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 ENOG4107QW4 alcohol dehydrogenase -0.021873
2 ENOG4105GH9 galactofuranosyltransferase -0.020204
3 ENOG4105CG3 alpha amylase, catalytic region 0.018581
4 ENOG4106AFX NA -0.017206
5 ENOG4105VXN addiction module toxin, RelE StbE family 0.016308
6 ENOG4105FDK ABC transporter 0.016266
7 ENOG4105CZG Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity) 0.015803
8 ENOG4108JKK conserved domain protein -0.015802
9 ENOG4105HTX biosynthesis protein -0.015361
10 ENOG4105C09 Bile acid 0.015324
11 ENOG4105KAF membrAne 0.015218
12 ENOG4105C1I TRANSCRIPTIONAl REGULATOR GntR family 0.015218
13 ENOG4107QSK Phage infection protein 0.015202
14 ENOG4108ZBF iron (metal) dependent repressor, dtxr family 0.015162
15 ENOG4108Z0A Cupin 2, conserved barrel domain protein -0.015090
16 ENOG4108RDQ ABC transporter -0.014986
17 ENOG4105QBX endodeoxyribonuclease RusA -0.014978
18 ENOG4108IMX DNA-binding helix-turn-helix protein -0.014922
19 ENOG4106BHR ftsk SpoIIIE family protein 0.014850
20 ENOG4105CXR Phospho-2-dehydro-3-deoxyoctonate aldolase -0.014761
21 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.014694
22 ENOG4105KRF dihydroneopterin aldolase 0.014598
23 ENOG4108HKT sucrose-6-phosphate hydrolase -0.014501
24 ENOG41080NU peptidase 0.014425
25 ENOG4105C0A alcohol dehydrogenase 0.014398
26 ENOG4108M60 Transcriptional regulator 0.014312
27 ENOG4105CYC Transferase -0.014278
28 ENOG4105EYH Exonuclease 0.014217
29 ENOG4108JJ8 (ABC) transporter 0.014192
30 ENOG4105MBY Addiction module antitoxin, RelB DinJ family 0.014171
31 ENOG4105CH6 catalase 0.014168
32 ENOG4106XIN polysaccharide biosynthesis protein 0.014092
33 ENOG4105CT5 Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate (By similarity) -0.014049
34 ENOG4105EE0 oxidoreductase 0.014015
35 ENOG4108IQK o-acetylhomoserine -0.013776
36 ENOG4105DA5 (ABC) transporter 0.013732
37 ENOG4107X35 defense response to bacterium 0.013668
38 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.013592
39 ENOG4105CEU Arginine dihydrolase 0.013533
40 ENOG4108FPF anti-repressor -0.013458
41 ENOG4105CQ9 aldose 1-epimerase 0.013418
42 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) -0.013410
43 ENOG4108VJJ Nitroreductase -0.013230
44 ENOG41090XC Abortive infection protein -0.013174
45 ENOG4106HCK NA -0.013096
46 ENOG4108Z86 Glutamine amidotransferase 0.013086
47 ENOG4105EUJ GTP cyclohydrolase i 0.013084
48 ENOG4105KG3 cytidine deaminase -0.013048
49 ENOG4108HQ0 Exopolysaccharide biosynthesis protein 0.012895
50 ENOG4107YWF Appr-1-P Processing -0.012873
51 ENOG41079VY methyltransferase -0.012858
52 ENOG4105DEU major facilitator superfamily 0.012761
53 ENOG4105CJQ hydrolase, family 31 0.012748
54 ENOG4107QJZ Glycosyl transferase, family 2 -0.012730
55 ENOG4106F1P AAA ATPase, central domain protein -0.012710
56 ENOG4108EQA pts system 0.012657
57 ENOG4107SNF Na H antiporter -0.012650
58 ENOG4105G6Z alkaline phosphatase -0.012610
59 ENOG4105Y0F caax amino terminal protease family protein 0.012554
60 ENOG4105FF5 Membrane 0.012534
61 ENOG4105EJQ L-serine dehydratase 0.012472
62 ENOG4105EFP binding-protein-dependent transport systems inner membrane Component -0.012464
63 ENOG4105D59 Tetracycline resistance protein 0.012440
64 ENOG4105RSI Galactose-6-phosphate isomerase subunit LacA 0.012406
65 ENOG4105DAA L-lactate 0.012405
66 ENOG4107T52 Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity) 0.012376
67 ENOG4105PAX Conserved Protein 0.012350
68 ENOG410724J NA 0.012289
69 ENOG41085ZR 50S ribosomal protein L36 0.011915
70 ENOG410814C multidrug resistance protein 0.011762
71 ENOG4107R5U Periplasmic binding protein LacI transcriptional regulator 0.011695
72 ENOG4105CJW magnesium transporter -0.011637
73 ENOG4105CFC Transporter -0.011632
74 ENOG41062B0 ABC transporter, permease 0.011579
75 ENOG4105KY0 addiction module toxin, Txe YoeB family 0.011538
76 ENOG4105FJQ ParB-like nuclease domain 0.011514
77 ENOG4105C1G acyl-Coa dehydrogenase -0.011507
78 ENOG4108KMV Glycosyl transferase (Group 1 -0.011486
79 ENOG4105C02 permease 0.011482
80 ENOG4107SSC biotin acetyl-CoA-carboxylase ligase -0.011463
81 ENOG41068PG O-Antigen polymerase -0.011351
82 ENOG4107R9N ABC transporter 0.011321
83 ENOG4108JQ7 (ABC) transporter 0.011256
84 ENOG4108HWY Beta-lactamase -0.011250
85 ENOG4107QR9 Iron-sulfur cluster binding protein 0.011205
86 ENOG4108N80 biosynthesis protein -0.011138
87 ENOG4105EB3 Histidine kinase 0.011112
88 ENOG4107UNG Ser Thr phosphatase family protein -0.011108
89 ENOG4105DVK Precorrin-2 c20-methyltransferase 0.011102
90 ENOG4105KVH Transcriptional regulator 0.011093
91 ENOG4105CTR Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity) 0.011085
92 ENOG4107QQN 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) 0.011063
93 ENOG4105PXR Erf family -0.010921
94 ENOG4105DMS mur ligase 0.010918
95 ENOG4105FAV ABC, transporter 0.010915
96 ENOG4108N34 Vanz family 0.010885
97 ENOG4105F27 Major Facilitator -0.010882
98 ENOG4105KRQ Addiction module toxin, Txe YoeB family 0.010868
99 ENOG4107QMS site-determining protein 0.010842
100 ENOG4108JB7 carboxylase 0.010769
101 ENOG4105CAG UPF0210 protein 0.010764
102 ENOG4108Z3G 3H domain protein -0.010624
103 ENOG4105ZWK Inherit from COG: Low-potential electron donor to a number of redox enzymes (By similarity) -0.010616
104 ENOG4108W89 Membrane 0.010603
105 ENOG4108KHX Diguanylate cyclase 0.010565
106 ENOG4105CID antiterminator 0.010565
107 ENOG4108JB8 alcohol dehydrogenase -0.010530
108 ENOG4108TMY O-Methyltransferase -0.010525
109 ENOG41082WH Nudix family 0.010501
110 ENOG4107T27 Major Facilitator -0.010500
111 ENOG4105CD5 CoA-binding domain protein -0.010500
112 ENOG4107V9M epimerase dehydratase -0.010483
113 ENOG4105NQQ topology modulation protein 0.010472
114 ENOG4106EG9 Catalyzes the decarboxylation of orotidine 5'- monophosphate (OMP) to uridine 5'-monophosphate (UMP) (By similarity) 0.010418
115 ENOG4105CQS hydrogenase expression formation protein HypD 0.010403
116 ENOG4105EJ9 Membrane 0.010402
117 ENOG4108SAI NA 0.010397
118 ENOG4105W5D IS66 Orf2 family protein 0.010367
119 ENOG4105EN1 NA 0.010363
120 ENOG4105HMI Membrane 0.010352
121 ENOG4105D5D udp-galactopyranose mutase -0.010325
122 ENOG4108C1E Inherit from COG: transposase 0.010323
123 ENOG4105GRC Transposase -0.010322
124 ENOG4105DPE Conserved Protein 0.010317
125 ENOG41080RE Glycine sarcosine betaine reductase 0.010308
126 ENOG4107QMH DNA methylase 0.010289
127 ENOG4105DNM Glycosyl transferase (Group 1 0.010278
128 ENOG4105DCU 2-hydroxyglutaryl-CoA dehydratase -0.010246
129 ENOG410849E Transcriptional regulator 0.010240
130 ENOG4107STQ Multicopper oxidase -0.010235
131 ENOG4105CB7 polysaccharide biosynthesis protein -0.010227
132 ENOG4105EEQ Na H antiporter 0.010216
133 ENOG4105E4P ATPase (AAA 0.010216
134 ENOG4108JA2 transcriptioN-repair coupling factor 0.010213
135 ENOG4105NMU Transcriptional regulator 0.010212
136 ENOG4105C7J ABC transporter, permease 0.010210
137 ENOG4105NI8 Cytosine-specific methyltransferase 0.010200
138 ENOG4108JU6 CBS domain protein 0.010195
139 ENOG4107ZCW Low molecular weight phosphotyrosine protein phosphatase 0.010184
140 ENOG4108FUT Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system) (By similarity) -0.010173
141 ENOG4107QYD Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.010161
142 ENOG4107QM2 Aldo Keto reductase 0.010159
143 ENOG4105CVJ phosphoglycerate mutase -0.010150
144 ENOG4108HRG Involved in the cleavage of the C1-C2 bond of 3D- (3,5 4)-trihydroxycyclohexane-1,2-dione (THcHDO) to yield 5-deoxy- glucuronate (5DG) (By similarity) -0.010126
145 ENOG4105XDZ Tripartite ATP-independent periplasmic transporter 0.010116
146 ENOG4107H8F NA -0.010110
147 ENOG4105CNA YD repeat protein -0.010084
148 ENOG4107RDH sufB sufD domain protein 0.010074
149 ENOG4108VQJ O-methyltransferase 0.010055
150 ENOG4105BZJ Electron transfer flavoprotein -0.010031
151 ENOG4105U0N Putative trans-membrane protein 0.010005
152 ENOG41065J1 NA 0.010004
153 ENOG4105IG6 Phage terminase, large subunit -0.010003
154 ENOG4105WF1 Addiction module antitoxin, RelB DinJ family 0.010000
155 ENOG4107QRR aspartate -0.009983
156 ENOG4105D2S major facilitator superfamily 0.009982
157 ENOG4105MZU cell filamentation protein 0.009973
158 ENOG4105D75 Capsular exopolysaccharide family -0.009961
159 ENOG4105WZQ Membrane 0.009945
160 ENOG4105K8R UPF0145 protein -0.009941
161 ENOG4105U87 Transposase 0.009937
162 ENOG4105NAE bifunctional deaminase-reductase domain protein -0.009922
163 ENOG4107UH8 sugar kinase -0.009918
164 ENOG4107S7W Dipeptidase 0.009904
165 ENOG4105WJW Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S- specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX (By similarity) 0.009894
166 ENOG4107V82 transporter gate domain protein -0.009878
167 ENOG4105ENN converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity) 0.009852
168 ENOG4105CJN penicillin-binding protein 0.009844
169 ENOG4105NI1 DNA-binding protein with PD1-like DNA-binding motif -0.009839
170 ENOG4107RE8 Integrase 0.009815
171 ENOG4105CQX Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.009810
172 ENOG4105DBU Hnh endonuclease 0.009794
173 ENOG4105EN6 Membrane 0.009759
174 ENOG41090CA NA 0.009748
175 ENOG4105GBN NA -0.009744
176 ENOG4105DIQ Transcriptional regulator -0.009654
177 ENOG41082IU Biotin-requiring enzyme 0.009644
178 ENOG4105F0R Cytidylyltransferase 0.009632
179 ENOG4108UMN azlc family 0.009628
180 ENOG4105VJZ Helix-turn-helix domain protein -0.009626
181 ENOG4105C5B carbamate kinase 0.009625
182 ENOG4105CGQ conserved protein UCP033563 -0.009620
183 ENOG4108IQE Amp-dependent synthetase and ligase -0.009611
184 ENOG4105Y93 regulatoR 0.009611
185 ENOG41066YJ Beta-lactamase -0.009609
186 ENOG4108VTX Hhh-gpd family 0.009601
187 ENOG4105EQ8 radical SAM domain protein -0.009592
188 ENOG4105CHW UPF0052 protein -0.009590
189 ENOG4108RTX Nitroreductase -0.009581
190 ENOG4107QYE Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.009577
191 ENOG4105VEZ toxin-antitoxin system, antitoxin component, ribbon-helix-helix 0.009576
192 ENOG4105EGG ABC transporter 0.009556
193 ENOG41085S6 NA -0.009555
194 ENOG4105UY6 5'-phosphate oxidase -0.009554
195 ENOG4105XWI UPF0304 protein -0.009550
196 ENOG4105HK2 serine threonine protein kinase -0.009540
197 ENOG4105D3H Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol (By similarity) -0.009528
198 ENOG4105E80 TraG TraD family protein -0.009522
199 ENOG4108UMA 3-octaprenyl-4-hydroxybenzoate carboxy-lyase -0.009505
200 ENOG4105DRC Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.009500
201 ENOG4105CMT Dihydroxyacetone kinase 0.009476
202 ENOG4105EMN RNA polymerase sigma factor -0.009472
203 ENOG4105CIF Ornithine Cyclodeaminase -0.009469
204 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.009465
205 ENOG4105W8X HesB YadR YfhF-family protein 0.009460
206 ENOG4107TFU periplasmic 0.009459
207 ENOG41085NV Membrane 0.009459
208 ENOG4105GDU serine acetyltransferase -0.009451
209 ENOG4108IJ8 ABC transporter 0.009446
210 ENOG4105MN3 Resolvase 0.009443
211 ENOG4107RVV histidinol phosphate phosphatase, hisj family -0.009441
212 ENOG4105C1N GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis (By similarity) -0.009429
213 ENOG4105MY8 Transcriptional regulator 0.009424
214 ENOG41066UZ arginase EC 3.5.3.1 0.009411
215 ENOG4105FCI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate (By similarity) 0.009410
216 ENOG4105CJT Mannose-1-phosphate guanylyltransferase 0.009402
217 ENOG4105N5G Hydrolase 0.009400
218 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) -0.009397
219 ENOG4108YYR NA 0.009358
220 ENOG4105N86 NA 0.009324
221 ENOG4105F2M alpha beta hydrolase fold-3 domain protein 0.009316
222 ENOG4107VHK HTH_XRE 0.009315
223 ENOG4106DXE bacteriocin-associated integral membrane protein 0.009305
224 ENOG4107T99 Guanine deaminase 0.009304
225 ENOG4105CMH dehydratase -0.009289
226 ENOG4105GF1 NA 0.009285
227 ENOG4108X80 Transposase 0.009281
228 ENOG4108FT7 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) 0.009275
229 ENOG4106KZR phosphorylase 0.009265
230 ENOG4105CII The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision (By similarity) 0.009248
231 ENOG4105FF2 Type I DHQase -0.009238
232 ENOG4107R7I amino acid -0.009232
233 ENOG4108MPM Sulfite exporter TauE/SafE 0.009226
234 ENOG4105E5H Transposase 0.009223
235 ENOG4108X4P NA 0.009221
236 ENOG4105C85 amino acid 0.009215
237 ENOG4105C44 Serine transporter 0.009201
238 ENOG4105C3R Methionine synthase -0.009173
239 ENOG4105CY2 Citrate transporter 0.009172
240 ENOG4108NZA Cobalt transport protein 0.009169
241 ENOG4107QR6 type I restriction-modification system 0.009167
242 ENOG4108IQD Involved in the biosynthesis of D-alanyl-lipoteichoic acid (LTA). Catalyzes an ATP-dependent two-step reaction where it forms a high energy D-alanyl AMP intermediate and transfers the alanyl residues from AMP to Dcp (By similarity) -0.009152
243 ENOG4108RBF ROK family -0.009146
244 ENOG4105KK4 UPF0060 membrane protein 0.009114
245 ENOG410623V transcriptional regulator 0.009114
246 ENOG41067V7 50S ribosomal protein L36 -0.009101
247 ENOG4107YT9 Methyltransferase 0.009095
248 ENOG4108Z9I -acetyltransferase -0.009094
249 ENOG4108VZS Transporter YvqF 0.009086
250 ENOG41067QW Transcriptional regulator 0.009085