Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C258
  Reference Plasmid   LR962408.1
  Reference Plasmid Size   83430
  Reference Plasmid GC Content   0.35
  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
M0149993 FOIBDFAG_00090 72797 4 Gut 1.00 protein_coding synonymous_variant LOW 426T>C Gly142Gly
M0149994 FOIBDFAG_00090 72833 4 Gut 1.00 protein_coding synonymous_variant LOW 390T>C His130His
M0149995 FOIBDFAG_00090 72839 4 Gut 1.00 protein_coding synonymous_variant LOW 384C>T Ile128Ile
M0149996 FOIBDFAG_00090 72908 4 Gut 1.00 protein_coding synonymous_variant LOW 315C>T Phe105Phe
M0149997 FOIBDFAG_00090 72918 4 Gut 1.00 protein_coding missense_variant MODERATE 305T>C Val102Ala
M0149998 FOIBDFAG_00090 73004 4 Gut 1.00 protein_coding synonymous_variant LOW 219G>T Ala73Ala
M0149999 FOIBDFAG_00090 73025 4 Gut 1.00 protein_coding synonymous_variant LOW 198C>T Ala66Ala
M0150000 FOIBDFAG_00090 73046 4 Gut 1.00 protein_coding synonymous_variant LOW 177G>A Val59Val
M0150001 FOIBDFAG_00090 73073 4 Gut 1.00 protein_coding synonymous_variant LOW 150T>C Asp50Asp
M0150002 FOIBDFAG_00090 73085 4 Gut 1.00 protein_coding synonymous_variant LOW 138A>G Leu46Leu
M0150003 FOIBDFAG_00090 73091 4 Gut 1.00 protein_coding synonymous_variant LOW 132A>G Arg44Arg
M0150004 FOIBDFAG_00090 73115 4 Gut 1.00 protein_coding synonymous_variant LOW 108G>A Thr36Thr
M0150005 FOIBDFAG_00090 73124 4 Gut 1.00 protein_coding synonymous_variant LOW 99A>G Gly33Gly
M0150006 FOIBDFAG_00090 73127 4 Gut 1.00 protein_coding synonymous_variant LOW 96T>C Ile32Ile
M0150007 FOIBDFAG_00090 73172 4 Gut 1.00 protein_coding synonymous_variant LOW 51A>G Leu17Leu
M0150008 FOIBDFAG_00090 73205 4 Gut 1.00 protein_coding synonymous_variant LOW 18T>C Asp6Asp
M0150009 FOIBDFAG_00086 73240 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2614G>T None
M0150010 FOIBDFAG_00086 73276 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2650C>T None
M0150011 FOIBDFAG_00086 73293 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2667G>A None
M0150012 FOIBDFAG_00086 73295 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2669T>A None
M0150013 FOIBDFAG_00086 73312 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2686G>A None
M0150014 FOIBDFAG_00086 73329 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2703A>G None
M0150015 FOIBDFAG_00086 73331 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2705G>A None
M0150016 FOIBDFAG_00086 73381 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -2755G>T None
M0150017 FOIBDFAG_00091 73849 4 Gut 1.00 protein_coding synonymous_variant LOW 93C>A Gly31Gly
M0150018 FOIBDFAG_00091 73905 4 Gut 1.00 protein_coding missense_variant MODERATE 149A>G Asp50Gly
M0150019 FOIBDFAG_00086 72621 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1995C>T None
M0150020 FOIBDFAG_00086 72623 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -1997C>T None
M0150021 FOIBDFAG_00086 72630 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -2004A>G None
M0150022 FOIBDFAG_00090 72637 3 Gut 0.75 protein_coding synonymous_variant LOW 586T>C Leu196Leu
M0150023 FOIBDFAG_00090 72653 3 Gut 0.75 protein_coding synonymous_variant LOW 570A>C Ala190Ala
M0150024 FOIBDFAG_00090 72656 3 Gut 0.75 protein_coding synonymous_variant LOW 567C>T Thr189Thr
M0150025 FOIBDFAG_00090 72665 3 Gut 0.75 protein_coding synonymous_variant LOW 558T>C Asp186Asp
M0150026 FOIBDFAG_00090 72674 3 Gut 0.75 protein_coding synonymous_variant LOW 549T>C Thr183Thr






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
FOIBDFAG_00072 Copper (Cu) 100 2.8e-85 1 151 1.0000 1.0000 experiment
FOIBDFAG_00076 Copper (Cu) 100 1.4e-31 1 68 1.0000 1.0000 experiment
FOIBDFAG_00077 Copper (Cu) 99.9 0 1 710 1.0000 1.0000 experiment
FOIBDFAG_00064 Copper (Cu), Cobalt (Co) 97.9 3.6e-306 1 528 1.0000 1.0000 prediction
FOIBDFAG_00072 Copper (Cu) 100 6.5e-83 1 151 1.0000 1.0000 prediction
FOIBDFAG_00076 Copper (Cu) 100 3.2e-29 1 68 1.0000 1.0000 prediction
FOIBDFAG_00077 Copper (Cu) 100 0 1 710 1.0000 1.0000 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
FOIBDFAG_00027 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
FOIBDFAG_00028 ARO:3002897 99.4 1.34e-130 1 180 1.0000 1.0000 nucleoside antibiotic streptothricin acetyltransferase (SAT) antibiotic inactivation
FOIBDFAG_00029 ARO:3002647 100 6.41e-197 1 261 1.0000 0.9886 aminoglycoside antibiotic APH(3') 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
FOIBDFAG_00006 PHI:2999 EF0026 98.8 1.5e-91 1 162 1.0000 1.0000 moths nosocomial infection None increased virulence (hypervirulence)






        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
FOIBDFAG_00077 3.A.3.5.16 99.9 0 1 710 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily