Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C143
  Reference Plasmid   CP088611.1
  Reference Plasmid Size   155469
  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
M0145184 HOGEEGCH_00097 88884 9 Gut 0.90 protein_coding missense_variant MODERATE 167T>C Met56Thr
M0145185 HOGEEGCH_00098 89403 10 Gut 1.00 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0145186 HOGEEGCH_00098 89566 9 Gut 0.90 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0145187 HOGEEGCH_00099 90011 9 Gut 0.90 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0145188 HOGEEGCH_00099 90068 9 Gut 0.90 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0145189 HOGEEGCH_00100 90222 9 Gut 0.90 protein_coding missense_variant MODERATE 460A>T Arg154Trp
M0145190 HOGEEGCH_00100 90380 10 Gut 1.00 protein_coding missense_variant MODERATE 302T>A Leu101Gln
M0145191 HOGEEGCH_00100 90382 10 Gut 1.00 protein_coding missense_variant MODERATE 300C>A Asp100Glu
M0145192 HOGEEGCH_00100 90391 10 Gut 1.00 protein_coding synonymous_variant LOW 291G>C Leu97Leu
M0145193 HOGEEGCH_00100 90393 10 Gut 1.00 protein_coding missense_variant MODERATE 289C>A Leu97Met
M0145194 HOGEEGCH_00094 90943 10 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4132A>G None
M0145195 HOGEEGCH_00094 91018 8 Gut 0.80 protein_coding upstream_gene_variant MODIFIER -4207G>A None
M0145196 HOGEEGCH_00102 91078 6 Gut 0.60 protein_coding synonymous_variant LOW 39G>A Gln13Gln
M0145197 HOGEEGCH_00102 91079 6 Gut 0.60 protein_coding synonymous_variant LOW 40A>C Arg14Arg
M0145198 HOGEEGCH_00102 91084 6 Gut 0.60 protein_coding synonymous_variant LOW 45G>A Ala15Ala
M0145199 HOGEEGCH_00102 91085 6 Gut 0.60 protein_coding missense_variant MODERATE 46A>G Ile16Val
M0145200 HOGEEGCH_00102 91087 6 Gut 0.60 protein_coding synonymous_variant LOW 48T>C Ile16Ile
M0145201 HOGEEGCH_00102 91126 6 Gut 0.60 protein_coding synonymous_variant LOW 87G>A Gln29Gln
M0145202 HOGEEGCH_00102 91133 6 Gut 0.60 protein_coding missense_variant MODERATE 94G>A Ala32Thr
M0145203 HOGEEGCH_00102 91150 6 Gut 0.60 protein_coding synonymous_variant LOW 111C>T Ala37Ala
M0145204 HOGEEGCH_00102 91168 6 Gut 0.60 protein_coding synonymous_variant LOW 129A>G Thr43Thr
M0145205 HOGEEGCH_00102 91187 6 Gut 0.60 protein_coding missense_variant MODERATE 148T>C Trp50Arg
M0145206 HOGEEGCH_00102 91192 6 Gut 0.60 protein_coding synonymous_variant LOW 153A>T Val51Val
M0145207 HOGEEGCH_00102 91216 6 Gut 0.60 protein_coding synonymous_variant LOW 177A>G Gly59Gly
M0145208 HOGEEGCH_00102 91228 6 Gut 0.60 protein_coding synonymous_variant LOW 189C>T Gly63Gly
M0145209 HOGEEGCH_00102 91270 6 Gut 0.60 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0145210 HOGEEGCH_00102 91345 4 Gut 0.40 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0145211 HOGEEGCH_00102 91363 5 Gut 0.50 protein_coding synonymous_variant LOW 324G>A Lys108Lys
M0145212 HOGEEGCH_00103 91390 5 Gut 0.50 protein_coding missense_variant MODERATE 25A>G Lys9Glu
M0145213 HOGEEGCH_00103 91394 5 Gut 0.50 protein_coding missense_variant MODERATE 29T>A Leu10Gln
M0145214 HOGEEGCH_00103 91411 5 Gut 0.50 protein_coding missense_variant MODERATE 46G>C Val16Leu
M0145215 HOGEEGCH_00103 91419 5 Gut 0.50 protein_coding synonymous_variant LOW 54T>C Ser18Ser
M0145216 HOGEEGCH_00103 91425 5 Gut 0.50 protein_coding synonymous_variant LOW 60A>G Leu20Leu
M0145217 HOGEEGCH_00103 91476 5 Gut 0.50 protein_coding synonymous_variant LOW 111T>G Pro37Pro
M0145218 HOGEEGCH_00103 91529 4 Gut 0.40 protein_coding missense_variant MODERATE 164T>A Leu55Gln
M0145219 HOGEEGCH_00103 91544 4 Gut 0.40 protein_coding missense_variant MODERATE 179G>A Gly60Glu
M0145220 HOGEEGCH_00103 91545 4 Gut 0.40 protein_coding synonymous_variant LOW 180G>A Gly60Gly
M0145221 HOGEEGCH_00103 91551 4 Gut 0.40 protein_coding synonymous_variant LOW 186T>C His62His
M0145222 HOGEEGCH_00103 91552 4 Gut 0.40 protein_coding missense_variant MODERATE 187C>A Gln63Lys
M0145223 HOGEEGCH_00103 91599 4 Gut 0.40 protein_coding synonymous_variant LOW 234A>T Gly78Gly
M0145224 HOGEEGCH_00103 91605 4 Gut 0.40 protein_coding synonymous_variant LOW 240G>A Arg80Arg
M0145225 HOGEEGCH_00103 91608 4 Gut 0.40 protein_coding synonymous_variant LOW 243A>G Val81Val
M0145226 HOGEEGCH_00103 91617 4 Gut 0.40 protein_coding synonymous_variant LOW 252T>C Cys84Cys
M0145227 HOGEEGCH_00103 91620 4 Gut 0.40 protein_coding synonymous_variant LOW 255A>T Thr85Thr
M0145228 HOGEEGCH_00103 91626 4 Gut 0.40 protein_coding synonymous_variant LOW 261G>A Ala87Ala
M0145229 HOGEEGCH_00103 91629 4 Gut 0.40 protein_coding synonymous_variant LOW 264C>T Arg88Arg
M0145230 HOGEEGCH_00103 91680 4 Gut 0.40 protein_coding synonymous_variant LOW 315C>T Arg105Arg
M0145231 HOGEEGCH_00103 91683 4 Gut 0.40 protein_coding synonymous_variant LOW 318T>G Thr106Thr
M0145232 HOGEEGCH_00103 91687 4 Gut 0.40 protein_coding missense_variant MODERATE 322G>A Val108Ile
M0145233 HOGEEGCH_00103 91734 4 Gut 0.40 protein_coding synonymous_variant LOW 369T>C Phe123Phe
M0145234 HOGEEGCH_00103 91746 4 Gut 0.40 protein_coding synonymous_variant LOW 381T>A Arg127Arg
M0145235 HOGEEGCH_00103 91756 4 Gut 0.40 protein_coding synonymous_variant LOW 391T>C Leu131Leu
M0145236 HOGEEGCH_00098 89411 8 Gut 0.80 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0145237 HOGEEGCH_00100 90173 8 Gut 0.80 protein_coding missense_variant MODERATE 509A>C Gln170Pro






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
HOGEEGCH_00091 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
HOGEEGCH_00153 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
HOGEEGCH_00091 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
HOGEEGCH_00153 VFG033944 Aerobactin 100 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor precusor IutA 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
HOGEEGCH_00124 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






        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
HOGEEGCH_00040 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
HOGEEGCH_00122 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
HOGEEGCH_00123 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
HOGEEGCH_00124 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
HOGEEGCH_00125 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
HOGEEGCH_00133 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) 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
HOGEEGCH_00091 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
HOGEEGCH_00092 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
HOGEEGCH_00093 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
HOGEEGCH_00094 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
HOGEEGCH_00121 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
HOGEEGCH_00153 PHI:6563 iucA 99.7 0 1 732 1.0000 0.9986 rodents pneumonia aerobactin 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
HOGEEGCH_00019 AKD26598.1|GH23 100 3.49e-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
HOGEEGCH_00040 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)
HOGEEGCH_00041 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
HOGEEGCH_00062 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
HOGEEGCH_00092 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
HOGEEGCH_00093 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
HOGEEGCH_00114 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
HOGEEGCH_00115 2.A.108.2.10 99.8 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
HOGEEGCH_00127 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