Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C312
  Reference Plasmid   NC_013507.1
  Reference Plasmid Size   67094
  Reference Plasmid GC Content   0.51
  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
M0152787 HEMNDAFI_00057 45816 3 Gut 0.21 protein_coding synonymous_variant LOW 72A>G Ser24Ser
M0152788 HEMNDAFI_00057 45840 3 Gut 0.21 protein_coding synonymous_variant LOW 48A>C Ala16Ala
M0152789 HEMNDAFI_00058 46008 3 Gut 0.21 protein_coding synonymous_variant LOW 5170A>C Arg1724Arg
M0152790 HEMNDAFI_00058 46019 3 Gut 0.21 protein_coding missense_variant MODERATE 5159A>G Gln1720Arg
M0152791 HEMNDAFI_00058 46079 3 Gut 0.21 protein_coding missense_variant MODERATE 5099A>C Asp1700Ala
M0152792 HEMNDAFI_00058 46108 3 Gut 0.21 protein_coding synonymous_variant LOW 5070A>G Glu1690Glu
M0152793 HEMNDAFI_00058 46132 3 Gut 0.21 protein_coding synonymous_variant LOW 5046T>C Gly1682Gly
M0152794 HEMNDAFI_00058 46312 3 Gut 0.21 protein_coding synonymous_variant LOW 4866T>C Gly1622Gly
M0152795 HEMNDAFI_00058 46564 3 Gut 0.21 protein_coding synonymous_variant LOW 4614T>C Ser1538Ser
M0152796 HEMNDAFI_00058 46571 3 Gut 0.21 protein_coding missense_variant MODERATE 4607G>C Gly1536Ala
M0152797 HEMNDAFI_00038 32499 4 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -4105G>A None
M0152798 HEMNDAFI_00038 32573 4 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -4179T>C None
M0152799 HEMNDAFI_00043 32928 4 Gut 0.29 protein_coding missense_variant MODERATE 1246C>T His416Tyr
M0152800 HEMNDAFI_00043 33150 4 Gut 0.29 protein_coding synonymous_variant LOW 1024C>T Leu342Leu
M0152801 HEMNDAFI_00044 34437 4 Gut 0.29 protein_coding synonymous_variant LOW 456T>C Arg152Arg
M0152802 HEMNDAFI_00043 34931 4 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -758G>A None
M0152803 HEMNDAFI_00043 34932 4 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -759C>T None
M0152804 HEMNDAFI_00045 35459 4 Gut 0.29 protein_coding synonymous_variant LOW 426A>G Leu142Leu
M0152805 HEMNDAFI_00045 35462 4 Gut 0.29 protein_coding synonymous_variant LOW 429T>C Val143Val
M0152806 HEMNDAFI_00045 35504 4 Gut 0.29 protein_coding synonymous_variant LOW 471C>A Leu157Leu
M0152807 HEMNDAFI_00045 35519 4 Gut 0.29 protein_coding synonymous_variant LOW 486G>A Ala162Ala
M0152808 HEMNDAFI_00046 35691 4 Gut 0.29 protein_coding synonymous_variant LOW 48A>G Val16Val
M0152809 HEMNDAFI_00046 35869 4 Gut 0.29 protein_coding missense_variant MODERATE 226C>T His76Tyr
M0152810 HEMNDAFI_00046 35937 4 Gut 0.29 protein_coding synonymous_variant LOW 294T>G Gly98Gly
M0152811 HEMNDAFI_00046 36174 4 Gut 0.29 protein_coding synonymous_variant LOW 531C>T Arg177Arg
M0152812 HEMNDAFI_00047 36596 4 Gut 0.29 protein_coding synonymous_variant LOW 153T>C His51His






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
HEMNDAFI_00029 VFG036068 Heat-labile toxin (LT) 100 4.8e-67 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
HEMNDAFI_00030 VFG036066 Heat-labile toxin (LT) 100 1.4e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
HEMNDAFI_00038 VFG002039 Heat-stable toxin (ST) 100 7.4e-36 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
HEMNDAFI_00029 VFG036068 Heat-labile toxin (LT) 100 3.6e-66 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
HEMNDAFI_00030 VFG036066 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
HEMNDAFI_00038 VFG002039 Heat-stable toxin (ST) 100 5.5e-35 1 72 1.0 1 Exotoxin heat stable enterotoxin I 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
HEMNDAFI_00042 ARO:3002641 98.2 3.76e-207 1 271 1.0000 1.0000 aminoglycoside antibiotic APH(3') antibiotic inactivation






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
HEMNDAFI_00029 PHI:699 CtxB 78.2 1.9e-51 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
HEMNDAFI_00030 PHI:698 CtxA 80.3 1.1e-105 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) 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
HEMNDAFI_00001 CBJ04400.1|GH23 100 8.23e-123 1 169 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
HEMNDAFI_00030 1.C.72.4.1 100 8.3e-130 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family