Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C359
  Reference Plasmid   NZ_AP019409.1
  Reference Plasmid Size   153750
  Reference Plasmid GC Content   0.35
  Reference Plasmid Mobility Type   non-mobilizable





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
M0154332 NLDGNLKI_00079 68916 3 Gut 0.50 protein_coding missense_variant MODERATE 91A>G Asn31Asp
M0154333 NLDGNLKI_00079 68966 3 Gut 0.50 protein_coding missense_variant MODERATE 41C>A Thr14Lys
M0154334 NLDGNLKI_00080 69229 3 Gut 0.50 protein_coding synonymous_variant LOW 636T>C Ala212Ala
M0154335 NLDGNLKI_00080 69844 3 Gut 0.50 protein_coding synonymous_variant LOW 21G>A Val7Val
M0154336 NLDGNLKI_00077 70711 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -2628A>G None
M0154337 NLDGNLKI_00082 70886 3 Gut 0.50 protein_coding synonymous_variant LOW 678G>A Gly226Gly
M0154338 NLDGNLKI_00077 71642 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3559A>G None
M0154339 NLDGNLKI_00077 71653 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -3570A>C None
M0154340 NLDGNLKI_00083 71960 3 Gut 0.50 protein_coding stop_gained HIGH 145C>T Arg49*
M0154341 NLDGNLKI_00083 72068 3 Gut 0.50 protein_coding missense_variant MODERATE 253T>C Phe85Leu
M0154342 NLDGNLKI_00083 72509 3 Gut 0.50 protein_coding missense_variant MODERATE 694T>G Cys232Gly
M0154343 NLDGNLKI_00083 72609 3 Gut 0.50 protein_coding missense_variant MODERATE 794G>A Gly265Asp
M0154344 NLDGNLKI_00083 72693 3 Gut 0.50 protein_coding missense_variant MODERATE 878C>T Thr293Ile
M0154345 NLDGNLKI_00078 73260 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4851T>G None






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







        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
NLDGNLKI_00026 PHI:5205 HMPREF0351_10118 (WxL locusC) 97.1 5.4e-33 1 69 0.9324 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00027 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1.6e-27 1 57 0.7403 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00028 PHI:5205 HMPREF0351_10118 (WxL locusC) 84.7 6.3e-77 1 170 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00039 PHI:5205 HMPREF0351_10118 (WxL locusC) 77.9 2e-23 13 80 0.8095 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00074 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
NLDGNLKI_00083 PHI:5205 HMPREF0351_10118 (WxL locusC) 70.7 2.9e-162 1 388 0.9974 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00111 PHI:5205 HMPREF0351_10118 (WxL locusC) 100 1.1e-29 44 106 0.5943 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00116 PHI:5205 HMPREF0351_10118 (WxL locusC) 74 2.4e-172 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
NLDGNLKI_00157 PHI:5205 HMPREF0351_10118 (WxL locusC) 78.8 1.1e-180 1 392 0.9899 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
NLDGNLKI_00045 QMV94891.1|GH32 100 0 1 479 1 1
NLDGNLKI_00133 CCO10203.2|GH1 86.9 1.56e-244 1 390 1 1
NLDGNLKI_00142 BBI40560.1|GH32 100 0 1 446 1 1
NLDGNLKI_00144 BBI40562.1|GH36 100 0 1 730 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
NLDGNLKI_00024 1.C.90.3.3 100 2.3e-38 1 87 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.90 The Carnocyclin A (Carnocyclin) Family