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 ENOG4105E2D ec 3.2.1.52 0.015638
2 ENOG4108IQC 2,3-dihydroxybenzoate-AMP ligase 0.010948
3 ENOG4105DZR Type I site-specific deoxyribonuclease 0.010813
4 ENOG4108TSE Transferase 0.009516
5 ENOG4107WN4 Polygalacturonase -0.008924
6 ENOG4108KGY deoR family transcriptional regulator 0.008922
7 ENOG4105JZC GHMP kinase 0.008918
8 ENOG4107QZU type I restriction-modification system 0.008476
9 ENOG4108KDD Involved in the transport of maltose and maltodextrins (By similarity) 0.008442
10 ENOG4108XMV regulator, lux-R family 0.008413
11 ENOG4108RPY Dehydrogenase 0.008174
12 ENOG4108MJ5 VirK protein 0.008169
13 ENOG4106KR7 LysR family Transcriptional regulator 0.008092
14 ENOG4108JQB penicillin-binding protein 1C 0.007991
15 ENOG4108HRK Histidine kinase 0.007975
16 ENOG4105D6R Binding-protein-dependent transport systems, inner membrane component -0.007916
17 ENOG41069U0 P2 GpE family -0.007832
18 ENOG4105HB7 Glyoxalase Bleomycin resistance protein (Dioxygenase 0.007760
19 ENOG4105X17 23-dihydro-2,3-dihydroxybenzoate dehydrogenase 0.007680
20 ENOG4105VEV -acetyltransferase 0.007613
21 ENOG4106F3G Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5- dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon (By similarity) 0.007587
22 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) 0.007561
23 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.007429
24 ENOG4105VMP Transcriptional regulator 0.007375
25 ENOG4108DWY NAD(P) transhydrogenase (Alpha subunit 0.007375
26 ENOG4105DT2 Terminase ATPase subunit -0.007360
27 ENOG4105EU5 type VI secretion system effector, hcp1 family -0.007224
28 ENOG4108V7B Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide (By similarity) 0.007217
29 ENOG41067Y0 NA -0.007189
30 ENOG4105XJ3 exported protein 0.007162
31 ENOG4105MQ8 Phage virion morphogenesis protein -0.007140
32 ENOG4105DJ2 Major Facilitator Superfamily 0.007111
33 ENOG4107S6X Glycosyl transferase, family 2 0.007093
34 ENOG4105CMW The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity) 0.007083
35 ENOG4105CSJ Enoyl- acyl-carrier-protein reductase NADH 0.007071
36 ENOG4107FKK extracellular solute-binding protein family 1 0.007044
37 ENOG4105KAF membrAne 0.007039
38 ENOG4108RNG Permease of the drug metabolite transporter -0.006963
39 ENOG4108RG5 PTS system N-acetylgalactosamine-specific transporter subunit IIB 0.006925
40 ENOG4105D4Y metalloprotease 0.006923
41 ENOG4105ES1 acyl-CoA reductase 0.006861
42 ENOG4105EM7 Selenocysteine-specific translation elongation factor 0.006853
43 ENOG4105EG2 ABC transporter, permease 0.006832
44 ENOG4105G5F extracellular solute-binding protein family 1 -0.006821
45 ENOG4105DCY Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide (By similarity) 0.006794
46 ENOG4105C8C binding-protein-dependent transport systems inner membrane Component -0.006720
47 ENOG4105U0F oligosaccharide H symporter, major facilitator superfamily (MFS) -0.006715
48 ENOG41080HT Transcriptional regulator, arsr family 0.006656
49 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) -0.006639
50 ENOG4108F3C rhs element vgr protein -0.006593
51 ENOG410662T chitinase 0.006593
52 ENOG4108CA4 Bacterial protein of unknown function (DUF934) 0.006572
53 ENOG4106AXJ AraC family transcriptional regulator 0.006569
54 ENOG4108CNU Entericidin EcnA/B family -0.006523
55 ENOG4105C54 Major Facilitator superfamily -0.006509
56 ENOG4105JSJ NA 0.006463
57 ENOG4108I9J Transcriptional regulator, ARAC family -0.006444
58 ENOG4108ZDJ NA -0.006441
59 ENOG4106FE2 Flagellar export protein flij -0.006415
60 ENOG4105GD2 NA 0.006391
61 ENOG4105NQ7 acetyltransferase -0.006385
62 ENOG4105E2K Glycosyl transferase (Group 1 -0.006382
63 ENOG4105EF1 ribulokinase -0.006380
64 ENOG4105EV9 Alpha Beta Hydrolase 0.006367
65 ENOG4107SNM Phosphoesterase, PA-phosphatase related -0.006347
66 ENOG4105D4B ABC, transporter -0.006338
67 ENOG4105BZG amino acid carrier protein 0.006310
68 ENOG4106B3Q phage holin 0.006293
69 ENOG4108P62 biosynthesis protein (CbiG) 0.006285
70 ENOG4108KI7 Diguanylate cyclase 0.006276
71 ENOG4105E4F Isochorismate synthase 0.006269
72 ENOG4106NDP Transcriptional regulator -0.006268
73 ENOG4108EKG Sodium hydrogen exchanger 0.006264
74 ENOG4107QWS glycogen debranching enzyme glgx -0.006234
75 ENOG4105EA6 outer membrane usher protein 0.003116
75 ENOG4106J8C Chaperone 0.003116
76 ENOG4108ZEY Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity) -0.006228
77 ENOG4107WSI Pfam:DUF395 -0.006217
78 ENOG4107RCJ Phage Tail Tape Measure Protein -0.006203
79 ENOG4106NV4 (ABC) transporter -0.006202
80 ENOG4108Q2J Inner membrane protein YebE 0.006196
81 ENOG4107W52 maltose operon periplasmic protein 0.006181
82 ENOG4105C0K Gdp-mannose 4,6-dehydratase -0.006168
83 ENOG4105TVJ transport system, permease 0.006166
84 ENOG4105C0W non-ribosomal peptide synthetase 0.006160
85 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) 0.002044
85 ENOG4105CIA precorrin-4 C(11)-methyltransferase 0.002044
85 ENOG4105DH2 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group (By similarity) 0.002044
86 ENOG41084S7 Plasmid maintenance system antidote protein 0.006131
87 ENOG4106JHG type VI secretion system effector, hcp1 family 0.006128
88 ENOG4107QQ4 Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans (By similarity) 0.006124
89 ENOG4106HK8 GPR1 FUN34 yaaH family protein 0.006118
90 ENOG4108YRF PTS System -0.006115
91 ENOG4105FPH Repressor protein 0.006081
92 ENOG4105STD Prophage CP4-57 regulatory -0.006065
93 ENOG4105CXC rtn protein 0.006061
94 ENOG4107SI7 Substrate-binding region of abc-type glycine betaine transport system 0.006053
95 ENOG4105G3H inositol mono-phosphatase 0.006044
96 ENOG4107SI4 ImcF domain-containing protein -0.002998
96 ENOG4108RV3 Type VI secretion -0.002998
97 ENOG4107QZB decarboxylase 0.005989
98 ENOG4107UUW glycyl-radical enzyme activating protein family -0.005989
99 ENOG4108530 peptidase 0.005988
100 ENOG4105Z6B inner membrane protein yjfl 0.005985
101 ENOG4108SZQ NA 0.005965
102 ENOG41090BB DNA mismatch endonuclease (vsr) -0.005946
103 ENOG4108W8P Diguanylate cyclase with PAS PAC sensor 0.005932
104 ENOG4105J7H Type IV VI secretion system protein, DotU family -0.005927
105 ENOG41061ZR Transcriptional regulator 0.005923
106 ENOG4105D56 permease protein 0.005903
107 ENOG4107QIJ Aconitate hydratase 2 0.005863
108 ENOG4108Z3M integral membrane protein 0.005856
109 ENOG4105CTD carboxy-peptidase 0.005812
110 ENOG4108EKE The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. This system is involved in N-acetylmuramic acid (MurNAc) transport, yielding cytoplasmic MurNAc-6-P. Is also able to take up anhydro-N-acetylmuramic acid (anhMurNAc), but cannot phosphorylate the carbon 6, probably because of the 1,6-anhydro ring (By similarity) 0.005804
111 ENOG4108A5K Protein of unknown function (DUF1044) -0.005802
112 ENOG4107SPW HsdM N-terminal domain 0.005790
113 ENOG4108U18 CAAX amino terminal protease family protein 0.005789
114 ENOG4106MZ1 Methyl-accepting chemotaxis sensory transducer -0.005757
115 ENOG4108F2V Transcriptional regulator (XRE family 0.005750
116 ENOG4105EE8 May catalyze the methylation of C-1 in cobalt-precorrin- 5 and the subsequent extrusion of acetic acid from the resulting intermediate to form cobalt-precorrin-6A (By similarity) 0.005744
117 ENOG4108RPX mosc domain containing protein 0.005742
118 ENOG4105CB3 Required for the thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32) (By similarity) 0.005734
119 ENOG4108Q79 6-phosphogluconolactonase (EC 3.1.1.31) 0.005731
120 ENOG4108RKU Protein of unknown function (DUF2612) -0.005721
121 ENOG4105M24 Pfam:DUF2241 0.005719
122 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin 0.005705
123 ENOG4105D1Z hydroxypyruvate reductase 0.005703
124 ENOG4105ECQ AraC Family Transcriptional Regulator 0.005674
125 ENOG4105QUC reductase 0.005660
126 ENOG4105DVK Precorrin-2 c20-methyltransferase 0.002830
126 ENOG41081F0 Precorrin-8x methylmutase 0.002830
127 ENOG4105IQ3 FHA domain 0.005656
128 ENOG4105BZX nudix hydrolase 0.005656
129 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase 0.005649
130 ENOG4108RMY Aminoglycoside phosphotransferase -0.005640
131 ENOG4105MZU cell filamentation protein 0.005633
132 ENOG4107T60 oxidoreductase 0.005620
133 ENOG4105GN1 Diguanylate cyclase 0.005612
134 ENOG4105CBZ Short-chain dehydrogenase reductase Sdr 0.005599
135 ENOG4105N1E membrAne -0.005586
136 ENOG41060SR sugar ABC transporter (Permease) -0.005586
137 ENOG4108AZI Catalyzes the hydrolysis of 4-amino-2-methyl-5- hydroxymethylpyrimidine pyrophosphate (HMP-PP) to 4-amino-2- methyl-5-hydroxymethylpyrimidine phosphate (HMP-P) (By similarity) 0.005586
138 ENOG4107S4Z Activates expression of the rhaBAD and rhaT operons (By similarity) -0.005577
139 ENOG4105FH0 Fimbrial protein 0.005566
140 ENOG4107BJW polysaccharide deacetylase 0.005561
141 ENOG4107U3U Sodium hydrogen exchanger -0.005557
142 ENOG4108NI7 LysR family Transcriptional regulator 0.005547
143 ENOG4105WQI isochorismatase 0.005544
144 ENOG4108WF3 methyltransferase -0.005543
145 ENOG4105CZX twitching motility protein 0.005542
146 ENOG4105EKS Tetr family transcriptional regulator 0.005540
147 ENOG4105RKW reductase (By -0.005525
148 ENOG4106TC3 peptidase -0.005522
149 ENOG41066DU Protein of unknown function (DUF2622) 0.005520
150 ENOG4105CYB regulatoR 0.005520
151 ENOG4105CU3 Type VI secretion protein IcmF 0.005513
152 ENOG4106JF3 nnrs family 0.005500
153 ENOG4105C1Y Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity) 0.005494
154 ENOG4105D3Y Na H antiporter 0.005493
155 ENOG4105D1V cellulose synthase operon protein YhjU 0.005492
156 ENOG4105DZT Gentisate 1,2-dioxygenase -0.005490
157 ENOG4108YH3 Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) -0.005489
158 ENOG4107SXU methyl-accepting chemotaxis 0.005472
159 ENOG4105PIA abc transporter atp-binding protein -0.005464
160 ENOG4108S8Y NA -0.005464
161 ENOG4107AQH NA -0.005462
162 ENOG4107QQ7 Outer membrane porin 0.005453
163 ENOG4105DG4 malate L-lactate dehydrogenase -0.005439
164 ENOG4108KYS NA 0.002714
164 ENOG4108PZ2 Phage Mu protein F like protein 0.002714
165 ENOG4106H1J Required for entry into the host cell through presentation or delivery of SipC at the host cell plasma membrane. Along with SipC, is necessary for the transfer of other effector proteins into the host cell. Induces macrophage apoptosis either by binding and activating the proapoptotic enzyme caspase-1 (caspase-1 dependent), resulting in the release of interleukin-1 beta active form, or by disrupting mitochondria and inducing autophagy (caspase-1 independent). The former is dependent of its membrane-fusion activity. The SipBC complex, in association with its chaperone SicA, is regulated by binding of InvE -0.005424
166 ENOG4105XDF Protein of unknown function (DUF1272) -0.005416
167 ENOG4105DDV Transcriptional regulator (LacI family 0.005413
168 ENOG4105CIX lrgb family 0.005401
169 ENOG4107SP0 drug resistance transporter, EmrB QacA subfamily 0.005398
170 ENOG4108J59 Extracellular solute-binding protein, family 5 0.005395
171 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) 0.005394
172 ENOG4105DGU Histone deacetylase 0.005392
173 ENOG41063B9 Siphovirus Gp157 -0.005379
174 ENOG4105IUQ nucleoprotein polynucleotide-associated enzyme -0.005376
175 ENOG4105EST Metal Dependent Phosphohydrolase 0.005370
176 ENOG4107T4E abc transporter permease protein -0.002682
176 ENOG4108W7X ABC transporter, permease -0.002682
177 ENOG4107RWZ Extracellular solute-binding protein, family 5 -0.005365
178 ENOG4105U74 cellulose biosynthesis protein BcsE 0.005363
179 ENOG4105DJN thiJ pfpI 0.005343
180 ENOG4107USW pfkb domain protein -0.005325
181 ENOG4108U9G peptidase M4 and M36 0.005320
182 ENOG41067B5 Histone deacetylase superfamily protein 0.005319
183 ENOG41068R2 flagellar protein -0.005301
184 ENOG4108TJN glycosyl transferase group 1 -0.005291
185 ENOG4106TKZ peptidase M23 -0.005285
186 ENOG4105DQ5 transport system permease protein 0.005283
187 ENOG4105XS7 NA -0.005278
188 ENOG4105X44 SMC domain protein 0.005273
189 ENOG4108XVQ NA -0.005269
190 ENOG4105DMF Dehydrogenase 0.005263
191 ENOG4107ANE NA -0.005261
192 ENOG4105I8U ABC phosphate phosphonate transporter periplasmic ligand binding protein 0.005260
193 ENOG4108PZU transcriptional regulator, lysR family -0.005260
194 ENOG410702I response regulator -0.005258
195 ENOG4105HZ2 Diguanylate cyclase 0.005253
196 ENOG4105V99 Domain of unknown function (DUF1795) 0.005250
197 ENOG4106N4H Non-LEE-encoded type III effector F -0.005250
198 ENOG4105E93 esterase 0.005247
199 ENOG41080J9 Membrane -0.005247
200 ENOG4107RGM aldo keto reductase 0.005242
201 ENOG4108YXU transcriptional regulator AsnC family 0.005234
202 ENOG41082H6 flagellar basal body rod modification protein -0.005234
203 ENOG4107XSI cobalt-precorrin-6y C15-methyltransferase 0.002616
203 ENOG4108DR9 Cobalt-precorrin-6Y C(5)-methyltransferase 0.002616
204 ENOG4107PPM cobalt chelatase 0.005233
205 ENOG4107T7X Aminotransferase -0.005231
206 ENOG4108KEM LysR family transcriptional regulator 0.005230
207 ENOG4105ENN converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity) -0.005228
208 ENOG4105DEJ cobaltochelatase, CobS subunit -0.005228
209 ENOG4107RPX Bacteriophage protein -0.005225
210 ENOG41082MF Hydrogenase assembly chaperone hypC hupF -0.005211
211 ENOG4108HRG Involved in the cleavage of the C1-C2 bond of 3D- (3,5 4)-trihydroxycyclohexane-1,2-dione (THcHDO) to yield 5-deoxy- glucuronate (5DG) (By similarity) 0.005210
212 ENOG41067TB Fimbrial assembly family protein -0.005209
213 ENOG4105HA9 of methanol dehydrogenase type 0.005198
214 ENOG4108HHM Glycosyl transferase, family 2 -0.005196
215 ENOG4105CJ4 Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids (By similarity) 0.005186
216 ENOG4107VMU Membrane 0.005182
217 ENOG4108KUX Phosphoadenosine phosphosulfate reductase -0.005181
218 ENOG4107RUZ Sss sodium solute transporter superfamily 0.005179
219 ENOG4105DZG Dehydrogenase -0.005163
220 ENOG4105G5A Protein of unknown function (DUF2877) -0.002578
220 ENOG4107653 Transcriptional regulator -0.002578
221 ENOG4108S9Q Repressor protein 0.005144
222 ENOG41060W2 glyoxylate carboligase -0.005140
223 ENOG41079C0 AraC family transcriptional regulator 0.005132
224 ENOG4105CKT filamentous hemagglutinin -0.005121
225 ENOG4108P0I Capsid scaffolding protein -0.005112
226 ENOG4108NNZ chitinase 0.005109
227 ENOG4107QKS N-acylglucosamine 2-epimerase -0.005106
228 ENOG4107YTJ transcriptional regulator 0.005103
229 ENOG4105CPQ Dehydrogenase -0.005103
230 ENOG4107J5X Diguanylate cyclase with PAS PAC sensor 0.005095
231 ENOG4106MZZ glycerophosphoryl diester phosphodiesterase 0.005090
232 ENOG4105NYC Head Completion -0.005090
233 ENOG4107SM8 Adenylate Guanylate cyclase 0.005084
234 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) 0.005079
235 ENOG4108HW8 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) -0.005078
236 ENOG4105DD8 Cobalt chelatase, pCobT subunit -0.005078
237 ENOG410846Z Transcriptional regulator (XRE family 0.005076
238 ENOG410671D Branched-chain amino acid transport protein (AzlD) 0.005075
239 ENOG4105CYM Glutathione S-transferase 0.005067
240 ENOG4105CAU Arsenical resistance protein, ArsH 0.005066
241 ENOG4108P6Y Inherit from COG: Outer membrane autotransporter -0.005066