Model overview

PhenDB uses Support Vector Machine (SVM) models for the prediction of traits. Below is a list of all models (click model name for further information). For each model, the maximal mean balanced accuracy (given a 100% complete, 0% contaminated metagenomic bin) is given.

Legend: T = from text mining E = from expert opinion M = inferred from marker gene presence C = from Feldbauer et al 2015

Model name Description Training date Maximal accuracy
ARCHAEA Organism is an archaeon (C) 2018-06-19 08:50:24
PEN_180 Organism is resistant to penicillin (trained on S. aureus) (E) 2018-06-19 08:55:24
THERM Organism has a thermophilic lifestyle (C) 2018-06-19 08:58:05
THERM_OR_TOLERANT Organism has a thermophilic lifestyle or is thermotolerant (C) 2018-06-19 08:58:27
Aerobe Organism is capable of aerobic respiration (T) 2018-06-19 08:59:19
Anaerobe Organism is capable of anaerobic respiration (T) 2018-06-19 08:59:52
gram_stain Cells of organism stain Gram-positive (+) or Gram-negative (-) (T) 2018-06-19 09:00:19
motility Organism is capable of self-propelled motion (T) 2018-06-19 09:00:54
sporulation Organism is capable of producing endospores for persistence (T) 2018-06-19 09:01:24
Sulfate_reducer Organism is capable of using sulfate as terminal electron acceptor (T) 2018-06-19 09:01:56
amikacin_resistant Organism is resistant to amikacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:47
ciprofloxacin_resistant Organism is resistant to ciprofloxacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:49
alkb Organism is capable of degrading alkanes (M) 2019-02-01 14:12:13
AOB Organism is part of the clade of ammonia-oxidizing bacteria (E) 2019-02-01 14:12:28
ars Organism is capable of arsenic detoxification (M) 2019-02-01 14:12:36
avre Organism is a plant pathogen (based on AvrE virulence factor) (M) 2019-02-01 14:12:49
baicd Organism is capable of producing secondary bile acids (M) 2019-02-01 14:12:54
bena Organism is capable of degrading benzoate via hydroxylation (M) 2019-02-01 14:13:02
bpp Organism is capable of hydrolyzing phytate (M) 2019-02-01 14:13:21
bsh Organism is capable of deconjugating glycine and taurine from bile salts (M) 2019-02-01 14:13:29
buk2 Organism is capable of producing butyrate (M) 2019-02-01 14:13:37
chb Organism is capable of degrading chitine (M) 2019-02-01 14:13:59
cnta Organism is capable of aromatic ring hydroxylation (M) 2019-02-01 14:14:07
coos Organism is capable of assimilating CO (M) 2019-02-01 14:14:12
cutc Organism is capable of producing trimethylamine via choline (M) 2019-02-01 14:14:28
dbfa4 Organism is capable of performing dibenzofuran degradation (M) 2019-02-01 14:14:38
FACULTATIVE Organism is a facultative anaerobe (C) 2019-02-01 14:14:59
HALO Organism has a halophilic lifestyle (C) 2019-02-01 14:15:25
hsdh Organism is capable of degrading bile acids (M) 2019-02-01 14:15:40
hyda Organism is capable of producing H2 gas (M) 2019-02-01 14:15:49
METHANOTROPH Organism is capable of growth with methane as the sole carbon source (C) 2019-02-01 14:16:08
naph2 Organism is capable of degrading naphtalene (M) 2019-02-01 14:16:25
nif Organism is capable of fixing N2 (E) 2019-02-01 14:16:31
NOB Organism is part of the clade of nitrite-oxidizing bacteria (E) 2019-02-01 14:16:53
p450 Organism is capable of degrading fatty acids (M) 2019-02-01 14:16:59
phnx Organism is capable of hydrolyzing phosphonate (M) 2019-02-01 14:17:19
phod Organism is capable of recycling organic phosphorus (M) 2019-02-01 14:17:45
PHOTO Organism is capable of photon capture for energy acquisition (C) 2019-02-01 14:18:05
psa Organism is capable of synthesizing capsular polysaccharide (M) 2019-02-01 14:18:23
PSYCHRO Organism has a psychrophilic lifestyle (C) 2019-02-01 14:18:28
soxb Organism is capable of oxidizing thiosulfate (M) 2019-02-01 14:18:55
SYMBIONT Organism has an obligate intracellular lifestyle (C) 2019-02-01 14:19:08
T3SS Organism expresses a Type III secretion system (C) 2019-02-01 14:19:22
T4SS Organism expresses a Type IV secretion system (C) 2019-02-01 14:19:48
T6SS Organism expresses a Type VI secretion system (C) 2019-02-01 14:20:09
txta Organism is a plant pathogen (based on thaxtomin synthesis capability) (M) 2019-02-01 14:20:35
urea Organism is capable of degrading urea (M) 2019-02-01 14:20:49
xen Organism is capable of reducing various alpha-beta-unsaturated and nitro compounds (M) 2019-02-01 14:21:02
AUTO Organism is capable of growth with CO2 as sole carbon source (C) 2019-02-01 14:21:46