Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C919
  Reference Plasmid   NZ_CP077935.1
  Reference Plasmid Size   256180
  Reference Plasmid GC Content   0.33
  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
M0104802 NJENCGFH_00160 165863 3 Skin 0.20 protein_coding missense_variant MODERATE 365G>A Ser122Asn






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
NJENCGFH_00128 VFG001292 Delta-hemolysin 97.7 1.2e-17 1 44 1.0 1 Exotoxin delta-hemolysin experiment
NJENCGFH_00141 VFG001798 Beta-hemolysin 100 2.1e-194 2 331 0.997 1 Exotoxin beta-hemolysin experiment
NJENCGFH_00142 VFG004566 Eap/Map 88.8 8.3e-287 1 582 0.9966 1.0017 Adherence extracellular adherence protein Eap/Map experiment
HGMKMHHB_00128 VFG001292 Delta-hemolysin 97.7 1.2e-17 1 44 1.0 1 Exotoxin delta-hemolysin experiment
HGMKMHHB_00141 VFG001798 Beta-hemolysin 100 2.1e-194 2 331 0.997 1 Exotoxin beta-hemolysin experiment
HGMKMHHB_00142 VFG004566 Eap/Map 88.8 8.3e-287 1 582 0.9966 1.0017 Adherence extracellular adherence protein Eap/Map experiment
NJENCGFH_00128 VFG004796 -hemolysin 100 1.9e-17 1 44 1.0 1 Exotoxin delta-hemolysin prediction
NJENCGFH_00139 VFG044014 PVL 100 6.5e-198 1 351 1.0 1 Exotoxin bi-component leukocidin LukGH subunit H prediction
NJENCGFH_00140 VFG044013 PVL 100 2.2e-198 1 338 1.0 1 Exotoxin bi-component leukocidin LukGH subunit G prediction
NJENCGFH_00141 VFG001798 Beta-hemolysin 100 1.6e-193 2 331 0.997 1 Exotoxin beta-hemolysin prediction
NJENCGFH_00142 VFG004563 Eap/Map 100 0 1 584 1.0 1 Adherence MHC class II analog protein prediction
HGMKMHHB_00128 VFG004796 -hemolysin 100 1.9e-17 1 44 1.0 1 Exotoxin delta-hemolysin prediction
HGMKMHHB_00139 VFG044014 PVL 100 6.5e-198 1 351 1.0 1 Exotoxin bi-component leukocidin LukGH subunit H prediction
HGMKMHHB_00140 VFG044013 PVL 100 2.2e-198 1 338 1.0 1 Exotoxin bi-component leukocidin LukGH subunit G prediction
HGMKMHHB_00141 VFG001798 Beta-hemolysin 100 1.6e-193 2 331 0.997 1 Exotoxin beta-hemolysin prediction
HGMKMHHB_00142 VFG004563 Eap/Map 100 0 1 584 1.0 1 Adherence MHC class II analog protein 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
NJENCGFH_00225 Hydrogen Peroxide (H2O2) [class: Peroxides] 100 6.2e-85 1 148 1.0000 1.0000 experiment
HGMKMHHB_00225 Hydrogen Peroxide (H2O2) [class: Peroxides] 100 6.2e-85 1 148 1.0000 1.0000 experiment
NJENCGFH_00225 Hydrogen Peroxide (H2O2) [class: Peroxides] 100 1.4e-82 1 148 1.0000 1.0000 prediction
HGMKMHHB_00225 Hydrogen Peroxide (H2O2) [class: Peroxides] 100 1.4e-82 1 148 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
NJENCGFH_00058 ARO:3003776 99.5 4.15e-298 1 421 1.0000 1.0000 phosphonic acid antibiotic antibiotic-resistant murA transferase antibiotic target alteration
NJENCGFH_00069 ARO:3003074 99.8 0 1 494 1.0000 1.0000 peptide antibiotic daptomycin resistant cls antibiotic target alteration
NJENCGFH_00079 ARO:3004047 98.5 0 1 885 1.0000 1.0000 aminoglycoside antibiotic kdpDE antibiotic efflux
NJENCGFH_00161 ARO:3000621 94.7 1.08e-186 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase antibiotic inactivation
HGMKMHHB_00058 ARO:3003776 99.5 4.15e-298 1 421 1.0000 1.0000 phosphonic acid antibiotic antibiotic-resistant murA transferase antibiotic target alteration
HGMKMHHB_00069 ARO:3003074 99.8 0 1 494 1.0000 1.0000 peptide antibiotic daptomycin resistant cls antibiotic target alteration
HGMKMHHB_00079 ARO:3004047 98.5 0 1 885 1.0000 1.0000 aminoglycoside antibiotic kdpDE antibiotic efflux
HGMKMHHB_00161 ARO:3000621 94.7 1.08e-186 1 281 1.0000 1.0000 penicillin beta-lactam BlaZ beta-lactamase 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
NJENCGFH_00033 PHI:6903 FbaA 100 4.8e-162 1 286 1.0000 1.0000 moths white muscardine fructose-bisphosphate aldolase reduced virulence
NJENCGFH_00037 PHI:8558 Rho 99.8 7.4e-247 1 438 1.0000 0.9887 rodents nosocomial infection transcriptional regulator increased virulence (hypervirulence)
NJENCGFH_00043 PHI:11296 ptpB 100 1.1e-76 1 139 1.0000 1.0000 primates pneumonia low molecular weight protein-tyrosine-phosphatase reduced virulence
NJENCGFH_00053 PHI:10773 atpA 100 1.5e-283 1 502 1.0000 1.0000 primates prosthetic joint infection ATP synthase subunit alpha reduced virulence
NJENCGFH_00054 PHI:8019 atpG 100 8e-157 1 288 1.0000 1.0000 rodents sepsis F1F0 ATPase reduced virulence
NJENCGFH_00058 PHI:10276 murA 100 6.3e-235 1 421 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease UDP-N-acetylglucosamine 1-carboxyvinyltransferase increased virulence (hypervirulence)
NJENCGFH_00089 PHI:9882 mazF 100 3.4e-61 1 120 1.0000 1.0000 rodents abscess; sepsis endoribonuclease increased virulence (hypervirulence)
NJENCGFH_00093 PHI:9446 sigB 99.6 8.7e-139 1 256 1.0000 1.0000 rodents bovine mastitis RNA polymerase sigma factor reduced virulence
NJENCGFH_00124 PHI:8330 agrA 100 8.4e-136 1 238 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease virulence gene transcription factor increased virulence (hypervirulence)
NJENCGFH_00125 PHI:9880 agrC 100 5.4e-226 1 430 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
NJENCGFH_00126 PHI:9879 agrD 100 3e-21 1 46 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
NJENCGFH_00127 PHI:9878 agrB 99.5 2.8e-95 19 207 0.9130 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
NJENCGFH_00132 PHI:9877 SAUSA300_1984 (mroQ) 100 2.7e-129 1 247 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease membrane protease regulator of Agr quorum sensing reduced virulence
NJENCGFH_00143 PHI:9852 eap 100 9.1e-49 1 96 1.0000 1.0000 moths skin infection; food poisoning; respiratory disease adherence protein unaffected pathogenicity
NJENCGFH_00146 PHI:10290 yhcF 100 1.2e-64 1 126 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease GntR family transcriptional regulator unaffected pathogenicity
NJENCGFH_00164 PHI:124259 pgl (SAUSA300_1902) 100 7.9e-204 1 342 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease hypothetical protein reduced virulence
NJENCGFH_00171 PHI:3285 saNOS 98.6 4.2e-216 1 358 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease NO-synthase reduced virulence
NJENCGFH_00177 PHI:11229 scpA 99.5 8.7e-223 1 388 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease staphopain A increased virulence (hypervirulence)
NJENCGFH_00178 PHI:7345 PurB 100 4.6e-249 1 431 1.0000 1.0000 bony fishes skin infection; food poisoning; respiratory disease adenylosuccinate lyase reduced virulence
NJENCGFH_00201 PHI:8947 vraS 100 3.9e-190 1 347 1.0000 1.0000 moths pneumonia sensor protein increased virulence (hypervirulence)
NJENCGFH_00202 PHI:8948 vraR 99.5 5.9e-109 1 209 1.0000 1.0000 moths pneumonia response regulator protein increased virulence (hypervirulence)
NJENCGFH_00225 PHI:4991 PerR 100 1e-83 1 148 1.0000 1.0000 nematodes skin infection; food poisoning; respiratory disease hydrogen peroxide sensor reduced virulence
HGMKMHHB_00033 PHI:6903 FbaA 100 4.8e-162 1 286 1.0000 1.0000 moths white muscardine fructose-bisphosphate aldolase reduced virulence
HGMKMHHB_00037 PHI:8558 Rho 99.8 7.4e-247 1 438 1.0000 0.9887 rodents nosocomial infection transcriptional regulator increased virulence (hypervirulence)
HGMKMHHB_00043 PHI:11296 ptpB 100 1.1e-76 1 139 1.0000 1.0000 primates pneumonia low molecular weight protein-tyrosine-phosphatase reduced virulence
HGMKMHHB_00053 PHI:10773 atpA 100 1.5e-283 1 502 1.0000 1.0000 primates prosthetic joint infection ATP synthase subunit alpha reduced virulence
HGMKMHHB_00054 PHI:8019 atpG 100 8e-157 1 288 1.0000 1.0000 rodents sepsis F1F0 ATPase reduced virulence
HGMKMHHB_00058 PHI:10276 murA 100 6.3e-235 1 421 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease UDP-N-acetylglucosamine 1-carboxyvinyltransferase increased virulence (hypervirulence)
HGMKMHHB_00089 PHI:9882 mazF 100 3.4e-61 1 120 1.0000 1.0000 rodents abscess; sepsis endoribonuclease increased virulence (hypervirulence)
HGMKMHHB_00093 PHI:9446 sigB 99.6 8.7e-139 1 256 1.0000 1.0000 rodents bovine mastitis RNA polymerase sigma factor reduced virulence
HGMKMHHB_00124 PHI:8330 agrA 100 8.4e-136 1 238 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease virulence gene transcription factor increased virulence (hypervirulence)
HGMKMHHB_00125 PHI:9880 agrC 100 5.4e-226 1 430 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
HGMKMHHB_00126 PHI:9879 agrD 100 3e-21 1 46 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
HGMKMHHB_00127 PHI:9878 agrB 99.5 2.8e-95 19 207 0.9130 1.0000 rodents skin infection; food poisoning; respiratory disease accessory gene regulator protein reduced virulence
HGMKMHHB_00132 PHI:9877 SAUSA300_1984 (mroQ) 100 2.7e-129 1 247 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease membrane protease regulator of Agr quorum sensing reduced virulence
HGMKMHHB_00143 PHI:9852 eap 100 9.1e-49 1 96 1.0000 1.0000 moths skin infection; food poisoning; respiratory disease adherence protein unaffected pathogenicity
HGMKMHHB_00146 PHI:10290 yhcF 100 1.2e-64 1 126 1.0000 1.0000 primates skin infection; food poisoning; respiratory disease GntR family transcriptional regulator unaffected pathogenicity
HGMKMHHB_00164 PHI:124259 pgl (SAUSA300_1902) 100 7.9e-204 1 342 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease hypothetical protein reduced virulence
HGMKMHHB_00171 PHI:3285 saNOS 98.6 4.2e-216 1 358 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease NO-synthase reduced virulence
HGMKMHHB_00177 PHI:11229 scpA 99.5 8.7e-223 1 388 1.0000 1.0000 rodents skin infection; food poisoning; respiratory disease staphopain A increased virulence (hypervirulence)
HGMKMHHB_00178 PHI:7345 PurB 100 4.6e-249 1 431 1.0000 1.0000 bony fishes skin infection; food poisoning; respiratory disease adenylosuccinate lyase reduced virulence
HGMKMHHB_00201 PHI:8947 vraS 100 3.9e-190 1 347 1.0000 1.0000 moths pneumonia sensor protein increased virulence (hypervirulence)
HGMKMHHB_00202 PHI:8948 vraR 99.5 5.9e-109 1 209 1.0000 1.0000 moths pneumonia response regulator protein increased virulence (hypervirulence)
HGMKMHHB_00225 PHI:4991 PerR 100 1e-83 1 148 1.0000 1.0000 nematodes skin infection; food poisoning; respiratory disease hydrogen peroxide sensor 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
NJENCGFH_00062 QCV68762.1|GH23 99.6 1.05e-151 1 231 1 1
NJENCGFH_00122 AWR10858.1|GH32 100 0 1 494 1 1
NJENCGFH_00212 AWR34034.1|GT51 100 5.09e-171 1 269 1 1
HGMKMHHB_00062 QCV68762.1|GH23 99.6 1.05e-151 1 231 1 1
HGMKMHHB_00122 AWR10858.1|GH32 100 0 1 494 1 1
HGMKMHHB_00212 AWR34034.1|GT51 100 5.09e-171 1 269 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
NJENCGFH_00012 2.A.4.1.2 97.9 5.3e-173 1 326 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.4 The Cation Diffusion Facilitator (CDF) Family
NJENCGFH_00048 1.A.77.3.20 100 4.1e-59 1 117 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.77 The Mg2+/Ca2+ Uniporter (MCU) Family
NJENCGFH_00053 3.A.2.1.14 75.3 5.4e-217 1 502 1.0000 1.7552 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
NJENCGFH_00055 3.A.2.1.14 81.5 7.3e-216 4 470 0.9936 1.6434 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
NJENCGFH_00127 9.B.46.1.1 78.6 1.2e-77 19 205 0.9034 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.46 The <I>Staphylococcus aureus</I> Putative Quorum Sensing Peptide Exporter, AgrB (AgrB) Family
NJENCGFH_00135 2.A.38.4.6 99.8 2e-231 1 435 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.38 The K+ Transporter (Trk) Family
NJENCGFH_00136 3.A.1.14.7 100 3.4e-174 1 303 1.0000 1.1434 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
NJENCGFH_00169 2.A.47.1.11 99.8 3.9e-287 1 520 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.47 The Divalent Anion:Na+ Symporter (DASS) Family
NJENCGFH_00184 2.A.21.2.2 100 2.1e-285 1 512 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
NJENCGFH_00220 3.A.1.106.2 100 0 1 578 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
HGMKMHHB_00012 2.A.4.1.2 97.9 5.3e-173 1 326 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.4 The Cation Diffusion Facilitator (CDF) Family
HGMKMHHB_00048 1.A.77.3.20 100 4.1e-59 1 117 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.77 The Mg2+/Ca2+ Uniporter (MCU) Family
HGMKMHHB_00053 3.A.2.1.14 75.3 5.4e-217 1 502 1.0000 1.7552 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
HGMKMHHB_00055 3.A.2.1.14 81.5 7.3e-216 4 470 0.9936 1.6434 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
HGMKMHHB_00127 9.B.46.1.1 78.6 1.2e-77 19 205 0.9034 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.46 The <I>Staphylococcus aureus</I> Putative Quorum Sensing Peptide Exporter, AgrB (AgrB) Family
HGMKMHHB_00135 2.A.38.4.6 99.8 2e-231 1 435 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.38 The K+ Transporter (Trk) Family
HGMKMHHB_00136 3.A.1.14.7 100 3.4e-174 1 303 1.0000 1.1434 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
HGMKMHHB_00169 2.A.47.1.11 99.8 3.9e-287 1 520 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.47 The Divalent Anion:Na+ Symporter (DASS) Family
HGMKMHHB_00184 2.A.21.2.2 100 2.1e-285 1 512 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.21 The Solute:Sodium Symporter (SSS) Family
HGMKMHHB_00220 3.A.1.106.2 100 0 1 578 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