Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C92
  Reference Plasmid   CP052009.1
  Reference Plasmid Size   43963
  Reference Plasmid GC Content   0.29
  Reference Plasmid Mobility Type   mobilizable





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
M0059306 LGLOEKLK_00039 30417 5 Skin 0.12 protein_coding synonymous_variant LOW 855C>T Phe285Phe
M0059307 LGLOEKLK_00039 30801 4 Skin 0.10 protein_coding synonymous_variant LOW 471T>C His157His
M0059308 LGLOEKLK_00039 31191 5 Skin 0.12 protein_coding synonymous_variant LOW 81C>T Tyr27Tyr
M0059309 LGLOEKLK_00039 31201 5 Skin 0.12 protein_coding missense_variant MODERATE 71G>A Gly24Asp
M0059310 LGLOEKLK_00038 31628 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -1922A>G None
M0059311 LGLOEKLK_00049 39338 6 Skin 0.15 protein_coding missense_variant MODERATE 314A>G Lys105Arg
M0059312 LGLOEKLK_00049 39381 7 Skin 0.17 protein_coding missense_variant MODERATE 271A>G Lys91Glu
M0059313 LGLOEKLK_00049 39400 7 Skin 0.17 protein_coding missense_variant MODERATE 252T>G Asp84Glu
M0059314 LGLOEKLK_00049 39448 7 Skin 0.17 protein_coding missense_variant MODERATE 204A>G Ile68Met
M0059315 LGLOEKLK_00049 39511 5 Skin 0.12 protein_coding synonymous_variant LOW 141C>T Ile47Ile
M0059316 LGLOEKLK_00047 39654 6 Skin 0.15 protein_coding upstream_gene_variant MODIFIER -1763T>C None
M0059317 LGLOEKLK_00047 39660 7 Skin 0.17 protein_coding upstream_gene_variant MODIFIER -1769C>T None
M0059318 LGLOEKLK_00050 39703 7 Skin 0.17 protein_coding synonymous_variant LOW 585T>C Asp195Asp
M0059319 LGLOEKLK_00050 39804 7 Skin 0.17 protein_coding missense_variant MODERATE 484T>G Ser162Ala
M0059320 LGLOEKLK_00050 39858 7 Skin 0.17 protein_coding synonymous_variant LOW 430C>T Leu144Leu
M0059321 LGLOEKLK_00050 40036 4 Skin 0.10 protein_coding synonymous_variant LOW 252A>G Val84Val
M0059322 LGLOEKLK_00050 40143 5 Skin 0.12 protein_coding missense_variant MODERATE 145G>A Ala49Thr
M0059323 LGLOEKLK_00050 40186 4 Skin 0.10 protein_coding synonymous_variant LOW 102A>G Lys34Lys
M0059324 LGLOEKLK_00050 40189 5 Skin 0.12 protein_coding synonymous_variant LOW 99G>A Lys33Lys
M0059325 LGLOEKLK_00050 40202 4 Skin 0.10 protein_coding missense_variant MODERATE 86G>A Arg29Lys
M0059326 LGLOEKLK_00050 40219 4 Skin 0.10 protein_coding synonymous_variant LOW 69A>G Leu23Leu
M0059327 LGLOEKLK_00047 40319 4 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -2428C>T None
M0059328 LGLOEKLK_00006 5815 3 Skin 0.07 protein_coding synonymous_variant LOW 286T>C Leu96Leu
M0059329 LGLOEKLK_00039 30564 3 Skin 0.07 protein_coding synonymous_variant LOW 708C>T Asn236Asn
M0059330 LGLOEKLK_00050 39712 4 Skin 0.10 protein_coding synonymous_variant LOW 576T>A Ile192Ile
M0059331 LGLOEKLK_00050 39763 4 Skin 0.10 protein_coding synonymous_variant LOW 525T>C Ser175Ser
M0059332 LGLOEKLK_00050 39865 3 Skin 0.07 protein_coding missense_variant MODERATE 423A>C Leu141Phe
M0059333 LGLOEKLK_00039 30668 3 Skin 0.07 protein_coding missense_variant MODERATE 604C>A Gln202Lys
M0059334 LGLOEKLK_00039 30846 4 Skin 0.10 protein_coding missense_variant MODERATE 426A>T Lys142Asn
M0059335 LGLOEKLK_00039 30995 5 Skin 0.12 protein_coding missense_variant MODERATE 277C>A Leu93Ile
M0059336 LGLOEKLK_00050 40255 3 Skin 0.07 protein_coding synonymous_variant LOW 33T>G Leu11Leu
M0059337 LGLOEKLK_00047 40324 3 Skin 0.07 protein_coding upstream_gene_variant MODIFIER -2433T>C 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







        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
LGLOEKLK_00050 Cadmium (Cd), Zinc (Zn) 93.2 6.5e-101 1 205 1.0000 1.0000 experiment
JEAHIGJD_00050 Cadmium (Cd), Zinc (Zn) 93.2 6.5e-101 1 205 1.0000 1.0000 experiment
HNIKLEBO_00050 Cadmium (Cd), Zinc (Zn) 93.2 6.5e-101 1 205 1.0000 1.0000 experiment
LGLOEKLK_00050 Cadmium (Cd), Zinc (Zn) 100 1e-102 1 205 1.0000 1.0000 prediction
JEAHIGJD_00050 Cadmium (Cd), Zinc (Zn) 100 1e-102 1 205 1.0000 1.0000 prediction
HNIKLEBO_00050 Cadmium (Cd), Zinc (Zn) 100 1e-102 1 205 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
LGLOEKLK_00020 ARO:3008823 97.9 1.23e-192 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
LGLOEKLK_00026 ARO:3007069 99.3 1.11e-105 1 140 1.0000 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase antibiotic inactivation
LGLOEKLK_00038 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
LGLOEKLK_00039 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
LGLOEKLK_00052 ARO:3002623 99.2 2.96e-189 4 256 0.9883 1.0000 aminoglycoside antibiotic ANT(4') antibiotic inactivation
JEAHIGJD_00020 ARO:3008823 97.9 1.23e-192 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
JEAHIGJD_00026 ARO:3007069 99.3 1.11e-105 1 140 1.0000 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase antibiotic inactivation
JEAHIGJD_00038 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JEAHIGJD_00039 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
JEAHIGJD_00052 ARO:3002623 99.2 2.96e-189 4 256 0.9883 1.0000 aminoglycoside antibiotic ANT(4') antibiotic inactivation
HNIKLEBO_00020 ARO:3008823 97.9 1.23e-192 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
HNIKLEBO_00026 ARO:3007069 99.3 1.11e-105 1 140 1.0000 1.0000 phosphonic acid antibiotic fosfomycin thiol transferase antibiotic inactivation
HNIKLEBO_00038 ARO:3000319 98.7 1.82e-228 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
HNIKLEBO_00039 ARO:3000251 95.7 2.0997789948253e-320 1 488 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
HNIKLEBO_00052 ARO:3002623 99.2 2.96e-189 4 256 0.9883 1.0000 aminoglycoside antibiotic ANT(4') 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






        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





        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
LGLOEKLK_00039 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
LGLOEKLK_00050 2.A.77.1.1 92.7 5.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
JEAHIGJD_00039 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JEAHIGJD_00050 2.A.77.1.1 92.7 5.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family
HNIKLEBO_00039 3.A.1.121.1 98.8 5.7e-272 1 488 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
HNIKLEBO_00050 2.A.77.1.1 92.7 5.4e-99 1 205 1.0000 0.9809 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.77 The Cadmium Resistance (CadD) Family