Model Internals

Each PhenDB model is trained on sets of bacterial ENOGs (orthologous groups from EggNOG 4.5), which have or have not been identified in the training genomes. Each ENOG is given a weight, with the magnitude of the weight being the importance of that ENOG for the final prediction. The sign of the weight indicates whether the presence (positive weight) or absence (negative weight) of this ENOG is indicative of the trait.

This table lists the 250 highest-ranking ENOGs of this model.

rank in model enog name enog description weight in model
1 ENOG4105CKM Branched-chain carboxylic acid kinase 0.093280
2 ENOG4107RE7 phosphate butyryltransferase 0.044495
3 ENOG4105CYC Transferase 0.041728
4 ENOG4105CHU acetyl-coa acetyltransferase 0.028318
5 ENOG4105E39 Enoyl-CoA hydratase 0.027533
6 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase 0.024067
7 ENOG4105C1G acyl-Coa dehydrogenase 0.023346
8 ENOG4108M36 Histidine kinase 0.019495
9 ENOG4108JQ1 Dehydrogenase 0.018637
10 ENOG4108T5Q phosphate 0.018217
11 ENOG4108Z0Z intracellular protease Pfpi family 0.018119
12 ENOG4105CCS Glutamate formiminotransferase 0.018048
13 ENOG4108UQV Membrane 0.017887
14 ENOG4108V1J Has antioxidant activity. Could remove peroxides or H(2)O(2) (By similarity) 0.017650
15 ENOG4108JUB Transcriptional regulator 0.017536
16 ENOG4105CDM Glutamate-1-semialdehyde aminotransferase -0.017377
17 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) 0.017025
18 ENOG4105C6Y Udp-glucose 6-dehydrogenase 0.017018
19 ENOG4105C7E Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA) (By similarity) -0.016846
20 ENOG4105CIF Ornithine Cyclodeaminase 0.016622
21 ENOG4108JJ7 ABC transporter 0.016411
22 ENOG4105FBU hydrolase family 16 0.016000
23 ENOG4105FKQ transcriptional regulator 0.015822
24 ENOG4108ZRZ Transcriptional regulator (AsnC family) 0.015789
25 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.015684
26 ENOG4105E79 Binding Domain protein 0.015673
27 ENOG4105C6I Resolvase 0.015519
28 ENOG4105CHD Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1- P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity) 0.015428
29 ENOG4105E37 hemerythrin hhe cation binding domain protein 0.015307
30 ENOG4105VPX protein, conserved in bacteria 0.015307
31 ENOG4105KME endoribonuclease L-psp 0.015257
32 ENOG4108IQF Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA (By similarity) -0.015162
33 ENOG4105C10 Electron transfer flavoprotein 0.015061
34 ENOG4105G5W regulator Fur family 0.015049
35 ENOG4105C7S Dehydrogenase 0.014982
36 ENOG4105D6W Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps (By similarity) -0.014846
37 ENOG4105K4S protein with conserved CXXC pairs 0.014789
38 ENOG4108MY4 Endonuclease Exonuclease phosphatase 0.014786
39 ENOG4105DU0 nucleoside hydrolase -0.014699
40 ENOG4105QTV Membrane 0.014627
41 ENOG4105D52 delta-aminolevulinic acid dehydratase -0.014278
42 ENOG4105D5U fad dependent oxidoreductase 0.014264
43 ENOG4105VM8 Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity) 0.014217
44 ENOG4105PW4 Sugar fermentation stimulation protein homolog 0.014114
45 ENOG4107YWT Membrane 0.014099
46 ENOG4107QQI Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity) -0.014015
47 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.013979
48 ENOG4107Z9Z Hydrolase 0.013968
49 ENOG4105VDU S-adenosyl-l-methionine hydroxide adenosyltransferase 0.013894
50 ENOG4105C84 Histidine ammonia-lyase 0.013552
51 ENOG4105CGP Urocanate hydratase 0.013409
52 ENOG41069SU NA 0.013378
53 ENOG4105E90 ABC transporter 0.013333
54 ENOG4105CGZ zinc metallopeptidase 0.013267
55 ENOG4108HHA Transketolase -0.013209
56 ENOG4108RF9 lipolytic protein, gdsl family -0.013162
57 ENOG4105WAN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.013067
58 ENOG4105FCI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate (By similarity) 0.013003
59 ENOG4105ZZ1 Membrane -0.012927
60 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase 0.012850
61 ENOG4107QU8 Transferase -0.012788
62 ENOG4105EMZ Hydrogenase large subunit domain protein 0.012771
63 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) 0.012744
64 ENOG4105CZ1 Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (By similarity) 0.012727
65 ENOG4107QYA phosphate 0.012723
66 ENOG4105D8X mechanosensitive ion channel 0.012679
67 ENOG4105EI2 Pseudouridine synthase -0.012657
68 ENOG41090A1 ferritin 0.012653
69 ENOG4107QPR SAICAR synthetase -0.012638
70 ENOG4106KUD Membrane 0.012565
71 ENOG4108DFD Uba ThiF-type NAD FAD-binding protein -0.012544
72 ENOG4105CVJ phosphoglycerate mutase 0.012520
73 ENOG4108C33 Resolvase -0.012509
74 ENOG4105DUM transcriptional regulator, lysR family 0.012475
75 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase 0.012466
76 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.012387
77 ENOG4105J9S Membrane 0.012359
78 ENOG4108VZ1 Uncharacterised ACR, YkgG family COG1556 0.012347
79 ENOG4107RUY (E1 component), alpha subunit 0.012285
80 ENOG4105EE0 oxidoreductase 0.012258
81 ENOG4108IJ8 ABC transporter 0.012251
82 ENOG4105C4U 4-methyl-5-beta-hydroxyethylthiazole kinase 0.012240
83 ENOG4108QF3 pyruvate flavodoxin ferredoxin oxidoreductase 0.012201
84 ENOG4107RSS Hydrogenase accessory protein HypB -0.012132
85 ENOG4105I09 ABC, transporter -0.012130
86 ENOG4105DZW Dipeptidase 0.012097
87 ENOG4105BZJ Electron transfer flavoprotein 0.012078
88 ENOG4105NMU Transcriptional regulator -0.012059
89 ENOG4105C4B ABC transporter, permease -0.012023
90 ENOG4108RTW conjugative transposon membrane protein 0.011992
91 ENOG4105CRQ synthase (Component I) -0.011976
92 ENOG4107S6Z Na H antiporter 0.011922
93 ENOG4105PV6 Rhodanese domain protein -0.011898
94 ENOG4105CI2 imidazolone-5-propionate hydrolase 0.011868
95 ENOG4105CPP Dehydrogenase, E1 component 0.011866
96 ENOG4105D82 Glutamate dehydrogenase 0.011801
97 ENOG4105EMD TRANSCRIPTIONal 0.011768
98 ENOG4105KGS Membrane -0.011739
99 ENOG4105C0N N-acetylglutamate semialdehyde dehydrogenase -0.011725
100 ENOG4107QSE Dipeptidase -0.011716
101 ENOG4105EW4 (LipO)protein -0.011702
102 ENOG4105C56 H( )-stimulated, divalent metal cation uptake system (By similarity) 0.011696
103 ENOG4105DAP Nicotinate phosphoribosyltransferase -0.011660
104 ENOG4107WM1 Major Intrinsic Protein -0.011643
105 ENOG4108UUM single-stranded DNA-binding protein 0.011642
106 ENOG4107QHI -hydrogenase 0.011621
107 ENOG4105DWF phosphomethylpyrimidine kinase 0.011620
108 ENOG4108UT2 hemolysin iii 0.011533
109 ENOG4106UJV Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity) 0.011519
110 ENOG4105EH4 helicase 0.011485
111 ENOG4105D78 K07001 NTE family protein 0.011481
112 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.011474
113 ENOG4105C0X amino acid -0.011424
114 ENOG4108QXE glycerophosphoryl diester phosphodiesterase 0.011423
115 ENOG41068WG NA 0.011388
116 ENOG4105KA6 Transcriptional regulator, TetR family 0.011367
117 ENOG4105KPB redox protein, regulator of disulfide bond -0.011360
118 ENOG4106VXV Conserved Protein -0.011273
119 ENOG4108KN7 Removes 5-oxoproline from various penultimate amino acid residues except L-proline (By similarity) 0.011271
120 ENOG4108ZHB oxidoreductase 0.011208
121 ENOG4108RAV Conserved protein -0.011191
122 ENOG4105NAX ABC-type nitrate sulfonate bicarbonate transport 0.011140
123 ENOG4107QVE (Anaerobic) ribonucleoside-triphosphate reductase 0.011125
124 ENOG4108RVE abc transporter atp-binding protein -0.011108
125 ENOG4108FV8 A G-specific adenine glycosylase -0.011102
126 ENOG4107RKZ ld-carboxypeptidase 0.011093
127 ENOG4105C26 Dehydrogenase 0.011091
128 ENOG4108XAU NA -0.011043
129 ENOG4107QW4 alcohol dehydrogenase 0.011034
130 ENOG4105CJG carbon-monoxide dehydrogenase catalytic subunit -0.011018
131 ENOG4105HMI Membrane 0.011001
132 ENOG4108RVA ribokinase -0.011000
133 ENOG4105C0A alcohol dehydrogenase 0.010998
134 ENOG4105DZR Type I site-specific deoxyribonuclease -0.010993
135 ENOG410813P histidinol phosphate phosphatase hisj family -0.010993
136 ENOG4105E2R ROK family -0.010980
137 ENOG4107XRV hypoxanthine phosphoribosyltransferase -0.010974
138 ENOG4107RBB ABC transporter, permease 0.010858
139 ENOG4107RDT Channel that permits osmotically driven movement of water in both directions. It is involved in the osmoregulation and in the maintenance of cell turgor during volume expansion in rapidly growing cells. It mediates rapid entry or exit of water in response to abrupt changes in osmolarity (By similarity) 0.010848
140 ENOG4105C3S Mate efflux family protein 0.010824
141 ENOG4107RVA Phosphate acetyl/butaryl transferase 0.010823
142 ENOG41080R1 Dinitrogenase iron-molybdenum cofactor 0.010820
143 ENOG4107RBM d-lactate dehydrogenase 0.010783
144 ENOG4105ERH Fumarylacetoacetate hydrolase 0.010777
145 ENOG4105CJ2 (LipO)protein 0.010748
146 ENOG4105CVG Homoserine O-transsuccinylase -0.010706
147 ENOG4107QSA Oxaloacetate decarboxylase 0.010697
148 ENOG4107XVE Cupin domain -0.010691
149 ENOG4105C03 ribonuclease 0.010683
150 ENOG4105HEJ Aminoglycoside phosphotransferase -0.010666
151 ENOG4107A20 Pilin isopeptide linkage domain protein -0.010663
152 ENOG4105C3Y UTP-glucose-1-phosphate uridylyltransferase -0.010661
153 ENOG410800P CobW/HypB/UreG, nucleotide-binding domain 0.010650
154 ENOG4108F2A regulatory protein 0.010638
155 ENOG4105C1W two component, sigma54 specific, transcriptional regulator, Fis family 0.010609
156 ENOG4106F9V transposase IS116 IS110 IS902 family protein -0.010565
157 ENOG4105C7Q Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity) 0.010562
158 ENOG4105KUR CAAX amino terminal protease family protein -0.010551
159 ENOG4108UZ3 Transporter -0.010537
160 ENOG4105DQC protein, conserved in bacteria -0.010527
161 ENOG4105C5R Aminotransferase 0.010498
162 ENOG4107YHQ hydrolase 0.010479
163 ENOG4105D49 3-dehydroquinate synthase -0.010473
164 ENOG410803F peptidylprolyl cis-trans isomerase 0.010454
165 ENOG4105CTK cobaltochelatase, cobn subunit -0.010447
166 ENOG4106093 NA -0.010443
167 ENOG4105CD9 Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring (By similarity) -0.010442
168 ENOG4105DPH UPF0371 protein -0.010433
169 ENOG4108X61 Nitroreductase -0.010417
170 ENOG4107R76 Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) 0.010408
171 ENOG4105C6H Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction (By similarity) 0.010388
172 ENOG4108ZAW ABC transporter, permease protein -0.010364
173 ENOG4108IQC 2,3-dihydroxybenzoate-AMP ligase 0.010360
174 ENOG4108UV6 Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) (By similarity) 0.010353
175 ENOG4105CUB amino acid 0.010279
176 ENOG41069J2 Hydrolase 0.010232
177 ENOG4105HA9 of methanol dehydrogenase type -0.010230
178 ENOG4105CSV Glutaminase 0.010221
179 ENOG4105W6F restriction endonuclease -0.010209
180 ENOG4105FAB Fumarate reductase succinate dehydrogenase flavoprotein domain protein 0.010204
181 ENOG4108XXK NUDIX hydrolase -0.010174
182 ENOG4106KBT YibE F family protein -0.010134
183 ENOG4107WAU Protein tyrosine phosphatase -0.010132
184 ENOG4105CYH conjugative transposon membrane protein 0.010131
185 ENOG4107QZ5 glutamate synthase 0.010122
186 ENOG41086B8 CoB-CoM heterodisulfide reductase -0.010099
187 ENOG4107V4I ABC transporter, permease -0.010087
188 ENOG4108RJJ Histidine kinase -0.010085
189 ENOG4105SSR PTS System -0.010075
190 ENOG4105D37 Low-affinity potassium transport system. Interacts with Trk system potassium uptake protein TrkA (By similarity) 0.010068
191 ENOG4107QNW Aldolase 0.010041
192 ENOG4107SX2 Transcriptional Regulator AraC Family 0.010020
193 ENOG4106IVZ signal transduction Histidine kinase 0.010015
194 ENOG4105FF6 Modulates transcription in response to changes in cellular NADH NAD( ) redox state (By similarity) 0.010013
195 ENOG4107QZU type I restriction-modification system -0.009984
196 ENOG4105C6N Formate acetyltransferase 0.009975
197 ENOG4105CFC Transporter 0.009974
198 ENOG4105MBT YolD-like protein 0.009968
199 ENOG4105KE9 The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity) 0.009955
200 ENOG4105ZW9 acetyltransferase, (GNAT) family 0.009953
201 ENOG4105NZE NA 0.009946
202 ENOG4105E2A Dehydrogenase -0.009940
203 ENOG4108JQ6 ABC transporter -0.009899
204 ENOG4105DUX Transporter 0.009884
205 ENOG4105CI1 PTS System 0.009865
206 ENOG4105NI8 Cytosine-specific methyltransferase -0.009852
207 ENOG4108MUG Signal transduction histidine kinase, lyts -0.009838
208 ENOG4105E0M Sulfatase 0.009832
209 ENOG4105C0G Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives (By similarity) 0.009829
210 ENOG4105VXN addiction module toxin, RelE StbE family -0.009825
211 ENOG4105JPD (Anaerobic) ribonucleoside-triphosphate reductase activating protein 0.009812
212 ENOG4105E05 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.009793
213 ENOG4105QA4 4Fe-4S Ferredoxin, iron-sulfur binding domain protein -0.009784
214 ENOG4108R8Y Beta-lactamase domain protein 0.009773
215 ENOG41087GE Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate (By similarity) 0.009734
216 ENOG41090Y0 FMN-binding protein 0.009725
217 ENOG4108YXY alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.009707
218 ENOG4105CTS PTS system mannitol-specific 0.009702
219 ENOG4106034 NA -0.009697
220 ENOG4105DME alpha-galactosidase -0.009696
221 ENOG41060V9 Cysteine-rich small domain protein 0.009667
222 ENOG41083MR nifu domain-containing protein 0.009649
223 ENOG4105VF1 iron-only hydrogenase system regulator 0.009647
224 ENOG4108WZA zeta toxin -0.009636
225 ENOG4108ZNQ Saccharopine dehydrogenase 0.009632
226 ENOG4108YNE Inherit from COG: esterase 0.009627
227 ENOG4108C3H Magnesium-importing ATPase 0.009626
228 ENOG4105WDY DNA (cytosine-5-)-methyltransferase 0.009626
229 ENOG4108H18 Polysaccharide biosynthesis protein 0.009610
230 ENOG4108Z66 YbaK ebsC protein 0.009608
231 ENOG4108IIZ The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane 0.009605
232 ENOG4108Z86 Glutamine amidotransferase -0.009593
233 ENOG4105ETE Transcriptional regulator (LacI family -0.009588
234 ENOG41061W4 NA 0.009588
235 ENOG410695F Crispr-associated protein, Csm1 family -0.009565
236 ENOG4106HFG hydrolase 0.009552
237 ENOG4107TGE l-asparaginase (EC 3.5.1.1) 0.009545
238 ENOG41064Q9 (CBS) domain 0.009535
239 ENOG4105CB8 Multifunctional enzyme that catalyzes the SAM-dependent methylation of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 and then position C-12 or C-18 to form trimethylpyrrocorphin 2. It also catalyzes the conversion of precorrin-2 into siroheme. This reaction consists of the NAD- dependent oxidation of precorrin-2 into sirohydrochlorin and its subsequent ferrochelation into siroheme (By similarity) -0.009508
240 ENOG4107ZCW Low molecular weight phosphotyrosine protein phosphatase -0.009496
241 ENOG41090K1 Metal dependent hydrolase 0.009461
242 ENOG4105MJ6 selenium-dependent hydroxylase accessory protein YqeC 0.009443
243 ENOG4108BDP Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate (By similarity) 0.009443
244 ENOG4107UGU thymidine kinase 0.009431
245 ENOG4105XKW domain protein -0.009426
246 ENOG4106Q2T NA -0.009423
247 ENOG4105CBF Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction (By similarity) 0.009396
248 ENOG4107Y8E Secondary thiamine-phosphate synthase enzyme 0.009381
249 ENOG41072A1 esterase 0.009379
250 ENOG4105CF9 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation dephosphorylation (By similarity) 0.009375