Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1261
  Reference Plasmid   NZ_CP145149.1
  Reference Plasmid Size   164347
  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
M0205016 BAAFECOA_00055 51897 3 Gut 0.25 protein_coding synonymous_variant LOW 1266T>C Gly422Gly
M0205017 BAAFECOA_00055 52011 3 Gut 0.25 protein_coding missense_variant MODERATE 1152T>G Asp384Glu






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
BAAFECOA_00024 VFG000417 Pla 81.7 2.7e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor experiment
BAAFECOA_00118 VFG034679 Ibes 71.9 5.2e-183 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
BAAFECOA_00024 VFG003087 Pla 82.1 5.3e-151 1 311 1.0 0.9968 Exoenzyme plasminogen activator protease precursor prediction
BAAFECOA_00118 VFG034652 Ibes 71.9 1e-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
BAAFECOA_00103 Copper (Cu), Silver (Ag) 88.9 6.5e-63 1 144 1.0000 1.0000 experiment
BAAFECOA_00104 Copper (Cu) 99.4 1.5e-262 1 466 1.0000 1.0000 experiment
BAAFECOA_00105 Copper (Cu) 100 1.7e-126 1 226 1.0000 1.0000 experiment
BAAFECOA_00106 Copper (Cu) 99.4 1.3e-164 1 309 1.0000 1.0000 experiment
BAAFECOA_00107 Copper (Cu) 100 4.9e-67 1 126 1.0000 1.0000 experiment
BAAFECOA_00108 Copper (Cu) 100 1.5e-175 1 296 1.0000 1.0000 experiment
BAAFECOA_00109 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
BAAFECOA_00113 Silver (Ag) 95.7 0 1 815 1.0012 0.9903 experiment
BAAFECOA_00115 Silver (Ag) 99.4 0 1 1048 1.0000 1.0000 experiment
BAAFECOA_00116 Silver (Ag) 98.1 9.4e-243 1 430 1.0000 1.0000 experiment
BAAFECOA_00117 Silver (Ag) 98.9 3.1e-47 28 117 0.7692 0.9375 experiment
BAAFECOA_00118 Silver (Ag) 99.3 1.8e-255 1 461 1.0000 1.0000 experiment
BAAFECOA_00119 Silver (Ag) 95.2 1.1e-117 1 226 1.0088 1.0000 experiment
BAAFECOA_00120 Silver (Ag) 90.6 1.3e-243 1 485 0.9939 0.9839 experiment
BAAFECOA_00121 Silver (Ag) 95.8 1.2e-72 1 143 1.0000 1.0000 experiment
BAAFECOA_00147 Nickel (Ni), Cobalt (Co) 91.5 4.3e-160 1 318 1.0000 1.0000 experiment
BAAFECOA_00148 Nickel (Ni), Cobalt (Co) 79.2 2.6e-115 1 255 1.0000 1.0000 experiment
BAAFECOA_00103 Copper (Cu), Silver (Ag) 98.6 3.9e-69 1 144 1.0000 1.0000 prediction
BAAFECOA_00104 Copper (Cu) 100 3.7e-262 1 466 1.0000 1.0000 prediction
BAAFECOA_00105 Copper (Cu) 100 3.9e-124 1 226 1.0000 0.9741 prediction
BAAFECOA_00106 Copper (Cu) 100 4.4e-163 1 309 1.0000 1.0000 prediction
BAAFECOA_00107 Copper (Cu) 100 1.1e-64 1 126 1.0000 1.0000 prediction
BAAFECOA_00108 Copper (Cu) 100 3.5e-173 1 296 1.0000 0.9900 prediction
BAAFECOA_00109 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
BAAFECOA_00113 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
BAAFECOA_00115 Silver (Ag) 100 0 1 1048 1.0000 1.0000 prediction
BAAFECOA_00116 Silver (Ag) 100 3.2e-244 1 430 1.0000 1.0000 prediction
BAAFECOA_00117 Silver (Ag) 100 1.6e-60 1 117 1.0000 1.0000 prediction
BAAFECOA_00118 Silver (Ag) 100 2.8e-254 1 461 1.0000 1.0000 prediction
BAAFECOA_00119 Silver (Ag) 99.6 6.6e-124 1 226 1.0000 1.0000 prediction
BAAFECOA_00120 Silver (Ag) 100 8.9e-275 1 492 1.0000 1.0000 prediction
BAAFECOA_00121 Silver (Ag) 100 6.8e-74 1 143 1.0000 1.0000 prediction
BAAFECOA_00147 Nickel (Ni), Cobalt (Co) 100 1.4e-172 1 318 1.0000 1.0000 prediction
BAAFECOA_00148 Nickel (Ni), Cobalt (Co) 99.6 8.8e-141 1 255 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
BAAFECOA_00134 PHI:3531 pld1 98.5 2.4e-29 1 65 1.0000 1.0000 rodents urinary tract infection; nosocomial pneumonia; abdominal infection lipid metabolism loss of pathogenicity
BAAFECOA_00142 PHI:8004 fecI 97.1 1e-90 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
BAAFECOA_00143 PHI:8005 fecR 98.4 9e-178 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
BAAFECOA_00144 PHI:8006 fecA 98.7 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
BAAFECOA_00145 PHI:8007 fecB 95.3 4e-159 1 300 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate-binding periplasmic protein reduced virulence
BAAFECOA_00146 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
BAAFECOA_00147 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
BAAFECOA_00148 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
BAAFECOA_00155 PHI:6268 lacZ 96.4 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
BAAFECOA_00155 ASC20425.1|GH2 100 0 1 1024 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
BAAFECOA_00024 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
BAAFECOA_00106 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
BAAFECOA_00108 1.B.76.1.5 100 5.7e-174 1 296 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.76 The Copper Resistance Putative Porin (CopB) Family
BAAFECOA_00111 1.A.34.1.3 100 1.1e-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
BAAFECOA_00113 3.A.3.5.4 95.7 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
BAAFECOA_00115 2.A.6.1.3 99.4 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
BAAFECOA_00118 1.B.17.3.4 99.3 6.6e-254 1 461 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.17 The Outer Membrane Factor (OMF) Family
BAAFECOA_00144 1.B.14.1.20 98.7 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
BAAFECOA_00145 3.A.1.14.1 95.3 8.9e-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
BAAFECOA_00146 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
BAAFECOA_00147 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
BAAFECOA_00148 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
BAAFECOA_00156 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)