Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C145
  Reference Plasmid   CP088630.1
  Reference Plasmid Size   162324
  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
M0145388 MFAPLIII_00128 119734 12 Gut 0.92 protein_coding upstream_gene_variant MODIFIER -3901T>C None
M0145389 MFAPLIII_00133 120253 12 Gut 0.92 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0145390 MFAPLIII_00133 120261 11 Gut 0.85 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0145391 MFAPLIII_00133 120416 12 Gut 0.92 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0145392 MFAPLIII_00134 120861 12 Gut 0.92 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0145393 MFAPLIII_00134 120918 12 Gut 0.92 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0145394 MFAPLIII_00135 121023 11 Gut 0.85 protein_coding missense_variant MODERATE 509A>C Gln170Pro
M0145395 MFAPLIII_00135 121072 12 Gut 0.92 protein_coding missense_variant MODERATE 460A>T Arg154Trp
M0145396 MFAPLIII_00130 121793 11 Gut 0.85 protein_coding upstream_gene_variant MODIFIER -4156A>G None
M0145397 MFAPLIII_00130 121868 9 Gut 0.69 protein_coding upstream_gene_variant MODIFIER -4231G>A None
M0145398 MFAPLIII_00137 121928 6 Gut 0.46 protein_coding synonymous_variant LOW 39G>A Gln13Gln
M0145399 MFAPLIII_00137 121929 6 Gut 0.46 protein_coding synonymous_variant LOW 40A>C Arg14Arg
M0145400 MFAPLIII_00137 121934 6 Gut 0.46 protein_coding synonymous_variant LOW 45G>A Ala15Ala
M0145401 MFAPLIII_00137 121935 6 Gut 0.46 protein_coding missense_variant MODERATE 46A>G Ile16Val
M0145402 MFAPLIII_00137 121937 6 Gut 0.46 protein_coding synonymous_variant LOW 48T>C Ile16Ile
M0145403 MFAPLIII_00137 121976 5 Gut 0.38 protein_coding synonymous_variant LOW 87G>A Gln29Gln
M0145404 MFAPLIII_00137 121983 5 Gut 0.38 protein_coding missense_variant MODERATE 94G>A Ala32Thr
M0145405 MFAPLIII_00137 122000 5 Gut 0.38 protein_coding synonymous_variant LOW 111C>T Ala37Ala
M0145406 MFAPLIII_00137 122018 5 Gut 0.38 protein_coding synonymous_variant LOW 129A>G Thr43Thr
M0145407 MFAPLIII_00137 122037 5 Gut 0.38 protein_coding missense_variant MODERATE 148T>C Trp50Arg
M0145408 MFAPLIII_00137 122042 5 Gut 0.38 protein_coding synonymous_variant LOW 153A>T Val51Val
M0145409 MFAPLIII_00137 122066 5 Gut 0.38 protein_coding synonymous_variant LOW 177A>G Gly59Gly
M0145410 MFAPLIII_00137 122078 5 Gut 0.38 protein_coding synonymous_variant LOW 189C>A Gly63Gly
M0145411 MFAPLIII_00137 122120 5 Gut 0.38 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0145412 MFAPLIII_00137 122195 3 Gut 0.23 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0145413 MFAPLIII_00137 122213 3 Gut 0.23 protein_coding synonymous_variant LOW 324G>A Lys108Lys
M0145414 MFAPLIII_00138 122240 3 Gut 0.23 protein_coding missense_variant MODERATE 25A>G Lys9Glu
M0145415 MFAPLIII_00138 122244 3 Gut 0.23 protein_coding missense_variant MODERATE 29T>A Leu10Gln
M0145416 MFAPLIII_00138 122261 3 Gut 0.23 protein_coding missense_variant MODERATE 46G>C Val16Leu
M0145417 MFAPLIII_00138 122269 3 Gut 0.23 protein_coding synonymous_variant LOW 54T>C Ser18Ser
M0145418 MFAPLIII_00138 122275 3 Gut 0.23 protein_coding synonymous_variant LOW 60A>G Leu20Leu
M0145419 MFAPLIII_00138 122326 3 Gut 0.23 protein_coding synonymous_variant LOW 111T>G Pro37Pro
M0145420 MFAPLIII_00135 121230 11 Gut 0.85 protein_coding missense_variant MODERATE 302T>A Leu101Gln
M0145421 MFAPLIII_00135 121232 11 Gut 0.85 protein_coding missense_variant MODERATE 300C>A Asp100Glu
M0145422 MFAPLIII_00135 121241 11 Gut 0.85 protein_coding synonymous_variant LOW 291G>C Leu97Leu
M0145423 MFAPLIII_00135 121243 11 Gut 0.85 protein_coding missense_variant MODERATE 289C>A Leu97Met






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
MFAPLIII_00127 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
MFAPLIII_00174 VFG048621 Aerobactin 99.7 0 1 732 1.0 0.9986 Nutritional/Metabolic factor ferric aerobactin receptor IutA experiment
MFAPLIII_00127 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction
MFAPLIII_00174 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
MFAPLIII_00108 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
MFAPLIII_00097 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
MFAPLIII_00101 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
MFAPLIII_00102 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
MFAPLIII_00107 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
MFAPLIII_00108 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
MFAPLIII_00109 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
MFAPLIII_00110 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement






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
MFAPLIII_00111 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
MFAPLIII_00127 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
MFAPLIII_00128 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
MFAPLIII_00129 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
MFAPLIII_00130 PHI:10792 cjrA 100 3.6e-162 1 283 1.0000 0.9725 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
MFAPLIII_00174 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
MFAPLIII_00032 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
MFAPLIII_00073 1.E.53.1.11 100 1.1e-21 1 49 1.0000 0.7206 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
MFAPLIII_00096 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
MFAPLIII_00097 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)
MFAPLIII_00106 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
MFAPLIII_00128 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
MFAPLIII_00129 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
MFAPLIII_00149 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
MFAPLIII_00150 2.A.108.2.10 99.6 8.1e-307 1 553 1.0000 3.1965 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family