Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C115
  Reference Plasmid   CP057974.1
  Reference Plasmid Size   94695
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   conjugative





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
M0144507 GKMGEDBK_00083 79734 3 Gut 0.75 protein_coding missense_variant MODERATE 576G>A Met192Ile
M0144508 GKMGEDBK_00085 80257 4 Gut 1.00 protein_coding missense_variant MODERATE 268G>T Asp90Tyr
M0144509 GKMGEDBK_00078 80598 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4980C>T None
M0144510 GKMGEDBK_00078 80612 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4994A>G None
M0144511 GKMGEDBK_00079 80735 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4141T>G None
M0144512 GKMGEDBK_00079 80762 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4168T>C None
M0144513 GKMGEDBK_00079 80765 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4171C>T None
M0144514 GKMGEDBK_00079 80784 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4190T>C None
M0144515 GKMGEDBK_00079 80787 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4193T>C None
M0144516 GKMGEDBK_00079 80839 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4245A>C None
M0144517 GKMGEDBK_00079 80842 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4248T>C None
M0144518 GKMGEDBK_00079 80846 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4252T>C None
M0144519 GKMGEDBK_00079 80869 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4275C>T None
M0144520 GKMGEDBK_00079 80883 4 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4289A>G None
M0144521 GKMGEDBK_00087 81376 4 Gut 1.00 protein_coding missense_variant MODERATE 217G>T Val73Leu
M0144522 GKMGEDBK_00088 82459 4 Gut 1.00 protein_coding missense_variant MODERATE 287C>T Ser96Leu
M0144523 GKMGEDBK_00089 83954 4 Gut 1.00 protein_coding missense_variant MODERATE 692C>T Ala231Val
M0144524 GKMGEDBK_00089 83964 4 Gut 1.00 protein_coding missense_variant MODERATE 682G>A Ala228Thr
M0144525 GKMGEDBK_00089 83965 4 Gut 1.00 protein_coding synonymous_variant LOW 681C>T Leu227Leu
M0144526 GKMGEDBK_00089 83991 4 Gut 1.00 protein_coding missense_variant MODERATE 655T>G Ser219Ala
M0144527 GKMGEDBK_00090 84807 4 Gut 1.00 protein_coding synonymous_variant LOW 1320C>T Ser440Ser
M0144528 GKMGEDBK_00090 85137 4 Gut 1.00 protein_coding synonymous_variant LOW 990T>A Pro330Pro
M0144529 GKMGEDBK_00090 85380 4 Gut 1.00 protein_coding synonymous_variant LOW 747T>C Asp249Asp
M0144530 GKMGEDBK_00090 86054 4 Gut 1.00 protein_coding missense_variant MODERATE 73T>C Trp25Arg
M0144531 GKMGEDBK_00092 86691 4 Gut 1.00 protein_coding synonymous_variant LOW 18C>A Ile6Ile
M0144532 GKMGEDBK_00093 87551 4 Gut 1.00 protein_coding missense_variant MODERATE 1825C>T Arg609Trp
M0144533 GKMGEDBK_00093 88416 4 Gut 1.00 protein_coding synonymous_variant LOW 960C>T Ala320Ala
M0144534 GKMGEDBK_00093 88608 4 Gut 1.00 protein_coding synonymous_variant LOW 768C>T Tyr256Tyr
M0144535 GKMGEDBK_00094 89950 4 Gut 1.00 protein_coding synonymous_variant LOW 222C>T Arg74Arg
M0144536 GKMGEDBK_00095 90039 4 Gut 1.00 protein_coding synonymous_variant LOW 54G>A Leu18Leu
M0144537 GKMGEDBK_00096 90711 4 Gut 1.00 protein_coding synonymous_variant LOW 231A>G Val77Val






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
GKMGEDBK_00005 PHI:6531 HlyF 99.7 9.7e-216 1 369 1.0000 1.0000 birds colibacillosis hemolysin reduced virulence






        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
GKMGEDBK_00056 QAZ75040.1|GH23 100 4.96e-124 1 169 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
GKMGEDBK_00006 9.B.50.1.1 73.2 3.9e-144 1 317 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family
GKMGEDBK_00020 1.E.53.1.11 98.5 1.1e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family