Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C76
  Reference Plasmid   CP033042.1
  Reference Plasmid Size   78861
  Reference Plasmid GC Content   0.35
  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
M0143643 EFFNKKGE_00017 14004 3 Gut 0.43 protein_coding synonymous_variant LOW 333C>T Ser111Ser
M0143644 EFFNKKGE_00018 14349 4 Gut 0.57 protein_coding missense_variant MODERATE 890C>T Thr297Met
M0143645 EFFNKKGE_00019 15298 3 Gut 0.43 protein_coding missense_variant MODERATE 547C>A Leu183Ile
M0143646 EFFNKKGE_00019 15838 4 Gut 0.57 protein_coding missense_variant MODERATE 7A>G Lys3Glu
M0143647 EFFNKKGE_00011 15860 4 Gut 0.57 protein_coding upstream_gene_variant MODIFIER -4689G>A None
M0143648 EFFNKKGE_00011 15884 4 Gut 0.57 protein_coding upstream_gene_variant MODIFIER -4713C>T None
M0143649 EFFNKKGE_00020 16035 4 Gut 0.57 protein_coding missense_variant MODERATE 34G>A Glu12Lys
M0143650 EFFNKKGE_00020 16051 4 Gut 0.57 protein_coding synonymous_variant LOW 18C>T His6His
M0143651 EFFNKKGE_00021 16093 4 Gut 0.57 protein_coding synonymous_variant LOW 1668G>T Thr556Thr
M0143652 EFFNKKGE_00021 16395 4 Gut 0.57 protein_coding missense_variant MODERATE 1366G>T Ala456Ser
M0143653 EFFNKKGE_00021 16400 3 Gut 0.43 protein_coding missense_variant MODERATE 1361A>C Glu454Ala






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
EFFNKKGE_00048 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 0 1 696 1.0 1 Adherence minor pilin subunit prediction
EFFNKKGE_00049 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
EFFNKKGE_00050 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 100 2.4e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
EFFNKKGE_00051 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 4.1e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
EFFNKKGE_00052 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 98.5 0 1 658 0.991 1 Adherence PilA prediction
EFFNKKGE_00053 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 98.7 1.4e-124 15 237 0.9409 1 Adherence putative housekeeping sortase 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
EFFNKKGE_00001 PHI:5205 HMPREF0351_10118 (WxL locusC) 74.2 8.4e-173 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
EFFNKKGE_00077 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.8 1.2e-168 1 389 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
EFFNKKGE_00006 VEF84274.1|GH32 100 0 1 479 1 1
EFFNKKGE_00008 CCO10203.2|GH1 87.9 9.57e-247 14 401 0.9628 0.9949
EFFNKKGE_00034 AYM74319.1|GH73 100 7.45e-276 1 401 1 1
EFFNKKGE_00062 CCO10203.2|GH1 87.9 9.57e-247 14 401 0.9628 0.9949
EFFNKKGE_00073 CCO10203.2|GH1 87.9 9.57e-247 14 401 0.9628 0.9949





        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