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 ENOG4105DGI Alkaline phosphatase 0.027078
2 ENOG4106032 Glutathionylspermidine synthase 0.011243
3 ENOG4105CPD ethanolamine ammonia-lyase 0.011107
4 ENOG4108IAJ Nad-dependent epimerase dehydratase -0.010529
5 ENOG4105JSC dimethylmenaquinone methyltransferase -0.010192
6 ENOG4105HJ4 Major pilin protein fimA -0.009911
7 ENOG4105EUS Binding-protein-dependent transport systems, inner membrane component 0.009819
8 ENOG4105VU6 Protein of unknown function (DUF497) 0.009592
9 ENOG4105C80 Catalyzes the reversible oxidation of malate to oxaloacetate (By similarity) 0.009556
10 ENOG4105CFP Peptidase U32 0.009481
11 ENOG4105CNV Aldolase -0.009374
12 ENOG4108RNG Permease of the drug metabolite transporter 0.009350
13 ENOG4105CRW Short chain fatty acid transporter -0.009032
14 ENOG4105JAB phenazine biosynthesis protein, phzf family -0.008974
15 ENOG4107QWP ABC-2 type transporter 0.008822
16 ENOG4105F27 Major Facilitator 0.008814
17 ENOG41061TZ Short-chain dehydrogenase reductase Sdr 0.008792
18 ENOG4105QGQ ycii-related protein -0.008691
19 ENOG4107FQ9 ethanolamine ammonia-lyase 0.008606
20 ENOG4106NZI LysR family Transcriptional regulator -0.008582
21 ENOG4105PHQ Protein of unknown function (DUF1311) -0.008544
22 ENOG4105CBP Major Facilitator -0.008534
23 ENOG4105CI2 imidazolone-5-propionate hydrolase 0.008529
24 ENOG4108ZN5 PilT protein domain protein 0.008516
25 ENOG4105MZW acyl-Coa dehydrogenase -0.008483
26 ENOG4105F0H myo-inositol catabolism protein 0.008413
27 ENOG4105EBG alcohol dehydrogenase 0.008323
28 ENOG4108SPA endoribonuclease L-psp -0.008299
29 ENOG4105ECR NmrA family 0.008290
30 ENOG4105EDD Bacterial protein of unknown function (DUF899) -0.008275
31 ENOG4105ETT transcriptional Regulator, LysR family -0.008270
32 ENOG4108NNV aspartate racemase -0.008264
33 ENOG4105W1Y Transcriptional regulator 0.008260
34 ENOG4105EEH Integrase, catalytic region 0.008245
35 ENOG4105X1V Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity (By similarity) 0.007992
36 ENOG4105QSA Protein of unknown function (DUF962) 0.007978
37 ENOG4105CC1 hydrolase, CocE NonD family protein -0.007977
38 ENOG4108Z7T Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) 0.007973
39 ENOG4105KDM Diguanylate cyclase with gaf sensor -0.007973
40 ENOG4105HFT AraC family transcriptional regulator -0.007945
41 ENOG4108I4G D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain -0.007910
42 ENOG4105DGJ Short-chain dehydrogenase reductase Sdr 0.007890
43 ENOG4105FFF abc transporter permease protein 0.007780
44 ENOG4108IV0 ABC, transporter 0.007773
45 ENOG4108HRC Alpha beta hydrolase fold protein -0.007713
46 ENOG4106MZZ glycerophosphoryl diester phosphodiesterase 0.007693
47 ENOG4107RAY Capsular exopolysaccharide family 0.007617
48 ENOG4105M0J Toxic component of a toxin-antitoxin (TA) module. A 0.007614
49 ENOG4107WH5 Integrase 0.007566
50 ENOG4108R3Z Response regulator receiver domain protein 0.007529
51 ENOG4108HH4 Major Facilitator Superfamily 0.007512
52 ENOG4105CC9 acyl-Coa dehydrogenase -0.007482
53 ENOG4105DFS Conserved Protein 0.007482
54 ENOG4105CJ1 ABC, transporter 0.007377
55 ENOG4108NZH Efflux transporter rnd family, mfp subunit 0.007365
56 ENOG4105QJW tonB-dependent Receptor -0.007344
57 ENOG4105KKX ATPase associated with various cellular activities aaa_5 0.007337
58 ENOG4108K2R Glutathione-regulated potassium-efflux system ancillary protein 0.007326
59 ENOG4105CHH sulfate transporter 0.007301
60 ENOG4107HG3 Helix-turn-helix type 11 domain protein 0.007293
61 ENOG4105FF2 Type I DHQase 0.007255
62 ENOG4105EXC Acyl-transferase 0.007253
63 ENOG4108IJF Heavy metal efflux pump, CzcA 0.007249
64 ENOG4108ZA9 Transcriptional regulator, TetR family 0.007208
65 ENOG4107RDJ Sulfotransferase 0.007205
66 ENOG41063Z6 transcriptional regulator, lysR family 0.007185
67 ENOG4105MZU cell filamentation protein 0.007155
68 ENOG41068T7 NA -0.007115
69 ENOG4105PKU glutathione-dependent formaldehyde-activating Gfa 0.007104
70 ENOG4105ZJV Uncharacterized conserved protein (DUF2267) 0.007069
71 ENOG4105QTV Membrane -0.007065
72 ENOG4105RE0 Asp Glu hydantoin racemase -0.007035
73 ENOG4105WS7 Cation transport regulator 0.007035
74 ENOG4105F0R Cytidylyltransferase -0.007033
75 ENOG4105NN7 muconolactone delta-isomerase -0.007029
76 ENOG4105VTW prevent-host-death family -0.007027
77 ENOG4105DHF Membrane -0.007026
78 ENOG4105CMR udp-glucose 4-epimerase 0.007014
79 ENOG4105ENE Histidine kinase 0.007014
80 ENOG4105DUX Transporter 0.006989
81 ENOG4108UKV benzoate 1,2-dioxygenase -0.006989
82 ENOG4105E0K tonB-dependent siderophore receptor 0.006987
83 ENOG4108N23 SpoOM-related protein 0.006978
84 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) -0.006948
85 ENOG4105CAA catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) -0.006933
86 ENOG4105D29 Helix-turn-helix type 11 domain protein 0.006931
87 ENOG4105X7U Transcriptional regulator, ARAC family -0.006923
88 ENOG4105N78 Plasmid maintenance system killer 0.006887
89 ENOG4107QZU type I restriction-modification system 0.006881
90 ENOG4108ZJF Glcg protein -0.006874
91 ENOG4106EBY NA 0.006868
92 ENOG4108KDV TniB family 0.006850
93 ENOG4108IE1 l-carnitine dehydratase bile acid-inducible protein F 0.006820
94 ENOG41066BY Binding-protein-dependent transport systems, inner membrane component 0.006820
95 ENOG4105NC1 PRS2 protein -0.006814
96 ENOG4108UQS dipeptidase 0.006803
97 ENOG41082PI Sel1 domain protein repeat-containing protein -0.006802
98 ENOG4105EWV Sodium calcium exchanger membrane region -0.006799
99 ENOG4105VJY transcriptional regulator 0.006791
100 ENOG4108IJ1 Dehydrogenase 0.006784
101 ENOG4107T8P acyl-Coa dehydrogenase -0.006779
102 ENOG4108KZZ accessory colonization factor ACFC 0.006772
103 ENOG4108ZFK Gcn5-related n-acetyltransferase -0.006767
104 ENOG4108C33 Resolvase 0.006763
105 ENOG4108UKI Enoyl-CoA hydratase -0.006755
106 ENOG41061C9 NA 0.006748
107 ENOG4105E4M (twin-arginine translocation) pathway signal 0.006747
108 ENOG4108JIK carboxylase 0.006746
109 ENOG4107V0B transcriptional regulator 0.006742
110 ENOG4105CBZ Short-chain dehydrogenase reductase Sdr 0.006726
111 ENOG41082V1 Tetr family transcriptional regulator 0.006700
112 ENOG41060W2 glyoxylate carboligase -0.006674
113 ENOG41087S2 NA -0.006672
114 ENOG4106YN8 Prenyltransferase 0.006669
115 ENOG4107VBF NA 0.006657
116 ENOG41088CQ domain protein -0.006656
117 ENOG4108VFE Methyltransferase 0.006645
118 ENOG4107RBX acriflavin resistance protein 0.006596
119 ENOG4108M7J Carbamoyl phosphate synthase-like protein -0.006591
120 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) 0.006562
121 ENOG4105KZE Death-On-Curing Family 0.006550
122 ENOG4105CW7 secretion protein, HlyD family 0.006546
123 ENOG4106PUJ Ornithine Cyclodeaminase 0.006544
124 ENOG4108JJA ABC, transporter 0.006544
125 ENOG4105TNC Membrane 0.006538
126 ENOG4105N1V MEKHLA domain protein 0.006536
127 ENOG410795E Major Facilitator Superfamily -0.006509
128 ENOG4105Y4T Tetr family transcriptional regulator 0.006482
129 ENOG4108MM0 NA -0.006481
130 ENOG4105M2Z protein tyrosine serine phosphatase -0.006474
131 ENOG4107R91 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position (By similarity) 0.006469
132 ENOG4105EIG urea carboxylase-associated protein 1 0.006460
133 ENOG4106FND NAD dependent epimerase dehydratase family 0.006455
134 ENOG4105MWN Alpha beta hydrolase -0.006442
135 ENOG4108VTW Thioesterase -0.006425
136 ENOG4108X7C Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity (By similarity) -0.006422
137 ENOG4108RG3 short-chain dehydrogenase reductase 0.006418
138 ENOG4105VD2 PilT protein domain protein 0.006390
139 ENOG4108YSS Bacterial protein of unknown function (DUF925) -0.006386
140 ENOG4105DDI hemolysin-type calcium-binding region 0.006358
141 ENOG4108YDC PAS PAC sensor protein -0.006357
142 ENOG4108DNE DNA internalization-related competence protein ComEC Rec2 -0.006350
143 ENOG4105F7Z ABC transporter -0.006347
144 ENOG4105F7Q Rieske (2fe-2S) 0.006336
145 ENOG4108Y9J Nucleoside-binding outer membrane protein -0.006335
146 ENOG4106C19 NA -0.006331
147 ENOG4107U3U Sodium hydrogen exchanger -0.006329
148 ENOG4105C79 DNA protecting protein DprA 0.006325
149 ENOG4105V9J phenylacetic acid degradation operon negative regulatory protein -0.006316
150 ENOG4107Z6A sulfate abc transporter permease 0.006310
151 ENOG4108WDN NA -0.006308
152 ENOG4105E0Y RtcB Protein 0.006304
153 ENOG4107CMW Auxin Efflux Carrier -0.006299
154 ENOG4105VPB 50S ribosomal protein L30 -0.006291
155 ENOG4107R9J drug resistance transporter, EmrB QacA subfamily 0.006290
156 ENOG4105CA0 peroxidase 0.006287
157 ENOG4105X44 SMC domain protein -0.006279
158 ENOG4105CJM Binding-protein-dependent transport systems, inner membrane component 0.006278
159 ENOG4108Y37 Glycosyl transferase (Group 1 0.006276
160 ENOG4107QKP alkaline phosphatase 0.006250
161 ENOG4107ZI0 Inherit from NOG: 4fe-4S ferredoxin iroN-sulfur binding 0.006241
162 ENOG4105CRU nitrate reductase, alpha subunit 0.006237
163 ENOG4108E83 oxidoreductase 0.006236
164 ENOG4105T6U NA 0.006231
165 ENOG4105EZS DNA RNA NON-specific endonuclease 0.006221
166 ENOG4105DC6 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex (By similarity) -0.006220
167 ENOG4107QJT sodium dicarboxylate symporter 0.006190
168 ENOG4107URN dipeptidase -0.006189
169 ENOG4106AAS Uncharacterized protein conserved in bacteria (DUF2171) -0.006180
170 ENOG41065PU cytochrome C -0.006159
171 ENOG4105EVH UPF0753 protein 0.006149
172 ENOG4105DMT epimerase dehydratase 0.006147
173 ENOG4105EDQ levansucrase EC 2.4.1.10 0.006121
174 ENOG4105MYC pyridoxamine 5'-phosphate oxidase-related, FMN-binding -0.006119
175 ENOG41063RB Lysine exporter protein (Lyse ygga) -0.006055
176 ENOG4108VK3 Cupin 2 Conserved Barrel Domain Protein 0.006051
177 ENOG4105CE1 Ferrous iron transport protein b 0.006024
178 ENOG4105XGU Inherit from COG: ketosteroid isomerase-like protein -0.005990
179 ENOG4105C7W Xanthine dehydrogenase 0.005980
180 ENOG4107SNH Integrase 0.005979
181 ENOG4105MP9 class II Aldolase -0.005975
182 ENOG4105CCD The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase (By similarity) 0.005969
183 ENOG4105MBG Low affinity iron permease -0.005955
184 ENOG4107EBW NA 0.005941
185 ENOG4107RHE UDP-glucose 6-dehydrogenase 0.005927
186 ENOG41062F8 Tetr family transcriptional regulator -0.005925
187 ENOG410816S Transcriptional regulator 0.005894
188 ENOG4105DBA pectate lyase 0.005876
189 ENOG4105DRR Transcriptional regulator, GntR family 0.005873
190 ENOG4108UPT UPF0178 protein -0.005866
191 ENOG4107QR7 peptidase S8 and S53, subtilisin, kexin, sedolisin 0.005861
192 ENOG4108TQ3 Enoyl-CoA hydratase 0.005853
193 ENOG4105CGP Urocanate hydratase 0.005853
194 ENOG4105ES4 Nitrilase 0.005852
195 ENOG4105PNH acetyltransferase, (GNAT) family -0.005848
196 ENOG4108RIR Molybdenum cofactor biosynthesis protein 0.005844
197 ENOG4108ZZW HIRAN domain -0.005832
198 ENOG4108UFQ NA -0.005832
199 ENOG4107T5M major facilitator superfamily -0.005825
200 ENOG4108ZZR RimK domain protein ATP-grasp 0.005821
201 ENOG4105D8V Glucose sorbosone dehydrogenase 0.005813
202 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase 0.005809
203 ENOG4107TQD glycosyl hydrolase (Family 0.005804
204 ENOG4108SNZ NA -0.005802
205 ENOG4105DC7 peptidase M24 -0.005797
206 ENOG4105KHS type IV fimbrial pilin protein -0.005785
207 ENOG4105E1C Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a) (By similarity) -0.005784
208 ENOG4108KB3 pectate lyase -0.005780
209 ENOG4108YYQ gCN5-related N-acetyltransferase 0.005777
210 ENOG4108N99 uba thif-type nad fad binding protein 0.005775
211 ENOG4108URA DSBA oxidoreductase -0.005773
212 ENOG4105GFX Transcriptional regulator 0.005773
213 ENOG4106RXY Transcriptional regulator -0.005773
214 ENOG4105ETF fumarylacetoacetate (faa) hydrolase -0.005769
215 ENOG4105CNG UPF0061 protein -0.005765
216 ENOG4108S9X Glutathione S-transferase -0.005763
217 ENOG4105P2E Endoribonuclease L-PSP -0.005743
218 ENOG4107R3A FAD linked oxidase domain protein 0.005742
219 ENOG4108SFV integral membrane protein 0.005734
220 ENOG4105EAG UDP-N-acetylglucosamine 2-epimerase 0.005734
221 ENOG4105CZH peptidase 0.005733
222 ENOG4108JJ7 ABC transporter 0.005733
223 ENOG41090KQ Glyoxalase Bleomycin resistance protein (Dioxygenase 0.005733
224 ENOG4105E2Q 3-(3-hydroxy-phenyl)propionate hydroxylase -0.005729
225 ENOG4108U1V ABC transporter, permease 0.005724
226 ENOG4105NV2 SnoaL-like polyketide cyclase 0.005718
227 ENOG4107SGM protein serine threonine phosphatase -0.005718
228 ENOG4105NX3 Membrane -0.005714
229 ENOG4106GA3 conserved membrane protein -0.005705
230 ENOG4108UNS ycii-related protein -0.005692
231 ENOG4105JHE Major Facilitator Superfamily -0.005688
232 ENOG4105ZTE gas vesicle protein 0.005664
233 ENOG4105DIN metallophosphoesterase 0.005654
234 ENOG4107SVJ Dehydrogenase -0.005653
235 ENOG41063I7 Protein of unknown function (DUF1778) -0.005651
236 ENOG4105T1S Transposase 0.005641
237 ENOG4106MYB Major Facilitator superfamily -0.005636
238 ENOG4105P4U NA 0.005633
239 ENOG4107SZ2 fumarylacetoacetate (Faa) hydrolase 0.005625
240 ENOG4105NHX Domain of unknown function (DU1801) -0.005620
241 ENOG4108KI4 LysR family transcriptional Regulator -0.005619
242 ENOG4105CSA Coproporphyrinogen iii oxidase 0.005619
243 ENOG4107RRE RNA-directed DNA polymerase -0.005618
244 ENOG4105G7D MltA-interacting MipA family protein 0.005616
245 ENOG41066CM NA 0.005609
246 ENOG41065XD Transcriptional regulator -0.005598
247 ENOG4105D6J arsenicaL-resistance protein 0.005584
248 ENOG4105WGJ thioesterase Superfamily protein 0.005578
249 ENOG4106ZAI extracellular solute-binding protein family 1 0.005563
250 ENOG4108IGT Dipeptidase 0.005558