Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2578
  Reference Plasmid   1111525849853957_bin.13__k141_574860
  Reference Plasmid Size   5152
  Reference Plasmid GC Content   0.62
  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
M0129667 APGFMAPD_00003 3215 3 Oral 0.60 protein_coding synonymous_variant LOW 231T>C His77His
M0129668 APGFMAPD_00004 3856 3 Oral 0.60 protein_coding synonymous_variant LOW 777T>C His259His
M0129669 APGFMAPD_00004 4179 3 Oral 0.60 protein_coding missense_variant MODERATE 454A>G Ser152Gly
M0129670 APGFMAPD_00004 4338 4 Oral 0.80 protein_coding missense_variant MODERATE 295G>A Gly99Ser
M0129671 APGFMAPD_00004 4465 4 Oral 0.80 protein_coding synonymous_variant LOW 168G>A Gly56Gly
M0129672 APGFMAPD_00004 4495 4 Oral 0.80 protein_coding synonymous_variant LOW 138G>A Ser46Ser
M0129673 APGFMAPD_00004 4531 4 Oral 0.80 protein_coding synonymous_variant LOW 102T>C Ser34Ser
M0129674 APGFMAPD_00005 4795 4 Oral 0.80 protein_coding synonymous_variant LOW 345A>G Leu115Leu
M0129675 APGFMAPD_00005 4848 4 Oral 0.80 protein_coding missense_variant MODERATE 292C>A Gln98Lys
M0129676 APGFMAPD_00005 4884 4 Oral 0.80 protein_coding missense_variant MODERATE 256G>A Gly86Ser
M0129677 APGFMAPD_00005 4899 4 Oral 0.80 protein_coding missense_variant MODERATE 241A>G Thr81Ala
M0129678 APGFMAPD_00005 4978 4 Oral 0.80 protein_coding synonymous_variant LOW 162G>A Ser54Ser
M0129679 APGFMAPD_00004 4474 3 Oral 0.60 protein_coding synonymous_variant LOW 159G>T Ala53Ala
M0129680 APGFMAPD_00004 4477 3 Oral 0.60 protein_coding synonymous_variant LOW 156T>C Ser52Ser
M0129681 APGFMAPD_00004 4486 3 Oral 0.60 protein_coding synonymous_variant LOW 147A>G Ala49Ala
M0129682 APGFMAPD_00001 47 3 Oral 0.60 protein_coding missense_variant MODERATE 30C>G Ile10Met
M0129683 APGFMAPD_00001 122 3 Oral 0.60 protein_coding synonymous_variant LOW 105A>G Ala35Ala
M0129684 APGFMAPD_00002 503 3 Oral 0.60 protein_coding synonymous_variant LOW 213G>C Gly71Gly
M0129685 APGFMAPD_00001 680 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *414A>G None
M0129686 APGFMAPD_00001 719 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *453G>A None
M0129687 APGFMAPD_00001 797 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *531A>G None
M0129688 APGFMAPD_00001 1151 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *885C>A None
M0129689 APGFMAPD_00001 1163 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *897T>C None
M0129690 APGFMAPD_00001 1256 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *990A>C None
M0129691 APGFMAPD_00001 1278 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1012A>G None
M0129692 APGFMAPD_00001 1373 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1107A>G None
M0129693 APGFMAPD_00001 1424 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1158A>G None
M0129694 APGFMAPD_00001 1448 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1182T>C None
M0129695 APGFMAPD_00001 1463 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1197A>G None
M0129696 APGFMAPD_00001 1592 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1326A>G None
M0129697 APGFMAPD_00001 1642 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1376C>A None
M0129698 APGFMAPD_00001 1972 3 Oral 0.60 protein_coding downstream_gene_variant MODIFIER *1706T>C None
M0129699 APGFMAPD_00003 2138 3 Oral 0.60 protein_coding synonymous_variant LOW 1308A>G Ala436Ala
M0129700 APGFMAPD_00003 2273 3 Oral 0.60 protein_coding synonymous_variant LOW 1173T>C Asp391Asp
M0129701 APGFMAPD_00003 2275 3 Oral 0.60 protein_coding missense_variant MODERATE 1171G>A Asp391Asn
M0129702 APGFMAPD_00003 2882 3 Oral 0.60 protein_coding synonymous_variant LOW 564A>G Leu188Leu
M0129703 APGFMAPD_00003 2921 3 Oral 0.60 protein_coding synonymous_variant LOW 525T>G Leu175Leu
M0129704 APGFMAPD_00003 2924 3 Oral 0.60 protein_coding synonymous_variant LOW 522A>G Lys174Lys






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