Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1257
  Reference Plasmid   NZ_CP143951.1
  Reference Plasmid Size   6295
  Reference Plasmid GC Content   0.42
  Reference Plasmid Mobility Type   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
M0204902 APPIBEKP_00005 3029 3 Gut 0.33 protein_coding missense_variant MODERATE 821T>C Val274Ala
M0204903 APPIBEKP_00005 3085 3 Gut 0.33 protein_coding synonymous_variant LOW 765T>G Arg255Arg
M0204904 APPIBEKP_00005 3122 3 Gut 0.33 protein_coding missense_variant MODERATE 728A>G Asn243Ser
M0204905 APPIBEKP_00005 3181 4 Gut 0.44 protein_coding synonymous_variant LOW 669A>G Lys223Lys
M0204906 APPIBEKP_00005 3190 5 Gut 0.56 protein_coding synonymous_variant LOW 660A>C Ile220Ile
M0204907 APPIBEKP_00005 3313 5 Gut 0.56 protein_coding synonymous_variant LOW 537C>T Phe179Phe
M0204908 APPIBEKP_00005 3319 3 Gut 0.33 protein_coding synonymous_variant LOW 531A>C Gly177Gly
M0204909 APPIBEKP_00005 3322 3 Gut 0.33 protein_coding synonymous_variant LOW 528G>A Lys176Lys
M0204910 APPIBEKP_00005 3451 5 Gut 0.56 protein_coding synonymous_variant LOW 399T>C Phe133Phe
M0204911 APPIBEKP_00005 3477 5 Gut 0.56 protein_coding missense_variant MODERATE 373G>A Val125Ile
M0204912 APPIBEKP_00006 4011 5 Gut 0.56 protein_coding synonymous_variant LOW 438A>C Ile146Ile
M0204913 APPIBEKP_00006 4101 3 Gut 0.33 protein_coding synonymous_variant LOW 348G>A Glu116Glu
M0204914 APPIBEKP_00006 4110 5 Gut 0.56 protein_coding synonymous_variant LOW 339T>C Asp113Asp
M0204915 APPIBEKP_00006 4425 3 Gut 0.33 protein_coding synonymous_variant LOW 24A>G Thr8Thr
M0204916 APPIBEKP_00005 4471 5 Gut 0.56 protein_coding upstream_gene_variant MODIFIER -622G>A None
M0204917 APPIBEKP_00003 1833 3 Gut 0.33 protein_coding synonymous_variant LOW 510T>A Thr170Thr
M0204918 APPIBEKP_00003 1834 3 Gut 0.33 protein_coding missense_variant MODERATE 511T>A Phe171Ile
M0204919 APPIBEKP_00003 1836 3 Gut 0.33 protein_coding missense_variant MODERATE 513C>A Phe171Leu
M0204920 APPIBEKP_00003 1839 3 Gut 0.33 protein_coding synonymous_variant LOW 516A>G Gly172Gly
M0204921 APPIBEKP_00004 2367 3 Gut 0.33 protein_coding missense_variant MODERATE 477A>G Ile159Met
M0204922 APPIBEKP_00004 2490 3 Gut 0.33 protein_coding synonymous_variant LOW 600C>T Ser200Ser
M0204923 APPIBEKP_00005 3202 3 Gut 0.33 protein_coding synonymous_variant LOW 648C>T Ser216Ser
M0204924 APPIBEKP_00005 3203 3 Gut 0.33 protein_coding missense_variant MODERATE 647G>C Ser216Thr
M0204925 APPIBEKP_00005 3709 3 Gut 0.33 protein_coding synonymous_variant LOW 141T>A Ser47Ser
M0204926 APPIBEKP_00005 3844 3 Gut 0.33 protein_coding synonymous_variant LOW 6T>C Asn2Asn
M0204927 APPIBEKP_00006 3871 3 Gut 0.33 protein_coding missense_variant MODERATE 578A>G Lys193Arg
M0204928 APPIBEKP_00006 3875 3 Gut 0.33 protein_coding missense_variant MODERATE 574A>G Lys192Glu
M0204929 APPIBEKP_00006 3891 3 Gut 0.33 protein_coding synonymous_variant LOW 558C>T Asp186Asp
M0204930 APPIBEKP_00006 3942 3 Gut 0.33 protein_coding synonymous_variant LOW 507A>G Gln169Gln
M0204931 APPIBEKP_00006 3944 3 Gut 0.33 protein_coding missense_variant MODERATE 505C>A Gln169Lys
M0204932 APPIBEKP_00006 3945 3 Gut 0.33 protein_coding missense_variant MODERATE 504G>T Met168Ile
M0204933 APPIBEKP_00006 3946 3 Gut 0.33 protein_coding missense_variant MODERATE 503T>A Met168Lys
M0204934 APPIBEKP_00006 3947 3 Gut 0.33 protein_coding missense_variant MODERATE 502A>T Met168Leu
M0204935 APPIBEKP_00006 3951 3 Gut 0.33 protein_coding synonymous_variant LOW 498G>A Lys166Lys
M0204936 APPIBEKP_00006 3954 3 Gut 0.33 protein_coding synonymous_variant LOW 495C>T Leu165Leu
M0204937 APPIBEKP_00006 3956 3 Gut 0.33 protein_coding missense_variant MODERATE 493C>A Leu165Ile
M0204938 APPIBEKP_00006 3957 3 Gut 0.33 protein_coding synonymous_variant LOW 492A>G Gln164Gln
M0204939 APPIBEKP_00001 402 3 Gut 0.33 protein_coding synonymous_variant LOW 363T>C Phe121Phe
M0204940 APPIBEKP_00004 2666 3 Gut 0.33 protein_coding missense_variant MODERATE 776A>T Tyr259Phe






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
APPIBEKP_00004 ARO:3003097 80.3 2.84e-171 1 315 0.9937 0.9517 cephalosporin CfxA beta-lactamase antibiotic inactivation






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