Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C242
  Reference Plasmid   LR213460.1
  Reference Plasmid Size   91948
  Reference Plasmid GC Content   0.53
  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
M0149556 MCJOFBCH_00019 14345 4 Gut 0.16 protein_coding synonymous_variant LOW 24C>T Ile8Ile
M0149557 MCJOFBCH_00021 15187 3 Gut 0.12 protein_coding synonymous_variant LOW 459C>T Pro153Pro
M0149558 MCJOFBCH_00021 15380 4 Gut 0.16 protein_coding missense_variant MODERATE 266G>A Arg89Lys
M0149559 MCJOFBCH_00021 15392 3 Gut 0.12 protein_coding missense_variant MODERATE 254C>T Ala85Val
M0149560 MCJOFBCH_00021 15395 3 Gut 0.12 protein_coding missense_variant MODERATE 251G>T Gly84Val
M0149561 MCJOFBCH_00018 14101 3 Gut 0.12 protein_coding synonymous_variant LOW 252C>T Ser84Ser
M0149562 MCJOFBCH_00020 14893 3 Gut 0.12 protein_coding synonymous_variant LOW 153G>C Leu51Leu






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







        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
MCJOFBCH_00041 ARO:3002660 99.6 5.98e-177 15 257 0.9455 0.8741 aminoglycoside antibiotic APH(6) antibiotic inactivation
MCJOFBCH_00044 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
MCJOFBCH_00045 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
MCJOFBCH_00046 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement






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






        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
MCJOFBCH_00086 SPE00673.1|GH23 100 1.33e-115 1 161 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
MCJOFBCH_00048 3.A.7.10.1 79.6 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
MCJOFBCH_00050 3.A.7.10.1 76.1 1.1e-189 1 401 0.9218 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
MCJOFBCH_00059 1.E.53.1.10 100 2e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
MCJOFBCH_00063 9.B.40.1.2 70.1 3.4e-289 1 720 0.9986 0.9678 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
MCJOFBCH_00074 3.A.7.10.1 74.6 4.2e-138 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
MCJOFBCH_00076 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
MCJOFBCH_00079 3.A.7.10.1 77.8 1.7e-175 1 379 0.9921 3.9479 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
MCJOFBCH_00080 3.A.7.10.1 77.9 6.6e-124 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