Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C459
  Reference Plasmid   NZ_CP017930.1
  Reference Plasmid Size   114139
  Reference Plasmid GC Content   0.51
  Reference Plasmid Mobility Type   non-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
M0088719 JIKIAAMK_00079 72573 4 Skin 0.33 protein_coding missense_variant MODERATE 1263T>G Ile421Met






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
JIKIAAMK_00076 VFG000417 Pla 81.7 2.7e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor experiment
ADFLINNE_00076 VFG000417 Pla 81.7 2.7e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor experiment
JIKIAAMK_00076 VFG003087 Pla 82.1 5.3e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor prediction
ADFLINNE_00076 VFG003087 Pla 82.1 5.3e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor 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
JIKIAAMK_00021 Copper (Cu) 98 1.1e-249 1 448 1.0000 0.9614 experiment
JIKIAAMK_00022 Copper (Cu), Silver (Ag) 91.7 3.7e-66 1 144 1.0000 1.0000 experiment
JIKIAAMK_00023 Nickel (Ni) 74.1 2.4e-162 1 369 1.0081 0.9947 experiment
JIKIAAMK_00024 Cobalt (Co), Nickel (Ni), Iron (Fe) 92.2 8.7e-42 1 90 1.0000 1.0000 experiment
JIKIAAMK_00041 Arsenic (As), Antimony (Sb) 90 2.4e-70 1 140 0.9929 0.9929 experiment
JIKIAAMK_00042 Arsenic (As), Antimony (Sb) 86.5 9.8e-208 1 429 1.0000 1.0000 experiment
JIKIAAMK_00043 Arsenic (As) 84.3 1.2e-42 1 89 0.8396 0.7607 experiment
JIKIAAMK_00044 Arsenic (As) 83.8 2e-114 1 234 1.0000 1.0086 experiment
ADFLINNE_00021 Copper (Cu) 98 1.1e-249 1 448 1.0000 0.9614 experiment
ADFLINNE_00022 Copper (Cu), Silver (Ag) 91.7 3.7e-66 1 144 1.0000 1.0000 experiment
ADFLINNE_00023 Nickel (Ni) 74.1 2.4e-162 1 369 1.0081 0.9947 experiment
ADFLINNE_00024 Cobalt (Co), Nickel (Ni), Iron (Fe) 92.2 8.7e-42 1 90 1.0000 1.0000 experiment
ADFLINNE_00041 Arsenic (As), Antimony (Sb) 90 2.4e-70 1 140 0.9929 0.9929 experiment
ADFLINNE_00042 Arsenic (As), Antimony (Sb) 86.5 9.8e-208 1 429 1.0000 1.0000 experiment
ADFLINNE_00043 Arsenic (As) 84.3 1.2e-42 1 89 0.8396 0.7607 experiment
ADFLINNE_00044 Arsenic (As) 83.8 2e-114 1 234 1.0000 1.0086 experiment
JIKIAAMK_00021 Copper (Cu) 100 5.1e-253 1 448 1.0000 1.0000 prediction
JIKIAAMK_00022 Copper (Cu), Silver (Ag) 100 1.3e-69 1 144 1.0000 1.0000 prediction
JIKIAAMK_00023 Nickel (Ni) 74.5 1.5e-160 1 370 1.0135 0.9973 prediction
JIKIAAMK_00024 Cobalt (Co), Nickel (Ni), Iron (Fe) 100 1.1e-42 1 90 1.0000 1.0000 prediction
JIKIAAMK_00041 Arsenic (As) 100 9.3e-76 1 141 1.0000 1.0000 prediction
JIKIAAMK_00042 Arsenic (As), Antimony (Sb) 86.9 1.2e-206 1 429 1.0000 1.0000 prediction
JIKIAAMK_00043 Arsenic (As) 100 2.1e-56 1 106 1.0000 1.0000 prediction
JIKIAAMK_00044 Arsenic (As) 100 2.3e-119 27 234 0.8889 1.0000 prediction
ADFLINNE_00021 Copper (Cu) 100 5.1e-253 1 448 1.0000 1.0000 prediction
ADFLINNE_00022 Copper (Cu), Silver (Ag) 100 1.3e-69 1 144 1.0000 1.0000 prediction
ADFLINNE_00023 Nickel (Ni) 74.5 1.5e-160 1 370 1.0135 0.9973 prediction
ADFLINNE_00024 Cobalt (Co), Nickel (Ni), Iron (Fe) 100 1.1e-42 1 90 1.0000 1.0000 prediction
ADFLINNE_00041 Arsenic (As) 100 9.3e-76 1 141 1.0000 1.0000 prediction
ADFLINNE_00042 Arsenic (As), Antimony (Sb) 86.9 1.2e-206 1 429 1.0000 1.0000 prediction
ADFLINNE_00043 Arsenic (As) 100 2.1e-56 1 106 1.0000 1.0000 prediction
ADFLINNE_00044 Arsenic (As) 100 2.3e-119 27 234 0.8889 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
JIKIAAMK_00001 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JIKIAAMK_00005 ARO:3002735 99.5 2.28e-107 1 214 1.0000 0.9469 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
JIKIAAMK_00007 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JIKIAAMK_00010 ARO:3003015 99.5 1.01e-134 1 189 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
JIKIAAMK_00013 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
JIKIAAMK_00014 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
JIKIAAMK_00019 ARO:3004684 100 0 1 539 1.0000 1.0000 peptide antibiotic MCR phosphoethanolamine transferase antibiotic target alteration
JIKIAAMK_00050 ARO:3002641 99.1 1.68e-167 1 220 1.0000 0.8118 aminoglycoside antibiotic APH(3') antibiotic inactivation
JIKIAAMK_00129 ARO:3002603 98.5 1.45e-185 39 301 0.8738 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
ADFLINNE_00001 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
ADFLINNE_00005 ARO:3002735 99.5 2.28e-107 1 214 1.0000 0.9469 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
ADFLINNE_00007 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
ADFLINNE_00010 ARO:3003015 99.5 1.01e-134 1 189 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
ADFLINNE_00013 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
ADFLINNE_00014 ARO:3002660 99.6 1.07e-205 1 278 1.0000 1.0000 aminoglycoside antibiotic APH(6) antibiotic inactivation
ADFLINNE_00019 ARO:3004684 100 0 1 539 1.0000 1.0000 peptide antibiotic MCR phosphoethanolamine transferase antibiotic target alteration
ADFLINNE_00050 ARO:3002641 99.1 1.68e-167 1 220 1.0000 0.8118 aminoglycoside antibiotic APH(3') antibiotic inactivation
ADFLINNE_00129 ARO:3002603 98.5 1.45e-185 39 301 0.8738 1.0000 aminoglycoside antibiotic ANT(3'') 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
JIKIAAMK_00012 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
JIKIAAMK_00128 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
ADFLINNE_00012 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
ADFLINNE_00128 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase 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





        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
JIKIAAMK_00023 2.A.113.1.2 74.1 9e-161 1 369 0.9946 0.9947 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.113 The Nickel/cobalt Transporter (NicO) Family
JIKIAAMK_00039 2.A.53.3.1 99.8 1.2e-269 1 492 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
JIKIAAMK_00042 3.A.4.1.1 86.5 8.2e-206 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
JIKIAAMK_00076 9.B.50.1.4 82.1 4.2e-151 1 311 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family
ADFLINNE_00023 2.A.113.1.2 74.1 9e-161 1 369 0.9946 0.9947 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.113 The Nickel/cobalt Transporter (NicO) Family
ADFLINNE_00039 2.A.53.3.1 99.8 1.2e-269 1 492 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.53 The Sulfate Permease (SulP) Family
ADFLINNE_00042 3.A.4.1.1 86.5 8.2e-206 1 429 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
ADFLINNE_00076 9.B.50.1.4 82.1 4.2e-151 1 311 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.50 The Outer Membrane Beta-barrel Endoprotease, Omptin (Omptin) Family