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 ENOG4105D5D udp-galactopyranose mutase -0.019285
2 ENOG4107R9Y phosphoglycerol transferase alkaline phosphatase superfamily protein 0.017738
3 ENOG4105MBY Addiction module antitoxin, RelB DinJ family -0.016297
4 ENOG4108M4B domain protein -0.016223
5 ENOG4107Z6X Transcriptional regulator -0.015953
6 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) -0.015502
7 ENOG4107R0P L-ribulose-5-phosphate 4-epimerase 0.015443
8 ENOG4106AA1 Histidine kinase -0.015424
9 ENOG4105EQK -acetyltransferase 0.015346
10 ENOG4105EEW auxin efflux carrier 0.015206
11 ENOG4105DF9 Lipoate-protein, ligase 0.015060
12 ENOG4108KMV Glycosyl transferase (Group 1 -0.015003
13 ENOG4107YX4 Amino acid ABC transporter substrate-binding protein 0.015002
14 ENOG4107QQ8 peptidase 0.015001
15 ENOG4105DRP amino acid AbC transporter 0.014926
16 ENOG4105YRW Domain of unknown function (DUF1836) 0.014912
17 ENOG4105CGH 5'-nucleotidase -0.014898
18 ENOG4105EW4 (LipO)protein 0.014827
19 ENOG4105C1I TRANSCRIPTIONAl REGULATOR GntR family 0.014792
20 ENOG4105D1M ATP-dependent endonuclease of the OLD 0.014491
21 ENOG4105K5P Membrane 0.014453
22 ENOG4108IE0 Dehydrogenase 0.014450
23 ENOG4105D7T ABC transporter 0.014396
24 ENOG41083RF phosphoribosyl-ATP pyrophosphatase 0.014385
25 ENOG41085UN Transcriptional regulator (XRE family 0.014379
26 ENOG4105DJ2 Major Facilitator Superfamily 0.014182
27 ENOG4105NC8 NA 0.014157
28 ENOG41066JZ Integrase -0.014120
29 ENOG4108SGB Transcriptional regulator -0.014115
30 ENOG4107EFR Flavocytochrome c -0.014077
31 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.014054
32 ENOG4107RBP Transcriptional regulator -0.013842
33 ENOG4105HRZ Inherit from COG: permease -0.013706
34 ENOG4105C5I Dehydrogenase 0.013683
35 ENOG4105D0I Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity) 0.013637
36 ENOG4107RKN regulatoR 0.013635
37 ENOG4105H6Q decarboxylase 0.013527
38 ENOG4105DTV traE protein -0.013428
39 ENOG4105KVH Transcriptional regulator 0.013384
40 ENOG4107QM5 aconitate hydratase -0.013322
41 ENOG4105ETU transcriptional activator (TenA 0.013218
42 ENOG4107S6X Glycosyl transferase, family 2 0.013192
43 ENOG4106DR7 MORN repeat protein 0.013166
44 ENOG4107XD6 NA 0.013150
45 ENOG4108ITR TRANSCRIPTIONal 0.013141
46 ENOG41074UY bacteriocin-associated integral membrane 0.013130
47 ENOG4107S7Q NAD dependent epimerase/dehydratase family -0.013054
48 ENOG4105E80 TraG TraD family protein -0.013017
49 ENOG4105ESV Glycosyl transferase, family 4 -0.012927
50 ENOG4106AIG Preprotein translocase subunit SecB -0.012916
51 ENOG4107TIF Phenazine biosynthesis protein, PhzF family 0.012908
52 ENOG4105C4N this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis (By similarity) -0.012887
53 ENOG4105CN1 protease -0.012867
54 ENOG4105FCD Major Facilitator 0.012760
55 ENOG4108N1N Glycosyl hydrolase family 1 0.012743
56 ENOG4107SJB teichoic acid biosynthesis -0.012670
57 ENOG4105KNA -acetyltransferase 0.012662
58 ENOG41089BQ Inherit from COG: Membrane 0.012633
59 ENOG4107Z9Z Hydrolase -0.012609
60 ENOG4105CF4 DegT DnrJ EryC1 StrS aminotransferase -0.012579
61 ENOG4108HHA Transketolase -0.012524
62 ENOG4107QXA Aminotransferase 0.012515
63 ENOG4106GQV Protein of unknown function (DUF3021) 0.012497
64 ENOG4105DA5 (ABC) transporter 0.012414
65 ENOG4107FYG PRD domain protein 0.012362
66 ENOG4105ZZ9 Membrane -0.012307
67 ENOG4105MGU response regulator 0.012270
68 ENOG4105UKW Inherit from COG: PAAR repeat-containing protein -0.012262
69 ENOG4108ZME abc transporter atp-binding protein 0.012252
70 ENOG4108UTW Plays a role in the regulation of phosphate uptake 0.012179
71 ENOG4108JJV Major Facilitator 0.012143
72 ENOG4105C2U cobyrinic Acid a,c-diamide synthase -0.012118
73 ENOG4105X0E operon (Activator) -0.012116
74 ENOG4108UHC Glycosyl transferase, wecb taga cpsf family -0.012111
75 ENOG4107UIB metallophosphoesterase 0.012091
76 ENOG4108N80 biosynthesis protein -0.012082
77 ENOG4105TAQ integral membrane protein 0.012075
78 ENOG4105CAC Catalyzes the conversion of L-arabinose to L-ribulose (By similarity) 0.012030
79 ENOG4105CER acetyl-CoA carboxylase biotin carboxylase 0.011956
80 ENOG4108JII Oxaloacetate decarboxylase 0.011936
81 ENOG4108IYH Dna topoisomerase -0.011915
82 ENOG4105D9Q decarboxylase (Beta subunit) 0.011879
83 ENOG41067RE Hnh endonuclease 0.011868
84 ENOG4105CJ1 ABC, transporter 0.011834
85 ENOG4105HF7 type i restriction modification DNA specificity domain protein -0.011800
86 ENOG4108W2Y isochorismatase 0.011789
87 ENOG4107YSK Glycerol-3-phosphate cytidylyltransferase -0.011758
88 ENOG4106D1Q NA -0.011746
89 ENOG4108QHG Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) -0.011727
90 ENOG410631I Domain of unknown function (DUF3173) -0.011686
91 ENOG4105HMI Membrane 0.011637
92 ENOG4108IYU L-aspartate oxidase 0.011595
93 ENOG4107R37 Glutamate dehydrogenase 0.011595
94 ENOG4106BHR ftsk SpoIIIE family protein 0.011558
95 ENOG4107VJT sorbitol operon transcription regulator -0.011557
96 ENOG4105C1G acyl-Coa dehydrogenase -0.011529
97 ENOG41066RB phage protein -0.011505
98 ENOG4105NDF NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. May also have NAD-dependent lysine demalonylase and desuccinylase activity (By similarity) -0.011491
99 ENOG4107XDY Nicotinamide Mononucleotide Transporter 0.011485
100 ENOG4108ZV3 isochorismatase 0.011472
101 ENOG4105FAV ABC, transporter -0.011386
102 ENOG4106DP4 NA 0.011382
103 ENOG41065DE NA -0.011343
104 ENOG410610U NA 0.011335
105 ENOG4108KAZ Involved in phosphonate degradation (By similarity) 0.011275
106 ENOG4105F2S Abortive infection protein AbiGII -0.011261
107 ENOG4105N04 SNARE associated Golgi protein 0.011245
108 ENOG4108WCK Erf family 0.011233
109 ENOG4105EN6 Membrane 0.011191
110 ENOG4108FW6 Catalyzes the folate-dependent formation of 5-methyl- uridine at position 54 (M-5-U54) in all tRNAs (By similarity) -0.011191
111 ENOG4108YBA Histidine kinase 0.011189
112 ENOG4108YBP pseudouridine synthase 0.011179
113 ENOG4105BZN citrate synthase -0.011150
114 ENOG4108WM5 site-specific recombinase, phage integrase family 0.011141
115 ENOG4105J6G PTS System 0.011104
116 ENOG41063JJ Phage derived protein Gp49-like (DUF891) -0.011097
117 ENOG4105GI3 Cell wall anchor domain protein 0.011080
118 ENOG4105HUF DNA protection during starvation protein -0.011026
119 ENOG4106FEC NA -0.010968
120 ENOG41090RU Pyridoxamine 5'-phosphate oxidase 0.010965
121 ENOG4108I0Q anthranilate phosphoribosyltransferase -0.010938
122 ENOG410814C multidrug resistance protein -0.010915
123 ENOG41089BK Glutamine amido-transferase 0.010897
124 ENOG4105D3D Catalyzes the decarboxylation of carboxynorspermidine and carboxyspermidine (By similarity) 0.010894
125 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.010865
126 ENOG4106B6K Membrane 0.010819
127 ENOG4105KZP HD domain protein 0.010808
128 ENOG4105DQ6 Transposase 0.010769
129 ENOG41076YM VRR-NUC domain protein 0.010757
130 ENOG4105C84 Histidine ammonia-lyase -0.010749
131 ENOG4105CNT hydrolase family 2 0.010731
132 ENOG4107QQ0 gntp family 0.010717
133 ENOG4105KE9 The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity) 0.010712
134 ENOG4108ZEE acetyltransferase, (GNAT) family 0.010708
135 ENOG4105WKN Transcriptional regulator Cro CI family -0.010692
136 ENOG4107EXU Short-chain dehydrogenase reductase Sdr 0.010666
137 ENOG4105GJU NA -0.010648
138 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) 0.010633
139 ENOG4105VEQ Cold shock protein -0.010590
140 ENOG4106G3J NA 0.010564
141 ENOG4105EJJ Dehydrogenase -0.010560
142 ENOG4106I21 NA 0.010539
143 ENOG4107RZX Teichoic acid biosynthesis protein -0.010535
144 ENOG4105C8P )-transporter -0.010521
145 ENOG4106V6D heparinase ii 0.010516
146 ENOG4105E39 Enoyl-CoA hydratase -0.010507
147 ENOG4105G8G Hydrolase -0.010491
148 ENOG4106UKV TonB family -0.010460
149 ENOG4105EP8 Glycosyl Hydrolase Family 88 0.010459
150 ENOG4108R5P Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery (By similarity) -0.010458
151 ENOG4105C6Z Gluconate 0.010458
152 ENOG4105ESI atpase involved in dna repair 0.010455
153 ENOG4105W8Z 4'-phosphopantetheinyl transferase 0.010436
154 ENOG4105E2Y ABC, transporter 0.010434
155 ENOG4105X3U lytTr DNA-binding domain protein -0.010427
156 ENOG4108QXE glycerophosphoryl diester phosphodiesterase -0.010408
157 ENOG4105Z0K NA 0.010385
158 ENOG4105WKZ CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease (By similarity) -0.010325
159 ENOG4108XXH specificity 0.010313
160 ENOG4105UQY Transcriptional regulator, TetR family 0.010291
161 ENOG4105F27 Major Facilitator 0.010279
162 ENOG41068XQ NA 0.010273
163 ENOG4108K4B hydrolase -0.010273
164 ENOG4105CPN adenine deaminase 0.010264
165 ENOG4105WPN DNA integration recombination invertion protein -0.010249
166 ENOG410905X membrane-flanked domain protein -0.010201
167 ENOG4106UFR NA -0.010174
168 ENOG41090F4 NA -0.010139
169 ENOG41077EQ NA 0.010127
170 ENOG4105CJX Molecular chaperone. Has ATPase activity (By similarity) 0.010091
171 ENOG4108ZKP Bacteriocin ABC exporter, ATP binding permease protein -0.010075
172 ENOG4105NJS thiw protein 0.010073
173 ENOG4105E2D ec 3.2.1.52 -0.010058
174 ENOG41062BI Domain of unknown function (DUF1851) -0.010040
175 ENOG4105SUZ NA 0.010030
176 ENOG4105WH1 Two component transcriptional regulator luxr family 0.009998
177 ENOG410712E NA -0.009984
178 ENOG4107QY7 Major Facilitator 0.009982
179 ENOG4105CG3 alpha amylase, catalytic region 0.009976
180 ENOG4107TEC Thiamine pyrophosphate enzyme, C-terminal TPP binding domain -0.009957
181 ENOG4105C2C drug resistance transporter, Bcr CflA -0.009957
182 ENOG4108UHX Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS (By similarity) 0.009952
183 ENOG41063G6 hmm pf04634 -0.009949
184 ENOG4105CJ2 (LipO)protein -0.009944
185 ENOG4105F1T DNA repair protein -0.009929
186 ENOG4108SJI hydrolase, family 25 -0.009923
187 ENOG4105CFT Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) -0.009896
188 ENOG41066XA Bacterial regulatory proteins, luxR family -0.009878
189 ENOG4108TMZ NA 0.009876
190 ENOG4105C8H hydrogenase maturation protein Hypf 0.009872
191 ENOG4107STF Involved in phosphonate degradation (By similarity) 0.009861
192 ENOG4105NMU Transcriptional regulator -0.009839
193 ENOG4108I8K Carboxymuconolactone decarboxylase family 0.009833
194 ENOG4107VBZ Transaldolase 0.009806
195 ENOG41088M9 Inherit from NOG: Nad-dependent epimerase dehydratase 0.009796
196 ENOG4105Y33 Xylose Isomerase Domain-Containing protein 0.009764
197 ENOG4106DH0 conserved domain protein 0.009755
198 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) 0.009749
199 ENOG4105WCN acetyltransferase -0.009711
200 ENOG4105FRU acetyltransferase, (GNAT) family 0.009709
201 ENOG4105BZ3 General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) (By similarity) 0.009701
202 ENOG4108UXR Transcriptional regulator, ARAC family 0.009693
203 ENOG4108VH3 NA -0.009690
204 ENOG4106FI4 Bacterial mobilization protein (MobC) 0.009687
205 ENOG4108QZM esterase 0.009675
206 ENOG4106128 DNA-binding helix-turn-helix protein -0.009659
207 ENOG4105CG5 Glycosyl transferase (Group 1 -0.009659
208 ENOG4105GVB Replication Protein 0.009658
209 ENOG4108WIN Transcriptional regulator -0.009638
210 ENOG4105CUP Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6- dimethylbenzimidazole (DMB) (By similarity) 0.009625
211 ENOG4108Z2U ureidoglycolate hydrolase 0.009624
212 ENOG4108SDJ NA 0.009615
213 ENOG4107ZAM ABC transporter 0.009603
214 ENOG4108MES Periplasmic binding protein -0.009570
215 ENOG4108S0Z ABC transporter, permease 0.009570
216 ENOG4105GVF (ABC) transporter 0.009564
217 ENOG4108R3I dna polymerase iii -0.009541
218 ENOG4106WZ2 NA -0.009538
219 ENOG4105C85 amino acid 0.009538
220 ENOG41080UH degv family -0.009524
221 ENOG4105HIK Protein of unknown function (DUF1697) 0.009522
222 ENOG4105C87 Aminotransferase class I and II -0.009500
223 ENOG4107BHU NA 0.009469
224 ENOG4105W5D IS66 Orf2 family protein -0.009468
225 ENOG4105PUK Membrane 0.009466
226 ENOG4105NI6 heptaprenyl diphosphate synthase component I -0.009456
227 ENOG4108PZN Polysaccharide Biosynthesis Protein 0.009451
228 ENOG4107R8N Glycosyl transferase, family 2 -0.009450
229 ENOG41081NX Carboxymuconolactone decarboxylase family 0.009447
230 ENOG4107179 Matrixin 0.009431
231 ENOG410800A inner membrane protein YbaN 0.009425
232 ENOG4105DRR Transcriptional regulator, GntR family 0.009420
233 ENOG4107QZ6 oxidoreductase 0.009384
234 ENOG4105CJW magnesium transporter -0.009381
235 ENOG4108RDR Transcriptional Regulator AraC Family 0.009371
236 ENOG41069KV Bacterial regulatory proteins, tetR family 0.009346
237 ENOG4107RBJ symporter 0.009334
238 ENOG4108THW HD domain protein 0.009310
239 ENOG4107G2C Protein of unknown function (DUF2680) 0.009281
240 ENOG4105D7N magnesium and cobalt transport protein CorA -0.009272
241 ENOG4107RV4 alkaline phosphatase 0.009269
242 ENOG4105F1F Uncharacterized protein conserved in bacteria (DUF2130) 0.009262
243 ENOG4108UT2 hemolysin iii 0.009258
244 ENOG4108RV2 acetyltransferase 0.009251
245 ENOG4105XE0 NA -0.009233
246 ENOG4106Z0T transcriptional regulator -0.009231
247 ENOG4106GG2 Bacteriophage holin -0.009229
248 ENOG4105ZW9 acetyltransferase, (GNAT) family -0.009214
249 ENOG4108HMX isocitrate dehydrogenase (NADP) -0.009213
250 ENOG4105EUZ Beta-lactamase domain protein 0.009200