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 ENOG4105EEF Alkane 1-monooxygenase 0.024909
2 ENOG4108W0N membrAne 0.014590
3 ENOG4105C5G amine oxidase 0.014215
4 ENOG4107GJV short-chain dehydrogenase reductase 0.013406
5 ENOG4108KCE plasmid partition ParA protein 0.012788
6 ENOG41084UD rubredoxin 0.011300
7 ENOG4107ZQV short-chain dehydrogenase reductase 0.011089
8 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F 0.011014
9 ENOG4105K6S Short-chain dehydrogenase reductase Sdr 0.010989
10 ENOG4105C9H acyl-CoA dehydrogenase 0.010841
11 ENOG41090P8 phosphoglycerate mutase 0.010797
12 ENOG410736V Aminoglycoside phosphotransferase 0.010562
13 ENOG41061TZ Short-chain dehydrogenase reductase Sdr 0.010435
14 ENOG4105CT3 Monooxygenase 0.010162
15 ENOG4107YAQ Catalyzes the reduction of FMN to FMNH2 which is used to reduce pyrimidine by RutA via the Rut pathway (By similarity) -0.009976
16 ENOG4105DZR Type I site-specific deoxyribonuclease 0.009711
17 ENOG4108ZVJ dinb family 0.009672
18 ENOG4107RIY acyl-Coa dehydrogenase 0.009404
19 ENOG4105FEU K -dependent Na -Ca exchanger 0.009091
20 ENOG4108ZAF Molybdopterin 0.009087
21 ENOG4107VHS Restriction modification system DNA (Specificity 0.008996
22 ENOG4105CW0 outer membrane usher protein 0.008782
23 ENOG4105DZS Phenylacetate-CoA ligase -0.008624
24 ENOG4105CNS Protein of unknown function (DUF1446) 0.008492
25 ENOG4108IXY short-chain dehydrogenase reductase 0.008437
26 ENOG4105X17 23-dihydro-2,3-dihydroxybenzoate dehydrogenase 0.008385
27 ENOG41067WK Transcriptional regulator 0.008358
28 ENOG4107QKC Oxidoreductase alpha (molybdopterin) subunit 0.008276
29 ENOG4105D29 Helix-turn-helix type 11 domain protein 0.008267
30 ENOG4107R72 Ceramidase 0.008188
31 ENOG4105K6V RNA polymerase 0.008171
32 ENOG4105R1U AraC Family Transcriptional Regulator 0.008145
33 ENOG4105XIV Mercuric transport protein, periplasmic component 0.008125
34 ENOG4105EG6 Saccharopine dehydrogenase 0.008101
35 ENOG4108RGJ Transcriptional Regulator AraC Family 0.008084
36 ENOG4105CRW Short chain fatty acid transporter -0.008016
37 ENOG4105V9V Short-chain dehydrogenase reductase Sdr 0.007960
38 ENOG4108UIR multimeric flavodoxin wrba 0.007940
39 ENOG4105CPP Dehydrogenase, E1 component 0.007900
40 ENOG4107S4N sulfate transporter -0.007825
41 ENOG4105GQR Chaperone 0.007797
42 ENOG4108IJE Histidine kinase 0.007777
43 ENOG4107QR6 type I restriction-modification system 0.007745
44 ENOG4105QE3 oxidoreductase 0.007717
45 ENOG41078CP metal-dependent hydrolase 0.007685
46 ENOG4105VPW Protein of unknown function (DUF2805) 0.007677
47 ENOG4105C54 Major Facilitator superfamily -0.007669
48 ENOG4105GSG merR family transcriptional Regulator 0.007663
49 ENOG4107QZF nitrite reductase NADPH large subunit 0.007500
50 ENOG4105CQF Transcriptional regulator -0.007484
51 ENOG4105D5Q Arginine ornithine antiporter 0.007452
52 ENOG4107XHY Alpha beta hydrolase 0.007432
53 ENOG4108IJ9 (ABC) transporter -0.007411
54 ENOG410678H NA 0.007405
55 ENOG4108KYP polysaccharide deacetylase 0.007378
56 ENOG41090MJ Fimbrial 0.007362
57 ENOG4107QZ8 phenylacetate-CoA oxygenase reductase PaaK subunit -0.007345
58 ENOG4105D9S phenylacetate-CoA oxygenase PaaI subunit -0.007345
59 ENOG4107RGR short-chain dehydrogenase reductase -0.007328
60 ENOG4107RZ5 peptidase, M24 0.007297
61 ENOG4105JQZ Methyltransferase 0.007291
62 ENOG4108VBZ doxx family 0.007290
63 ENOG4105CND Glycosyl transferase, family 2 0.007290
64 ENOG4105CQH Protein of unknown function (DUF1254) 0.007258
65 ENOG4106G1T NA 0.007251
66 ENOG4108UKV benzoate 1,2-dioxygenase -0.007201
67 ENOG4108RNB homoserine dehydrogenase 0.007192
68 ENOG41080HT Transcriptional regulator, arsr family 0.007169
69 ENOG4105C08 Histidine kinase 0.007141
70 ENOG4109003 Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis (By similarity) -0.007124
71 ENOG4105C18 Uncharacterized protein conserved in bacteria (DUF2252) 0.007066
72 ENOG4105G7F Cyclase dehydrase 0.007066
73 ENOG4107XEC aspartate racemase 0.007034
74 ENOG41060J2 metal-dependent hydrolase 0.007009
75 ENOG4108202 K01087 trehalose 6-phosphate phosphatase EC 3.1.3.12 -0.007001
76 ENOG4105ZUZ Enoyl-CoA hydratase 0.006991
77 ENOG4105EVH UPF0753 protein 0.006980
78 ENOG4108ZA2 phenylacetate-CoA oxygenase PaaJ subunit -0.006961
79 ENOG4105E18 UPF0276 protein 0.006958
80 ENOG4105EJ9 Membrane 0.006950
81 ENOG4105N76 Phenylacetate-CoA oxygenase, subunit -0.006909
82 ENOG4105E7U AraC family transcriptional regulator 0.006892
83 ENOG4105KFG YeeE YedE family protein 0.003443
83 ENOG4105MD1 YeeE YedE family protein 0.003443
84 ENOG4105EAD ABC transporter -0.006879
85 ENOG4105CMG Carbohydrate kinase 0.006867
86 ENOG410795E Major Facilitator Superfamily -0.006866
87 ENOG4105CRS phenylacetate-CoA oxygenase PaaG subunit -0.006784
88 ENOG4105X0I Fimbrial 0.006781
89 ENOG4107YJJ HPP family 0.006778
90 ENOG4105D2S major facilitator superfamily -0.006772
91 ENOG4105GN1 Diguanylate cyclase -0.006770
92 ENOG41068Z8 NA 0.006749
93 ENOG4105YJ4 PAAR repeat-containing protein -0.006731
94 ENOG4107AQZ Membrane -0.006727
95 ENOG4105EUS Binding-protein-dependent transport systems, inner membrane component 0.006693
96 ENOG4108YYX Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome (By similarity) 0.006677
97 ENOG4108JPW Aminotransferase 0.006676
98 ENOG4107U2P Uracil permease -0.006669
99 ENOG4105DMY Choloylglycine hydrolase 0.006666
100 ENOG4105KF3 Short-chain dehydrogenase reductase Sdr 0.006660
101 ENOG4105S6Z atpase involved in dna repair 0.006645
102 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) 0.006634
103 ENOG4107QX3 carboxylase 0.006632
104 ENOG4105MH4 Lipolytic enzyme, GDSL 0.006577
105 ENOG4105Q9P Inherit from COG: UPF0754 membrane protein 0.006569
106 ENOG4107R8Z faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.006551
107 ENOG4105GW5 Histidine kinase 0.006542
108 ENOG4105F95 Monooxygenase 0.006542
109 ENOG4108UWE Acyltransferase 0.006532
110 ENOG4108ZY0 Glyoxalase Bleomycin resistance protein (Dioxygenase 0.006518
111 ENOG4107RF9 Periplasmic binding protein 0.006495
112 ENOG4108TWJ NADH dehydrogenase subunit 5 0.006494
113 ENOG4106FTQ Taurine ABC transporter, periplasmic 0.006491
114 ENOG4108YXW Together with MoaA, is involved in the conversion of 5'- GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.006483
115 ENOG4105C36 SPFH domain, Band 7 family protein -0.006481
116 ENOG4108UUF peptidase C13, legumain asparaginyl peptidase -0.006478
117 ENOG410633P Hydantoin racemase 0.006456
118 ENOG4107SUD Esterase -0.006386
119 ENOG4108XP1 Tetr family transcriptional regulator 0.006385
120 ENOG4108Q9N NAD(P)H quinone reductase 0.006373
121 ENOG4105KVH Transcriptional regulator 0.006362
122 ENOG4105JPG D-isomer specific 2-hydroxyacid dehydrogenase -0.006344
123 ENOG4108BVK Alpha beta hydrolase 0.006336
124 ENOG4105CJ1 ABC, transporter 0.006336
125 ENOG410906A Beta-Ig-H3 fasciclin 0.006335
126 ENOG4108DTZ ABC transporter 0.006320
127 ENOG4105N3I Involved in formation and maintenance of cell shape (By similarity) 0.006311
128 ENOG4107REU MgtE intracellular region 0.006304
129 ENOG4107QR7 peptidase S8 and S53, subtilisin, kexin, sedolisin 0.006301
130 ENOG4105CSU acyl-Coa dehydrogenase 0.006299
131 ENOG4107T2Q AcrB AcrD AcrF family protein 0.006292
132 ENOG4105F2Z 3-oxoadipate enol-lactonase -0.006280
133 ENOG4105M35 NA 0.006276
134 ENOG4107U1G Cysteine desulfurase -0.006263
135 ENOG4105VG5 Membrane 0.006261
136 ENOG4106MZZ glycerophosphoryl diester phosphodiesterase 0.006260
137 ENOG4105W44 ompa motb domain protein -0.006240
138 ENOG4105WRT Inherit from COG: Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity) -0.006233
139 ENOG4105F7J membrane-bound serine protease -0.006231
140 ENOG4105EDD Bacterial protein of unknown function (DUF899) -0.006222
141 ENOG4107Y0X (LipO)protein 0.006219
142 ENOG4105VMP Transcriptional regulator -0.006206
143 ENOG4108WT1 Transcriptional regulator 0.006204
144 ENOG4107RHE UDP-glucose 6-dehydrogenase 0.006196
145 ENOG4106TC3 peptidase -0.006190
146 ENOG4107D0A Flavoprotein monooxygenase required for N-hydroxylation of the two acylated lysine residues during mycobactin assembly, thus producing the hydroxamate groups necessary for iron sequestration. Is also able, but less efficiently, to hydroxylate L-lysine (non acylated) in vitro 0.006186
147 ENOG4105J2M HNH endonuclease 0.006176
148 ENOG4105CJD (Anaerobic) ribonucleoside-triphosphate reductase -0.006174
149 ENOG4105D5N isocitrate dehydrogenase (NADP) 0.006172
150 ENOG4105E7N gluconolactonase (EC 3.1.1.17) -0.006163
151 ENOG4105CN2 monooxygenase, FAD-binding 0.006163
152 ENOG4105VEQ Cold shock protein 0.006145
153 ENOG4106NQW sterol desaturase 0.006141
154 ENOG4105CE1 Ferrous iron transport protein b -0.006140
155 ENOG4108MKW Pfam:DUF88 -0.006129
156 ENOG4105F2M alpha beta hydrolase fold-3 domain protein 0.006128
157 ENOG4105DHU Bile acid -0.006120
158 ENOG4105DY8 decarboxylase -0.006120
159 ENOG4108Y44 NA 0.006109
160 ENOG4105JSC dimethylmenaquinone methyltransferase -0.006097
161 ENOG4107AY9 taurine catabolism dioxygenase -0.006095
162 ENOG41064Y7 Protein of unknown function (DUF2946) -0.006082
163 ENOG4106A3C Protein of unknown function (DUF2845) -0.006063
164 ENOG4105DUX Transporter 0.006054
165 ENOG4107QSA Oxaloacetate decarboxylase -0.006052
166 ENOG4105EXQ uroporphyrinogen iii synthase hem4 0.006040
167 ENOG41061KK NA 0.006028
168 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) 0.006016
169 ENOG4107XY0 Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit (By similarity) -0.005992
170 ENOG4107V5X Glycerophosphoryl diester phosphodiesterase family 0.005988
171 ENOG4108QK1 type VI secretion system, lysozyme-related protein 0.005976
172 ENOG4105D98 threonine synthase -0.005970
173 ENOG4105CK0 Membrane bOund o-acyl transferase mboat family protein -0.005968
174 ENOG4105SPT Transcriptional regulator 0.005961
175 ENOG4107R3A FAD linked oxidase domain protein 0.005957
176 ENOG4108TQ3 Enoyl-CoA hydratase 0.005956
177 ENOG4108QU1 NA 0.005946
178 ENOG4108KQ5 Integrase catalytic subunit 0.005937
179 ENOG4105P14 thioesterase Superfamily protein 0.005931
180 ENOG4105FBC mechanosensitive ion channel 0.005930
181 ENOG4105CV9 cyclopropane-fatty-acyl-phospholipid synthase 0.005930
182 ENOG4107UWK alpha amylase, catalytic -0.005923
183 ENOG4105C0W non-ribosomal peptide synthetase 0.005923
184 ENOG4105HNQ LysR family Transcriptional regulator 0.005917
185 ENOG4108Z4C Uncharacterized protein conserved in bacteria (DUF2237) 0.005902
186 ENOG41068P4 Acyltransferase family 0.005894
187 ENOG4105VWP Inherit from COG: 4Fe-4S ferredoxin, iron-sulfur binding -0.005892
188 ENOG4107RV4 alkaline phosphatase 0.005889
189 ENOG41060DV molybdenum cofactor biosynthesis protein 0.005889
190 ENOG4105ENR peptidase, M24 -0.005888
191 ENOG4108ZHR arsR family transcriptional regulator -0.005860
192 ENOG4105NDT Rhomboid family -0.005859
193 ENOG4105CE5 Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) -0.005843
194 ENOG4105WZK nitrite reductase NADPH small subunit 0.005836
195 ENOG41060SZ Protein of unknown function (DUF1049) 0.005832
196 ENOG4107RUY (E1 component), alpha subunit 0.005821
197 ENOG4108Z1M DSBA oxidoreductase 0.005801
198 ENOG4108R52 Type VI secretion protein, VC_A0107 family -0.005798
199 ENOG4108KC1 acyl-Coa dehydrogenase 0.005795
200 ENOG4108JIK carboxylase 0.005779
201 ENOG41084V6 Protein CrcB homolog 0.005778
202 ENOG4105TFN Glutathione-dependent formaldehyde-activating Gfa -0.005770
203 ENOG4108MDU Tetr family transcriptional regulator 0.005769
204 ENOG4108RPI (ABC) transporter -0.005768
205 ENOG4105G4N Gcn5-related n-acetyltransferase -0.005767
206 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) -0.005766
207 ENOG4105CVK Glutamate decarboxylase 0.005765
208 ENOG4105JIX pgap1 family 0.005762
209 ENOG4105QNF Outer membrane lipoprotein 0.005741
210 ENOG4108BUD transposase -0.005736
211 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) 0.005730
212 ENOG4105DXM phenylacetic acid degradation protein -0.005723
213 ENOG4105SJ4 replicase 0.005722
214 ENOG4105CQ3 Poorly processive error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. Exhibits no 3-5 exonuclease (proofreading) activity. May be involved in translesional synthesis in conjunction with the beta clamp from polIII (By similarity) 0.005710
215 ENOG4106CD9 glycosyl transferase group 1 0.005709
216 ENOG4108ISU Inherit from COG: Methyltransferase -0.005704
217 ENOG4107QV0 amino acid -0.005698
218 ENOG4108S9R Auxin Efflux Carrier -0.005691
219 ENOG4107QK5 Homocysteine s-methyltransferase 0.005683
220 ENOG4107QX8 SPFH domain, Band 7 family protein 0.005682
221 ENOG4108ZA6 Thioesterase 0.005677
222 ENOG4105XNY Alpha beta hydrolase 0.005671
223 ENOG4105G1P ec 3.1.3.12 0.005665
224 ENOG4106F2G NA -0.005656
225 ENOG4105PEH alcohol dehydrogenase 0.005646
226 ENOG4107R4J Chloride channel 0.005645
227 ENOG4106I0I NA 0.005644
228 ENOG4105I59 Glutathione S-transferase 0.005637
229 ENOG4107R7U type II secretion system protein E 0.005632
230 ENOG4105QCW NA 0.005632
231 ENOG4105DFK Polyphosphate glucokinase -0.005631
232 ENOG4108RYK Nad-dependent epimerase dehydratase 0.005631
233 ENOG41071M6 RNA methyltransferase 0.002814
233 ENOG4107QV9 transporter DctM subunit 0.002814
234 ENOG4108IQC 2,3-dihydroxybenzoate-AMP ligase 0.005627
235 ENOG4107RGH Aldehyde dehydrogenase 0.005625
236 ENOG41083ZX major facilitator superfamily 0.005620
237 ENOG4108T58 Mg2 transport protein CorA 0.005588
238 ENOG4105DC8 reductase 0.005584
239 ENOG4108DKR ABC transporter, permease -0.005583
240 ENOG4105EGJ LysR family Transcriptional regulator -0.005577
241 ENOG4105IHJ enoyl-CoA hydratase isomerase 0.005577
242 ENOG4107QZU type I restriction-modification system 0.005575
243 ENOG4106KVQ PAP2 superfamily 0.005566
244 ENOG4105QW5 phosphate-starvation-inducible E 0.005566
245 ENOG4105DNA ATP GTP Binding Protein 0.005552
246 ENOG4105PHQ Protein of unknown function (DUF1311) -0.005550
247 ENOG4108KT4 Ectoine hydroxyectoine ABC transporter solute-binding protein -0.005548
248 ENOG4105E3W Two component transcriptional regulator (Winged helix family 0.005547