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 1.00
PEN_180 Organism is resistant to penicillin (trained on S. aureus) (E) 2018-06-19 08:55:24 0.96
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
Aerobe Organism is capable of aerobic respiration (T) 2018-06-19 08:59:19 0.96
Anaerobe Organism is capable of anaerobic respiration (T) 2018-06-19 08:59:52 0.93
gram_stain Cells of organism stain Gram-positive (+) or Gram-negative (-) (T) 2018-06-19 09:00:19 0.98
motility Organism is capable of self-propelled motion (T) 2018-06-19 09:00:54 0.95
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
amikacin_resistant Organism is resistant to amikacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:47 0.83
ciprofloxacin_resistant Organism is resistant to ciprofloxacin. (Trained on Acinetobacter baumannii.) (E) 2018-09-11 09:32:49 0.92
alkb Organism is capable of degrading alkanes (M) 2019-02-01 14:12:13 0.83
AOB Organism is part of the clade of ammonia-oxidizing bacteria (E) 2019-02-01 14:12:28 0.96
ars Organism is capable of arsenic detoxification (M) 2019-02-01 14:12:36 0.67
avre Organism is a plant pathogen (based on AvrE virulence factor) (M) 2019-02-01 14:12:49 0.88
baicd Organism is capable of producing secondary bile acids (M) 2019-02-01 14:12:54 0.56
bena Organism is capable of degrading benzoate via hydroxylation (M) 2019-02-01 14:13:02 0.81
bpp Organism is capable of hydrolyzing phytate (M) 2019-02-01 14:13:21 0.54
bsh Organism is capable of deconjugating glycine and taurine from bile salts (M) 2019-02-01 14:13:29 0.85
buk2 Organism is capable of producing butyrate (M) 2019-02-01 14:13:37 0.87
chb Organism is capable of degrading chitine (M) 2019-02-01 14:13:59 0.82
cnta Organism is capable of aromatic ring hydroxylation (M) 2019-02-01 14:14:07 0.74
coos Organism is capable of assimilating CO (M) 2019-02-01 14:14:12 0.82
cutc Organism is capable of producing trimethylamine via choline (M) 2019-02-01 14:14:28 0.79
dbfa4 Organism is capable of performing dibenzofuran degradation (M) 2019-02-01 14:14:38 0.69
FACULTATIVE Organism is a facultative anaerobe (C) 2019-02-01 14:14:59 0.82
HALO Organism has a halophilic lifestyle (C) 2019-02-01 14:15:25 0.75
hsdh Organism is capable of degrading bile acids (M) 2019-02-01 14:15:40 0.83
hyda Organism is capable of producing H2 gas (M) 2019-02-01 14:15:49 0.80
METHANOTROPH Organism is capable of growth with methane as the sole carbon source (C) 2019-02-01 14:16:08 0.97
naph2 Organism is capable of degrading naphtalene (M) 2019-02-01 14:16:25 0.57
nif Organism is capable of fixing N2 (E) 2019-02-01 14:16:31 0.91
NOB Organism is part of the clade of nitrite-oxidizing bacteria (E) 2019-02-01 14:16:53 0.86
p450 Organism is capable of degrading fatty acids (M) 2019-02-01 14:16:59 0.75
phnx Organism is capable of hydrolyzing phosphonate (M) 2019-02-01 14:17:19 0.84
phod Organism is capable of recycling organic phosphorus (M) 2019-02-01 14:17:45 0.83
PHOTO Organism is capable of photon capture for energy acquisition (C) 2019-02-01 14:18:05 0.92
psa Organism is capable of synthesizing capsular polysaccharide (M) 2019-02-01 14:18:23 0.65
PSYCHRO Organism has a psychrophilic lifestyle (C) 2019-02-01 14:18:28 0.69
soxb Organism is capable of oxidizing thiosulfate (M) 2019-02-01 14:18:55 0.79
SYMBIONT Organism has an obligate intracellular lifestyle (C) 2019-02-01 14:19:08 0.99
T3SS Organism expresses a Type III secretion system (C) 2019-02-01 14:19:22 0.91
T4SS Organism expresses a Type IV secretion system (C) 2019-02-01 14:19:48 0.91
T6SS Organism expresses a Type VI secretion system (C) 2019-02-01 14:20:09 0.90
txta Organism is a plant pathogen (based on thaxtomin synthesis capability) (M) 2019-02-01 14:20:35 0.53
urea Organism is capable of degrading urea (M) 2019-02-01 14:20:49 0.86
xen Organism is capable of reducing various alpha-beta-unsaturated and nitro compounds (M) 2019-02-01 14:21:02 0.84
AUTO Organism is capable of growth with CO2 as sole carbon source (C) 2019-02-01 14:21:46 0.81
ac Organism is producing acetic_acid 2019-11-21 13:10:13 0.78
actn_R Organism is producing R_acetoin 2019-11-21 13:10:25 0.88
Asaccharolytic Organism has a Asaccharolytic lifestyle 2019-11-21 13:10:32 0.76
btoh Organism is producing 1_butanol 2019-11-21 13:10:43 0.98
but Organism is producing butyric_acid 2019-11-21 13:10:47 0.94
etoh Organism is producing ethanol 2019-11-21 13:10:56 0.83
Fermentative Organism has a Fermentative lifestyle 2019-11-21 13:11:06 0.83
for Organism is producing formic_acid 2019-11-21 13:11:16 0.82
glc_D Organism is producing D_glucose 2019-11-21 13:11:26 0.79
h2 Organism is producing hydrogen 2019-11-21 13:11:30 0.87
indole Organism is producing indole 2019-11-21 13:11:39 0.80
isobut Organism is producing isobutyric_acid 2019-11-21 13:11:46 0.87
isoval Organism is producing isovaleric_acid 2019-11-21 13:11:53 0.92
lac_D Organism is producing D_lactic_acid 2019-11-21 13:12:00 0.88
lac_L Organism is producing L_lactic_acid 2019-11-21 13:12:11 0.84
nonfermentative Organism has a nonfermentative lifestyle 2019-11-21 13:12:21 0.67
ppa Organism is producing propionic_acid 2019-11-21 13:12:32 0.87
Saccharolytic Organism has a Saccharolytic lifestyle 2019-11-21 13:12:41 0.90
succ Organism is producing succinic_acid 2019-11-21 13:12:50 0.90
nanoaerobemicro Organism has a nanoaerobemicro lifestyle 2019-11-21 13:13:00 0.92