Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C958
  Reference Plasmid   NZ_CP084247.1
  Reference Plasmid Size   292841
  Reference Plasmid GC Content   0.37
  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
M0191071 EHEPJDKE_00028 25283 4 Gut 0.15 protein_coding missense_variant MODERATE 653A>G Asp218Gly
M0191072 EHEPJDKE_00195 178129 3 Gut 0.11 protein_coding synonymous_variant LOW 390A>G Ser130Ser
M0191073 EHEPJDKE_00248 225945 4 Gut 0.15 protein_coding missense_variant MODERATE 76A>C Ile26Leu
M0191074 EHEPJDKE_00244 227339 3 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -4862T>C None
M0191075 EHEPJDKE_00252 230003 3 Gut 0.11 protein_coding synonymous_variant LOW 24T>C Ile8Ile






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
EHEPJDKE_00095 VFG042998 Bee (biofilm enhancer in enterococci) 97.9 1.2e-205 1 373 1.0 1 Adherence Srt2 prediction
EHEPJDKE_00096 VFG042997 Bee (biofilm enhancer in enterococci) 98.5 8.7e-223 1 398 1.0 1 Adherence Srt1 prediction
EHEPJDKE_00097 VFG042996 Bee (biofilm enhancer in enterococci) 97.4 1.5e-272 1 495 1.0 1 Adherence Bee3 prediction
EHEPJDKE_00098 VFG042995 Bee (biofilm enhancer in enterococci) 96 2.4e-130 1 249 1.0 1.0247 Adherence Bee2 prediction
EHEPJDKE_00099 VFG042994 Bee (biofilm enhancer in enterococci) 98.4 0 1 1085 1.0 1.0018 Adherence Bee1 prediction
EHEPJDKE_00277 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.2 5.2e-124 1 223 1.0 1 Adherence putative housekeeping sortase prediction
EHEPJDKE_00278 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 0 1 658 1.0 1 Adherence PilA prediction
EHEPJDKE_00279 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 99.2 2.4e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
EHEPJDKE_00280 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 95.7 9.7e-127 1 253 1.0 1.008 Adherence cell wall-associated LPXTG-like protein prediction
EHEPJDKE_00281 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
EHEPJDKE_00282 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.4 0 1 696 1.0 1 Adherence minor pilin subunit 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
EHEPJDKE_00062 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1e-226 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EHEPJDKE_00067 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.4 1.2e-154 1 348 0.9694 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EHEPJDKE_00084 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.3 1.7e-114 1 279 0.9859 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EHEPJDKE_00086 PHI:3317 hsdR 76.2 0 7 1030 0.9922 0.9912 rodents Glasser's disease involved in pathogenicity reduced virulence
EHEPJDKE_00138 PHI:8586 mntH1 77.4 9.1e-223 17 530 0.9607 0.9737 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity
EHEPJDKE_00174 PHI:8586 mntH1 77.4 9.1e-223 17 530 0.9607 0.9737 moths nosocomial infection divalent metal cation transporter 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
EHEPJDKE_00019 QZK92746.1|GH1 100 0 1 468 1 1
EHEPJDKE_00040 VEF84274.1|GH32 100 0 1 479 1 1
EHEPJDKE_00224 UBX35808.1|GH0 100 0 1 776 1 1
EHEPJDKE_00293 UBX35873.1|GH73 100 1.18e-272 1 401 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
EHEPJDKE_00018 4.A.3.1.1 71.7 4.4e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
EHEPJDKE_00054 1.C.24.1.10 100 7.8e-37 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family
EHEPJDKE_00085 3.A.7.14.1 84 2.2e-111 1 276 1.0000 1.5410 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
EHEPJDKE_00093 3.A.7.14.1 98.1 3.3e-167 1 322 1.0000 1.7596 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
EHEPJDKE_00120 2.A.7.5.3 95.6 3.8e-154 1 295 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
EHEPJDKE_00142 1.C.24.1.10 95.8 4.3e-35 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family
EHEPJDKE_00178 1.C.24.1.10 95.8 4.3e-35 1 71 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family