Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C147
  Reference Plasmid   CP088697.1
  Reference Plasmid Size   150404
  Reference Plasmid GC Content   0.52
  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
M0145426 JDBEOEKE_00071 64120 3 Gut 0.75 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0145427 JDBEOEKE_00072 64274 3 Gut 0.75 protein_coding missense_variant MODERATE 481A>T Arg161Trp
M0145428 JDBEOEKE_00072 64633 3 Gut 0.75 protein_coding missense_variant MODERATE 122A>G Asn41Ser
M0145429 JDBEOEKE_00073 64858 3 Gut 0.75 protein_coding missense_variant MODERATE 154A>G Thr52Ala
M0145430 JDBEOEKE_00073 64938 3 Gut 0.75 protein_coding missense_variant MODERATE 74A>G Tyr25Cys
M0145431 JDBEOEKE_00068 65016 3 Gut 0.75 protein_coding upstream_gene_variant MODIFIER -4138A>G None
M0145432 JDBEOEKE_00074 65257 3 Gut 0.75 protein_coding missense_variant MODERATE 148T>C Trp50Arg
M0145433 JDBEOEKE_00074 65376 3 Gut 0.75 protein_coding synonymous_variant LOW 267T>C Ile89Ile
M0145434 JDBEOEKE_00074 65415 3 Gut 0.75 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0145435 JDBEOEKE_00075 65577 3 Gut 0.75 protein_coding missense_variant MODERATE 145A>G Asn49Asp






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
JDBEOEKE_00144 VFG000940 Aerobactin 94.8 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD experiment
JDBEOEKE_00145 VFG000939 Aerobactin 96.2 1.7e-190 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB experiment
JDBEOEKE_00146 VFG000938 Aerobactin 97.4 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC experiment
JDBEOEKE_00147 VFG000937 Aerobactin 97.9 1.3e-252 1 425 1.0 0.9551 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD experiment
JDBEOEKE_00148 VFG048621 Aerobactin 99.7 0 1 733 1.0 1 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
JDBEOEKE_00159 VFG000942 Dr adhesins 100 2.8e-57 1 101 1.0 1 Adherence cytoplamic protein DraA experiment
JDBEOEKE_00160 VFG000943 Dr adhesins 100 1.8e-135 1 239 0.9019 0.9676 Adherence chaperone protein DraB experiment
JDBEOEKE_00161 VFG000944 Dr adhesins 98.7 0 1 860 1.0 1.0012 Adherence usher protein DraC experiment
JDBEOEKE_00162 VFG000945 Dr adhesins 100 5.6e-83 1 147 1.0 1 Adherence DraD, periplasmic protein experiment
JDBEOEKE_00163 VFG000946 Dr adhesins 100 1.1e-29 1 57 1.0 1 Adherence DraP experiment
JDBEOEKE_00124 VFG012575 Iron/manganese transport 99.7 2.2e-173 1 304 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter substrate-binding protein SitA prediction
JDBEOEKE_00125 VFG034214 Iron/manganese transport 100 5.5e-152 1 275 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter ATP-binding protein SitB prediction
JDBEOEKE_00126 VFG012585 Iron/manganese transport 100 1.4e-153 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitC prediction
JDBEOEKE_00127 VFG012590 Iron/manganese transport 100 3.8e-148 1 285 1.0 1 Nutritional/Metabolic factor iron/manganese ABC transporter permease subunit SitD prediction
JDBEOEKE_00144 VFG012526 Aerobactin 99.8 0 1 574 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucD prediction
JDBEOEKE_00145 VFG033993 Aerobactin 99.7 3.2e-196 1 315 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucB prediction
JDBEOEKE_00146 VFG012522 Aerobactin 99.8 0 1 580 1.0 1 Nutritional/Metabolic factor aerobactin siderophore biosynthesis protein IucC prediction
JDBEOEKE_00147 VFG033958 Aerobactin 100 3.7e-256 1 425 1.0 1 Nutritional/Metabolic factor L-lysine 6-monooxygenase IucD prediction
JDBEOEKE_00148 VFG033944 Aerobactin 100 0 1 733 1.0 1 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA prediction
JDBEOEKE_00157 VFG042429 Afa/Dr family 100 5e-43 1 85 1.0 1 Adherence AfaF-III prediction
JDBEOEKE_00159 VFG000942 Dr adhesins 100 2.1e-56 1 101 1.0 1 Adherence cytoplamic protein DraA prediction
JDBEOEKE_00160 VFG046077 Afimbrial adhesin AFA-I 99.2 3.2e-149 1 265 1.0 1 Adherence Dr fimbrial biogenesis chaperone DraB prediction
JDBEOEKE_00161 VFG042425 Dr adhesins 99.5 0 1 860 1.0 1 Adherence usher AfaC prediction
JDBEOEKE_00162 VFG000945 Dr adhesins 100 4.2e-82 1 147 1.0 1 Adherence DraD, periplasmic protein prediction
JDBEOEKE_00163 VFG000946 Dr adhesins 100 8e-29 1 57 1.0 1 Adherence DraP 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
JDBEOEKE_00021 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
JDBEOEKE_00124 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 75.8 1.5e-133 8 304 0.9770 0.9738 experiment
JDBEOEKE_00125 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 77.7 3.7e-115 2 266 0.9636 0.9707 experiment
JDBEOEKE_00126 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87 9e-133 1 277 0.9719 0.9685 experiment
JDBEOEKE_00124 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 76.4 5.2e-132 8 304 0.9770 0.9738 prediction
JDBEOEKE_00125 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 81.1 2.3e-118 2 266 0.9636 0.9707 prediction
JDBEOEKE_00126 Manganese (Mn), Iron (Fe), Hydrogen Peroxide (H2O2) [class: Peroxides] 87.8 3.4e-133 1 279 0.9789 0.9789 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
JDBEOEKE_00019 ARO:3002858 100 4.78e-119 1 165 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
JDBEOEKE_00020 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
JDBEOEKE_00021 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
JDBEOEKE_00022 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JDBEOEKE_00027 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JDBEOEKE_00028 ARO:3000316 100 1.13e-217 1 301 0.9901 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JDBEOEKE_00031 ARO:3000375 98 7.97e-174 1 245 1.0000 0.9879 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
JDBEOEKE_00037 ARO:3004623 100 4.76e-213 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
JDBEOEKE_00041 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
JDBEOEKE_00018 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
JDBEOEKE_00124 PHI:10082 STM14_RS15345 75.8 2.5e-132 8 304 0.9770 0.9705 eudicots infection manganese/iron ABC transporter ATP-binding protein unaffected pathogenicity
JDBEOEKE_00125 PHI:10083 STM14_RS15350 77.7 6.1e-114 2 266 0.9636 0.9707 eudicots infection iron ABC transporter permease unaffected pathogenicity
JDBEOEKE_00126 PHI:10084 STM14_RS15355 87 1.5e-131 1 277 0.9719 0.9685 eudicots infection iron ABC transporter permease unaffected pathogenicity
JDBEOEKE_00144 PHI:124067 iucA (PAGR_g3927) 78.5 7.4e-271 1 573 0.9983 0.9598 monocots None aerobactin siderophores unaffected pathogenicity
JDBEOEKE_00145 PHI:124068 iucB (PAGR_g3926) 80 1.2e-158 1 315 1.0000 1.0000 monocots None aerobactin siderophores unaffected pathogenicity
JDBEOEKE_00146 PHI:124069 iucC (PAGR_g3925) 83.7 2e-300 1 577 0.9948 0.9983 monocots None aerobactin siderophores unaffected pathogenicity
JDBEOEKE_00147 PHI:3610 iucD 100 1.3e-256 1 425 1.0000 1.0000 birds colibacillosis aerobactin reduced virulence
JDBEOEKE_00148 PHI:6563 iucA 99.7 0 1 733 1.0000 1.0000 rodents pneumonia aerobactin 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
JDBEOEKE_00091 AXI38019.1|GH23 98.8 5.79e-123 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
JDBEOEKE_00008 2.A.108.2.10 100 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JDBEOEKE_00009 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
JDBEOEKE_00023 2.A.51.1.7 99.5 5.1e-210 1 376 0.9377 0.9666 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
JDBEOEKE_00124 3.A.1.15.7 75.8 5.5e-132 8 304 0.9770 0.9705 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JDBEOEKE_00125 3.A.1.15.7 77.7 1.4e-113 2 266 0.9636 0.8689 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JDBEOEKE_00126 3.A.1.15.7 87 3.4e-131 1 277 0.9719 0.9082 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily