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 ENOG41068IA nitrate reductase molybdenum cofactor assembly chaperone 0.010308
2 ENOG4108V7B Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide (By similarity) 0.009929
3 ENOG4107QWJ nitrate reductase beta subunit 0.009499
4 ENOG4105C3U ABC transporter -0.009444
5 ENOG4105CD5 CoA-binding domain protein -0.008593
6 ENOG4105HVG nitrogen regulatory protein PII 0.008465
7 ENOG4105EVH UPF0753 protein 0.008419
8 ENOG4105EWF repeat protein 0.008341
9 ENOG41090MV Histidine kinase 0.008332
10 ENOG41076YT nitrate reductase, gamma subunit 0.008309
11 ENOG4105DRC Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.008250
12 ENOG4105DC4 trap transporter, 4tm 12tm fusion protein -0.008135
13 ENOG4105DDI hemolysin-type calcium-binding region 0.008101
14 ENOG4105K4P CoA-binding domain protein -0.007897
15 ENOG4105TMB Formate nitrite transporter 0.007829
16 ENOG4105WG3 lipid A biosynthesis 0.007776
17 ENOG4105EIT integrase catalytic 0.007644
18 ENOG4105D4P Coproporphyrinogen iii oxidase -0.007608
19 ENOG4105D7T ABC transporter -0.007600
20 ENOG4105DPX Hydrogenase, large subunit -0.007479
21 ENOG4107V7F Amidase (EC -0.007473
22 ENOG4105CNG UPF0061 protein 0.007458
23 ENOG4105CGZ zinc metallopeptidase 0.007408
24 ENOG4105DG4 malate L-lactate dehydrogenase -0.007365
25 ENOG4105DS9 AAA ATPase, central domain protein 0.007356
26 ENOG4108VQJ O-methyltransferase 0.007355
27 ENOG4108YZY peptidylprolyl cis-trans isomerase 0.007338
28 ENOG4105XHW Sel1 domain protein repeat-containing protein 0.007292
29 ENOG4105VDW Csbd family 0.007273
30 ENOG4105E1N methyl-accepting chemotaxis -0.007218
31 ENOG4105DAA L-lactate -0.007084
32 ENOG41060RY XRE family Transcriptional regulator 0.007035
33 ENOG4105D2T synthase 0.007002
34 ENOG4108RUB cytochrome C, class I 0.006981
35 ENOG4105CBS Chea signal transduction histidine kinase -0.006979
36 ENOG4107REZ Sodium hydrogen exchanger 0.006975
37 ENOG4108YYH Nadph-dependent fmn reductase 0.006959
38 ENOG4108TWJ NADH dehydrogenase subunit 5 0.006959
39 ENOG4105RSF C4-dicarboxylate transporter malic acid transport protein 0.006928
40 ENOG4105X9Y Hydrogenase assembly chaperone hypC hupF -0.006906
41 ENOG41067QW Transcriptional regulator 0.003451
41 ENOG41060Y5 NA 0.003451
42 ENOG4108UVN methyltransferase 0.006902
43 ENOG4105CIZ coA-substrate-specific enzyme activase -0.006860
44 ENOG41081J6 Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity) -0.006841
45 ENOG4105DH4 Periplasmic copper-binding protein -0.006821
46 ENOG4105ET3 Reduction of activated sulfate into sulfite (By similarity) 0.006793
47 ENOG4106G2I secreted hydrolase-like protein 0.006722
48 ENOG4108J5G 6-phosphogluconate dehydrogenase 0.006701
49 ENOG4105XUJ Polysaccharide chain length determinant protein 0.006680
50 ENOG4105VZ9 UPF0235 protein 0.006679
51 ENOG4105K78 MarR family Transcriptional regulator 0.006678
52 ENOG4105W43 methyltransferase Fkbm family 0.006660
53 ENOG4108VMV Chlorite dismutase 0.006648
54 ENOG41067SM Transcriptional regulator, luxr family 0.006640
55 ENOG4105WER RNA polymerase sigma-24 subunit, ECF subfamily 0.006621
56 ENOG4105CSH Transporter -0.006595
57 ENOG4105CRU nitrate reductase, alpha subunit 0.006584
58 ENOG4108PNF NA 0.006563
59 ENOG4107SE4 UDP-N-acetylglucosamine 2-epimerase 0.006557
60 ENOG4105CTC Lipopolysaccharide biosynthesis protein-like protein 0.006541
61 ENOG4108IQE Amp-dependent synthetase and ligase -0.006518
62 ENOG4105H1G trap transporter solute receptor taxi family -0.006516
63 ENOG4105E3S small subunit -0.006497
64 ENOG4105E78 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity) 0.006479
65 ENOG4105CE7 Amidase, hydantoinase carbamoylase family -0.006477
66 ENOG4108WWH tetratricopeptide 0.006462
67 ENOG4108USZ hydrogenase -0.006437
68 ENOG4105F7H FIST C domain 0.006434
69 ENOG4105DKB L-sorbosone dehydrogenase 0.006416
70 ENOG4105CXE carboxysome shell 0.001587
70 ENOG4105KIX carboxysome peptide A 0.001587
70 ENOG4105WT7 carboxysome peptide B 0.001587
70 ENOG41068NB Pterin 4 alpha carbinolamine dehydratase 0.001587
71 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase -0.006335
72 ENOG4105E8G Major facilitator Superfamily -0.006326
73 ENOG4107RFB Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine (By similarity) 0.006313
74 ENOG4108ZZR RimK domain protein ATP-grasp 0.006303
75 ENOG4108VPQ HhH-GPD domain protein 0.006303
76 ENOG4107TY6 Acylneuraminate cytidylyltransferase 0.006297
77 ENOG4105WJY cytochrome C oxidoreductase subunit B 0.006275
78 ENOG4107QXP Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine (By similarity) -0.006237
79 ENOG4108YXD 3-demethylubiquinone-9 3-methyltransferase 0.006229
80 ENOG4107YTI Protein of unknown function (DUF2958) 0.006194
81 ENOG4105HMI Membrane -0.006188
82 ENOG4107XZC Restriction modification system DNA (Specificity 0.006173
83 ENOG4105CHI Involved in the active translocation of vitamin B12 (cyanocobalamin) across the outer membrane to the periplasmic space. It derives its energy for transport by interacting with the trans-periplasmic membrane protein TonB (By similarity) 0.006159
84 ENOG4108NJQ AAA ATPase, central domain protein 0.006149
85 ENOG4107V1D Peptidoglycan binding domain protein 0.006125
86 ENOG4105VNT transposase (IS4 family) protein 0.006114
87 ENOG4105CFY cytochrome d ubiquinol oxidase, subunit ii -0.006099
88 ENOG4105DMH Transposase 0.006097
89 ENOG4105NQN cytochrome C 0.006092
90 ENOG4108ESZ Glycogen debranching enzyme 0.006087
91 ENOG4105DJY efflux transporter, rnd family, mfp subunit 0.006086
92 ENOG4107XYJ ROK family 0.006068
93 ENOG4108Z1M DSBA oxidoreductase -0.006060
94 ENOG4107RSS Hydrogenase accessory protein HypB -0.006058
95 ENOG410682Z Lactamase_B 0.006025
96 ENOG4107SIB radical SAM domain protein 0.006016
97 ENOG4105KK6 nuclease 0.006005
98 ENOG4105E00 20S proteasome, A and B subunits -0.006002
99 ENOG41063I7 Protein of unknown function (DUF1778) 0.005980
100 ENOG4105CG5 Glycosyl transferase (Group 1 0.005978
101 ENOG4105CKU formyltetrahydrofolate synthetase -0.005972
102 ENOG4108KR5 Type iv secretory pathway vird4 0.005970
103 ENOG4105D20 Nad-dependent epimerase dehydratase 0.005956
104 ENOG4105DN3 alpha-2-macroglobulin domain protein 0.005955
105 ENOG4108I5A Tetratricopeptide tpr_2 repeat protein 0.005950
106 ENOG4105C4M (Ubiquinol oxidase) subunit I -0.005939
107 ENOG4105CPK Glycosyl transferase (Group 1 0.005923
108 ENOG4105D22 carbon starvation protein 0.005921
109 ENOG4105DRE desaturase 0.005920
110 ENOG4105VGN Protein of unknown function (DUF1499) 0.005913
111 ENOG4105KIP Thioesterase -0.005911
112 ENOG4105CED cation diffusion facilitator family transporter 0.005893
113 ENOG4105G3U fad dependent oxidoreductase -0.005874
114 ENOG4108RVA ribokinase -0.005870
115 ENOG4105N29 PRC-barrel domain protein 0.005860
116 ENOG4105CJM Binding-protein-dependent transport systems, inner membrane component -0.005857
117 ENOG4108K6H transposase 0.005854
118 ENOG4108Z33 Thiol disulfide Interchange Protein 0.005851
119 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) -0.005848
120 ENOG4107NQ8 LysR family Transcriptional regulator -0.005839
121 ENOG4107Y3K Glycosyl transferase, family 4 0.005829
122 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase 0.005826
123 ENOG4105C0Y Responsible for the amidation of carboxylic groups at position A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) -0.005792
124 ENOG4105DRF Glycosyl transferase (Group 1 0.005778
125 ENOG4105W1Y Transcriptional regulator 0.005775
126 ENOG41082J7 Rhodanese domain protein 0.005766
127 ENOG4105CF5 Short-chain dehydrogenase reductase Sdr 0.005763
128 ENOG4105DH2 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group (By similarity) -0.002875
128 ENOG4108YZT Adenosylcobinamide kinase -0.002875
129 ENOG4105F9X Microcompartments protein 0.002871
129 ENOG4105KNY Microcompartments protein 0.002871
130 ENOG4108372 Uncharacterized ACR, COG1430 0.005731
131 ENOG4105D82 Glutamate dehydrogenase 0.005715
132 ENOG4105FP9 thiamine pyrophosphate 0.005701
133 ENOG41089BK Glutamine amido-transferase -0.005697
134 ENOG4105DMP NA 0.005697
135 ENOG4108U78 Glutathione S-transferase -0.005689
136 ENOG4108IJ8 ABC transporter 0.005687
137 ENOG4107RBX acriflavin resistance protein -0.005685
138 ENOG4105IBQ Peptidase S16, lon domain protein 0.005682
139 ENOG4108EK3 Regulatory protein NosR -0.001892
139 ENOG4108T0W nitrous oxide maturation protein NosY -0.001892
139 ENOG4108X6V nitrous oxide reductase accessory protein -0.001892
140 ENOG4107QZH ABC transporter, permease 0.001891
140 ENOG4105EF8 ABC transporter, permease 0.001891
140 ENOG4105F9I RND Family Efflux Transporter MFP Subunit 0.001891
141 ENOG4107T0B glycosyl transferase 0.005671
142 ENOG41083QE Glycosyl transferase, family 2 0.000942
142 ENOG4108SG0 PepSY-associated TM helix 0.000942
142 ENOG4107U0S ABC transporter periplasmic protein 0.000942
142 ENOG4108SQH Phage-related protein 0.000942
142 ENOG4105KN6 Periplasmic Protein 0.000942
142 ENOG4105VF4 Methyltransferase domain 0.000942
143 ENOG4105DF0 Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrD type B subunit to the ultimate electron acceptor NAD( ) (By similarity) -0.005653
144 ENOG4105CNM Receptor 0.005619
145 ENOG4105C8W ABC transporter -0.005607
146 ENOG4105E2X shikimate dehydrogenase -0.005605
147 ENOG4105CJW magnesium transporter 0.005586
148 ENOG4106FEU of the drug metabolite transporter, DMT superfamily -0.005576
149 ENOG4105CGY Dna recombination protein -0.005576
150 ENOG4105QRJ Transcriptional Regulator, LuxR family 0.001858
150 ENOG4105PER PRC-barrel domain 0.001858
150 ENOG41083E3 cytochrome C 0.001858
151 ENOG4105CRY pfkb domain protein 0.005568
152 ENOG4108IEF Nitrate reductase -0.005562
153 ENOG4105PV2 FimH-like protein 0.005559
154 ENOG41082Z0 chrd domain containing protein 0.005550
155 ENOG4105KT7 mgtC SapB transporter -0.005537
156 ENOG4105KRB Glutaredoxin -0.005521
157 ENOG4105E40 K01470 creatinine amidohydrolase EC 3.5.2.10 -0.005517
158 ENOG4105MME Sugar o-acyltransferase, sialic acid o-acetyltransferase neud family 0.005515
159 ENOG4105C3V 40-residue yvtn family beta-propeller repeat protein 0.005515
160 ENOG4108EN3 Metal binding domain of Ada 0.005512
161 ENOG4106DQ1 NA 0.005512
162 ENOG4105CPF Cell wall formation (By similarity) -0.005504
163 ENOG4105EDT of the drug metabolite transporter -0.005496
164 ENOG4105F1Q DNA mismatch repair protein 0.005487
165 ENOG4105CBB PepSY-associated TM helix domain protein 0.005487
166 ENOG4105EPU Molybdenum cofactor synthesis domain protein -0.005466
167 ENOG4105FEE aaa atpase central domain protein 0.005455
168 ENOG4105DQ6 Transposase 0.005449
169 ENOG4107RU8 SPFH domain, Band 7 family protein 0.005443
170 ENOG41087Y0 Glycosyl transferase, family 2 0.005414
171 ENOG4108WSZ paraquat-inducible protein a 0.005412
172 ENOG4105CVP deoxyribo-dipyrimidine photolyase -0.005394
173 ENOG4107JEE Short-chain dehydrogenase reductase Sdr 0.005389
174 ENOG4105FQ6 thiopurine methyltransferase 0.005389
175 ENOG4105W0R Phage-Associated Protein 0.005378
176 ENOG4105C1D Membrane -0.005375
177 ENOG4105CUC YeeE YedE family protein -0.005373
178 ENOG4105D3Z quinone oxidoreductase, yhdh yhfp family -0.005367
179 ENOG4105EFZ amidohydrolase -0.005367
180 ENOG4105DN2 repeat protein 0.005363
181 ENOG4107ST1 Methyl-accepting chemotaxis -0.005361
182 ENOG4107QY8 reductase -0.005360
183 ENOG4108UJJ activator of Hsp90 ATPase 1 family protein 0.005357
184 ENOG4105MHZ Amino acid-binding act domain protein 0.005351
185 ENOG4105D85 methylase 0.005350
186 ENOG4105DXI Major Facilitator superfamily -0.005345
187 ENOG4105C8H hydrogenase maturation protein Hypf -0.005341
188 ENOG41090VX general secretion pathway protein L 0.005339
189 ENOG4105VKX TadE family 0.005334
190 ENOG410600T transposase 0.005331
191 ENOG4105XZT Protein of unknown function (DUF2892) -0.005330
192 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) -0.005301
193 ENOG4105E1F short-chain dehydrogenase reductase 0.005297
194 ENOG4105CUB amino acid 0.005292
195 ENOG4105KNJ Glycosyl transferase, family 2 0.005286
196 ENOG4108IJ7 Glycine betaine -0.005284
197 ENOG4105CKH Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation (By similarity) -0.002641
197 ENOG4105FE9 pseudouridine synthase -0.002641
198 ENOG4105C07 amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity) -0.005283
199 ENOG4106IK7 Uncharacterised ArCR, COG2043 0.005283
200 ENOG4107JTW chlorite dismutase 0.005277
201 ENOG4105E6M Sulphatase-modifying factor protein 0.005266
202 ENOG4107SN8 glycosyl transferase family 0.005259
203 ENOG4108MUX N-hydroxyarylamine O-acetyltransferase 0.005257
204 ENOG4107R9B monooxygenase, FAD-binding 0.005242
205 ENOG4108J2C peptidase, M48 0.005232
206 ENOG4105DPT Diguanylate cyclase phosphodiesterase -0.001743
206 ENOG4108WHK AraC Family Transcriptional Regulator -0.001743
206 ENOG4108N7M cbb3-type cytochrome c oxidase subunit II -0.001743
207 ENOG4108V4V acetyltransferase 0.005221
208 ENOG4105VK6 HNH endonuclease 0.005216
209 ENOG4108VA7 Cupin 2, conserved barrel domain protein 0.005212
210 ENOG4107TME TrkA-N domain protein -0.005203
211 ENOG4108GQT Transposase 0.005186
212 ENOG4105C1B dTDP-glucose 4-6-dehydratase 0.005185
213 ENOG4108RG3 short-chain dehydrogenase reductase -0.002587
213 ENOG4105IQ5 FAD linked oxidase domain protein -0.002587
214 ENOG4105F0R Cytidylyltransferase 0.005174
215 ENOG41067HS methyltransferase 0.005168
216 ENOG4108S4N thiJ PfpI domain-containing protein -0.005163
217 ENOG4106F1P AAA ATPase, central domain protein 0.005162
218 ENOG4108QH2 crispr-associated protein 0.005143
219 ENOG41069Z1 DNA binding domain protein, excisionase family 0.005119
220 ENOG4105EHI Phosphonate ABC transporter, periplasmic -0.002558
220 ENOG4107T5M major facilitator superfamily -0.002558
221 ENOG4105C0K Gdp-mannose 4,6-dehydratase 0.005111
222 ENOG4105F7R Short-chain dehydrogenase reductase Sdr -0.002552
222 ENOG4105EFP binding-protein-dependent transport systems inner membrane Component -0.002552
223 ENOG41074MP UPF0103 Mediator of ErbB2-driven cell motility-containing protein -0.005103
224 ENOG4107SBX Type I restriction-modification system R subunit 0.002542
224 ENOG4107UGN N-6 DNA Methylase 0.002542
225 ENOG4106BCY NA 0.005077
226 ENOG4105EQJ Nitrous-oxide reductase is part of a bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide (By similarity) -0.005076