Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1066
  Reference Plasmid   NZ_CP103563.1
  Reference Plasmid Size   241084
  Reference Plasmid GC Content   0.52
  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
M0195617 GDOBIMDK_00139 125083 3 Gut 0.50 protein_coding synonymous_variant LOW 195T>C Arg65Arg
M0195618 GDOBIMDK_00139 125203 3 Gut 0.50 protein_coding synonymous_variant LOW 75C>T Gly25Gly
M0195619 GDOBIMDK_00140 125525 3 Gut 0.50 protein_coding missense_variant MODERATE 136G>A Val46Met
M0195620 GDOBIMDK_00141 125910 3 Gut 0.50 protein_coding missense_variant MODERATE 2375G>A Arg792Lys
M0195621 GDOBIMDK_00141 126377 3 Gut 0.50 protein_coding synonymous_variant LOW 1908T>C Gly636Gly
M0195622 GDOBIMDK_00148 132808 3 Gut 0.50 protein_coding missense_variant MODERATE 94G>C Val32Leu
M0195623 GDOBIMDK_00149 133013 3 Gut 0.50 protein_coding synonymous_variant LOW 222A>T Arg74Arg
M0195624 GDOBIMDK_00149 133100 3 Gut 0.50 protein_coding synonymous_variant LOW 135A>G Ser45Ser
M0195625 GDOBIMDK_00149 133123 3 Gut 0.50 protein_coding missense_variant MODERATE 112A>G Ile38Val
M0195626 GDOBIMDK_00149 133133 3 Gut 0.50 protein_coding synonymous_variant LOW 102C>A Ala34Ala






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
GDOBIMDK_00061 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
GDOBIMDK_00152 VFG001445 TraJ 73.7 1.6e-76 2 191 0.8444 0.9453 Invasion unknown protein experiment
GDOBIMDK_00191 VFG000908 Alpha-Hemolysin 98.1 2.9e-253 1 478 1.0 1 Exotoxin Hemolysin D experiment
GDOBIMDK_00192 VFG000907 Alpha-Hemolysin 98.3 0 1 707 1.0 1 Exotoxin Hemolysin B experiment
GDOBIMDK_00196 VFG000906 Alpha-Hemolysin 98 0 1 790 0.9394 0.7715 Exotoxin Hemolysin A experiment
GDOBIMDK_00197 VFG000905 Alpha-Hemolysin 97.1 5.9e-100 1 170 1.0 1 Exotoxin Hemolysin C experiment
GDOBIMDK_00061 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
GDOBIMDK_00152 VFG001445 TraJ 73.7 1.2e-75 2 191 0.8444 0.9453 Invasion unknown protein prediction
GDOBIMDK_00191 VFG012472 -Hemolysin 98.3 7.4e-253 1 478 1.0 1 Exotoxin Hemolysin D prediction
GDOBIMDK_00192 VFG012478 -Hemolysin 98.6 0 1 707 1.0 1 Exotoxin Hemolysin B prediction
GDOBIMDK_00196 VFG000906 Alpha-Hemolysin 98 0 1 790 0.9394 0.7715 Exotoxin Hemolysin A prediction
GDOBIMDK_00197 VFG012491 -Hemolysin 98.2 4e-100 1 170 1.0 1 Exotoxin Hemolysin C 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
GDOBIMDK_00203 Mercury (Hg) 93.8 4e-73 1 144 1.0000 1.0000 experiment
GDOBIMDK_00204 Mercury (Hg) 100 1.2e-62 1 116 1.0000 1.0000 experiment
GDOBIMDK_00205 Mercury (Hg) 90.1 7e-39 1 91 1.0000 1.0000 experiment
GDOBIMDK_00207 Mercury (Hg) 85.3 5e-268 1 564 1.0018 1.0071 experiment
GDOBIMDK_00208 Mercury (Hg) 82.6 1.3e-48 1 120 1.0083 1.0000 experiment
GDOBIMDK_00209 Mercury (Hg) 78.2 4.9e-33 1 78 1.0000 1.0000 experiment
GDOBIMDK_00220 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
GDOBIMDK_00203 Mercury (Hg) 100 4.3e-76 1 144 1.0000 0.7619 prediction
GDOBIMDK_00204 Mercury (Hg) 99.1 3.5e-60 1 116 1.0000 1.0000 prediction
GDOBIMDK_00205 Mercury (Hg) 100 6.3e-41 1 91 1.0000 0.8835 prediction
GDOBIMDK_00207 Mercury (Hg), Phenylmercury Acetate [class: Organo-mercury] 100 0 1 564 1.0000 1.0000 prediction
GDOBIMDK_00208 Mercury (Hg) 91.7 5.5e-53 1 120 1.0000 1.0000 prediction
GDOBIMDK_00209 Mercury (Hg) 83.3 2.7e-32 1 78 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
GDOBIMDK_00040 ARO:3004621 99 6.49e-211 1 286 1.0000 1.0000 aminoglycoside antibiotic AAC(3) antibiotic inactivation
GDOBIMDK_00077 ARO:3001878 100 1.15e-202 1 291 1.0000 1.0000 cephalosporin CTX-M beta-lactamase antibiotic inactivation
GDOBIMDK_00080 ARO:3002581 98 1.4e-140 2 199 0.9950 0.9754 aminoglycoside antibiotic AAC(6') antibiotic inactivation
GDOBIMDK_00081 ARO:3001396 100 6.06e-199 16 291 0.9485 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
GDOBIMDK_00087 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GDOBIMDK_00201 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
GDOBIMDK_00213 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
GDOBIMDK_00214 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
GDOBIMDK_00219 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GDOBIMDK_00220 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
GDOBIMDK_00221 ARO:3002602 100 5.68e-187 1 259 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
GDOBIMDK_00222 ARO:3002858 100 4.78e-119 1 165 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
GDOBIMDK_00230 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
GDOBIMDK_00237 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux






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
GDOBIMDK_00061 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
GDOBIMDK_00062 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
GDOBIMDK_00063 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
GDOBIMDK_00064 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
GDOBIMDK_00193 PHI:7837 hlyA 95.3 1.9e-125 18 251 0.9323 1.0000 rodents neonatal meningitis pore forming toxin alpha-hemolysin unaffected pathogenicity
GDOBIMDK_00196 PHI:7837 hlyA 98.5 0 1 790 0.9394 1.0000 rodents neonatal meningitis pore forming toxin alpha-hemolysin unaffected pathogenicity
GDOBIMDK_00223 PHI:9804 int 97.3 1.2e-13 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
GDOBIMDK_00256 PHI:3317 hsdR 73.1 0 1 1038 1.0000 1.0000 rodents Glasser's disease involved in pathogenicity 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
GDOBIMDK_00154 QAZ75040.1|GH23 100 4.96e-124 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
GDOBIMDK_00011 2.A.10.1.2 71 7.9e-121 1 317 0.9875 0.9664 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.10 The 2-Keto-3-Deoxygluconate Transporter (KdgT) Family
GDOBIMDK_00026 2.A.108.2.10 100 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GDOBIMDK_00027 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
GDOBIMDK_00062 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
GDOBIMDK_00063 2.C.1.1.3 100 3.7e-137 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
GDOBIMDK_00087 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GDOBIMDK_00088 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
GDOBIMDK_00112 1.E.53.1.11 98.5 2.5e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
GDOBIMDK_00191 8.A.1.3.1 96.9 1.8e-249 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
GDOBIMDK_00192 3.A.1.109.1 97.6 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
GDOBIMDK_00196 1.C.11.1.3 98.5 0 1 790 0.9394 0.7713 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.11 The Pore-forming RTX Toxin (RTX-toxin) Family
GDOBIMDK_00204 1.A.72.3.1 87.9 3e-54 1 116 1.0000 1.2747 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GDOBIMDK_00205 1.A.72.3.1 90.1 2.6e-37 1 91 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GDOBIMDK_00209 1.A.72.5.1 100 1.8e-39 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
GDOBIMDK_00218 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
GDOBIMDK_00237 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
GDOBIMDK_00238 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
GDOBIMDK_00266 2.A.3.1.10 99.6 5e-265 9 475 0.9832 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family