Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2425
  Reference Plasmid   1111525849768046_bin.37__k141_214139
  Reference Plasmid Size   3741
  Reference Plasmid GC Content   0.40
  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
M0124820 PDOGNJAK_00002 195 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -2117T>C None
M0124821 PDOGNJAK_00002 207 4 Oral 0.80 protein_coding upstream_gene_variant MODIFIER -2105A>G None
M0124822 PDOGNJAK_00002 216 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2096T>C None
M0124823 PDOGNJAK_00002 330 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -1982A>G None
M0124824 PDOGNJAK_00001 632 3 Oral 0.60 protein_coding synonymous_variant LOW 1419C>T Phe473Phe
M0124825 PDOGNJAK_00001 941 3 Oral 0.60 protein_coding missense_variant MODERATE 1110G>T Met370Ile
M0124826 PDOGNJAK_00001 968 3 Oral 0.60 protein_coding synonymous_variant LOW 1083T>C Phe361Phe
M0124827 PDOGNJAK_00001 1106 4 Oral 0.80 protein_coding synonymous_variant LOW 945A>G Ser315Ser
M0124828 PDOGNJAK_00001 1145 4 Oral 0.80 protein_coding synonymous_variant LOW 906A>G Leu302Leu
M0124829 PDOGNJAK_00001 1490 4 Oral 0.80 protein_coding synonymous_variant LOW 561T>A Ile187Ile
M0124830 PDOGNJAK_00001 1502 3 Oral 0.60 protein_coding missense_variant MODERATE 549G>T Met183Ile
M0124831 PDOGNJAK_00001 1550 3 Oral 0.60 protein_coding synonymous_variant LOW 501C>T Gly167Gly
M0124832 PDOGNJAK_00001 1559 4 Oral 0.80 protein_coding synonymous_variant LOW 492C>T Ala164Ala
M0124833 PDOGNJAK_00001 1678 3 Oral 0.60 protein_coding missense_variant MODERATE 373A>C Ile125Leu
M0124834 PDOGNJAK_00001 1715 3 Oral 0.60 protein_coding synonymous_variant LOW 336T>C Leu112Leu
M0124835 PDOGNJAK_00001 1916 3 Oral 0.60 protein_coding missense_variant MODERATE 135A>G Ile45Met
M0124836 PDOGNJAK_00001 2027 3 Oral 0.60 protein_coding synonymous_variant LOW 24A>G Thr8Thr
M0124837 PDOGNJAK_00001 2058 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -8G>T None
M0124838 PDOGNJAK_00001 2219 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -169T>C None
M0124839 PDOGNJAK_00001 2224 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -174A>C None
M0124840 PDOGNJAK_00001 2235 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -185T>C None
M0124841 PDOGNJAK_00001 2268 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -218T>C None
M0124842 PDOGNJAK_00001 2284 5 Oral 1.00 protein_coding upstream_gene_variant MODIFIER -234T>C None
M0124843 PDOGNJAK_00002 2464 5 Oral 1.00 protein_coding missense_variant MODERATE 153G>T Arg51Ser
M0124844 PDOGNJAK_00002 2527 5 Oral 1.00 protein_coding synonymous_variant LOW 216A>C Ala72Ala
M0124845 PDOGNJAK_00002 2638 4 Oral 0.80 protein_coding synonymous_variant LOW 327T>C Pro109Pro
M0124846 PDOGNJAK_00002 2641 4 Oral 0.80 protein_coding synonymous_variant LOW 330T>G Ser110Ser
M0124847 PDOGNJAK_00002 2662 3 Oral 0.60 protein_coding synonymous_variant LOW 351T>C Gly117Gly
M0124848 PDOGNJAK_00002 2689 3 Oral 0.60 protein_coding synonymous_variant LOW 378G>A Glu126Glu
M0124849 PDOGNJAK_00002 2690 3 Oral 0.60 protein_coding synonymous_variant LOW 379C>T Leu127Leu
M0124850 PDOGNJAK_00002 2713 3 Oral 0.60 protein_coding synonymous_variant LOW 402A>G Leu134Leu
M0124851 PDOGNJAK_00002 2719 3 Oral 0.60 protein_coding synonymous_variant LOW 408T>C Asn136Asn
M0124852 PDOGNJAK_00002 2845 3 Oral 0.60 protein_coding synonymous_variant LOW 534T>C Gly178Gly
M0124853 PDOGNJAK_00002 2890 4 Oral 0.80 protein_coding synonymous_variant LOW 579A>T Ala193Ala
M0124854 PDOGNJAK_00002 2897 4 Oral 0.80 protein_coding missense_variant MODERATE 586A>G Thr196Ala
M0124855 PDOGNJAK_00002 2899 3 Oral 0.60 protein_coding synonymous_variant LOW 588T>C Thr196Thr
M0124856 PDOGNJAK_00002 2920 3 Oral 0.60 protein_coding synonymous_variant LOW 609T>C Asn203Asn
M0124857 PDOGNJAK_00002 3088 3 Oral 0.60 protein_coding synonymous_variant LOW 777T>C Gly259Gly
M0124858 PDOGNJAK_00002 3280 3 Oral 0.60 protein_coding synonymous_variant LOW 969G>A Gly323Gly
M0124859 PDOGNJAK_00002 3313 3 Oral 0.60 protein_coding synonymous_variant LOW 1002G>A Glu334Glu
M0124860 PDOGNJAK_00002 297 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2015T>C None
M0124861 PDOGNJAK_00002 561 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -1751T>C None
M0124862 PDOGNJAK_00001 834 3 Oral 0.60 protein_coding missense_variant MODERATE 1217G>A Ser406Asn
M0124863 PDOGNJAK_00001 2144 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -94T>C None
M0124864 PDOGNJAK_00001 2146 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -96G>T None
M0124865 PDOGNJAK_00001 2266 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -216C>T None
M0124866 PDOGNJAK_00002 2434 4 Oral 0.80 protein_coding synonymous_variant LOW 123A>T Val41Val
M0124867 PDOGNJAK_00002 2596 3 Oral 0.60 protein_coding synonymous_variant LOW 285A>G Lys95Lys
M0124868 PDOGNJAK_00002 84 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2228T>G None
M0124869 PDOGNJAK_00002 85 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2227T>G None
M0124870 PDOGNJAK_00002 86 3 Oral 0.60 protein_coding upstream_gene_variant MODIFIER -2226C>G None
M0124871 PDOGNJAK_00001 1706 3 Oral 0.60 protein_coding synonymous_variant LOW 345A>G Leu115Leu






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
PDOGNJAK_00002 EFC70604.2|GT4 98 1.36e-264 1 351 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