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 ENOG4107T32 3-phytase (EC 3.1.3.8) 0.037149
2 ENOG4108WNA (GGDEF) domain protein 0.036339
3 ENOG4108WHX Transcriptional Regulator AraC Family 0.034934
4 ENOG4105C4D tonB-dependent Receptor 0.031848
5 ENOG41061YN Tonb protein 0.016496
6 ENOG4105TAX Integrase 0.013080
7 ENOG4105CG3 alpha amylase, catalytic region 0.012923
8 ENOG4105DFP Integrase 0.012753
9 ENOG4108VBZ doxx family 0.012698
10 ENOG41086G8 propeptide, pepSY amd peptidase M4 -0.012317
11 ENOG4105KBS Plasmid maintenance system killer 0.011978
12 ENOG4105CHJ isochorismatase hydrolase 0.011853
13 ENOG4107QTA d-serine deaminase 0.011607
14 ENOG4108UQN AraC family transcriptional regulator 0.011419
15 ENOG4105IGJ Zn-dependent Hydrolase of the beta-lactamase fold protein 0.011054
16 ENOG4107U0S ABC transporter periplasmic protein 0.011045
17 ENOG4108WFR AraC Family Transcriptional Regulator -0.010574
18 ENOG4108HSU Gcn5-related n-acetyltransferase -0.010453
19 ENOG4105DZR Type I site-specific deoxyribonuclease 0.010347
20 ENOG41067QW Transcriptional regulator 0.010289
21 ENOG4107QQG Dehydrogenase 0.010201
22 ENOG4108UPG 'Phage' integrase family 0.010158
23 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) -0.010132
24 ENOG4107SPW HsdM N-terminal domain 0.010096
25 ENOG4105E5H Transposase 0.010010
26 ENOG4105F27 Major Facilitator 0.009875
27 ENOG41063HJ polysaccharide biosynthesis protein 0.009820
28 ENOG4108ENU TonB dependent receptor 0.009474
29 ENOG4105XDF Protein of unknown function (DUF1272) -0.009415
30 ENOG4106K1W GAF domain 0.009362
31 ENOG4105C1B dTDP-glucose 4-6-dehydratase -0.009293
32 ENOG4105G5K NIPSNAP family containing protein -0.009281
33 ENOG4108ZVJ dinb family 0.009275
34 ENOG4105FDP GntR family transcriptional regulator -0.009266
35 ENOG4108SG0 PepSY-associated TM helix 0.009205
36 ENOG4108NVR Methyl-accepting chemotaxis 0.009144
37 ENOG4108S1R peptidylprolyl cis-trans isomerase -0.009138
38 ENOG4105CPT Alpha beta hydrolase 0.009109
39 ENOG4105KWI UPF0339 protein 0.009050
40 ENOG4107SZI Methyl-accepting chemotaxis 0.009008
41 ENOG4108ZZ2 nucleotide-binding protein 0.008976
42 ENOG4105N51 Two component transcriptional regulator luxr family 0.008947
43 ENOG4105PEA Transcriptional regulator 0.008923
44 ENOG4105VY2 Fimbrial pilin related signal peptide protein 0.008912
45 ENOG4107E2C NA -0.008890
46 ENOG4108RPX mosc domain containing protein -0.008882
47 ENOG4105DND Transcriptional regulator -0.008880
48 ENOG4105ER5 DNA-binding protein 0.008841
49 ENOG4105E4M (twin-arginine translocation) pathway signal 0.008841
50 ENOG4107S65 Methyltransferase Type -0.008820
51 ENOG41069GT NA 0.008814
52 ENOG4105KT7 mgtC SapB transporter 0.008761
53 ENOG4108WN9 NA 0.008752
54 ENOG4105E7U AraC family transcriptional regulator 0.008741
55 ENOG4105D5V NA 0.008713
56 ENOG4108TGY Glutathione S-transferase -0.008672
57 ENOG4105D6J arsenicaL-resistance protein 0.008657
58 ENOG4105KRQ Addiction module toxin, Txe YoeB family 0.008619
59 ENOG4105EEH Integrase, catalytic region 0.008594
60 ENOG4108UUM single-stranded DNA-binding protein -0.008585
61 ENOG41085PU Protein of unknown function (DUF2384) 0.008565
62 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin -0.008559
63 ENOG4108P8R NA 0.008518
64 ENOG4108NGR Regulatory component of sensory transduction system -0.008514
65 ENOG4105VQU rdd domain containing protein 0.008507
66 ENOG410862C low temperature requirement 0.008483
67 ENOG4105DKE DNA helicase 0.008475
68 ENOG4106B0W Curli production assembly transport component CsgG 0.008413
69 ENOG4107MVG Inherit from COG: negative regulation of growth -0.008401
70 ENOG4105DDI hemolysin-type calcium-binding region 0.008401
71 ENOG4107XZC Restriction modification system DNA (Specificity 0.008385
72 ENOG4107RGU branched-chain amino acid ABC transporter, permease 0.008382
73 ENOG4108TU9 TRANSCRIPTIONal 0.008369
74 ENOG4108T2F Short chain dehydrogenase 0.008368
75 ENOG4105CI0 Citrate lyase -0.008365
76 ENOG4108XI3 Inner membrane protein YmfA 0.008351
77 ENOG4105MDH 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) -0.008344
78 ENOG4105M7S Transcriptional regulator -0.008341
79 ENOG4108KWN alpha beta 0.008325
80 ENOG410679B prophage CP4-57 regulatory protein alpA 0.008256
81 ENOG4105C5I Dehydrogenase 0.008246
82 ENOG4105VFA cytochrome 0.008227
83 ENOG4105CGZ zinc metallopeptidase 0.008219
84 ENOG4107RNS bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase 3'-nucleotidase periplasmic -0.008213
85 ENOG4105W4K NA 0.008197
86 ENOG4105ZX7 tail collar domain protein 0.008189
87 ENOG4108W8P Diguanylate cyclase with PAS PAC sensor 0.008149
88 ENOG4107QRN Major Facilitator 0.008137
89 ENOG4108HGT Histidine kinase 0.008125
90 ENOG4108MGI Transcriptional regulator 0.008120
91 ENOG4108MUX N-hydroxyarylamine O-acetyltransferase 0.008116
92 ENOG4108S01 response regulator 0.004052
92 ENOG4108ZGX Histidine kinase 0.004052
93 ENOG4105E2W cytoplasmic protein -0.008100
94 ENOG4105M6W Crispr-associated protein, Csy3 family 0.008054
95 ENOG4107DI8 domain protein 0.004022
95 ENOG4108XF7 MotA TolQ exbB proton channel 0.004022
96 ENOG4105C30 Nad-dependent epimerase dehydratase 0.008024
97 ENOG4105IUK Pin domain protein 0.008000
98 ENOG4105W3S hemerythrin-like, metal-binding protein -0.007950
99 ENOG41067WK Transcriptional regulator 0.007916
100 ENOG4108KEY CRISPR-associated protein (Cas_Csy2) 0.007910
101 ENOG4108JKD thiamine biosynthesis protein this 0.007890
102 ENOG4105UCJ NA -0.007886
103 ENOG4105CIS alcohol dehydrogenase 0.007849
104 ENOG4108T6S 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) -0.007825
105 ENOG4108XDK Chromosome (Plasmid) partitioning protein, ParB 0.007799
106 ENOG4108TKV Major Facilitator 0.007768
107 ENOG4105CRA 2Fe-2S iron-sulfur cluster binding domain-containing protein -0.003877
107 ENOG4107U36 Aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding -0.003877
108 ENOG4108HXG Beta-lactamase -0.007726
109 ENOG4108RR1 Bacterial TniB protein 0.007722
110 ENOG4108QBQ Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione (By similarity) -0.007703
111 ENOG4108Z9K Osmotically inducible protein 0.007694
112 ENOG4105GVR general secretion pathway protein D 0.007671
113 ENOG4108ID0 Protein of unknown function (DUF3772) -0.007661
114 ENOG41069YE inner membrane protein yohC -0.007652
115 ENOG410909K Domain of unknown function (DUF3332) 0.007650
116 ENOG4105EB3 Histidine kinase 0.007626
117 ENOG4105X5E Protein of unknown function, DUF606 0.003809
117 ENOG4106260 Protein of unknown function, DUF606 0.003809
118 ENOG41074JR NA 0.007600
119 ENOG4105DZK receptor 0.007526
120 ENOG4105CR4 methylisocitrate lyase -0.007524
121 ENOG4105DXW Membrane associated hydrolase 0.007516
122 ENOG4105R3A Nitrate reductase -0.007514
123 ENOG4105ESG NA 0.007489
124 ENOG4107RF4 Phosphodiesterase 0.007488
125 ENOG41065RQ ADP-ribosylation crystallin J1 -0.007484
126 ENOG4106JDM Transposase 0.007481
127 ENOG4105MCI (LipO)protein -0.007466
128 ENOG4105ETQ PIWI domain protein 0.007461
129 ENOG4105C6J response regulator 0.007433
130 ENOG4107RX5 permease -0.007426
131 ENOG4105KAC Antibiotic biosynthesis monooxygenase 0.007421
132 ENOG4108V3W Chemotaxis protein, CheW 0.007401
133 ENOG4105E0M Sulfatase 0.007396
134 ENOG4107ZSV Receptor 0.007394
135 ENOG4105DGI Alkaline phosphatase 0.007394
136 ENOG4105E1H DNA sulfur modification protein DndD -0.007380
137 ENOG4108M9J MaoC like domain protein -0.007369
138 ENOG4106CAN NA 0.003682
138 ENOG4106H9G NA 0.003682
139 ENOG4105KWG Pfam:DUF1696 0.007337
140 ENOG4105STD Prophage CP4-57 regulatory 0.007337
141 ENOG4107WH5 Integrase 0.007333
142 ENOG4105KWY NA 0.007330
143 ENOG4105C5B carbamate kinase -0.007323
144 ENOG4105I7Z Short-chain dehydrogenase reductase Sdr 0.007315
145 ENOG4105D7V transposase 0.007309
146 ENOG4105DGU Histone deacetylase -0.007297
147 ENOG4105DE9 3-keto-5-aminohexanoate cleavage enzyme -0.007296
148 ENOG4106A3M Cytochrome p-450 -0.007258
149 ENOG4105ETT transcriptional Regulator, LysR family -0.007257
150 ENOG4105Q06 Pfam:PhdYeFM -0.007249
151 ENOG4105DMF Dehydrogenase -0.007240
152 ENOG4105XAM NA -0.007229
153 ENOG4108I9P glycine cleavage 0.007229
154 ENOG4107VG6 Outer membrane efflux protein 0.007221
155 ENOG4108MU3 NA 0.007217
156 ENOG41060M0 Crispr-associated protein, cse4 family 0.003608
156 ENOG4108VWQ crispr-associated protein 0.003608
157 ENOG4107SJ3 cation diffusion facilitator family transporter -0.007189
158 ENOG4108Q4J peptidase m48, ste24p -0.007182
159 ENOG41067V8 cytochrome C oxidase -0.007179
160 ENOG4105NNN FxsA cytoplasmic membrane protein -0.007156
161 ENOG4107QKC Oxidoreductase alpha (molybdopterin) subunit 0.007152
162 ENOG4105KAF membrAne -0.007148
163 ENOG4108NU1 transcriptional regulator, lysR family 0.007144
164 ENOG4105D04 Cation efflux protein 0.007129
165 ENOG4107SA8 fad-dependent pyridine nucleotide-disulfide oxidoreductase -0.007123
166 ENOG4105JAB phenazine biosynthesis protein, phzf family -0.007119
167 ENOG4105EY9 peptidase S8 and S53, subtilisin, kexin, sedolisin -0.007112
168 ENOG4105CF7 AraC family transcriptional regulator 0.007108
169 ENOG4108HPH acetyltransferase, (GNAT) family 0.007094
170 ENOG4105VIR ycii-related 0.007073
171 ENOG4107UCX Nad-dependent epimerase dehydratase 0.007067
172 ENOG4105MD7 metal-dependent hydrolase 0.007058
173 ENOG4108PXT Sensor hybrid histidine kinase -0.007058
174 ENOG4105SX5 NA 0.007058
175 ENOG4105DU1 integral membrane protein, terc -0.007056
176 ENOG4105PGM cation diffusion facilitator family transporter 0.007047
177 ENOG4108P3M response regulator receiver modulated diguanylate cyclase phosphodiesterase 0.007044
178 ENOG4108T1P restriction endonuclease 0.007038
179 ENOG4107R60 Aldo/keto reductase family -0.007038
180 ENOG4105VRA Glyoxalase Bleomycin resistance protein (Dioxygenase 0.007034
181 ENOG4105M0P NA 0.007031
182 ENOG4105U51 Thioesterase 0.007028
183 ENOG4105DK4 Major Facilitator superfamily 0.007028
184 ENOG4105D70 Integrase catalytic subunit 0.007024
185 ENOG4107YX6 peptidase -0.007015
186 ENOG4108K9F Fe2 -dicitrate sensor, membrane component 0.007012
187 ENOG4107QZ7 Cellulose synthase catalytic subunit 0.007010
188 ENOG4105M3E Glyoxalase Bleomycin resistance protein (Dioxygenase 0.006999
189 ENOG4107V01 Methyl-accepting chemotaxis 0.006984
190 ENOG4107XQ8 Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (By similarity) 0.006974
191 ENOG410724M NA 0.006972
192 ENOG4106GTH NA -0.006971
193 ENOG4108ZFA transmembrane signal peptide protein 0.006962
194 ENOG4107UGY Proline imino-peptidase 0.006953
195 ENOG4105CNM Receptor 0.006944
196 ENOG4108STK glycosyl transferase family -0.006935
197 ENOG4108QGT oligogalacturonate-specific porin 0.006932
198 ENOG4108S67 amidohydrolase 2 -0.006917
199 ENOG4105EBU metallophosphoesterase 0.006907
200 ENOG4107FW8 Inherit from COG: Histidine kinase -0.006901
201 ENOG4105D8X mechanosensitive ion channel -0.006894
202 ENOG4105DGD Non-specific acid phosphatase 0.006882
203 ENOG4105YHG TonB family 0.006874
204 ENOG4108KEM LysR family transcriptional regulator -0.006849
205 ENOG4105C9Q fumarate hydratase class II -0.006849
206 ENOG4108PHS Dehydrogenase -0.002282
206 ENOG4108XDC Dehydrogenase -0.002282
206 ENOG4108YF6 methylamine dehydrogenase accessory protein MauD -0.002282
207 ENOG4105EQ0 Major Facilitator superfamily 0.006845
208 ENOG4105CSX c4-dicarboxylate anaerobic carrier -0.006841
209 ENOG4105CBB PepSY-associated TM helix domain protein -0.006837
210 ENOG4105F5W AtP-binding protein 0.006837
211 ENOG4107T6V glycerophosphoryl diester phosphodiesterase 0.006834
212 ENOG4108F2M FabA-like domain -0.006828
213 ENOG4108MID NA 0.006827
214 ENOG410607E NA -0.006818
215 ENOG41072A1 esterase 0.006815
216 ENOG4105SF6 cobyrinic Acid a,c-diamide synthase 0.006812
217 ENOG4107ENK receptor 0.006812
218 ENOG4105CD5 CoA-binding domain protein -0.006804
219 ENOG4107R0C GSCFA domain protein -0.006800
220 ENOG4108IPX Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system (By similarity) 0.006799
221 ENOG4107GQG Pfam:TonB 0.006789
222 ENOG41062ZG ion transport 2 domain protein 0.006779
223 ENOG4105CRU nitrate reductase, alpha subunit -0.002255
223 ENOG4105D0D Nitrate reductase 2, gamma subunit -0.002255
223 ENOG4108EAP nitrate reductase beta -0.002255
224 ENOG4105K0K Short-chain dehydrogenase reductase Sdr 0.006764
225 ENOG4108KB8 LysR family transcriptional regulator 0.006763
226 ENOG4105ETS cytosine purines uracil thiamine allantoin -0.006757
227 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) -0.006738
228 ENOG4107SCJ type I restriction enzyme EcoKI subunit R 0.006737
229 ENOG4108R6G acetyltransferase 0.006729
230 ENOG4105F0M Aldo Keto reductase 0.006712
231 ENOG41085IS Methyl-accepting chemotaxis -0.006710
232 ENOG4107RUP AcrB AcrD AcrF family protein -0.006707
233 ENOG4108EQ0 fad dependent oxidoreductase -0.006701
234 ENOG410664K NA 0.006692
235 ENOG4108IEH NADH dehydrogenase subunit g 0.006692
236 ENOG4105FEN Deacylase 0.006686
237 ENOG4107QZU type I restriction-modification system -0.006681
238 ENOG4105ECQ AraC Family Transcriptional Regulator 0.006679
239 ENOG4108KKK parallel beta-helix repeat protein 0.006679
240 ENOG4108VP3 Lysine exporter protein (LysE YggA) 0.006675