Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3359
  Reference Plasmid   MGYG000298860__MGYG000298860_55
  Reference Plasmid Size   10265
  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
M0136968 LOPKIHFC_00002 1562 3 Oral 1.00 protein_coding missense_variant MODERATE 47C>T Ser16Phe
M0136969 LOPKIHFC_00002 1636 3 Oral 1.00 protein_coding missense_variant MODERATE 121G>A Asp41Asn
M0136970 LOPKIHFC_00002 1656 3 Oral 1.00 protein_coding synonymous_variant LOW 141G>A Ser47Ser
M0136971 LOPKIHFC_00002 1681 3 Oral 1.00 protein_coding missense_variant MODERATE 166T>G Ser56Ala
M0136972 LOPKIHFC_00002 1696 3 Oral 1.00 protein_coding synonymous_variant LOW 181C>T Leu61Leu
M0136973 LOPKIHFC_00002 1830 3 Oral 1.00 protein_coding synonymous_variant LOW 315T>G Ala105Ala
M0136974 LOPKIHFC_00002 2005 3 Oral 1.00 protein_coding missense_variant MODERATE 490A>G Ser164Gly
M0136975 LOPKIHFC_00003 2856 3 Oral 1.00 protein_coding synonymous_variant LOW 75A>G Val25Val
M0136976 LOPKIHFC_00003 3156 3 Oral 1.00 protein_coding synonymous_variant LOW 375C>T Phe125Phe
M0136977 LOPKIHFC_00003 3357 3 Oral 1.00 protein_coding synonymous_variant LOW 576T>C Ile192Ile
M0136978 LOPKIHFC_00003 3489 3 Oral 1.00 protein_coding synonymous_variant LOW 708A>G Val236Val
M0136979 LOPKIHFC_00003 3656 3 Oral 1.00 protein_coding missense_variant MODERATE 875G>A Ser292Asn
M0136980 LOPKIHFC_00003 3723 3 Oral 1.00 protein_coding synonymous_variant LOW 942A>G Gly314Gly
M0136981 LOPKIHFC_00003 3876 3 Oral 1.00 protein_coding synonymous_variant LOW 1095C>T Gly365Gly
M0136982 LOPKIHFC_00003 3885 3 Oral 1.00 protein_coding synonymous_variant LOW 1104T>C Ala368Ala
M0136983 LOPKIHFC_00003 3898 3 Oral 1.00 protein_coding missense_variant MODERATE 1117A>G Ile373Val
M0136984 LOPKIHFC_00005 4769 3 Oral 1.00 protein_coding synonymous_variant LOW 201T>C Ser67Ser
M0136985 LOPKIHFC_00005 4829 3 Oral 1.00 protein_coding synonymous_variant LOW 261A>T Gly87Gly
M0136986 LOPKIHFC_00005 4833 3 Oral 1.00 protein_coding missense_variant MODERATE 265G>A Val89Ile
M0136987 LOPKIHFC_00005 4853 3 Oral 1.00 protein_coding synonymous_variant LOW 285T>C Asn95Asn
M0136988 LOPKIHFC_00005 4865 3 Oral 1.00 protein_coding synonymous_variant LOW 297A>G Leu99Leu
M0136989 LOPKIHFC_00005 4892 3 Oral 1.00 protein_coding synonymous_variant LOW 324A>G Gln108Gln
M0136990 LOPKIHFC_00005 5243 3 Oral 1.00 protein_coding synonymous_variant LOW 675T>C Phe225Phe
M0136991 LOPKIHFC_00005 5309 3 Oral 1.00 protein_coding synonymous_variant LOW 741T>C Phe247Phe
M0136992 LOPKIHFC_00005 5312 3 Oral 1.00 protein_coding synonymous_variant LOW 744A>G Glu248Glu
M0136993 LOPKIHFC_00005 5315 3 Oral 1.00 protein_coding synonymous_variant LOW 747G>A Gly249Gly
M0136994 LOPKIHFC_00005 5345 3 Oral 1.00 protein_coding synonymous_variant LOW 777G>A Pro259Pro
M0136995 LOPKIHFC_00005 5357 3 Oral 1.00 protein_coding synonymous_variant LOW 789G>A Val263Val
M0136996 LOPKIHFC_00005 5375 3 Oral 1.00 protein_coding synonymous_variant LOW 807G>A Glu269Glu
M0136997 LOPKIHFC_00005 5405 3 Oral 1.00 protein_coding synonymous_variant LOW 837A>G Glu279Glu
M0136998 LOPKIHFC_00005 5408 3 Oral 1.00 protein_coding synonymous_variant LOW 840C>G Leu280Leu
M0136999 LOPKIHFC_00005 5438 3 Oral 1.00 protein_coding synonymous_variant LOW 870T>C Asn290Asn
M0137000 LOPKIHFC_00006 6283 3 Oral 1.00 protein_coding synonymous_variant LOW 339G>C Val113Val
M0137001 LOPKIHFC_00007 7366 3 Oral 1.00 protein_coding missense_variant MODERATE 356T>C Val119Ala
M0137002 LOPKIHFC_00007 7862 3 Oral 1.00 protein_coding synonymous_variant LOW 852G>A Arg284Arg
M0137003 LOPKIHFC_00007 7874 3 Oral 1.00 protein_coding synonymous_variant LOW 864G>A Leu288Leu
M0137004 LOPKIHFC_00007 8219 3 Oral 1.00 protein_coding synonymous_variant LOW 1209G>A Lys403Lys
M0137005 LOPKIHFC_00007 8291 3 Oral 1.00 protein_coding synonymous_variant LOW 1281G>A Ser427Ser
M0137006 LOPKIHFC_00007 8715 3 Oral 1.00 protein_coding missense_variant MODERATE 1705C>T His569Tyr
M0137007 LOPKIHFC_00007 8729 3 Oral 1.00 protein_coding synonymous_variant LOW 1719G>A Glu573Glu






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