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
Aerobe Organism is capable of aerobic respiration (T) 2018-06-19 08:59:19 0.96
alkb Organism is capable of degrading alkanes (M) 2018-06-19 08:50:04 0.83
amikacin_resistant Organism is resistant to amikacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:47 0.83
Anaerobe Organism is capable of anaerobic respiration (T) 2018-06-19 08:59:52 0.93
AOB Organism is part of the clade of ammonia-oxidizing bacteria (E) 2018-06-19 08:50:17 0.96
ARCHAEA Organism is an archaeon (C) 2018-06-19 08:50:24 1.00
ars Organism is capable of arsenic detoxification (M) 2018-06-19 08:50:59 0.70
AUTO Organism is capable of growth with CO2 as sole carbon source (C) 2018-06-19 08:51:11 0.79
avre Organism is a plant pathogen (based on AvrE virulence factor) (M) 2018-06-19 08:51:24 0.88
baicd Organism is capable of producing secondary bile acids (M) 2018-06-19 08:51:28 0.55
bena Organism is capable of degrading benzoate via hydroxylation (M) 2018-06-19 08:51:35 0.81
bpp Organism is capable of hydrolyzing phytate (M) 2018-06-19 08:51:50 0.53
bsh Organism is capable of deconjugating glycine and taurine from bile salts (M) 2018-06-19 08:51:56 0.84
buk2 Organism is capable of producing butyrate (M) 2018-06-19 08:52:04 0.87
chb Organism is capable of degrading chitine (M) 2018-06-19 08:52:22 0.83
ciprofloxacin_resistant Organism is resistant to ciprofloxacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:49 0.92
cnta Organism is capable of aromatic ring hydroxylation (M) 2018-06-19 08:52:30 0.71
coos Organism is capable of assimilating CO (M) 2018-06-19 08:52:34 0.84
cutc Organism is capable of producing trimethylamine via choline (M) 2018-06-19 08:52:47 0.77
dbfa4 Organism is capable of performing dibenzofuran degradation (M) 2018-06-19 08:52:56 0.71
FACULTATIVE Organism is a facultative anaerobe (C) 2018-06-19 08:53:14 0.80
gram_stain Cells of organism stain Gram-positive (+) or Gram-negative (-) (T) 2018-06-19 09:00:19 0.98
HALO Organism has a halophilic lifestyle (C) 2018-06-19 08:53:37 0.73
hsdh Organism is capable of degrading bile acids (M) 2018-06-19 08:53:49 0.84
hyda Organism is capable of producing H2 gas (M) 2018-06-19 08:53:57 0.81
METHANOTROPH Organism is capable of growth with methane as the sole carbon source (C) 2018-06-19 08:54:17 0.84
motility Organism is capable of self-propelled motion (T) 2018-06-19 09:00:54 0.95
naph2 Organism is capable of degrading naphtalene (M) 2018-06-19 08:54:31 0.58
nif Organism is capable of fixing N2 (E) 2018-06-19 08:54:39 0.92
NOB Organism is part of the clade of nitrite-oxidizing bacteria (E) 2018-06-19 08:54:59 0.90
p450 Organism is capable of degrading fatty acids (M) 2018-06-19 08:55:05 0.72
PEN_180 Organism is resistant to penicillin (trained on S. aureus) (E) 2018-06-19 08:55:24 0.96
phnx Organism is capable of hydrolyzing phosphonate (M) 2018-06-19 08:55:25 0.85
phod Organism is capable of recycling organic phosphorus (M) 2018-06-19 08:55:49 0.81
PHOTO Organism is capable of photon capture for energy acquisition (C) 2018-06-19 08:56:05 0.93
psa Organism is capable of synthesizing capsular polysaccharide (M) 2018-06-19 08:56:22 0.64
PSYCHRO Organism has a psychrophilic lifestyle (C) 2018-06-19 08:56:26 0.70
soxb Organism is capable of oxidizing thiosulfate (M) 2018-06-19 08:56:50 0.79
sporulation Organism is capable of producing endospores for persistence (T) 2018-06-19 09:01:24 0.96
Sulfate_reducer Organism is capable of using sulfate as terminal electron acceptor (T) 2018-06-19 09:01:56 0.96
SYMBIONT Organism has an obligate intracellular lifestyle (C) 2018-06-19 08:57:03 1.00
T3SS Organism expresses a Type III secretion system (C) 2018-06-19 08:57:11 0.83
T4SS Organism expresses a Type IV secretion system (C) 2018-06-19 08:57:29 0.88
T6SS Organism expresses a Type VI secretion system (C) 2018-06-19 08:57:45 0.82
THERM Organism has a thermophilic lifestyle (C) 2018-06-19 08:58:05 0.78
THERM_OR_TOLERANT Organism has a thermophilic lifestyle or is thermotolerant (C) 2018-06-19 08:58:27 0.79
txta Organism is a plant pathogen (based on thaxtomin synthesis capability) (M) 2018-06-19 08:58:50 0.54
urea Organism is capable of degrading urea (M) 2018-06-19 08:59:03 0.87
xen Organism is capable of reducing various alpha-beta-unsaturated and nitro compounds (M) 2018-06-19 08:59:14 0.87