Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C824
  Reference Plasmid   NZ_CP068154.1
  Reference Plasmid Size   72354
  Reference Plasmid GC Content   0.49
  Reference Plasmid Mobility Type   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
M0184057 DLBNDPKM_00063 57059 3 Gut 0.38 protein_coding missense_variant MODERATE 188T>C Val63Ala
M0184058 DLBNDPKM_00063 57139 3 Gut 0.38 protein_coding synonymous_variant LOW 108T>C Leu36Leu
M0184059 DLBNDPKM_00063 57202 3 Gut 0.38 protein_coding synonymous_variant LOW 45A>G Leu15Leu
M0184060 DLBNDPKM_00057 57361 3 Gut 0.38 protein_coding upstream_gene_variant MODIFIER -4386C>T None
M0184061 DLBNDPKM_00064 57432 3 Gut 0.38 protein_coding synonymous_variant LOW 465C>T Ser155Ser
M0184062 DLBNDPKM_00064 57489 3 Gut 0.38 protein_coding synonymous_variant LOW 408A>T Ala136Ala
M0184063 DLBNDPKM_00064 57501 3 Gut 0.38 protein_coding synonymous_variant LOW 396C>T Gly132Gly
M0184064 DLBNDPKM_00064 57504 3 Gut 0.38 protein_coding synonymous_variant LOW 393A>G Thr131Thr
M0184065 DLBNDPKM_00064 57510 3 Gut 0.38 protein_coding synonymous_variant LOW 387G>A Leu129Leu
M0184066 DLBNDPKM_00064 57513 3 Gut 0.38 protein_coding synonymous_variant LOW 384A>G Pro128Pro
M0184067 DLBNDPKM_00064 57525 3 Gut 0.38 protein_coding synonymous_variant LOW 372G>A Thr124Thr
M0184068 DLBNDPKM_00064 57598 3 Gut 0.38 protein_coding missense_variant MODERATE 299T>C Val100Ala
M0184069 DLBNDPKM_00064 57605 3 Gut 0.38 protein_coding synonymous_variant LOW 292T>C Leu98Leu
M0184070 DLBNDPKM_00064 57619 3 Gut 0.38 protein_coding missense_variant MODERATE 278T>A Leu93His
M0184071 DLBNDPKM_00064 57735 3 Gut 0.38 protein_coding synonymous_variant LOW 162G>A Glu54Glu
M0184072 DLBNDPKM_00064 57743 3 Gut 0.38 protein_coding missense_variant MODERATE 154A>T Thr52Ser
M0184073 DLBNDPKM_00065 58053 3 Gut 0.38 protein_coding missense_variant MODERATE 92A>G Asn31Ser
M0184074 DLBNDPKM_00067 58483 3 Gut 0.38 protein_coding missense_variant MODERATE 528C>A Ser176Arg
M0184075 DLBNDPKM_00067 58825 3 Gut 0.38 protein_coding synonymous_variant LOW 186G>A Ala62Ala
M0184076 DLBNDPKM_00068 59597 3 Gut 0.38 protein_coding synonymous_variant LOW 855C>T Asn285Asn
M0184077 DLBNDPKM_00068 59600 3 Gut 0.38 protein_coding synonymous_variant LOW 852T>C Arg284Arg
M0184078 DLBNDPKM_00068 59609 3 Gut 0.38 protein_coding synonymous_variant LOW 843G>A Val281Val
M0184079 DLBNDPKM_00068 59612 3 Gut 0.38 protein_coding synonymous_variant LOW 840C>T Ile280Ile
M0184080 DLBNDPKM_00068 59913 3 Gut 0.38 protein_coding missense_variant MODERATE 539T>C Leu180Pro
M0184081 DLBNDPKM_00068 59975 3 Gut 0.38 protein_coding synonymous_variant LOW 477A>G Pro159Pro
M0184082 DLBNDPKM_00068 60044 3 Gut 0.38 protein_coding synonymous_variant LOW 408A>G Pro136Pro
M0184083 DLBNDPKM_00070 61336 3 Gut 0.38 protein_coding missense_variant MODERATE 397A>G Ile133Val
M0184084 DLBNDPKM_00071 61772 3 Gut 0.38 protein_coding synonymous_variant LOW 294T>C Phe98Phe






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
DLBNDPKM_00026 VFG033834 Pic 99.9 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
DLBNDPKM_00041 VFG020186 VirK 98.7 4.2e-188 1 316 1.0 1 Others virulence factor VirK prediction
DLBNDPKM_00042 VFG013087 MsbB2 97.5 1.4e-183 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase 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
DLBNDPKM_00021 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence
DLBNDPKM_00040 PHI:10400 Sfgtr4 (ORF186) 95.6 7.3e-208 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
DLBNDPKM_00040 AOT35667.1|GT4 100 7.65e-272 1 362 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