Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C889
  Reference Plasmid   NZ_CP072340.1
  Reference Plasmid Size   163652
  Reference Plasmid GC Content   0.45
  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
M0140836 BEGGJNFM_00035 27387 4 Oral 0.40 protein_coding synonymous_variant LOW 408T>C Ser136Ser
M0140837 BEGGJNFM_00035 27426 4 Oral 0.40 protein_coding synonymous_variant LOW 447T>C Ser149Ser
M0140838 BEGGJNFM_00035 27823 3 Oral 0.30 protein_coding missense_variant MODERATE 844C>A His282Asn
M0140839 BEGGJNFM_00035 27864 3 Oral 0.30 protein_coding synonymous_variant LOW 885A>G Leu295Leu
M0140840 BEGGJNFM_00035 28257 4 Oral 0.40 protein_coding synonymous_variant LOW 1278T>C Asn426Asn
M0140841 BEGGJNFM_00035 28473 3 Oral 0.30 protein_coding synonymous_variant LOW 1494A>G Lys498Lys
M0140842 BEGGJNFM_00035 28611 4 Oral 0.40 protein_coding synonymous_variant LOW 1632A>T Val544Val
M0140843 BEGGJNFM_00035 28635 4 Oral 0.40 protein_coding synonymous_variant LOW 1656T>C Cys552Cys
M0140844 BEGGJNFM_00035 28668 4 Oral 0.40 protein_coding synonymous_variant LOW 1689G>A Lys563Lys
M0140845 BEGGJNFM_00035 29067 3 Oral 0.30 protein_coding synonymous_variant LOW 2088T>C Ala696Ala
M0140846 BEGGJNFM_00035 29301 3 Oral 0.30 protein_coding synonymous_variant LOW 2322T>C Ala774Ala
M0140847 BEGGJNFM_00035 29304 3 Oral 0.30 protein_coding synonymous_variant LOW 2325A>G Gly775Gly
M0140848 BEGGJNFM_00035 29346 3 Oral 0.30 protein_coding synonymous_variant LOW 2367A>G Val789Val
M0140849 BEGGJNFM_00036 29657 5 Oral 0.50 protein_coding synonymous_variant LOW 207T>C Phe69Phe
M0140850 BEGGJNFM_00033 30284 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -4093G>A None
M0140851 BEGGJNFM_00033 30293 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -4102T>C None
M0140852 BEGGJNFM_00033 30377 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -4186C>T None
M0140853 BEGGJNFM_00033 30706 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -4515A>T None
M0140854 BEGGJNFM_00037 30887 4 Oral 0.40 protein_coding synonymous_variant LOW 162G>A Gly54Gly
M0140855 BEGGJNFM_00037 30890 4 Oral 0.40 protein_coding synonymous_variant LOW 165A>G Val55Val
M0140856 BEGGJNFM_00037 31004 3 Oral 0.30 protein_coding synonymous_variant LOW 279C>T Asn93Asn
M0140857 BEGGJNFM_00037 31211 4 Oral 0.40 protein_coding synonymous_variant LOW 486G>T Gly162Gly
M0140858 BEGGJNFM_00037 31214 4 Oral 0.40 protein_coding synonymous_variant LOW 489A>G Pro163Pro
M0140859 BEGGJNFM_00037 31508 5 Oral 0.50 protein_coding synonymous_variant LOW 783T>C Val261Val
M0140860 BEGGJNFM_00037 31919 4 Oral 0.40 protein_coding synonymous_variant LOW 1194A>T Ala398Ala
M0140861 BEGGJNFM_00037 32318 4 Oral 0.40 protein_coding synonymous_variant LOW 1593A>G Glu531Glu
M0140862 BEGGJNFM_00037 32495 5 Oral 0.50 protein_coding synonymous_variant LOW 1770T>C Gly590Gly
M0140863 BEGGJNFM_00037 32702 5 Oral 0.50 protein_coding synonymous_variant LOW 1977T>C Asn659Asn
M0140864 BEGGJNFM_00038 33293 4 Oral 0.40 protein_coding synonymous_variant LOW 63G>A Gly21Gly
M0140865 BEGGJNFM_00038 33455 5 Oral 0.50 protein_coding synonymous_variant LOW 225G>A Leu75Leu
M0140866 BEGGJNFM_00038 33917 5 Oral 0.50 protein_coding synonymous_variant LOW 687T>C Gly229Gly
M0140867 BEGGJNFM_00038 34301 5 Oral 0.50 protein_coding synonymous_variant LOW 1071A>G Leu357Leu
M0140868 BEGGJNFM_00039 35047 3 Oral 0.30 protein_coding synonymous_variant LOW 117C>T Ala39Ala
M0140869 BEGGJNFM_00032 24323 4 Oral 0.40 protein_coding missense_variant MODERATE 668C>T Ala223Val
M0140870 BEGGJNFM_00032 24336 4 Oral 0.40 protein_coding missense_variant MODERATE 655G>A Asp219Asn
M0140871 BEGGJNFM_00032 24408 4 Oral 0.40 protein_coding synonymous_variant LOW 583C>A Arg195Arg
M0140872 BEGGJNFM_00032 24418 4 Oral 0.40 protein_coding synonymous_variant LOW 573A>G Arg191Arg
M0140873 BEGGJNFM_00032 24426 4 Oral 0.40 protein_coding missense_variant MODERATE 565A>G Ile189Val
M0140874 BEGGJNFM_00032 24537 4 Oral 0.40 protein_coding missense_variant MODERATE 454A>T Asn152Tyr
M0140875 BEGGJNFM_00033 25067 3 Oral 0.30 protein_coding synonymous_variant LOW 1125C>T His375His
M0140876 BEGGJNFM_00035 27783 3 Oral 0.30 protein_coding synonymous_variant LOW 804T>C Asp268Asp
M0140877 BEGGJNFM_00035 23521 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -3459C>G None
M0140878 BEGGJNFM_00032 23743 3 Oral 0.30 protein_coding synonymous_variant LOW 1248A>T Val416Val
M0140879 BEGGJNFM_00032 23782 3 Oral 0.30 protein_coding synonymous_variant LOW 1209T>C Gly403Gly
M0140880 BEGGJNFM_00032 23826 3 Oral 0.30 protein_coding missense_variant MODERATE 1165C>T Arg389Cys
M0140881 BEGGJNFM_00032 23827 3 Oral 0.30 protein_coding synonymous_variant LOW 1164C>A Arg388Arg
M0140882 BEGGJNFM_00032 23980 3 Oral 0.30 protein_coding synonymous_variant LOW 1011G>C Pro337Pro
M0140883 BEGGJNFM_00032 24014 3 Oral 0.30 protein_coding missense_variant MODERATE 977T>G Leu326Arg
M0140884 BEGGJNFM_00032 24050 3 Oral 0.30 protein_coding missense_variant MODERATE 941G>A Gly314Asp
M0140885 BEGGJNFM_00032 24055 3 Oral 0.30 protein_coding missense_variant MODERATE 936G>T Met312Ile
M0140886 BEGGJNFM_00032 24058 3 Oral 0.30 protein_coding synonymous_variant LOW 933C>T Tyr311Tyr
M0140887 BEGGJNFM_00032 24070 3 Oral 0.30 protein_coding synonymous_variant LOW 921C>T Ser307Ser
M0140888 BEGGJNFM_00032 24093 3 Oral 0.30 protein_coding missense_variant MODERATE 898A>G Thr300Ala
M0140889 BEGGJNFM_00032 24114 3 Oral 0.30 protein_coding missense_variant MODERATE 877T>C Ser293Pro
M0140890 BEGGJNFM_00032 24170 3 Oral 0.30 protein_coding missense_variant MODERATE 821A>C Glu274Ala
M0140891 BEGGJNFM_00032 24189 3 Oral 0.30 protein_coding missense_variant MODERATE 802A>G Asn268Asp
M0140892 BEGGJNFM_00032 24211 3 Oral 0.30 protein_coding missense_variant MODERATE 780G>T Gln260His
M0140893 BEGGJNFM_00032 24220 3 Oral 0.30 protein_coding synonymous_variant LOW 771G>A Lys257Lys
M0140894 BEGGJNFM_00032 24250 3 Oral 0.30 protein_coding synonymous_variant LOW 741C>T Gly247Gly
M0140895 BEGGJNFM_00032 24325 3 Oral 0.30 protein_coding synonymous_variant LOW 666A>G Glu222Glu
M0140896 BEGGJNFM_00032 24496 3 Oral 0.30 protein_coding synonymous_variant LOW 495G>A Ala165Ala
M0140897 BEGGJNFM_00032 24499 3 Oral 0.30 protein_coding synonymous_variant LOW 492G>A Lys164Lys
M0140898 BEGGJNFM_00032 24767 3 Oral 0.30 protein_coding missense_variant MODERATE 224T>C Ile75Thr
M0140899 BEGGJNFM_00032 24832 3 Oral 0.30 protein_coding synonymous_variant LOW 159T>C Leu53Leu
M0140900 BEGGJNFM_00032 24959 3 Oral 0.30 protein_coding missense_variant MODERATE 32C>T Thr11Ile
M0140901 BEGGJNFM_00033 25367 3 Oral 0.30 protein_coding synonymous_variant LOW 825T>G Leu275Leu
M0140902 BEGGJNFM_00037 31322 3 Oral 0.30 protein_coding synonymous_variant LOW 597A>G Gln199Gln
M0140903 BEGGJNFM_00037 31325 3 Oral 0.30 protein_coding synonymous_variant LOW 600C>T Val200Val
M0140904 BEGGJNFM_00037 32009 3 Oral 0.30 protein_coding synonymous_variant LOW 1284A>G Glu428Glu
M0140905 BEGGJNFM_00037 32795 3 Oral 0.30 protein_coding synonymous_variant LOW 2070T>C Asp690Asp
M0140906 BEGGJNFM_00038 33848 3 Oral 0.30 protein_coding synonymous_variant LOW 618C>T Ser206Ser
M0140907 BEGGJNFM_00038 33872 3 Oral 0.30 protein_coding synonymous_variant LOW 642G>T Val214Val
M0140908 BEGGJNFM_00042 38077 3 Oral 0.30 protein_coding synonymous_variant LOW 1851A>G Val617Val
M0140909 BEGGJNFM_00042 38125 3 Oral 0.30 protein_coding synonymous_variant LOW 1899G>A Gly633Gly
M0140910 BEGGJNFM_00044 39066 3 Oral 0.30 protein_coding missense_variant MODERATE 83A>G Tyr28Cys
M0140911 BEGGJNFM_00044 39116 3 Oral 0.30 protein_coding missense_variant MODERATE 133A>G Met45Val
M0140912 BEGGJNFM_00044 39262 3 Oral 0.30 protein_coding synonymous_variant LOW 279A>G Ala93Ala
M0140913 BEGGJNFM_00045 39405 3 Oral 0.30 protein_coding synonymous_variant LOW 1209A>G Lys403Lys
M0140914 BEGGJNFM_00045 39585 3 Oral 0.30 protein_coding synonymous_variant LOW 1029A>T Thr343Thr






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
BEGGJNFM_00018 Arsenic (As), Antimony (Sb) 76.1 6.8e-144 2 344 0.9800 0.9800 prediction
OEFHJDCF_00018 Arsenic (As), Antimony (Sb) 76.1 6.8e-144 2 344 0.9800 0.9800 prediction






        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
BEGGJNFM_00008 QUB52973.1|GH24 100 9.27e-124 1 168 1 1
OEFHJDCF_00008 QUB52973.1|GH24 100 9.27e-124 1 168 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
BEGGJNFM_00018 2.A.59.1.5 72.5 1.9e-136 5 346 0.9771 1.1554 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.59 The Arsenical Resistance-3 (ACR3) Family
OEFHJDCF_00018 2.A.59.1.5 72.5 1.9e-136 5 346 0.9771 1.1554 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.59 The Arsenical Resistance-3 (ACR3) Family