Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C780
  Reference Plasmid   NZ_CP061330.1
  Reference Plasmid Size   127456
  Reference Plasmid GC Content   0.49
  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
M0177542 PEFOJEJG_00019 23036 11 Gut 0.20 protein_coding missense_variant MODERATE 613A>G Ser205Gly
M0177543 PEFOJEJG_00013 23940 12 Gut 0.21 protein_coding downstream_gene_variant MODIFIER *3301G>A None
M0177544 PEFOJEJG_00020 26883 12 Gut 0.21 protein_coding missense_variant MODERATE 1784T>C Met595Thr
M0177545 PEFOJEJG_00020 32584 14 Gut 0.25 protein_coding upstream_gene_variant MODIFIER -3918C>T None
M0177546 PEFOJEJG_00025 33914 7 Gut 0.13 protein_coding synonymous_variant LOW 753T>G Gly251Gly
M0177547 PEFOJEJG_00028 38019 12 Gut 0.21 protein_coding missense_variant MODERATE 19A>G Ser7Gly
M0177548 PEFOJEJG_00043 57672 3 Gut 0.05 protein_coding synonymous_variant LOW 852C>T Ala284Ala
M0177549 PEFOJEJG_00066 83445 3 Gut 0.05 protein_coding missense_variant MODERATE 485A>G Lys162Arg
M0177550 PEFOJEJG_00066 83644 3 Gut 0.05 protein_coding synonymous_variant LOW 684C>T Arg228Arg
M0177551 PEFOJEJG_00066 83669 3 Gut 0.05 protein_coding missense_variant MODERATE 709A>G Asn237Asp
M0177552 PEFOJEJG_00066 83701 3 Gut 0.05 protein_coding synonymous_variant LOW 741T>G Ala247Ala
M0177553 PEFOJEJG_00066 84569 3 Gut 0.05 protein_coding missense_variant MODERATE 1609G>A Asp537Asn
M0177554 PEFOJEJG_00013 19569 3 Gut 0.05 protein_coding missense_variant MODERATE 8260A>G Ser2754Gly
M0177555 PEFOJEJG_00013 19607 3 Gut 0.05 protein_coding synonymous_variant LOW 8298C>T Arg2766Arg
M0177556 PEFOJEJG_00013 19929 4 Gut 0.07 protein_coding missense_variant MODERATE 8620G>A Ala2874Thr
M0177557 PEFOJEJG_00013 19946 4 Gut 0.07 protein_coding synonymous_variant LOW 8637G>T Pro2879Pro
M0177558 PEFOJEJG_00013 19949 4 Gut 0.07 protein_coding synonymous_variant LOW 8640A>C Gly2880Gly
M0177559 PEFOJEJG_00013 20006 4 Gut 0.07 protein_coding synonymous_variant LOW 8697C>T Thr2899Thr
M0177560 PEFOJEJG_00013 20025 4 Gut 0.07 protein_coding missense_variant MODERATE 8716G>T Gly2906Cys
M0177561 PEFOJEJG_00013 20033 4 Gut 0.07 protein_coding synonymous_variant LOW 8724A>T Leu2908Leu
M0177562 PEFOJEJG_00015 21374 4 Gut 0.07 protein_coding missense_variant MODERATE 215G>T Gly72Val
M0177563 PEFOJEJG_00015 21507 3 Gut 0.05 protein_coding synonymous_variant LOW 348T>C Ala116Ala
M0177564 PEFOJEJG_00065 81617 3 Gut 0.05 protein_coding missense_variant MODERATE 436A>G Met146Val
M0177565 PEFOJEJG_00065 81626 3 Gut 0.05 protein_coding missense_variant MODERATE 445A>G Ser149Gly
M0177566 PEFOJEJG_00026 34603 3 Gut 0.05 protein_coding missense_variant MODERATE 257G>A Gly86Glu
M0177567 PEFOJEJG_00028 37871 3 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -130A>G None
M0177568 PEFOJEJG_00030 44656 4 Gut 0.07 protein_coding missense_variant MODERATE 194T>C Leu65Pro






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
PEFOJEJG_00020 VFG000903 Pic 99.9 0 1 1371 1.0 1 Effector delivery system Pic serine protease precursor, autotransporter experiment
PEFOJEJG_00037 VFG013418 LOS 74.5 2e-80 1 192 1.0 0.9897 Immune modulation phosphoheptose isomerase experiment
PEFOJEJG_00012 VFG036039 Contact-dependent inhibition CDI system 98.1 0 1 590 1.0 1 Effector delivery system ShlB/FhaC/HecB family hemolysin secretion/activation protein prediction
PEFOJEJG_00020 VFG000903 Pic 99.9 0 1 1371 1.0 1 Effector delivery system Pic serine protease precursor, autotransporter prediction
PEFOJEJG_00037 VFG013422 LOS 75 8.8e-80 1 192 1.0 0.9897 Immune modulation phosphoheptose isomerase prediction
PEFOJEJG_00065 VFG036037 Contact-dependent inhibition CDI system 96.6 0 1 588 1.0 1 Effector delivery system ShlB/FhaC/HecB family hemolysin secretion/activation protein prediction
PEFOJEJG_00093 VFG042533 CS31A capsule-like antigen 83.9 2e-81 1 180 1.0 1 Adherence ClpC prediction
PEFOJEJG_00094 VFG042494 Adhesive fimbriae 90.8 0 19 814 0.9779 0.995 Adherence cshB porin (usher) prediction
PEFOJEJG_00095 VFG042553 Adhesive fimbriae 94.6 1.4e-136 1 258 1.0 1 Adherence F4 (K88) fimbrial chaperone FaeE prediction
PEFOJEJG_00096 VFG042496 Adhesive fimbriae 82.2 1.2e-66 1 163 1.0 1 Adherence unknown protein prediction
PEFOJEJG_00098 VFG034600 Adhesive fimbriae 74.7 1.6e-108 1 265 1.0 1 Adherence fimbrial protein FaeH prediction
PEFOJEJG_00099 VFG043644 CS31A capsule-like antigen 70.9 2.7e-105 1 251 1.0 0.9882 Adherence CS31A minor subunit prediction
PEFOJEJG_00102 VFG035973 EspC 90.6 0 1 1309 1.0 1 Effector delivery system Type III secretion system secreted protein, serine protease prediction







        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
PEFOJEJG_00020 PHI:3792 pic 96.6 0 1 1371 1.0000 1.0000 birds colibacillosis; cellulitis; swollen head syndrome serin protease aut o transporter reduced virulence
PEFOJEJG_00035 PHI:2647 ivy 100 1.8e-86 1 157 1.0000 1.0000 birds colibacillosis; cellulitis; swollen head syndrome lysozyme inhibitor unaffected pathogenicity
PEFOJEJG_00102 PHI:3449 crc1 95.4 0 1 1309 1.0000 1.0000 rodents colitis class 1 serine protease autotransporter 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
PEFOJEJG_00012 1.B.20.1.3 93.1 0 1 590 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
PEFOJEJG_00020 1.B.12.4.5 96.6 0 1 1371 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
PEFOJEJG_00051 1.B.1.1.2 100 4.8e-204 1 351 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
PEFOJEJG_00065 1.B.20.1.3 100 0 1 588 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
PEFOJEJG_00094 1.B.11.1.1 89.5 0 5 814 0.9951 0.9975 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family