Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C247
  Reference Plasmid   LR961949.1
  Reference Plasmid Size   137069
  Reference Plasmid GC Content   0.34
  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
M0149596 POGFMHJC_00076 64981 3 Gut 0.30 protein_coding synonymous_variant LOW 807G>A Glu269Glu






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
POGFMHJC_00083 VFG002178 Cytolysin 99.7 9.3e-179 1 327 1.0 1 Exotoxin cytolysin immunity protein experiment
POGFMHJC_00084 VFG002177 Cytolysin 99.5 2.4e-232 1 412 1.0 1 Exotoxin cytolysin activator experiment
POGFMHJC_00085 VFG002176 Cytolysin 99.7 0 1 714 1.0 1 Exotoxin ABC-type transporter experiment
POGFMHJC_00086 VFG045474 Cytolysin 99.5 0 1 993 1.0 1 Exotoxin CylM; cytolysin subunit modifier experiment
POGFMHJC_00087 VFG045473 Cytolysin 100 8.1e-31 1 63 1.0 1 Exotoxin CylS; cytolysin subunit experiment
POGFMHJC_00088 VFG045472 Cytolysin 100 1.8e-31 1 68 1.0 1 Exotoxin CylL; cytolysin subunit experiment
POGFMHJC_00089 VFG002175 Cytolysin 97.9 2e-41 1 94 1.0 1 Exotoxin cytolysin regulator R1 experiment
POGFMHJC_00090 VFG045470 Cytolysin 98.5 2.2e-31 1 66 1.0 1 Exotoxin cytolysin regulator R2 experiment
POGFMHJC_00124 VFG002164 AS 95.7 0 1 1297 1.0 0.9939 Adherence aggregation substance PrgB/Asc10 experiment
POGFMHJC_00083 VFG002178 Cytolysin 99.7 7e-178 1 327 1.0 1 Exotoxin cytolysin immunity protein prediction
POGFMHJC_00084 VFG002177 Cytolysin 99.5 1.8e-231 1 412 1.0 1 Exotoxin cytolysin activator prediction
POGFMHJC_00085 VFG002176 Cytolysin 99.7 0 1 714 1.0 1 Exotoxin ABC-type transporter prediction
POGFMHJC_00086 VFG002169 Cytolysin 99.4 0 1 993 1.0 1 Exotoxin CylM; cytolysin subunit modifier prediction
POGFMHJC_00087 VFG045473 Cytolysin 100 6.1e-30 1 63 1.0 1 Exotoxin CylS; cytolysin subunit prediction
POGFMHJC_00088 VFG045472 Cytolysin 100 1.3e-30 1 68 1.0 1 Exotoxin CylL; cytolysin subunit prediction
POGFMHJC_00089 VFG002175 Cytolysin 97.9 1.5e-40 1 94 1.0 1 Exotoxin cytolysin regulator R1 prediction
POGFMHJC_00090 VFG045470 Cytolysin 98.5 1.7e-30 1 66 1.0 1 Exotoxin cytolysin regulator R2 prediction
POGFMHJC_00124 VFG002164 AS 95.7 0 1 1297 1.0 0.9939 Adherence aggregation substance PrgB/Asc10 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
POGFMHJC_00025 Arsenic (As) 72.9 1.9e-140 6 345 0.9770 0.9827 experiment
POGFMHJC_00039 Copper (Cu) 100 1.4e-31 1 68 1.0000 1.0000 experiment
POGFMHJC_00040 Copper (Cu) 99.9 0 1 710 1.0000 1.0000 experiment
POGFMHJC_00024 Arsenic (As), Antimony (Sb) 78.2 3.2e-149 2 349 0.9748 0.9748 prediction
POGFMHJC_00025 Arsenic (As) 79.1 8.3e-150 4 347 0.9885 0.9718 prediction
POGFMHJC_00039 Copper (Cu) 100 3.2e-29 1 68 1.0000 1.0000 prediction
POGFMHJC_00040 Copper (Cu) 100 0 1 710 1.0000 1.0000 prediction






        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
POGFMHJC_00145 ARO:3002628 100 1.04e-211 27 302 0.9139 1.0000 aminoglycoside antibiotic ANT(6) antibiotic inactivation
POGFMHJC_00147 ARO:3002647 100 1.07e-198 1 264 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation
POGFMHJC_00148 ARO:3000375 98 3.24e-173 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration






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
POGFMHJC_00050 PHI:5205 HMPREF0351_10118 (WxL locusC) 75 2.6e-174 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
POGFMHJC_00062 PHI:5205 HMPREF0351_10118 (WxL locusC) 92.6 4.6e-123 1 231 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis 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
POGFMHJC_00091 AAL59475.1|GT0 99.7 1.47e-211 116 430 0.7326 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
POGFMHJC_00024 2.A.59.1.6 72.6 1.5e-136 4 346 0.9608 1.1588 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.59 The Arsenical Resistance-3 (ACR3) Family
POGFMHJC_00025 2.A.59.1.2 72.9 7e-139 6 345 0.9770 0.9827 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.59 The Arsenical Resistance-3 (ACR3) Family
POGFMHJC_00040 3.A.3.5.16 99.9 0 1 710 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
POGFMHJC_00085 3.A.1.111.1 99.7 0 1 714 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
POGFMHJC_00087 1.C.60.1.1 100 4.8e-30 1 63 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.60 The Two-component <I>Enterococcus faecalis</I> Cytolysin (EFC) Family
POGFMHJC_00088 1.C.60.1.1 100 1e-30 1 68 1.0000 1.0794 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.60 The Two-component <I>Enterococcus faecalis</I> Cytolysin (EFC) Family
POGFMHJC_00099 3.A.7.19.1 93.9 4.9e-246 3 447 0.9955 0.7932 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
POGFMHJC_00101 3.A.7.19.1 99.6 0 1 561 1.0000 1.0000 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
POGFMHJC_00104 3.A.7.19.1 99.6 0 1 719 1.0000 1.2816 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
POGFMHJC_00105 3.A.7.19.1 99.5 0 1 609 1.0000 1.0856 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