Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3369
  Reference Plasmid   MGYG000298994__MGYG000298994_252
  Reference Plasmid Size   3813
  Reference Plasmid GC Content   0.42
  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
M0137503 PCEFHGHA_00001 313 3 Oral 0.75 protein_coding missense_variant MODERATE 281T>C Met94Thr
M0137504 PCEFHGHA_00001 314 3 Oral 0.75 protein_coding missense_variant MODERATE 282G>A Met94Ile
M0137505 PCEFHGHA_00001 374 3 Oral 0.75 protein_coding synonymous_variant LOW 342C>T Tyr114Tyr
M0137506 PCEFHGHA_00001 376 3 Oral 0.75 protein_coding missense_variant MODERATE 344T>C Val115Ala
M0137507 PCEFHGHA_00001 422 4 Oral 1.00 protein_coding synonymous_variant LOW 390A>G Ser130Ser
M0137508 PCEFHGHA_00001 476 3 Oral 0.75 protein_coding synonymous_variant LOW 444T>C Ser148Ser
M0137509 PCEFHGHA_00001 1259 3 Oral 0.75 protein_coding synonymous_variant LOW 1227T>C Ala409Ala
M0137510 PCEFHGHA_00001 1325 4 Oral 1.00 protein_coding synonymous_variant LOW 1293T>C His431His
M0137511 PCEFHGHA_00002 1623 3 Oral 0.75 protein_coding missense_variant MODERATE 35T>C Ile12Thr
M0137512 PCEFHGHA_00002 1678 3 Oral 0.75 protein_coding synonymous_variant LOW 90A>C Pro30Pro
M0137513 PCEFHGHA_00002 1708 3 Oral 0.75 protein_coding synonymous_variant LOW 120A>C Thr40Thr
M0137514 PCEFHGHA_00002 1741 3 Oral 0.75 protein_coding synonymous_variant LOW 153T>C Asn51Asn
M0137515 PCEFHGHA_00002 1756 4 Oral 1.00 protein_coding missense_variant MODERATE 168C>A His56Gln
M0137516 PCEFHGHA_00002 1861 3 Oral 0.75 protein_coding synonymous_variant LOW 273T>C Asn91Asn
M0137517 PCEFHGHA_00002 1909 4 Oral 1.00 protein_coding synonymous_variant LOW 321A>G Thr107Thr
M0137518 PCEFHGHA_00002 2017 4 Oral 1.00 protein_coding synonymous_variant LOW 429T>C Asp143Asp
M0137519 PCEFHGHA_00002 2074 3 Oral 0.75 protein_coding synonymous_variant LOW 486C>T Leu162Leu
M0137520 PCEFHGHA_00002 2104 4 Oral 1.00 protein_coding synonymous_variant LOW 516T>C Asn172Asn
M0137521 PCEFHGHA_00002 2128 4 Oral 1.00 protein_coding synonymous_variant LOW 540C>T Gly180Gly
M0137522 PCEFHGHA_00002 2197 4 Oral 1.00 protein_coding synonymous_variant LOW 609T>G Thr203Thr
M0137523 PCEFHGHA_00003 2583 4 Oral 1.00 protein_coding synonymous_variant LOW 79C>T Leu27Leu
M0137524 PCEFHGHA_00003 2647 4 Oral 1.00 protein_coding missense_variant MODERATE 143T>C Val48Ala
M0137525 PCEFHGHA_00003 2657 4 Oral 1.00 protein_coding synonymous_variant LOW 153A>G Thr51Thr
M0137526 PCEFHGHA_00003 2669 4 Oral 1.00 protein_coding synonymous_variant LOW 165T>C Pro55Pro
M0137527 PCEFHGHA_00003 2984 4 Oral 1.00 protein_coding synonymous_variant LOW 480A>G Glu160Glu
M0137528 PCEFHGHA_00003 3020 3 Oral 0.75 protein_coding synonymous_variant LOW 516T>A Thr172Thr
M0137529 PCEFHGHA_00003 3182 4 Oral 1.00 protein_coding synonymous_variant LOW 678T>C Asn226Asn
M0137530 PCEFHGHA_00003 3188 3 Oral 0.75 protein_coding synonymous_variant LOW 684A>G Ala228Ala
M0137531 PCEFHGHA_00003 3266 3 Oral 0.75 protein_coding synonymous_variant LOW 762C>T Gly254Gly
M0137532 PCEFHGHA_00002 2248 3 Oral 0.75 protein_coding synonymous_variant LOW 660T>C Gly220Gly
M0137533 PCEFHGHA_00003 2570 3 Oral 0.75 protein_coding synonymous_variant LOW 66T>C Phe22Phe






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