Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C574
  Reference Plasmid   NZ_CP033627.1
  Reference Plasmid Size   184083
  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
M0168797 ANDLEIPI_00084 74776 3 Gut 0.38 protein_coding missense_variant MODERATE 44G>T Arg15Leu
M0168798 ANDLEIPI_00096 87785 3 Gut 0.38 protein_coding stop_gained HIGH 95G>A Trp32*






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
ANDLEIPI_00018 VFG034679 Ibes 71.9 5.2e-183 1 459 0.9957 0.9978 Invasion Cu(+)/Ag(+) efflux RND transporter outer membrane channel CusC experiment
ANDLEIPI_00018 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
ANDLEIPI_00015 Silver (Ag) 91.6 5.4e-70 1 143 1.0000 1.0000 experiment
ANDLEIPI_00016 Silver (Ag) 93.9 7.6e-257 1 491 1.0081 0.9960 experiment
ANDLEIPI_00017 Silver (Ag) 95.2 1.1e-117 1 226 1.0088 1.0000 experiment
ANDLEIPI_00018 Silver (Ag) 99.3 1.8e-255 1 461 1.0000 1.0000 experiment
ANDLEIPI_00019 Silver (Ag) 98.9 3.1e-47 28 117 0.7692 0.9375 experiment
ANDLEIPI_00020 Silver (Ag) 97.7 6.1e-242 1 430 1.0000 1.0000 experiment
ANDLEIPI_00021 Silver (Ag) 98.9 0 1 1048 1.0000 1.0000 experiment
ANDLEIPI_00023 Silver (Ag) 94.5 0 1 815 1.0012 0.9903 experiment
ANDLEIPI_00027 Copper (Cu) 100 0 1 605 1.0000 1.0000 experiment
ANDLEIPI_00028 Copper (Cu) 100 1.5e-175 1 296 1.0000 1.0000 experiment
ANDLEIPI_00029 Copper (Cu) 100 4.9e-67 1 126 1.0000 1.0000 experiment
ANDLEIPI_00030 Copper (Cu) 99.7 2.5e-165 1 309 1.0000 1.0000 experiment
ANDLEIPI_00031 Copper (Cu) 100 1.7e-126 1 226 1.0000 1.0000 experiment
ANDLEIPI_00032 Copper (Cu) 99.1 2.6e-262 1 466 1.0000 1.0000 experiment
ANDLEIPI_00033 Copper (Cu), Silver (Ag) 94.4 8.7e-68 1 144 1.0000 1.0000 experiment
ANDLEIPI_00039 Arsenic (As) 82.7 6.4e-100 30 237 0.8776 0.8966 experiment
ANDLEIPI_00045 Arsenic (As), Antimony (Sb) 100 1.1e-78 1 141 1.0000 1.0000 experiment
ANDLEIPI_00046 Arsenic (As), Antimony (Sb) 100 3.9e-233 1 429 1.0000 1.0000 experiment
ANDLEIPI_00047 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 1.0000 experiment
ANDLEIPI_00048 Arsenic (As), Antimony (Sb) 91.7 6.4e-64 1 120 1.0000 1.0000 experiment
ANDLEIPI_00049 Arsenic (As), Antimony (Sb), Bismuth (Bi) 88.8 8.6e-58 1 116 1.0000 0.9915 experiment
ANDLEIPI_00106 Nickel (Ni), Cobalt (Co) 91.2 2.8e-159 1 318 1.0000 1.0000 experiment
ANDLEIPI_00107 Nickel (Ni), Cobalt (Co) 79.2 2.6e-115 1 255 1.0000 1.0000 experiment
ANDLEIPI_00179 Mercury (Hg) 96.2 2.7e-39 1 78 1.0000 1.0000 experiment
ANDLEIPI_00180 Mercury (Hg) 90.1 1.6e-54 1 121 1.0000 1.0000 experiment
ANDLEIPI_00181 Mercury (Hg) 92.5 8.4e-292 1 561 1.0000 1.0000 experiment
ANDLEIPI_00182 Mercury (Hg) 80.1 1.6e-61 1 141 1.0000 1.0000 experiment
ANDLEIPI_00183 Mercury (Hg) 85.7 4.5e-38 1 91 1.0000 1.0000 experiment
ANDLEIPI_00184 Mercury (Hg) 98.3 1.7e-61 7 121 0.9504 0.9914 experiment
ANDLEIPI_00185 Mercury (Hg) 88.7 5.5e-73 1 151 1.0000 1.0000 experiment
ANDLEIPI_00015 Silver (Ag) 100 6.1e-75 1 143 1.0000 1.0000 prediction
ANDLEIPI_00016 Silver (Ag) 99.8 8.9e-275 1 491 1.0000 1.0000 prediction
ANDLEIPI_00017 Silver (Ag) 99.6 6.6e-124 1 226 1.0000 1.0000 prediction
ANDLEIPI_00018 Silver (Ag) 100 2.8e-254 1 461 1.0000 1.0000 prediction
ANDLEIPI_00019 Silver (Ag) 100 1.6e-60 1 117 1.0000 1.0000 prediction
ANDLEIPI_00020 Silver (Ag) 99.8 7.1e-244 1 430 1.0000 1.0000 prediction
ANDLEIPI_00021 Silver (Ag) 100 0 1 1048 1.0000 0.9905 prediction
ANDLEIPI_00023 Silver (Ag) 100 0 1 815 1.0000 1.0000 prediction
ANDLEIPI_00027 Copper (Cu) 100 0 1 605 1.0000 0.9967 prediction
ANDLEIPI_00028 Copper (Cu) 100 3.5e-173 1 296 1.0000 0.9900 prediction
ANDLEIPI_00029 Copper (Cu) 100 1.1e-64 1 126 1.0000 1.0000 prediction
ANDLEIPI_00030 Copper (Cu) 100 4.4e-163 1 309 1.0000 1.0000 prediction
ANDLEIPI_00031 Copper (Cu) 100 3.9e-124 1 226 1.0000 0.9741 prediction
ANDLEIPI_00032 Copper (Cu) 100 3.7e-262 1 466 1.0000 1.0000 prediction
ANDLEIPI_00033 Copper (Cu), Silver (Ag) 100 8.6e-69 1 144 1.0000 1.0000 prediction
ANDLEIPI_00039 Arsenic (As) 82.3 3.7e-109 1 237 1.0000 1.0000 prediction
ANDLEIPI_00045 Arsenic (As) 100 2.5e-76 1 141 1.0000 1.0000 prediction
ANDLEIPI_00046 Arsenic (As), Antimony (Sb) 100 2.6e-230 2 429 0.9977 1.0000 prediction
ANDLEIPI_00047 Arsenic (As), Antimony (Sb) 100 0 1 583 1.0000 0.9848 prediction
ANDLEIPI_00048 Arsenic (As) 99.2 8.8e-67 1 120 1.0000 1.0000 prediction
ANDLEIPI_00049 Arsenic (As) 98.3 1.6e-60 1 116 1.0000 1.0000 prediction
ANDLEIPI_00107 Nickel (Ni), Cobalt (Co) 99.6 8.8e-141 1 255 1.0000 1.0000 prediction
ANDLEIPI_00179 Mercury (Hg) 98.7 5.1e-39 1 78 1.0000 1.0000 prediction
ANDLEIPI_00180 Mercury (Hg) 100 3.1e-59 1 121 1.0000 1.0000 prediction
ANDLEIPI_00181 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 99.8 0 1 561 1.0000 1.0000 prediction
ANDLEIPI_00182 Mercury (Hg) 80.9 3.2e-60 1 141 1.0000 1.0000 prediction
ANDLEIPI_00183 Mercury (Hg) 94.5 9.1e-40 1 91 1.0000 1.0000 prediction
ANDLEIPI_00184 Mercury (Hg) 100 9.2e-64 1 121 1.0000 1.0000 prediction
ANDLEIPI_00185 Mercury (Hg) 99.3 7.9e-81 1 151 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
ANDLEIPI_00067 PHI:3531 pld1 100 6.4e-30 1 65 1.0000 1.0000 rodents urinary tract infection; nosocomial pneumonia; abdominal infection lipid metabolism loss of pathogenicity
ANDLEIPI_00101 PHI:8004 fecI 97.1 1e-90 1 173 1.0000 1.0000 even-toed ungulates bovine mastitis RNA polymerase sigma factor reduced virulence
ANDLEIPI_00102 PHI:8005 fecR 98.4 9e-178 1 317 1.0000 1.0000 even-toed ungulates bovine mastitis Fec operon regulator reduced virulence
ANDLEIPI_00103 PHI:8006 fecA 98.4 0 1 774 1.0000 1.0000 even-toed ungulates bovine mastitis ferric citrate outer membrane transporter reduced virulence
ANDLEIPI_00104 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
ANDLEIPI_00105 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
ANDLEIPI_00106 PHI:8009 fecD 91.2 4.7e-158 1 318 1.0000 1.0000 even-toed ungulates bovine mastitis Fe(3+) dicitrate transport system permease protein reduced virulence
ANDLEIPI_00107 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
ANDLEIPI_00111 PHI:6268 lacZ 96.7 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
ANDLEIPI_00111 APM62253.1|GH2 100 0 1 1024 1 1
ANDLEIPI_00164 AWE04561.1|GH23 100 9.39e-116 1 161 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
ANDLEIPI_00018 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
ANDLEIPI_00021 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
ANDLEIPI_00023 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
ANDLEIPI_00025 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
ANDLEIPI_00028 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
ANDLEIPI_00030 9.B.62.1.1 99.7 9.5e-164 1 309 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.62 The Copper Resistance (CopD) Family
ANDLEIPI_00046 3.A.4.1.1 93.9 2.9e-219 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
ANDLEIPI_00047 3.A.4.1.1 87.3 2.3e-288 1 581 0.9966 1.3543 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.4 The Arsenite-Antimonite (ArsAB) Efflux Family
ANDLEIPI_00103 1.B.14.1.20 98.4 0 1 774 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
ANDLEIPI_00104 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
ANDLEIPI_00105 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
ANDLEIPI_00106 3.A.1.14.1 91.2 1e-157 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
ANDLEIPI_00107 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
ANDLEIPI_00112 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)
ANDLEIPI_00179 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
ANDLEIPI_00183 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
ANDLEIPI_00184 1.A.72.3.1 92.2 1.3e-55 7 121 0.9504 1.2637 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily