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 ENOG4108UKV benzoate 1,2-dioxygenase 0.046864
2 ENOG4108Q89 anthranilate 1,2-dioxygenase large subunit 0.043577
3 ENOG4107SEV 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 0.036937
4 ENOG4107TVJ ,Oxidoreductase FAD NAD(P)-binding 0.034367
5 ENOG4105NN7 muconolactone delta-isomerase 0.031247
6 ENOG410626B catechol 1,2-dioxygenase 0.029891
7 ENOG4105DTQ mandelate racemase muconate lactonizing 0.024988
8 ENOG4108KB2 LysR family Transcriptional regulator 0.022296
9 ENOG4105F2Z 3-oxoadipate enol-lactonase 0.020268
10 ENOG4105D2S major facilitator superfamily 0.014066
11 ENOG4105S0E allantoin catabolism protein 0.013671
12 ENOG4105GSG merR family transcriptional Regulator -0.011840
13 ENOG4107VZY mandelate racemase muconate lactonizing 0.011182
14 ENOG4107SJ3 cation diffusion facilitator family transporter 0.011169
15 ENOG4107SN1 CoA-transferase subunit A 0.010424
16 ENOG410633P Hydantoin racemase 0.010408
17 ENOG4107HP6 Transcriptional regulator 0.010292
18 ENOG4105CI0 Citrate lyase 0.010207
19 ENOG4107J8Z Flavoprotein involved in K transport 0.010023
20 ENOG4108Q26 Iclr family transcriptional regulator 0.009691
21 ENOG4105EU7 Protocatechuate 3,4-dioxygenase, beta 0.009577
22 ENOG4106NZI LysR family Transcriptional regulator 0.009550
23 ENOG41069M3 Transcriptional regulator 0.009326
24 ENOG4105RM9 Protocatechuate 3,4-dioxygenase alpha 0.009246
25 ENOG4105F76 Sarcosine oxidase 0.009211
26 ENOG4105DKK Benzoate 0.009148
27 ENOG4107RAW 3-carboxy-cis-cis-muconate cycloisomerase 0.009078
28 ENOG4105KT7 mgtC SapB transporter -0.008970
29 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) 0.008955
30 ENOG4108UWW Cmp dcmp deaminase zinc-binding 0.008893
31 ENOG4105KI2 Urea amidohydrolase subunit beta 0.008751
32 ENOG4108KEZ Dehydrogenase 0.008717
33 ENOG4105EB3 Histidine kinase 0.008670
34 ENOG4105GWW Protein of unknown function (DUF2938) 0.008650
35 ENOG4105DIE 6-aminohexanoate-dimer hydrolase 0.008615
36 ENOG4108K2P TRANSCRIPTIONal 0.008448
37 ENOG4105VEG Regulator protein 0.008437
38 ENOG4107SGC serine threonine protein kinase -0.008421
39 ENOG4105DMN coenzyme A transferase 0.008356
40 ENOG4108UM8 Spovr like family protein 0.008305
41 ENOG41090GV transcriptional regulator AsnC family 0.008295
42 ENOG4105DZI LysR family Transcriptional regulator 0.008143
43 ENOG4108MZC LysR family Transcriptional regulator -0.008117
44 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.008078
45 ENOG4108RPX mosc domain containing protein 0.008077
46 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.008070
47 ENOG4105PSI phosphoribosyl-dephospho-CoA transferase 0.004019
47 ENOG4107VVD malonate decarboxylase subunit epsilon 0.004019
48 ENOG4105NHA hicB family 0.008036
49 ENOG4107RZW Transferase 0.007998
50 ENOG4105CTU Proline racemase 0.007986
51 ENOG4105EN6 Membrane 0.007946
52 ENOG4107RUN Cytosolic protein 0.007921
53 ENOG4105CFQ glutamine synthetase 0.007850
54 ENOG4105CQM Urea amidohydrolase subunit alpha 0.007800
55 ENOG4108YSS Bacterial protein of unknown function (DUF925) -0.007784
56 ENOG4107S9B Shikimate dehydrogenase 0.007754
57 ENOG4108UVJ appr-1-p processing domain protein 0.007706
58 ENOG4105FP9 thiamine pyrophosphate -0.007682
59 ENOG4105R3G BNR Asp-box repeat protein 0.007664
60 ENOG4105D6B malonate decarboxylase alpha subunit 0.007660
61 ENOG4108PNY Short-chain dehydrogenase reductase Sdr 0.007658
62 ENOG4105D9P serine threonine protein kinase -0.007630
63 ENOG4108SNY Protein of unknown function (DUF3455) -0.007561
64 ENOG4105EQK -acetyltransferase -0.007521
65 ENOG4107RAP type iii restriction -0.007471
66 ENOG4107U2B Glucose sorbosone dehydrogenase 0.007452
67 ENOG4107R0A malonate decarboxylase subunit beta 0.007412
68 ENOG4105DVW rieske (2Fe-2S) 0.007389
69 ENOG4107RCH Diaminopropionate ammonia-lyase 0.007386
70 ENOG4107WD2 ec 2.7.10.2 -0.007379
71 ENOG4108RGX Xanthine dehydrogenase accessory protein XdhC 0.007291
72 ENOG4107BWH Tail assembly protein -0.007236
73 ENOG4107S5F Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG (By similarity) 0.007223
74 ENOG4108M9J MaoC like domain protein 0.007217
75 ENOG4108Z7F N-acetyltransferase -0.007215
76 ENOG4107QQG Dehydrogenase 0.007188
77 ENOG4105EVZ LysR family transcriptional regulator 0.007164
78 ENOG4108NFZ LuxR family Transcriptional regulator 0.007162
79 ENOG41076HS cation diffusion facilitator family transporter 0.007150
80 ENOG4108Y9J Nucleoside-binding outer membrane protein 0.007149
81 ENOG4105FAJ Minor tail protein -0.007096
82 ENOG4105QYX Minor tail protein -0.007074
83 ENOG4107QZK Ferredoxin oxidoreductase 0.007070
84 ENOG4108MSR malonate Decarboxylase Gamma Subunit 0.007069
85 ENOG4105CFM UPF0317 protein 0.007067
86 ENOG4107RDP Dehydrogenase 0.007061
87 ENOG4105CP3 Alpha Beta Hydrolase Fold protein 0.007055
88 ENOG4108YJK tail protein -0.007044
89 ENOG4108RYR transcriptional regulator AsnC family 0.007016
90 ENOG4108WJ6 Tail assembly protein -0.007001
91 ENOG4107QMZ Dehydrogenase 0.006974
92 ENOG4108XF4 Transcriptional regulator 0.006942
93 ENOG4108PXT Sensor hybrid histidine kinase 0.006941
94 ENOG4107R0M Integrase 0.006925
95 ENOG4105FX9 transmembrane pair domain-containing protein -0.006897
96 ENOG4108S5X Glutathione S-transferase 0.006892
97 ENOG4105VGJ Virulence-associated protein -0.006892
98 ENOG4105HA6 Glycosyl transferase, family 2 -0.006886
99 ENOG4105C6V Glycerol-3-phosphate dehydrogenase 0.006885
100 ENOG4105ESA extracellular ligand-binding receptor 0.006849
101 ENOG4107R8Z faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.006849
102 ENOG4105CND Glycosyl transferase, family 2 0.006833
103 ENOG4105XJI Host specificity protein -0.006822
104 ENOG4108M9X Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.006801
105 ENOG4105DFE Dna adenine methylase -0.006794
106 ENOG4108K6F triphosphoribosyl-dephospho-CoA synthase 0.006780
107 ENOG4105KJM monovalent cation h antiporter subunit g 0.006773
108 ENOG4105E7D Protein of unknown function (DUF3375) 0.006767
109 ENOG4105EGK Proline imino-peptidase 0.006753
110 ENOG4108EK7 Monovalent cation H antiporter subunit 0.006688
111 ENOG41062RA Transcriptional Regulator AraC Family 0.006684
112 ENOG4105DAA L-lactate 0.006667
113 ENOG4108IUY abc transporter atp-binding protein 0.006651
114 ENOG4105FDY integral membrane protein 0.006642
115 ENOG4105DCJ Xanthine dehydrogenase 0.006635
116 ENOG4107QYA phosphate 0.006631
117 ENOG4108PXA Replication Protein 0.006604
118 ENOG4105CW7 secretion protein, HlyD family 0.006598
119 ENOG41063N7 cyclase, family 0.006594
120 ENOG4105CBP Major Facilitator 0.006589
121 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component -0.006565
122 ENOG4106571 Short-chain dehydrogenase reductase Sdr 0.006561
123 ENOG4108KZT fad dependent oxidoreductase 0.006558
124 ENOG4107QRH Arylsulfatase (Ec 3.1.6.1) 0.006555
125 ENOG4105NUM transcriptional regulator AsnC family 0.006504
126 ENOG4105M4E phosphohistidine phosphatase, SixA 0.006492
127 ENOG4108E1A Oxidoreductase FAD-binding domain 0.006487
128 ENOG4105DX5 Two component transcriptional regulator (Winged helix family -0.006484
129 ENOG4105BZG amino acid carrier protein 0.006454
130 ENOG4105PI0 Ferredoxin 0.006450
131 ENOG4108HV6 Fosmidomycin resistance protein 0.006429
132 ENOG41081E8 Alpha beta hydrolase 0.006416
133 ENOG4105VT2 5-hydroxyisourate hydrolase 0.006410
134 ENOG4108PTX LysR family Transcriptional regulator 0.006397
135 ENOG4105KHS type IV fimbrial pilin protein 0.006396
136 ENOG4105E3J oxidoreductase 0.006385
137 ENOG4108NRF LysR family Transcriptional regulator -0.006381
138 ENOG4105C1X Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity (By similarity) 0.006374
139 ENOG4107QZR ABC, transporter 0.003184
139 ENOG4107RB5 abc transporter permease protein 0.003184
140 ENOG41088R0 Uncharacterized protein conserved in bacteria N-term (DUF3322) 0.006342
141 ENOG4105EJB Short-chain dehydrogenase reductase Sdr -0.006330
142 ENOG4108RDT NADH dehydrogenase NAD(P)H nitroreductase) 0.006325
143 ENOG4105YHG TonB family 0.006312
144 ENOG4105PMN Glutathione-dependent formaldehyde-activating Gfa 0.006312
145 ENOG4108TM1 Tetr family transcriptional regulator -0.006311
146 ENOG4105M5N Metal Dependent Phosphohydrolase 0.006304
147 ENOG4105DTR rard protein 0.006302
148 ENOG4107S7S glycoside hydrolase, family 3 domain protein -0.006302
149 ENOG4105CY2 Citrate transporter 0.006297
150 ENOG4105EDD Bacterial protein of unknown function (DUF899) 0.006296
151 ENOG4105MMR Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) 0.006290
152 ENOG4108VAU general secretion pathway protein G 0.006275
153 ENOG4105N2J Inclusion body protein 0.006273
154 ENOG4105WSE Subunit of malonate decarboxylase, it is an acyl carrier protein to which acetyl and malonyl thioester residues are bound via a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group and turn over during the catalytic mechanism (By similarity) 0.006267
155 ENOG4105KIR Thiol-disulfide oxidoreductase dcc -0.006265
156 ENOG4108IPZ Transporter 0.006254
157 ENOG4105CMF Pfam:DUF2086 -0.006251
158 ENOG4107RCI amp-dependent synthetase and ligase 0.006241
159 ENOG4105DQ4 alcohol dehydrogenase 0.006233
160 ENOG4105CV8 reductase 0.006227
161 ENOG4107SZI Methyl-accepting chemotaxis -0.006214
162 ENOG4105EFA 4-hydroxyphenylacetate 0.006206
163 ENOG4105TMB Formate nitrite transporter -0.006195
164 ENOG4108Q1K integrase family -0.006195
165 ENOG4107R55 ethanolamine transporter 0.006193
166 ENOG4108X5V major facilitator superfamily -0.006193
167 ENOG4105E09 nadh pyrophosphatase 0.006176
168 ENOG4107YNJ LysR family Transcriptional regulator 0.006166
169 ENOG4105EZS DNA RNA NON-specific endonuclease -0.006120
170 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) -0.006117
171 ENOG4105VJI Inherit from COG: response to pH 0.006117
172 ENOG4107WBS restriction modification system DNA specificity domain -0.006102
173 ENOG4108WQI RNA Polymerase 0.006101
174 ENOG4108UAJ Transcriptional regulator 0.006083
175 ENOG4108WP1 Histidine kinase -0.006068
176 ENOG4108I1J Integrase -0.006066
177 ENOG4105EYJ TRANSCRIPTIONal REGULATOR, lysR family 0.006064
178 ENOG4107T1M fad dependent oxidoreductase 0.006058
179 ENOG4105DVC DnaJ domain protein 0.006056
180 ENOG4108K70 Transcriptional regulator 0.006055
181 ENOG4105WF7 pyrroloquinoline quinone biosynthesis protein d 0.006052
182 ENOG41060HI Regulatory protein, FmdB family 0.006050
183 ENOG4106NXG Short chain dehydrogenase -0.006045
184 ENOG41080V8 GntR Family Transcriptional Regulator 0.006037
185 ENOG4108R3G Haloacid dehalogenase type II 0.006024
186 ENOG4105DQ5 transport system permease protein 0.006018
187 ENOG4105DD8 Cobalt chelatase, pCobT subunit 0.006017
188 ENOG4108K6I Transcriptional regulator, GntR family 0.006011
189 ENOG4105KH3 nitrite reductase (NAD(P)h) small subunit 0.006010
190 ENOG4105DSW Fusaric acid resistance protein 0.006009
191 ENOG4107YJJ HPP family -0.006001
192 ENOG4105CRZ Nucleotidyl transferase of unknown function (DUF1814) 0.005989
193 ENOG4105VQD rieske 2fe-2S domain-containing protein 0.005989
194 ENOG4105DMT epimerase dehydratase -0.005985
195 ENOG4105EV8 ectoine hydroxylase -0.005980
196 ENOG4107UZW von willebrand factor, type a -0.005971
197 ENOG4107QUY Guanine deaminase 0.005959
198 ENOG4105CP5 Pfam:DUF88 -0.005955
199 ENOG4105CQT polysaccharide deacetylase 0.005942
200 ENOG4106XE2 ATP-binding region, ATPase domain protein 0.005939
201 ENOG4105F11 amine oxidase 0.005938
202 ENOG4105P74 NA 0.005938
203 ENOG4105RZA cell wall assembly cell proliferation coordinating protein 0.005934
204 ENOG4107X36 Redoxin domain protein -0.005924
205 ENOG4105ECE NA -0.005920
206 ENOG4105MIR Phenylalanine 4-monooxygenase 0.005917
207 ENOG4105FQ6 thiopurine methyltransferase 0.005916
208 ENOG4105HYG antirestriction protein -0.005911
209 ENOG4107RIM Dehydrogenase 0.005908
210 ENOG4105EE5 Membrane protein terC -0.005908
211 ENOG4108U0T Iclr family transcriptional regulator 0.005905
212 ENOG4105CHH sulfate transporter 0.005889
213 ENOG4105QE3 oxidoreductase -0.005884
214 ENOG4105D9U N-acetyltransferase -0.005868
215 ENOG4105E7N gluconolactonase (EC 3.1.1.17) 0.005850
216 ENOG4108N19 Protein of unknown function (DUF3150) -0.005832
217 ENOG4105F8W Membrane 0.005830
218 ENOG4105ETT transcriptional Regulator, LysR family 0.005829
219 ENOG4108PGY Molybdenum cofactor biosynthesis protein F 0.005826
220 ENOG4106UW1 Major Facilitator superfamily -0.005820
221 ENOG4105DRI Involved in the oxidation of myo-inositol (MI) to 2- keto-myo-inositol (2KMI or 2-inosose) (By similarity) 0.005813
222 ENOG4107U81 Protein of unknown function (DUF1524) 0.005813
223 ENOG4107UEM Glycosyl transferase, family 2 0.005789
224 ENOG4108VFV resolvase -0.005787
225 ENOG41074JJ Transcriptional regulator 0.005782
226 ENOG4107S7K N-6 DNA Methylase -0.005775
227 ENOG4105CIY formyltetrahydrofolate deformylase 0.005774
228 ENOG41070EG Hydrolyzes cAMP to 5'-AMP. Plays an important regulatory role in modulating the intracellular concentration of cAMP, thereby influencing cAMP-dependent processes (By similarity) 0.005766
229 ENOG4107S0Z Chromate transporter, chromate ion transporter (CHR) family 0.005750
230 ENOG4107S3M amidohydrolase -0.005745
231 ENOG4107T4I Type I site-specific deoxyribonuclease 0.005743
232 ENOG4107TGF N-6 DNA Methylase 0.005743
233 ENOG4105E04 Beta-lactamase domain protein 0.005725
234 ENOG4107Y59 type iii secretion -0.005724
235 ENOG4105SC1 monovalent cation H antiporter subunit E 0.005721
236 ENOG4105DPE Conserved Protein 0.005702
237 ENOG4106DXM integrase family 0.005701
238 ENOG4106032 Glutathionylspermidine synthase 0.005690
239 ENOG4105G7D MltA-interacting MipA family protein -0.005689
240 ENOG4107R8R ATP-dependent DNA helicase RecQ 0.005685
241 ENOG4105C7I Dehydrogenase 0.005676
242 ENOG4108QK7 TRANSCRIPTIONal REGULATOR, IclR family -0.005671
243 ENOG4107SSX brancheD-chain amino acid aminotransferase -0.005670
244 ENOG4105F35 Catalyzes the NAD( )-dependent oxidation of L-carnitine to 3-dehydrocarnitine (By similarity) 0.005669
245 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.005667
246 ENOG4105G0T bifunctional deaminase-reductase domain protein 0.005661
247 ENOG4105MRF Integrase 0.005660
248 ENOG4108R3Q Short chain dehydrogenase 0.005659