Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1336
  Reference Plasmid   NZ_KU997026.1
  Reference Plasmid Size   217306
  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
M0206809 IGFFADPJ_00169 138020 3 Gut 1.00 protein_coding missense_variant MODERATE 37G>A Asp13Asn






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
IGFFADPJ_00141 Mercury (Hg) 88.7 5.5e-73 1 151 1.0000 1.0000 experiment
IGFFADPJ_00142 Mercury (Hg) 99.1 6e-62 7 121 0.9504 0.9914 experiment
IGFFADPJ_00143 Mercury (Hg) 85.7 4.5e-38 1 91 1.0000 1.0000 experiment
IGFFADPJ_00144 Mercury (Hg) 80.1 1.6e-61 1 141 1.0000 1.0000 experiment
IGFFADPJ_00145 Mercury (Hg) 92.5 2.9e-292 1 561 1.0000 1.0000 experiment
IGFFADPJ_00146 Mercury (Hg) 90.1 1.6e-54 1 121 1.0000 1.0000 experiment
IGFFADPJ_00147 Mercury (Hg) 96.2 2.7e-39 1 78 1.0000 1.0000 experiment
IGFFADPJ_00153 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
IGFFADPJ_00160 Nickel (Ni), Cobalt (Co) 79.2 2.6e-115 1 255 1.0000 1.0000 experiment
IGFFADPJ_00161 Nickel (Ni), Cobalt (Co) 91.5 4.3e-160 1 318 1.0000 1.0000 experiment
IGFFADPJ_00188 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
IGFFADPJ_00192 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
IGFFADPJ_00207 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
IGFFADPJ_00215 Mercury (Hg) 97.4 1.1e-40 1 78 1.0000 1.0000 experiment
IGFFADPJ_00216 Mercury (Hg) 99.2 1.2e-62 1 121 1.0000 1.0000 experiment
IGFFADPJ_00217 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 5e-120 1 212 1.0000 1.0000 experiment
IGFFADPJ_00222 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 96.6 4.8e-190 1 351 0.9145 0.7674 experiment
IGFFADPJ_00223 Mercury (Hg) 100 2.7e-43 1 91 1.0000 1.0000 experiment
IGFFADPJ_00224 Mercury (Hg) 100 2.3e-63 1 116 1.0000 1.0000 experiment
IGFFADPJ_00225 Mercury (Hg) 100 1.7e-79 1 144 1.0000 1.0000 experiment
IGFFADPJ_00141 Mercury (Hg) 99.3 7.9e-81 1 151 1.0000 1.0000 prediction
IGFFADPJ_00142 Mercury (Hg) 100 1.2e-63 1 121 1.0000 1.0000 prediction
IGFFADPJ_00143 Mercury (Hg) 94.5 9.1e-40 1 91 1.0000 1.0000 prediction
IGFFADPJ_00144 Mercury (Hg) 80.9 3.2e-60 1 141 1.0000 1.0000 prediction
IGFFADPJ_00145 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 561 1.0000 1.0000 prediction
IGFFADPJ_00146 Mercury (Hg) 100 3.1e-59 1 121 1.0000 1.0000 prediction
IGFFADPJ_00147 Mercury (Hg) 98.7 5.1e-39 1 78 1.0000 1.0000 prediction
IGFFADPJ_00160 Nickel (Ni), Cobalt (Co) 99.6 8.8e-141 1 255 1.0000 1.0000 prediction
IGFFADPJ_00161 Nickel (Ni), Cobalt (Co) 100 1.4e-172 1 318 1.0000 1.0000 prediction
IGFFADPJ_00207 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 prediction
IGFFADPJ_00214 Mercury (Hg) 91.2 1.2e-177 1 329 1.0000 0.8044 prediction
IGFFADPJ_00215 Mercury (Hg) 100 2.3e-39 1 78 1.0000 1.0000 prediction
IGFFADPJ_00216 Mercury (Hg) 99.2 2.8e-60 1 121 1.0000 1.0000 prediction
IGFFADPJ_00217 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury], Methylmercury Acetate [class: Organo-mercury] 100 1.1e-117 1 212 1.0000 1.0000 prediction
IGFFADPJ_00223 Mercury (Hg) 100 6.3e-41 1 91 1.0000 1.0000 prediction
IGFFADPJ_00224 Mercury (Hg) 100 5.3e-61 1 116 1.0000 1.0000 prediction
IGFFADPJ_00225 Mercury (Hg) 100 3.9e-77 1 144 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
IGFFADPJ_00152 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
IGFFADPJ_00153 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
IGFFADPJ_00154 ARO:3003022 100 8.64e-56 1 78 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
IGFFADPJ_00187 ARO:3000230 100 5.4e-134 39 215 0.8233 1.0000 aminoglycoside antibiotic ANT(2'') antibiotic inactivation
IGFFADPJ_00188 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
IGFFADPJ_00189 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
IGFFADPJ_00191 ARO:3003011 100 1.82e-136 1 187 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
IGFFADPJ_00192 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
IGFFADPJ_00193 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
IGFFADPJ_00204 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
IGFFADPJ_00210 ARO:3002683 100 3.08e-171 1 219 1.0000 1.0000 phenicol antibiotic chloramphenicol acetyltransferase (CAT) antibiotic inactivation
IGFFADPJ_00220 ARO:3002641 98.5 6.49e-208 1 271 1.0000 1.0000 aminoglycoside antibiotic APH(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
IGFFADPJ_00087 PHI:11406 dsbC 100 3.2e-135 1 235 1.0000 1.0000 rodents pneumonia thiol:disulfide interchange protein reduced virulence
IGFFADPJ_00155 PHI:9804 int 100 3e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
IGFFADPJ_00160 PHI:8010 fecE 79.2 4.3e-114 1 255 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport ATP-binding protein reduced virulence
IGFFADPJ_00161 PHI:8009 fecD 91.5 7.2e-159 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
IGFFADPJ_00162 PHI:8008 fecC 96.7 4e-176 1 332 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
IGFFADPJ_00163 PHI:8007 fecB 95.7 2.3e-159 1 300 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate-binding periplasmic protein reduced virulence
IGFFADPJ_00164 PHI:8006 fecA 98.6 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
IGFFADPJ_00165 PHI:8005 fecR 98.1 7.7e-177 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
IGFFADPJ_00166 PHI:8004 fecI 96.5 3e-90 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
IGFFADPJ_00186 PHI:9804 int 100 3e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
IGFFADPJ_00230 PHI:11588 PPECC33_0249 (Rhs1) 99.9 0 1 1051 0.9813 0.7417 primates infection classic rearrangement hotspot protein 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
IGFFADPJ_00241 AIO10552.2|GH23 100 6.52e-238 9 346 0.9769 1
IGFFADPJ_00243 AIO10245.2|GH23 100 0 1 1204 1 1
IGFFADPJ_00246 QDC33125.1|GH23 100 5.28e-123 1 177 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
IGFFADPJ_00142 1.A.72.3.1 93 4.4e-56 7 121 0.9504 1.2637 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IGFFADPJ_00143 1.A.72.3.1 85.7 1.7e-36 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IGFFADPJ_00147 1.A.72.5.1 80.8 7.5e-33 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IGFFADPJ_00160 3.A.1.14.1 79.2 9.7e-114 1 255 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
IGFFADPJ_00161 3.A.1.14.1 91.5 1.6e-158 1 318 1.0000 1.2471 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
IGFFADPJ_00162 3.A.1.14.1 96.7 8.9e-176 1 332 1.0000 1.3020 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
IGFFADPJ_00163 3.A.1.14.1 95.7 5.2e-159 1 300 1.0000 1.1765 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
IGFFADPJ_00164 1.B.14.1.20 98.6 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
IGFFADPJ_00215 1.A.72.5.1 80.8 7.5e-33 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IGFFADPJ_00223 1.A.72.3.1 94.5 2.2e-39 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
IGFFADPJ_00224 1.A.72.3.1 93.1 2.2e-57 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily