Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1397
  Reference Plasmid   NZ_OK236218.1
  Reference Plasmid Size   150191
  Reference Plasmid GC Content   0.51
  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
M0208891 LJAGLEHJ_00073 71423 3 Gut 0.11 protein_coding missense_variant MODERATE 199A>G Lys67Glu
M0208892 LJAGLEHJ_00073 71462 3 Gut 0.11 protein_coding missense_variant MODERATE 238C>T His80Tyr
M0208893 LJAGLEHJ_00073 71690 3 Gut 0.11 protein_coding missense_variant MODERATE 466A>T Ile156Phe
M0208894 LJAGLEHJ_00073 71694 3 Gut 0.11 protein_coding missense_variant MODERATE 470C>T Ser157Leu
M0208895 LJAGLEHJ_00073 71705 3 Gut 0.11 protein_coding missense_variant MODERATE 481T>G Phe161Val
M0208896 LJAGLEHJ_00073 71706 3 Gut 0.11 protein_coding missense_variant MODERATE 482T>C Phe161Ser
M0208897 LJAGLEHJ_00073 71727 3 Gut 0.11 protein_coding missense_variant MODERATE 503C>T Ala168Val
M0208898 LJAGLEHJ_00104 100362 3 Gut 0.11 protein_coding synonymous_variant LOW 5169T>C Val1723Val






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
LJAGLEHJ_00013 VFG034679 Ibes 71.9 4.8e-183 102 560 0.8167 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
LJAGLEHJ_00013 VFG034652 Ibes 71.9 9.5e-183 102 560 0.8167 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC 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
LJAGLEHJ_00010 Silver (Ag) 92.3 1.4e-70 1 143 1.0000 1.0000 experiment
LJAGLEHJ_00011 Silver (Ag) 92.9 4.2e-255 1 491 1.0081 0.9960 experiment
LJAGLEHJ_00012 Silver (Ag) 92.6 3.5e-93 1 186 1.0108 0.8246 experiment
LJAGLEHJ_00013 Silver (Ag) 99.3 1.6e-255 102 562 0.8203 1.0000 experiment
LJAGLEHJ_00014 Silver (Ag) 96.7 2e-46 28 117 0.7692 0.9375 experiment
LJAGLEHJ_00015 Silver (Ag) 96.7 3.3e-240 1 430 1.0000 1.0000 experiment
LJAGLEHJ_00016 Silver (Ag) 98.5 0 1 1048 1.0000 1.0000 experiment
LJAGLEHJ_00018 Silver (Ag) 94 0 1 815 1.0012 0.9903 experiment
LJAGLEHJ_00039 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 93.6 4.2e-54 1 110 1.0000 1.0000 experiment
LJAGLEHJ_00051 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 100 4.7e-217 1 391 1.0000 1.0000 experiment
LJAGLEHJ_00052 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 100 0 1 1050 1.0000 1.0000 experiment
LJAGLEHJ_00010 Silver (Ag) 100 8e-75 1 143 1.0000 1.0000 prediction
LJAGLEHJ_00011 Silver (Ag) 100 1.4e-275 1 491 1.0000 1.0000 prediction
LJAGLEHJ_00012 Silver (Ag) 100 8.5e-101 1 186 1.0000 0.8230 prediction
LJAGLEHJ_00013 Silver (Ag) 98.2 1.7e-309 1 562 1.0000 1.0000 prediction
LJAGLEHJ_00014 Silver (Ag) 99.1 2.7e-60 1 117 1.0000 1.0000 prediction
LJAGLEHJ_00015 Silver (Ag) 100 4.2e-244 1 430 1.0000 1.0000 prediction
LJAGLEHJ_00016 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
LJAGLEHJ_00018 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
LJAGLEHJ_00039 Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)] 100 1.7e-53 1 110 1.0000 1.0000 prediction
LJAGLEHJ_00051 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 100 1.1e-214 1 391 1.0000 1.0000 prediction
LJAGLEHJ_00052 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Clorine Dioxide (ClO2) [class: Halogens], Triclosan [class: Phenolic compounds], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Chlorhexidine [class: Biguanides], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Acriflavine [class: Acridine] 100 0 1 1050 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
LJAGLEHJ_00023 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
LJAGLEHJ_00024 ARO:3002605 99.6 3.17e-190 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LJAGLEHJ_00028 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LJAGLEHJ_00029 ARO:3002858 100 4.78e-119 1 165 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
LJAGLEHJ_00037 ARO:3000413 100 3.83e-187 1 263 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
LJAGLEHJ_00039 ARO:3005098 93.6 1.69e-70 1 110 1.0000 1.0000 disinfecting agents and antiseptics small multidrug resistance (SMR) antibiotic efflux pump antibiotic efflux
LJAGLEHJ_00040 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
LJAGLEHJ_00048 ARO:3004623 100 4.76e-213 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
LJAGLEHJ_00051 ARO:3003922 100 2.28e-273 1 391 1.0000 1.0000 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
LJAGLEHJ_00052 ARO:3003923 100 0 1 1050 1.0000 1.0000 fluoroquinolone antibiotic resistance-nodulation-cell division (RND) antibiotic efflux pump antibiotic efflux
LJAGLEHJ_00057 ARO:3002705 99.3 4.61e-275 1 404 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
LJAGLEHJ_00062 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM 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
LJAGLEHJ_00022 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
LJAGLEHJ_00030 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
LJAGLEHJ_00043 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
LJAGLEHJ_00051 PHI:6448 oqxA 99.7 3e-215 1 391 1.0000 1.0000 nematodes pneumonia RND family efflux transporter reduced virulence
LJAGLEHJ_00052 PHI:6449 oqxB 99.7 0 1 1050 1.0000 1.0000 nematodes pneumonia multidrug efflux pump reduced virulence






        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
LJAGLEHJ_00135 QAZ75040.1|GH23 100 4.96e-124 1 169 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
LJAGLEHJ_00013 1.B.17.3.4 99.3 6.2e-254 102 562 0.8203 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
LJAGLEHJ_00016 2.A.6.1.3 98.5 0 1 1048 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
LJAGLEHJ_00018 3.A.3.5.4 94 0 1 815 1.0000 0.9879 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.3 The P-type ATPase (P-ATPase) Superfamily
LJAGLEHJ_00052 2.A.6.2.47 99.7 0 1 1050 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.6 The Resistance-Nodulation-Cell Division (RND) Superfamily
LJAGLEHJ_00057 2.A.1.2.110 98.3 5.9e-214 1 404 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
LJAGLEHJ_00100 1.E.53.1.11 98.5 1.1e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family