Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3323
  Reference Plasmid   MGYG000298398__MGYG000298398_6
  Reference Plasmid Size   57742
  Reference Plasmid GC Content   0.39
  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
M0135353 LONAFIPB_00020 51052 3 Oral 0.60 protein_coding synonymous_variant LOW 138T>G Ala46Ala
M0135354 LONAFIPB_00020 51337 3 Oral 0.60 protein_coding synonymous_variant LOW 423T>C Gly141Gly
M0135355 LONAFIPB_00020 51356 3 Oral 0.60 protein_coding missense_variant MODERATE 442A>G Ile148Val
M0135356 LONAFIPB_00020 51358 3 Oral 0.60 protein_coding synonymous_variant LOW 444T>C Ile148Ile
M0135357 LONAFIPB_00020 51361 3 Oral 0.60 protein_coding synonymous_variant LOW 447T>C Tyr149Tyr
M0135358 LONAFIPB_00020 51382 3 Oral 0.60 protein_coding synonymous_variant LOW 468T>C Ser156Ser
M0135359 LONAFIPB_00020 51412 3 Oral 0.60 protein_coding synonymous_variant LOW 498G>A Ala166Ala
M0135360 LONAFIPB_00020 51598 3 Oral 0.60 protein_coding synonymous_variant LOW 684T>C Cys228Cys
M0135361 LONAFIPB_00020 51670 3 Oral 0.60 protein_coding synonymous_variant LOW 756T>C Ile252Ile
M0135362 LONAFIPB_00020 51676 3 Oral 0.60 protein_coding synonymous_variant LOW 762T>C Thr254Thr
M0135363 LONAFIPB_00020 51703 3 Oral 0.60 protein_coding synonymous_variant LOW 789T>C Asp263Asp
M0135364 LONAFIPB_00020 51704 3 Oral 0.60 protein_coding missense_variant MODERATE 790C>G Pro264Ala
M0135365 LONAFIPB_00020 51889 3 Oral 0.60 protein_coding synonymous_variant LOW 975T>C Tyr325Tyr
M0135366 LONAFIPB_00020 51895 3 Oral 0.60 protein_coding synonymous_variant LOW 981A>G Val327Val
M0135367 LONAFIPB_00021 53588 3 Oral 0.60 protein_coding synonymous_variant LOW 1116T>C Gly372Gly
M0135368 LONAFIPB_00022 54151 3 Oral 0.60 protein_coding synonymous_variant LOW 153G>A Leu51Leu
M0135369 LONAFIPB_00023 55136 3 Oral 0.60 protein_coding synonymous_variant LOW 693T>C Ala231Ala
M0135370 LONAFIPB_00023 55286 3 Oral 0.60 protein_coding synonymous_variant LOW 843A>G Thr281Thr
M0135371 LONAFIPB_00023 55730 3 Oral 0.60 protein_coding synonymous_variant LOW 1287G>A Gly429Gly
M0135372 LONAFIPB_00023 55838 3 Oral 0.60 protein_coding synonymous_variant LOW 1395T>G Pro465Pro






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
LONAFIPB_00009 ARI59740.1|GT2|GT8 100 0 1 697 1 1
LONAFIPB_00010 QEM33046.1|GT8 99.7 1.35e-202 1 291 1 1
LONAFIPB_00011 SQF75538.1|GT8 100 4.37e-305 1 402 1 1
LONAFIPB_00012 QEM33044.1|GT4 98.2 0 1 493 1 0.986
LONAFIPB_00013 SQF75540.1|GT8 99.8 1.46e-301 1 407 1 1
LONAFIPB_00014 CCB92926.1|GT113 100 3.37e-246 1 336 1 1
LONAFIPB_00015 AEJ53046.1|GT8 99.8 2.07e-306 3 411 0.9951 0.9669
LONAFIPB_00016 QEM33040.1|GT2 100 1.88e-215 1 294 1 1
LONAFIPB_00017 QEM33039.1|GT101|GT8 99.1 0 1 819 1 1
LONAFIPB_00018 ARI59747.1|GT8 99.3 1.6e-308 1 413 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