Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C74
  Reference Plasmid   CP029771.1
  Reference Plasmid Size   100894
  Reference Plasmid GC Content   0.48
  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
M0143628 IKDBGMFM_00019 16980 4 Gut 0.67 protein_coding upstream_gene_variant MODIFIER -3371A>C None
M0143629 IKDBGMFM_00024 18768 4 Gut 0.67 protein_coding synonymous_variant LOW 2109G>A Leu703Leu
M0143630 IKDBGMFM_00024 18987 4 Gut 0.67 protein_coding missense_variant MODERATE 1890A>G Ile630Met
M0143631 IKDBGMFM_00024 19007 4 Gut 0.67 protein_coding missense_variant MODERATE 1870C>T His624Tyr
M0143632 IKDBGMFM_00024 19183 4 Gut 0.67 protein_coding missense_variant MODERATE 1694G>A Gly565Asp
M0143633 IKDBGMFM_00024 19205 4 Gut 0.67 protein_coding missense_variant MODERATE 1672C>A Leu558Met
M0143634 IKDBGMFM_00025 21173 4 Gut 0.67 protein_coding missense_variant MODERATE 649T>C Phe217Leu
M0143635 IKDBGMFM_00026 22204 4 Gut 0.67 protein_coding missense_variant MODERATE 333A>G Ile111Met
M0143636 IKDBGMFM_00026 22514 4 Gut 0.67 protein_coding missense_variant MODERATE 23A>G Gln8Arg
M0143637 IKDBGMFM_00023 22955 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4409A>G None
M0143638 IKDBGMFM_00027 23250 3 Gut 0.50 protein_coding missense_variant MODERATE 170C>A Ala57Glu
M0143639 IKDBGMFM_00027 23252 3 Gut 0.50 protein_coding synonymous_variant LOW 168A>C Pro56Pro
M0143640 IKDBGMFM_00022 20959 3 Gut 0.50 protein_coding upstream_gene_variant MODIFIER -4442A>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
IKDBGMFM_00023 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
IKDBGMFM_00020 VFG043980 Colicin Ib 98.9 0 1 626 1.0 1 Exotoxin colicin-like pore-forming protein prediction
IKDBGMFM_00023 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB 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
IKDBGMFM_00007 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 82.9 9.9e-45 1 105 1.0000 1.0000 experiment
IKDBGMFM_00007 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate] 90.5 1.3e-45 1 105 1.0000 1.0000 prediction






        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
IKDBGMFM_00005 ARO:3002053 100 2.33e-286 1 381 1.0000 1.0000 cephalosporin CMY 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
IKDBGMFM_00005 PHI:6133 blaCMY-2 99.7 3.7e-226 1 381 1.0000 1.0000 rodents salmonellosis beta-lactamase reduced virulence
IKDBGMFM_00023 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
IKDBGMFM_00024 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
IKDBGMFM_00025 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
IKDBGMFM_00026 PHI:10792 cjrA 99.6 2.7e-134 1 235 1.0000 0.8076 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)






        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
IKDBGMFM_00098 AWT21935.1|GH23 100 6.12e-116 1 160 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
IKDBGMFM_00005 8.A.212.1.4 75.8 3.3e-174 1 380 0.9974 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.212 The d-Amino Acid Peptidase (dAAP) Family
IKDBGMFM_00007 2.A.7.1.10 86.7 9.7e-44 1 105 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
IKDBGMFM_00020 1.C.1.1.2 99.8 0 1 626 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
IKDBGMFM_00021 8.B.24.2.1 98.2 2.7e-55 1 110 0.9565 0.8661 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
IKDBGMFM_00024 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
IKDBGMFM_00025 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
IKDBGMFM_00061 3.A.7.10.1 99.6 0 1 763 1.0000 7.9479 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00062 3.A.7.10.1 96.3 6.6e-201 1 356 1.0000 3.7083 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00063 3.A.7.10.1 99 1.3e-242 1 402 1.0000 4.1875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00065 1.E.53.1.10 88.4 1.2e-15 9 51 0.8431 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
IKDBGMFM_00082 3.A.7.10.1 99.1 7.4e-183 1 327 1.0000 3.4063 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00083 3.A.7.10.1 98.7 1.6e-128 1 230 1.0000 2.3958 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00084 3.A.7.10.1 100 1.3e-57 1 115 1.0000 1.1979 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00087 3.A.7.10.1 99 4.6e-56 1 96 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00088 3.A.7.10.1 99.7 4.2e-222 1 382 1.0000 3.9792 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00089 3.A.7.10.1 99.3 2.8e-159 1 272 1.0000 2.8333 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
IKDBGMFM_00090 3.A.7.10.1 100 6e-87 1 152 1.0000 1.5833 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family