Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1206
  Reference Plasmid   NZ_CP134806.1
  Reference Plasmid Size   117740
  Reference Plasmid GC Content   0.50
  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
M0199500 BGHFBFCE_00086 76897 3 Gut 0.33 protein_coding missense_variant MODERATE 1526A>C Tyr509Ser
M0199501 BGHFBFCE_00087 77198 3 Gut 0.33 protein_coding synonymous_variant LOW 48T>G Leu16Leu
M0199502 BGHFBFCE_00087 77199 3 Gut 0.33 protein_coding missense_variant MODERATE 49A>G Ile17Val
M0199503 BGHFBFCE_00087 77205 3 Gut 0.33 protein_coding missense_variant MODERATE 55A>G Thr19Ala
M0199504 BGHFBFCE_00087 77243 3 Gut 0.33 protein_coding synonymous_variant LOW 93A>G Gly31Gly
M0199505 BGHFBFCE_00087 77504 4 Gut 0.44 protein_coding missense_variant MODERATE 354C>G Asn118Lys
M0199506 BGHFBFCE_00086 76049 3 Gut 0.33 protein_coding missense_variant MODERATE 678T>G Asp226Glu
M0199507 BGHFBFCE_00086 76482 3 Gut 0.33 protein_coding missense_variant MODERATE 1111G>C Val371Leu
M0199508 BGHFBFCE_00087 77597 3 Gut 0.33 protein_coding synonymous_variant LOW 447T>C Gly149Gly
M0199509 BGHFBFCE_00087 77630 4 Gut 0.44 protein_coding synonymous_variant LOW 480A>G Thr160Thr
M0199510 BGHFBFCE_00087 77816 4 Gut 0.44 protein_coding synonymous_variant LOW 666G>T Arg222Arg
M0199511 BGHFBFCE_00087 77817 5 Gut 0.56 protein_coding missense_variant MODERATE 667A>G Ile223Val
M0199512 BGHFBFCE_00087 77834 5 Gut 0.56 protein_coding synonymous_variant LOW 684C>T Arg228Arg
M0199513 BGHFBFCE_00087 77840 4 Gut 0.44 protein_coding missense_variant MODERATE 690T>A Ser230Arg
M0199514 BGHFBFCE_00087 77859 5 Gut 0.56 protein_coding missense_variant MODERATE 709A>G Asn237Asp
M0199515 BGHFBFCE_00087 78399 4 Gut 0.44 protein_coding missense_variant MODERATE 1249G>A Gly417Ser
M0199516 BGHFBFCE_00087 78414 4 Gut 0.44 protein_coding missense_variant MODERATE 1264G>A Asp422Asn
M0199517 BGHFBFCE_00087 78422 4 Gut 0.44 protein_coding synonymous_variant LOW 1272C>T Gly424Gly
M0199518 BGHFBFCE_00087 78440 4 Gut 0.44 protein_coding synonymous_variant LOW 1290T>C Gly430Gly
M0199519 BGHFBFCE_00087 78443 4 Gut 0.44 protein_coding synonymous_variant LOW 1293T>C Ala431Ala
M0199520 BGHFBFCE_00087 78452 4 Gut 0.44 protein_coding synonymous_variant LOW 1302G>A Gly434Gly
M0199521 BGHFBFCE_00087 78456 4 Gut 0.44 protein_coding missense_variant MODERATE 1306T>A Ser436Thr
M0199522 BGHFBFCE_00087 78522 4 Gut 0.44 protein_coding missense_variant MODERATE 1372G>A Val458Met
M0199523 BGHFBFCE_00087 78583 4 Gut 0.44 protein_coding missense_variant MODERATE 1433C>T Thr478Met
M0199524 BGHFBFCE_00087 78613 4 Gut 0.44 protein_coding missense_variant MODERATE 1463C>T Ser488Leu
M0199525 BGHFBFCE_00087 80085 3 Gut 0.33 protein_coding missense_variant MODERATE 2935A>G Ser979Gly
M0199526 BGHFBFCE_00087 81036 3 Gut 0.33 protein_coding missense_variant MODERATE 3886T>G Cys1296Gly






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
BGHFBFCE_00008 VFG001445 TraJ 97.5 8.1e-113 1 200 0.8772 0.995 Invasion unknown protein experiment
BGHFBFCE_00067 VFG000884 P fimbriae 72.1 0 1 819 1.0 0.9797 Adherence usher protein PapC experiment
BGHFBFCE_00068 VFG000885 P fimbriae 77.8 1.2e-106 1 239 0.9835 0.9795 Adherence chaperone protein PapD experiment
BGHFBFCE_00008 VFG001445 TraJ 97.5 6.1e-112 1 200 0.8772 0.995 Invasion unknown protein prediction
BGHFBFCE_00052 VFG042533 CS31A capsule-like antigen 92.2 4.7e-91 3 181 0.989 0.9944 Adherence ClpC prediction
BGHFBFCE_00053 VFG034596 Adhesive fimbriae 93 0 5 814 0.9951 0.9988 Adherence fimbrial usher protein FaeD prediction
BGHFBFCE_00054 VFG034597 Adhesive fimbriae 96.5 1.9e-138 1 258 1.0 1 Adherence fimbrial chaperone FaeE prediction
BGHFBFCE_00055 VFG043645 CS31A capsule-like antigen 87 8.3e-71 1 162 0.9939 0.9939 Adherence unknown protein prediction
BGHFBFCE_00057 VFG043647 CS31A capsule-like antigen 94 7.9e-141 26 290 0.9138 0.9962 Adherence fimbrial protein prediction
BGHFBFCE_00058 VFG043644 CS31A capsule-like antigen 96.5 2.4e-141 1 254 1.0 1 Adherence CS31A minor subunit prediction
BGHFBFCE_00065 VFG042583 Sfp fimbriae 75.6 1e-66 8 175 0.96 0.9655 Adherence type 1 fimbrial protein prediction
BGHFBFCE_00066 VFG042652 Pix pilus 90.3 9.2e-101 1 195 1.0 1.0052 Adherence PixH protein prediction
BGHFBFCE_00067 VFG042653 Pix pilus 94.6 0 1 819 1.0 0.9579 Adherence PixC protein prediction
BGHFBFCE_00068 VFG042586 Sfp fimbriae 90.1 1.9e-124 1 243 1.0 1 Adherence fimbria/pilus periplasmic chaperone prediction
BGHFBFCE_00086 VFG036037 Contact-dependent inhibition CDI system 96.4 0 1 588 1.0 1 Effector delivery system ShlB/FhaC/HecB family hemolysin secretion/activation protein prediction
BGHFBFCE_00087 VFG036031 Contact-dependent inhibition CDI system 94.3 0 1 3095 0.9503 0.9624 Effector delivery system contact-dependent inhibition effector tRNA nuclease prediction
BGHFBFCE_00100 VFG044067 Colicin Ia 99 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
BGHFBFCE_00110 VFG043979 Colicin B 99.8 6.2e-290 1 511 1.0 1 Exotoxin colicin B 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
BGHFBFCE_00078 PHI:2648 pliG 97.7 1.9e-68 1 133 1.0000 1.0000 birds colibacillosis; cellulitis; swollen head syndrome lysozyme inhibitor unaffected pathogenicity






        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
BGHFBFCE_00006 AZM68384.1|GH23 99.5 9.54e-156 1 215 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
BGHFBFCE_00047 1.E.53.1.11 100 5e-33 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
BGHFBFCE_00053 1.B.11.1.1 92.8 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
BGHFBFCE_00067 1.B.11.2.1 72.2 0 1 819 1.0000 0.9809 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
BGHFBFCE_00085 8.B.24.2.3 88.1 1.2e-44 1 101 0.8938 0.9806 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
BGHFBFCE_00086 1.B.20.1.3 97.3 0 1 588 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
BGHFBFCE_00100 1.C.1.1.1 98.9 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
BGHFBFCE_00107 8.B.24.3.1 99.1 3.2e-64 1 117 1.0000 0.8298 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
BGHFBFCE_00110 1.C.1.3.2 99.8 4.9e-290 1 511 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family