Ala177Ala
M0126513 PJNFMGDJ_00002 1305 5 Oral 0.63 protein_coding synonymous_variant LOW 75A>T Pro25Pro
M0126514 PJNFMGDJ_00002 1308 5 Oral 0.63 protein_coding synonymous_variant LOW 78A>G Val26Val
M0126515 PJNFMGDJ_00002 1311 5 Oral 0.63 protein_coding synonymous_variant LOW 81T>A Ile27Ile
M0126516 PJNFMGDJ_00002 1345 5 Oral 0.63 protein_coding missense_variant MODERATE 115C>G Leu39Val
M0126517 PJNFMGDJ_00002 1428 4 Oral 0.50 protein_coding synonymous_variant LOW 198C>T Phe66Phe
M0126518 PJNFMGDJ_00002 1458 7 Oral 0.88 protein_coding synonymous_variant LOW 228A>G Ala76Ala
M0126519 PJNFMGDJ_00002 1491 3 Oral 0.38 protein_coding synonymous_variant LOW 261C>T Gly87Gly
M0126520 PJNFMGDJ_00002 1740 7 Oral 0.88 protein_coding synonymous_variant LOW 510T>C His170His
M0126521 PJNFMGDJ_00002 1815 6 Oral 0.75 protein_coding synonymous_variant LOW 585T>A Thr195Thr
M0126522 PJNFMGDJ_00002 1828 3 Oral 0.38 protein_coding synonymous_variant LOW 598C>T Leu200Leu
M0126523 PJNFMGDJ_00002 1893 6 Oral 0.75 protein_coding synonymous_variant LOW 663A>T Gly221Gly
M0126524 PJNFMGDJ_00002 1932 5 Oral 0.63 protein_coding synonymous_variant LOW 702A>G Leu234Leu
M0126525 PJNFMGDJ_00002 2073 6 Oral 0.75 protein_coding synonymous_variant LOW 843T>C Asp281Asp
M0126526 PJNFMGDJ_00003 2379 6 Oral 0.75 protein_coding synonymous_variant LOW 150C>A Val50Val
M0126527 PJNFMGDJ_00003 2403 6 Oral 0.75 protein_coding synonymous_variant LOW 174T>C Thr58Thr
M0126528 PJNFMGDJ_00003 2427 4 Oral 0.50 protein_coding synonymous_variant LOW 198C>T Val66Val
M0126529 PJNFMGDJ_00003 2430 4 Oral 0.50 protein_coding synonymous_variant LOW 201T>A Leu67Leu
M0126530 PJNFMGDJ_00003 2577 4 Oral 0.50 protein_coding synonymous_variant LOW 348T>C Pro116Pro
M0126531 PJNFMGDJ_00003 2622 3 Oral 0.38 protein_coding synonymous_variant LOW 393C>T Thr131Thr
M0126532 PJNFMGDJ_00003 2790 6 Oral 0.75 protein_coding missense_variant MODERATE 561A>T Glu187Asp
M0126533 PJNFMGDJ_00003 2862 3 Oral 0.38 protein_coding synonymous_variant LOW 633C>T Phe211Phe
M0126534 PJNFMGDJ_00003 2883 6 Oral 0.75 protein_coding synonymous_variant LOW 654C>T Phe218Phe
M0126535 PJNFMGDJ_00001 3176 5 Oral 0.63 protein_coding downstream_gene_variant MODIFIER *1951C>G None
M0126536 PJNFMGDJ_00001 3366 4 Oral 0.50 protein_coding downstream_gene_variant MODIFIER *2141T>C None
M0126537 PJNFMGDJ_00001 3468 5 Oral 0.63 protein_coding downstream_gene_variant MODIFIER *2243C>T None
M0126538 PJNFMGDJ_00001 3510 3 Oral 0.38 protein_coding downstream_gene_variant MODIFIER *2285G>A None
M0126539 PJNFMGDJ_00001 3525 5 Oral 0.63 protein_coding downstream_gene_variant MODIFIER *2300T>C None
M0126540 PJNFMGDJ_00003 2763 3 Oral 0.38 protein_coding synonymous_variant LOW 534C>T Asn178Asn
M0126541 PJNFMGDJ_00003 2769 3 Oral 0.38 protein_coding synonymous_variant LOW 540A>T Ile180Ile
M0126542 PJNFMGDJ_00003 2781 3 Oral 0.38 protein_coding synonymous_variant LOW 552C>T Asn184Asn
M0126543 PJNFMGDJ_00003 2805 3 Oral 0.38 protein_coding synonymous_variant LOW 576C>T His192His
M0126544 PJNFMGDJ_00002 1386 3 Oral 0.38 protein_coding synonymous_variant LOW 156C>G Thr52Thr
M0126545 PJNFMGDJ_00002 1393 3 Oral 0.38 protein_coding missense_variant MODERATE 163C>T His55Tyr
M0126546 PJNFMGDJ_00002 1425 3 Oral 0.38 protein_coding synonymous_variant LOW 195C>T Tyr65Tyr






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