Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C303
  Reference Plasmid   NC_011754.1
  Reference Plasmid Size   119594
  Reference Plasmid GC Content   0.49
  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
M0151870 HBOCFJMJ_00080 56288 5 Gut 0.17 protein_coding missense_variant MODERATE 191A>G Gln64Arg
M0151871 HBOCFJMJ_00081 57629 5 Gut 0.17 protein_coding missense_variant MODERATE 649T>C Phe217Leu
M0151872 HBOCFJMJ_00073 54946 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3829A>T None
M0151873 HBOCFJMJ_00073 54955 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3838A>G None
M0151874 HBOCFJMJ_00073 54957 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3840G>C None
M0151875 HBOCFJMJ_00073 54964 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3847A>G None
M0151876 HBOCFJMJ_00073 54965 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3848C>T None
M0151877 HBOCFJMJ_00073 54974 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3857T>C None
M0151878 HBOCFJMJ_00073 55001 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3884C>A None
M0151879 HBOCFJMJ_00073 55009 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3892T>C None
M0151880 HBOCFJMJ_00073 55010 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3893G>A None
M0151881 HBOCFJMJ_00073 55019 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3902A>T None
M0151882 HBOCFJMJ_00073 55024 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3907A>G None
M0151883 HBOCFJMJ_00073 55032 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3915C>A None
M0151884 HBOCFJMJ_00073 55133 3 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -4016A>C None
M0151885 HBOCFJMJ_00056 38884 3 Gut 0.10 protein_coding synonymous_variant LOW 516A>T Gly172Gly






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
HBOCFJMJ_00083 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
HBOCFJMJ_00083 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






        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
HBOCFJMJ_00080 PHI:10792 cjrA 99.7 1.6e-165 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
HBOCFJMJ_00081 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
HBOCFJMJ_00082 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
HBOCFJMJ_00083 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin 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
HBOCFJMJ_00128 CAQ87348.1|GH23 100 2.05e-114 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
HBOCFJMJ_00007 1.A.73.1.3 93.2 7.1e-15 1 44 0.9565 0.9362 1 Channels/Pores 1.A α-Type Channels 1.A.73 The Colicin Lysis Protein (CLP) Family
HBOCFJMJ_00042 3.A.1.116.1 90.5 1.3e-98 19 207 0.8915 0.7652 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
HBOCFJMJ_00046 8.B.24.2.1 100 6.4e-57 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
HBOCFJMJ_00081 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
HBOCFJMJ_00082 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
HBOCFJMJ_00087 3.A.7.10.1 79.8 0 1 724 0.9439 7.5417 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
HBOCFJMJ_00089 3.A.7.10.1 75.3 1.6e-188 1 401 0.8852 4.1771 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
HBOCFJMJ_00096 1.E.53.1.10 95.2 3.7e-17 9 50 0.8400 0.9767 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
HBOCFJMJ_00112 3.A.7.10.1 76.5 1.3e-139 1 324 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
HBOCFJMJ_00114 3.A.7.10.1 73.3 1.9e-40 1 116 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
HBOCFJMJ_00117 3.A.7.10.1 78.7 2.7e-176 4 379 0.9843 3.9167 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
HBOCFJMJ_00118 3.A.7.10.1 78.6 7.8e-125 1 271 0.9748 2.8021 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