Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1010
  Reference Plasmid   NZ_CP093272.1
  Reference Plasmid Size   200578
  Reference Plasmid GC Content   0.52
  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
M0191768 BFMJPFMF_00085 86551 3 Gut 0.27 protein_coding missense_variant MODERATE 63A>G Ile21Met






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
BFMJPFMF_00055 VFG034679 Ibes 71.5 4.4e-182 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
BFMJPFMF_00055 VFG034652 Ibes 71.5 8.6e-182 1 459 0.9957 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
BFMJPFMF_00016 Arsenic (As), Antimony (Sb), Bismuth (Bi) 100 8.1e-64 1 117 1.0000 1.0000 experiment
BFMJPFMF_00017 Arsenic (As), Antimony (Sb) 98.3 1.6e-67 1 120 1.0000 1.0000 experiment
BFMJPFMF_00018 Arsenic (As), Antimony (Sb) 98.3 0 1 583 1.0000 1.0000 experiment
BFMJPFMF_00019 Arsenic (As), Antimony (Sb) 99.1 5.7e-232 1 429 1.0000 1.0000 experiment
BFMJPFMF_00020 Arsenic (As), Antimony (Sb) 95.7 9.4e-75 1 141 1.0000 1.0000 experiment
BFMJPFMF_00040 Copper (Cu), Silver (Ag) 88.2 4.9e-63 1 144 1.0000 1.0000 experiment
BFMJPFMF_00041 Copper (Cu) 98.3 9.2e-260 1 466 1.0000 1.0000 experiment
BFMJPFMF_00042 Copper (Cu) 99.6 2.9e-126 1 226 1.0000 1.0000 experiment
BFMJPFMF_00043 Copper (Cu) 99.4 1.3e-164 1 309 1.0000 1.0000 experiment
BFMJPFMF_00044 Copper (Cu) 100 4.9e-67 1 126 1.0000 1.0000 experiment
BFMJPFMF_00045 Copper (Cu) 100 2e-175 3 298 0.9933 1.0000 experiment
BFMJPFMF_00046 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
BFMJPFMF_00050 Silver (Ag) 94.5 0 1 815 1.0012 0.9903 experiment
BFMJPFMF_00052 Silver (Ag) 98.9 0 1 1048 1.0000 1.0000 experiment
BFMJPFMF_00053 Silver (Ag) 97.9 2.1e-242 1 430 1.0000 1.0000 experiment
BFMJPFMF_00054 Silver (Ag) 98.9 3.1e-47 28 117 0.7692 0.9375 experiment
BFMJPFMF_00055 Silver (Ag) 98.9 1.5e-254 1 461 1.0000 1.0000 experiment
BFMJPFMF_00056 Silver (Ag) 93.4 9.3e-117 1 226 1.0088 1.0000 experiment
BFMJPFMF_00057 Silver (Ag) 92.9 4.2e-255 1 491 1.0081 0.9960 experiment
BFMJPFMF_00058 Silver (Ag) 92.3 1.8e-70 40 182 0.7857 1.0000 experiment
BFMJPFMF_00081 Nickel (Ni), Cobalt (Co) 91.2 7.3e-160 1 318 1.0000 1.0000 experiment
BFMJPFMF_00082 Nickel (Ni), Cobalt (Co) 79.2 2.6e-115 1 255 1.0000 1.0000 experiment
BFMJPFMF_00085 Arsenic (As), Antimony (Sb) 83.7 5.3e-70 1 141 1.0000 1.0000 experiment
BFMJPFMF_00086 Arsenic (As) 90.9 1.7e-213 27 455 0.9429 1.0000 experiment
BFMJPFMF_00087 Arsenic (As) 91 1.5e-45 1 89 0.8396 0.7607 experiment
BFMJPFMF_00088 Arsenic (As) 91.4 4.3e-125 1 232 1.0000 1.0000 experiment
BFMJPFMF_00016 Arsenic (As) 100 1.9e-61 1 117 1.0000 1.0000 prediction
BFMJPFMF_00017 Arsenic (As) 100 4.4e-66 1 120 1.0000 1.0000 prediction
BFMJPFMF_00018 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 prediction
BFMJPFMF_00019 Arsenic (As), Antimony (Sb) 100 1.8e-231 1 429 1.0000 1.0000 prediction
BFMJPFMF_00020 Arsenic (As) 100 1.2e-75 1 141 1.0000 1.0000 prediction
BFMJPFMF_00040 Copper (Cu), Silver (Ag) 97.9 3e-69 1 144 1.0000 1.0000 prediction
BFMJPFMF_00041 Copper (Cu) 100 2.8e-262 1 466 1.0000 1.0000 prediction
BFMJPFMF_00042 Copper (Cu) 100 3.9e-124 1 226 1.0000 1.0000 prediction
BFMJPFMF_00043 Copper (Cu) 100 7.6e-163 1 309 1.0000 1.0000 prediction
BFMJPFMF_00044 Copper (Cu) 100 1.1e-64 1 126 1.0000 1.0000 prediction
BFMJPFMF_00045 Copper (Cu) 100 4.1e-174 1 298 1.0000 0.9967 prediction
BFMJPFMF_00046 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
BFMJPFMF_00050 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
BFMJPFMF_00052 Silver (Ag) 100 0 1 1048 1.0000 0.9905 prediction
BFMJPFMF_00053 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
BFMJPFMF_00054 Silver (Ag) 100 1.6e-60 1 117 1.0000 1.0000 prediction
BFMJPFMF_00055 Silver (Ag) 100 3.7e-254 1 461 1.0000 1.0000 prediction
BFMJPFMF_00056 Silver (Ag) 100 1e-124 1 226 1.0000 1.0000 prediction
BFMJPFMF_00057 Silver (Ag) 100 1.4e-275 1 491 1.0000 1.0000 prediction
BFMJPFMF_00058 Silver (Ag) 100 1e-74 40 182 0.7857 1.0000 prediction
BFMJPFMF_00081 Nickel (Ni), Cobalt (Co) 100 1.1e-172 1 318 1.0000 1.0000 prediction
BFMJPFMF_00082 Nickel (Ni), Cobalt (Co) 99.6 8.8e-141 1 255 1.0000 1.0000 prediction
BFMJPFMF_00085 Arsenic (As) 85.8 1.4e-68 1 141 1.0000 1.0000 prediction
BFMJPFMF_00086 Arsenic (As), Antimony (Sb) 99.3 1.3e-243 1 455 1.0000 1.0000 prediction
BFMJPFMF_00087 Arsenic (As) 95.3 8.9e-55 1 106 1.0000 1.0000 prediction
BFMJPFMF_00088 Arsenic (As) 100 8.6e-135 1 232 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






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
BFMJPFMF_00076 PHI:8004 fecI 97.1 1e-90 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
BFMJPFMF_00077 PHI:8005 fecR 98.4 9e-178 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
BFMJPFMF_00078 PHI:8006 fecA 98.3 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
BFMJPFMF_00079 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
BFMJPFMF_00080 PHI:8008 fecC 96.4 8.9e-176 1 332 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
BFMJPFMF_00081 PHI:8009 fecD 91.2 1.2e-158 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
BFMJPFMF_00082 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
BFMJPFMF_00095 PHI:6268 lacZ 96.6 0 1 1024 1.0000 1.0000 rodents urinary tract infection beta-galactosidase 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
BFMJPFMF_00024 ARB20136.1|GH3 100 0 1 908 1 1
BFMJPFMF_00025 UNI57221.1|CBM4|GH9 100 0 1 779 1 1
BFMJPFMF_00032 ARB20145.1|GH1 100 0 1 459 1 1
BFMJPFMF_00095 ARB20066.1|GH2 100 0 1 1024 1 1
BFMJPFMF_00121 ARB20088.1|GH23 100 9.66e-116 1 166 1 1
BFMJPFMF_00127 ARB20094.1|GH23 100 1.2e-111 1 156 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
BFMJPFMF_00018 3.A.4.1.1 85.7 3e-283 1 582 0.9983 1.3566 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
BFMJPFMF_00019 3.A.4.1.1 93.9 6.9e-221 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
BFMJPFMF_00043 9.B.62.1.1 99.4 4.7e-163 1 309 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family
BFMJPFMF_00045 1.B.76.1.5 100 7.5e-174 3 298 0.9933 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.76 The Copper Resistance Putative Porin (CopB) Family
BFMJPFMF_00048 1.A.34.1.3 99.6 4.3e-135 1 245 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.34 The <i>Bacillus</i> Gap Junction-like Channel-forming Complex (GJ-CC) Family
BFMJPFMF_00050 3.A.3.5.4 94.5 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
BFMJPFMF_00052 2.A.6.1.3 98.9 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
BFMJPFMF_00055 1.B.17.3.4 98.9 5.6e-253 1 461 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
BFMJPFMF_00078 1.B.14.1.20 98.3 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
BFMJPFMF_00079 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
BFMJPFMF_00080 3.A.1.14.1 96.4 2e-175 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
BFMJPFMF_00081 3.A.1.14.1 91.2 2.8e-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
BFMJPFMF_00082 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
BFMJPFMF_00086 3.A.4.1.1 88.1 2.6e-210 27 455 0.9429 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
BFMJPFMF_00090 2.A.51.1.7 77.4 6.3e-168 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
BFMJPFMF_00096 2.A.1.5.1 99.3 9.3e-231 1 417 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)