Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C419
  Reference Plasmid   NZ_CP010239.1
  Reference Plasmid Size   184614
  Reference Plasmid GC Content   0.51
  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
M0164229 JPCPDEEH_00040 31952 6 Gut 0.07 protein_coding missense_variant MODERATE 31T>C Cys11Arg
M0164230 JPCPDEEH_00040 31964 6 Gut 0.07 protein_coding missense_variant MODERATE 43T>C Ser15Pro
M0164231 JPCPDEEH_00032 32188 10 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -4252A>G None
M0164232 JPCPDEEH_00032 32402 11 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -4466G>A None
M0164233 JPCPDEEH_00042 33703 11 Gut 0.13 protein_coding synonymous_variant LOW 306C>T Thr102Thr
M0164234 JPCPDEEH_00043 34552 16 Gut 0.19 protein_coding missense_variant MODERATE 209C>T Pro70Leu
M0164235 JPCPDEEH_00043 34611 16 Gut 0.19 protein_coding missense_variant MODERATE 268A>G Ser90Gly
M0164236 JPCPDEEH_00043 35753 16 Gut 0.19 protein_coding missense_variant MODERATE 1410T>G His470Gln
M0164237 JPCPDEEH_00043 36590 16 Gut 0.19 protein_coding synonymous_variant LOW 2247A>G Gly749Gly
M0164238 JPCPDEEH_00046 37986 16 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -1120T>A None
M0164239 JPCPDEEH_00046 38320 16 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -786T>G None
M0164240 JPCPDEEH_00045 38724 16 Gut 0.19 protein_coding missense_variant MODERATE 52A>C Met18Leu
M0164241 JPCPDEEH_00045 38840 11 Gut 0.13 protein_coding upstream_gene_variant MODIFIER -65C>T None
M0164242 JPCPDEEH_00045 38933 7 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -158A>C None
M0164243 JPCPDEEH_00083 74168 7 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -3030C>T None
M0164244 JPCPDEEH_00088 74261 7 Gut 0.08 protein_coding synonymous_variant LOW 1452A>C Leu484Leu
M0164245 JPCPDEEH_00088 74547 7 Gut 0.08 protein_coding missense_variant MODERATE 1166T>C Phe389Ser
M0164246 JPCPDEEH_00088 75025 4 Gut 0.05 protein_coding missense_variant MODERATE 688C>A Leu230Met
M0164247 JPCPDEEH_00088 75035 4 Gut 0.05 protein_coding synonymous_variant LOW 678T>G Leu226Leu
M0164248 JPCPDEEH_00088 75359 3 Gut 0.03 protein_coding synonymous_variant LOW 354A>G Pro118Pro
M0164249 JPCPDEEH_00088 75623 4 Gut 0.05 protein_coding synonymous_variant LOW 90G>T Leu30Leu
M0164250 JPCPDEEH_00089 75795 6 Gut 0.07 protein_coding synonymous_variant LOW 315C>T Pro105Pro
M0164251 JPCPDEEH_00089 75929 5 Gut 0.06 protein_coding missense_variant MODERATE 181G>A Gly61Ser
M0164252 JPCPDEEH_00089 76087 5 Gut 0.06 protein_coding missense_variant MODERATE 23C>T Thr8Ile
M0164253 JPCPDEEH_00036 34235 10 Gut 0.12 protein_coding upstream_gene_variant MODIFIER -4039A>G None
M0164254 JPCPDEEH_00095 78351 3 Gut 0.03 protein_coding synonymous_variant LOW 237A>G Leu79Leu
M0164255 JPCPDEEH_00095 78441 3 Gut 0.03 protein_coding synonymous_variant LOW 147A>G Leu49Leu
M0164256 JPCPDEEH_00097 79444 3 Gut 0.03 protein_coding synonymous_variant LOW 90C>A Val30Val
M0164257 JPCPDEEH_00031 26853 3 Gut 0.03 protein_coding synonymous_variant LOW 1245C>T Asp415Asp






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
JPCPDEEH_00028 VFG000905 Alpha-Hemolysin 95.3 1.9e-98 1 170 1.0 1 Exotoxin Hemolysin C experiment
JPCPDEEH_00029 VFG000906 Alpha-Hemolysin 96.5 0 1 1024 1.0 1 Exotoxin Hemolysin A experiment
JPCPDEEH_00030 VFG000907 Alpha-Hemolysin 98.7 0 1 707 1.0 1 Exotoxin Hemolysin B experiment
JPCPDEEH_00031 VFG000908 Alpha-Hemolysin 96 6.2e-248 1 478 1.0 1 Exotoxin Hemolysin D experiment
JPCPDEEH_00044 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
JPCPDEEH_00055 VFG000862 Pet 99.4 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter experiment
JPCPDEEH_00065 VFG034837 TTSS secreted effectors 92 2.7e-212 1 402 1.0 1 Effector delivery system type III secretion system effector experiment
JPCPDEEH_00028 VFG033901 Hemolysin 99.4 1.4e-100 1 170 1.0 1 Exotoxin Hemolysin C prediction
JPCPDEEH_00029 VFG033893 Hemolysin 98.6 0 1 1024 1.0 1 Exotoxin Hemolysin A prediction
JPCPDEEH_00030 VFG033885 Hemolysin 99.6 0 1 707 1.0 1 Exotoxin Hemolysin B prediction
JPCPDEEH_00031 VFG033877 Hemolysin 98.7 3.9e-254 1 478 1.0 1 Exotoxin Hemolysin D prediction
JPCPDEEH_00044 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
JPCPDEEH_00055 VFG000862 Pet 99.4 0 1 1295 1.0 1 Effector delivery system Pet serine protease precursor, autotransporter prediction
JPCPDEEH_00064 VFG017870 Icm/dot type IVB locus 77.9 1e-89 1 208 0.9905 0.9952 Effector delivery system ParA family protein prediction
JPCPDEEH_00065 VFG034837 TTSS secreted effectors 92 2e-211 1 402 1.0 1 Effector delivery system type III secretion system effector 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
JPCPDEEH_00036 Cadmium (Cd), Mercury (Hg), Tributyltin (TBT) [class: Organo-tin], Hydrogen Peroxide (H2O2) [class: Peroxides], Hydrochloric acid (HCl) [class: Acid] 96.9 3e-65 1 127 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
JPCPDEEH_00196 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JPCPDEEH_00197 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
JPCPDEEH_00202 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
JPCPDEEH_00205 ARO:3002132 100 3.97e-277 1 379 1.0000 1.0000 cephalosporin DHA beta-lactamase antibiotic inactivation
JPCPDEEH_00212 ARO:3002737 92.6 5.96e-110 1 215 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection






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
JPCPDEEH_00029 PHI:4522 HlyA 98.6 0 1 1024 1.0000 1.0000 rodents urinary tract infection induces caspase-1/caspase-4-dependent inflammatory cell death in human urothelial cells unaffected pathogenicity
JPCPDEEH_00041 PHI:10792 cjrA 99.3 3.6e-165 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
JPCPDEEH_00042 PHI:10793 cjrB 99.6 1.1e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
JPCPDEEH_00043 PHI:10794 cjrC 99.1 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
JPCPDEEH_00044 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
JPCPDEEH_00204 PHI:10922 ampR 100 4.9e-170 1 291 1.0000 1.0000 rodents pneumonia regulator of the LysR family reduced virulence
JPCPDEEH_00207 PHI:7660 pspD 84.5 8.3e-29 1 71 0.9342 0.9861 rodents salmonellosis phage-shock protein reduced virulence
JPCPDEEH_00208 PHI:7659 pspC 87.4 2.6e-53 1 119 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
JPCPDEEH_00209 PHI:7658 pspB 89.2 6e-32 1 74 1.0000 1.0000 rodents salmonellosis phage-shock protein reduced virulence
JPCPDEEH_00210 PHI:7657 pspA 94.6 1e-103 1 222 1.0000 1.0000 rodents salmonellosis phage-shock 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
JPCPDEEH_00165 AXI38019.1|GH23 100 2.02e-123 1 169 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
JPCPDEEH_00029 1.C.11.1.3 96.7 0 1 1024 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
JPCPDEEH_00030 3.A.1.109.1 99.2 0 1 707 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
JPCPDEEH_00031 8.A.1.3.1 98.5 7.6e-253 1 478 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.A Auxiliary transport proteins 8.A.1 The Membrane Fusion Protein (MFP) Family
JPCPDEEH_00042 2.C.1.1.3 99.6 2.4e-136 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
JPCPDEEH_00043 1.B.14.7.1 99.1 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
JPCPDEEH_00055 1.B.12.4.4 99.4 0 1 1295 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
JPCPDEEH_00201 2.A.51.1.7 99.5 5.1e-210 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
JPCPDEEH_00210 9.B.100.1.1 94.6 2.3e-103 1 222 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.100 The Phage Shock Protein (Psp) Family