Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C504
  Reference Plasmid   NZ_CP024244.1
  Reference Plasmid Size   152012
  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
M0167548 NJEBBCIH_00180 144435 3 Gut 0.10 protein_coding synonymous_variant LOW 936C>T Thr312Thr
M0167549 NJEBBCIH_00039 29281 3 Gut 0.10 protein_coding synonymous_variant LOW 1527A>T Ala509Ala
M0167550 NJEBBCIH_00039 29288 3 Gut 0.10 protein_coding synonymous_variant LOW 1534C>T Leu512Leu
M0167551 NJEBBCIH_00039 29455 3 Gut 0.10 protein_coding synonymous_variant LOW 1701C>A Gly567Gly






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
NJEBBCIH_00018 VFG035923 Dispersin 78.4 6.3e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC experiment
NJEBBCIH_00180 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
NJEBBCIH_00181 VFG034541 EtpA 95 0 1 1513 1.0 0.9831 Adherence Two-partner secreted adhesin EtpA experiment
NJEBBCIH_00018 VFG035919 Dispersin 79.3 7.3e-88 1 208 0.9952 0.9952 Others ATP-binding protein AatC prediction
NJEBBCIH_00026 VFG043747 Heat-stable toxin (ST) 98.6 1.2e-34 1 72 1.0 1 Exotoxin unknown protein prediction
NJEBBCIH_00098 VFG042500 Adhesive fimbriae 100 8.5e-133 1 238 1.0 1 Adherence CS14 periplasmic chaperone prediction
NJEBBCIH_00099 VFG042501 Adhesive fimbriae 100 4.7e-85 1 169 1.0 1 Adherence CS14 major fimbrial subunit prediction
NJEBBCIH_00100 VFG042502 Adhesive fimbriae 100 2.1e-88 1 175 1.0 1 Adherence CS14 major fimbrial subunit prediction
NJEBBCIH_00101 VFG042503 Adhesive fimbriae 100 0 6 876 0.9943 1 Adherence outer membrane usher protein prediction
NJEBBCIH_00102 VFG042504 Adhesive fimbriae 100 1e-209 1 361 1.0 1 Adherence CS14 minor fimbrial subunit prediction
NJEBBCIH_00146 VFG044067 Colicin Ia 99.5 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
NJEBBCIH_00180 VFG042382 EtpA 98.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
NJEBBCIH_00181 VFG034541 EtpA 95 0 1 1513 1.0 0.9831 Adherence Two-partner secreted adhesin EtpA 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
NJEBBCIH_00112 PHI:11470 STM14_3563 88 1.7e-33 5 87 0.9432 0.9121 rodents salmonellosis putative transcriptional regulator 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
NJEBBCIH_00046 BAN82826.1|GH23 96.4 1.73e-114 1 168 1 0.7778





        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
NJEBBCIH_00001 9.B.127.1.3 97.6 6.7e-92 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
NJEBBCIH_00101 1.B.11.4.1 93.9 0 9 876 0.9909 0.9988 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
NJEBBCIH_00146 1.C.1.1.1 99.4 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
NJEBBCIH_00180 1.B.20.3.3 98.7 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family