Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C348
  Reference Plasmid   NZ_AP014804.1
  Reference Plasmid Size   146197
  Reference Plasmid GC Content   0.47
  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
M0153381 DGOMIHNH_00049 55503 4 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -3505G>A None
M0153382 DGOMIHNH_00120 106371 3 Gut 0.04 protein_coding synonymous_variant LOW 864C>T Asp288Asp
M0153383 DGOMIHNH_00105 96554 5 Gut 0.06 protein_coding missense_variant MODERATE 107G>T Gly36Val
M0153384 DGOMIHNH_00020 15254 5 Gut 0.06 protein_coding missense_variant MODERATE 174T>G Ile58Met
M0153385 DGOMIHNH_00035 24903 4 Gut 0.05 protein_coding synonymous_variant LOW 238C>T Leu80Leu
M0153386 DGOMIHNH_00072 76275 3 Gut 0.04 protein_coding synonymous_variant LOW 171A>G Leu57Leu
M0153387 DGOMIHNH_00072 76290 3 Gut 0.04 protein_coding synonymous_variant LOW 156C>T His52His
M0153388 DGOMIHNH_00075 78334 3 Gut 0.04 protein_coding synonymous_variant LOW 129C>T Val43Val






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
DGOMIHNH_00004 VFG042784 BFP 96.9 5.3e-97 1 193 1.0 1 Adherence major pilin structural unit bundlin experiment
DGOMIHNH_00005 VFG000750 BFP 98.5 1.4e-72 1 133 1.0 1 Adherence BFP biogenesis protein BfpG experiment
DGOMIHNH_00006 VFG000751 BFP 99.6 1.9e-301 1 552 1.0 1 Adherence BfpB secretin experiment
DGOMIHNH_00007 VFG000752 BFP 99.5 6.2e-241 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein experiment
DGOMIHNH_00008 VFG042788 BFP 98.1 1.4e-79 1 156 1.0 0.9512 Adherence periplasmic protein experiment
DGOMIHNH_00009 VFG042789 BFP 99.3 2e-308 1 534 1.0 0.9981 Adherence assembly ATPase experiment
DGOMIHNH_00010 VFG000755 BFP 99.4 1.6e-197 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein experiment
DGOMIHNH_00011 VFG042791 BFP 99.7 9.1e-179 1 318 1.0 0.9607 Adherence retraction ATPase experiment
DGOMIHNH_00012 VFG000757 BFP 98.8 4.8e-143 1 249 1.0 1 Adherence prepilin peptidase BfpP experiment
DGOMIHNH_00013 VFG042793 BFP 98 6.3e-82 1 148 1.0 1 Adherence lipoprotein experiment
DGOMIHNH_00014 VFG042794 BFP 99.4 1e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI experiment
DGOMIHNH_00015 VFG000760 BFP 100 8.8e-102 1 183 1.0 1 Adherence minor pilin subunit BfpJ experiment
DGOMIHNH_00016 VFG042796 BFP 98.1 7.8e-86 1 162 1.0 1 Adherence minor pilin subunit BfpK experiment
DGOMIHNH_00017 VFG000762 BFP 98 7.7e-80 1 149 1.0 1 Adherence BFP biogenesis protein BfpL experiment
DGOMIHNH_00027 VFG000763 Per 94.9 5.7e-145 1 274 1.0 1 Regulation BfpT experiment
DGOMIHNH_00029 VFG000765 Per 98.9 1.3e-45 1 89 1.0 1 Regulation BfpW experiment
DGOMIHNH_00040 VFG000845 ToxB 90.2 0 1 3166 1.0 0.9991 Effector delivery system cytotoxin experiment
DGOMIHNH_00004 VFG042784 BFP 96.9 3.9e-96 1 193 1.0 1 Adherence major pilin structural unit bundlin prediction
DGOMIHNH_00005 VFG000750 BFP 98.5 1e-71 1 133 1.0 1 Adherence BFP biogenesis protein BfpG prediction
DGOMIHNH_00006 VFG000751 BFP 99.6 1.4e-300 1 552 1.0 1 Adherence BfpB secretin prediction
DGOMIHNH_00007 VFG000752 BFP 99.5 4.6e-240 1 402 1.0 1 Adherence BfpC, bitopic inner membrane protein prediction
DGOMIHNH_00008 VFG042788 BFP 98.1 1e-78 1 156 1.0 0.9512 Adherence periplasmic protein prediction
DGOMIHNH_00009 VFG042789 BFP 99.3 1.5e-307 1 534 1.0 0.9981 Adherence assembly ATPase prediction
DGOMIHNH_00010 VFG000755 BFP 99.4 1.2e-196 1 352 1.0 1 Adherence BfpE, polytopic inner membrane protein prediction
DGOMIHNH_00011 VFG042791 BFP 99.7 6.8e-178 1 318 1.0 0.9607 Adherence retraction ATPase prediction
DGOMIHNH_00012 VFG000757 BFP 98.8 3.6e-142 1 249 1.0 1 Adherence prepilin peptidase BfpP prediction
DGOMIHNH_00013 VFG042793 BFP 98 4.7e-81 1 148 1.0 1 Adherence lipoprotein prediction
DGOMIHNH_00014 VFG042794 BFP 99.4 7.4e-97 1 181 1.0 1 Adherence minor pilin subunit BfpI prediction
DGOMIHNH_00015 VFG000760 BFP 100 6.6e-101 1 183 1.0 1 Adherence minor pilin subunit BfpJ prediction
DGOMIHNH_00016 VFG042796 BFP 98.1 5.9e-85 1 162 1.0 1 Adherence minor pilin subunit BfpK prediction
DGOMIHNH_00017 VFG000762 BFP 98 5.8e-79 1 149 1.0 1 Adherence BFP biogenesis protein BfpL prediction
DGOMIHNH_00027 VFG000763 Per 94.9 4.2e-144 1 274 1.0 1 Regulation BfpT prediction
DGOMIHNH_00029 VFG000765 Per 98.9 9.5e-45 1 89 1.0 1 Regulation BfpW prediction
DGOMIHNH_00040 VFG033077 ToxB 97.3 0 1 3166 1.0 1 Effector delivery system cytotoxin 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
DGOMIHNH_00065 ARO:3002863 100 3.34e-121 1 169 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
DGOMIHNH_00158 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase 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
DGOMIHNH_00027 PHI:3803 PerA 95.6 1e-145 1 274 1.0000 1.0000 nematodes hemorrhagic colitis; hemolytic uremic syndrome LPS O-side chain 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
DGOMIHNH_00013 BAU62016.1|GH23 100 1.6e-103 1 148 1 1
DGOMIHNH_00040 BAU62038.1|GT44 100 0 1 3166 1 1
DGOMIHNH_00048 BAU62044.1|GT44 100 0 1 2984 1 1
DGOMIHNH_00113 BAU62106.1|GH23 100 5.79e-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
DGOMIHNH_00006 1.B.22.7.1 99.6 1.1e-300 1 552 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.22 The Outer Bacterial Membrane Secretin (Secretin) Family
DGOMIHNH_00040 1.C.57.2.1 90.1 0 1 3166 1.0000 0.9997 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.57 The Clostridial Cytotoxin (CCT) Family