Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C333
  Reference Plasmid   NC_018995.1
  Reference Plasmid Size   91942
  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
M0153216 LFMOKLIM_00048 45277 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3214A>T None
M0153217 LFMOKLIM_00048 45755 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3692T>A None
M0153218 LFMOKLIM_00048 45756 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3693T>G None
M0153219 LFMOKLIM_00053 46603 9 Gut 0.33 protein_coding synonymous_variant LOW 42C>T Ala14Ala
M0153220 LFMOKLIM_00053 46630 9 Gut 0.33 protein_coding synonymous_variant LOW 15A>C Ile5Ile
M0153221 LFMOKLIM_00054 47064 9 Gut 0.33 protein_coding synonymous_variant LOW 318T>C Val106Val
M0153222 LFMOKLIM_00054 47168 9 Gut 0.33 protein_coding missense_variant MODERATE 422C>T Ala141Val
M0153223 LFMOKLIM_00057 48179 9 Gut 0.33 protein_coding missense_variant MODERATE 34A>G Thr12Ala
M0153224 LFMOKLIM_00050 48759 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4287A>G None
M0153225 LFMOKLIM_00050 49072 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4600C>T None
M0153226 LFMOKLIM_00050 49321 9 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -4849T>A None
M0153227 LFMOKLIM_00060 49507 9 Gut 0.33 protein_coding missense_variant MODERATE 1445G>A Arg482Gln
M0153228 LFMOKLIM_00044 36496 5 Gut 0.19 protein_coding synonymous_variant LOW 396G>T Ala132Ala
M0153229 LFMOKLIM_00043 35732 3 Gut 0.11 protein_coding synonymous_variant LOW 372G>A Glu124Glu






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
LFMOKLIM_00041 ARO:3002660 99.6 5.98e-177 15 257 0.9455 0.8741 aminoglycoside antibiotic APH(6) antibiotic inactivation
LFMOKLIM_00044 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
LFMOKLIM_00045 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
LFMOKLIM_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
LFMOKLIM_00085 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
LFMOKLIM_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
LFMOKLIM_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
LFMOKLIM_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
LFMOKLIM_00073 3.A.7.10.1 74.3 1.2e-137 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
LFMOKLIM_00075 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
LFMOKLIM_00078 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
LFMOKLIM_00079 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