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 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) -0.023485
2 ENOG4105C9K Endothelin-converting enzyme 1 -0.022732
3 ENOG4107TSB Polypeptide-transport-associated domain protein ShlB-type -0.019971
4 ENOG4107VQQ Glycosyl transferase, family 2 -0.019965
5 ENOG41069F6 NA -0.019874
6 ENOG4106U13 NA -0.019847
7 ENOG4106CZ6 NA -0.019814
8 ENOG4108VKT Abortive infection protein -0.019619
9 ENOG4108PPP Transcriptional regulator, ARAC family -0.019592
10 ENOG4105M33 TRANSCRIPTIONal -0.019207
11 ENOG41088CX ErfK YbiS YcfS YnhG -0.018816
12 ENOG4107QIW Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism (By similarity) 0.016208
13 ENOG4105CJQ hydrolase, family 31 0.015724
14 ENOG4107QND Nitrite extrusion protein 0.015419
15 ENOG4107RT8 yd repeat-containing protein 0.014738
16 ENOG4105UX5 NA 0.014598
17 ENOG4108X7A Terpene synthase metal-binding domain-containing protein 0.014211
18 ENOG4108VK9 NA 0.014177
19 ENOG4107SW5 Peptidase M16 domain protein 0.013805
20 ENOG41061H0 Monooxygenase 0.013764
21 ENOG41065KQ synthase 0.013708
22 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) 0.013669
23 ENOG4107RFG polymerase involved in DNA repair 0.013658
24 ENOG4105CMV Succinyl-CoA synthetase subunit beta 0.013618
25 ENOG4107UT5 site-determining protein 0.013562
26 ENOG4105EGG ABC transporter 0.013517
27 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F 0.013415
28 ENOG4105CH8 Succinyl-CoA ligase ADP-forming subunit alpha 0.013256
29 ENOG4107SYD Arginyl-tRNA synthetase 0.013108
30 ENOG4105WCN acetyltransferase 0.013083
31 ENOG4108TQF Hydrolase 0.013027
32 ENOG4105C57 major facilitator superfamily 0.012834
33 ENOG4105C0B DNA polymerase III (alpha subunit) 0.012743
34 ENOG4107ZED Uncharacterised protein family UPF0047 0.012589
35 ENOG4105E03 chitinase 0.012492
36 ENOG4105F0K SARP family transcriptional regulator 0.012348
37 ENOG4105DEV SARP family transcriptional regulator 0.012155
38 ENOG4105VQ0 flagellar hook-basal body complex protein fliE 0.012144
39 ENOG410805Z Gcn5-related n-acetyltransferase 0.012076
40 ENOG41061KA protein serine threonine phosphatase 0.011979
41 ENOG4105M8B Conserved domain protein, histidine-rich 0.011903
42 ENOG4107VBA oxidoreductase 0.011892
43 ENOG4105C5U The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate (By similarity) 0.011745
44 ENOG410907J dual specificity protein phosphatase 0.011724
45 ENOG4107YNN Transcriptional regulator 0.011724
46 ENOG4105E3X Lytic transglycosylase catalytic 0.011718
47 ENOG4105VEQ Cold shock protein 0.011644
48 ENOG4107QTI laci family transcriptional regulator 0.011614
49 ENOG4105W73 LamG domain-containing protein 0.011588
50 ENOG4105R4Y NA 0.011544
51 ENOG4105G8A Tetr family transcriptional regulator 0.011516
52 ENOG41067X5 VanZ-like protein 0.011473
53 ENOG4108J4Z RNA polymerase 0.011434
54 ENOG4105D6C Part of the ABC transporter complex MacAB involved in macrolide export. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation (By similarity) 0.011402
55 ENOG4107QW6 Glycoside hydrolase family 2 TIM barrel 0.011377
56 ENOG4105DH9 Beta-lactamase domain protein 0.011329
57 ENOG4105SG0 Membrane 0.011312
58 ENOG4107KTR stage II sporulation protein 0.011301
59 ENOG4105FCG Threonine dehydratase 0.011289
60 ENOG4108S7K FtsX-like permease family 0.011273
61 ENOG4108SGC Alpha beta hydrolase 0.011267
62 ENOG4105D6T Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine (By similarity) 0.011227
63 ENOG4107HZB Carbohydrate binding family 6 0.011154
64 ENOG4105QEZ Hydrolase 0.011110
65 ENOG4108ZVZ FtsX-like permease family 0.011092
66 ENOG4105I94 hydrolase 0.011006
67 ENOG4107JA4 regulatoR 0.010988
68 ENOG4105DB3 bacteriochlorophyll chlorophyll a synthase 0.010975
69 ENOG4105U9I Nudix Hydrolase 0.010956
70 ENOG4108ZNU Tetr family transcriptional regulator 0.010942
71 ENOG4108KT5 K06886 hemoglobin 0.010934
72 ENOG4107QK4 glycoside hydrolase, family 3 domain protein 0.010898
73 ENOG4105Y5M Membrane 0.010898
74 ENOG4105EX0 alpha-galactosidase 0.010881
75 ENOG4106JH8 cNMP 0.010842
76 ENOG4106GTI NA 0.010834
77 ENOG41066T1 NA 0.010823
78 ENOG4105TV4 AraC family transcriptional regulator 0.010815
79 ENOG4108HBX Transcriptional regulator 0.010756
80 ENOG4105DDC Oxidoreductase domain protein 0.010753
81 ENOG4108A1M Family Transcriptional Regulator 0.010748
82 ENOG4106BEU NA 0.010748
83 ENOG4105H5Y gCN5-related N-acetyltransferase 0.010747
84 ENOG4107BUS NA 0.010735
85 ENOG4107CZ0 NA 0.010735
86 ENOG4105MNR Tetr family transcriptional regulator 0.010695
87 ENOG4108K8Q Inherit from NOG: Xylosidase arabinosidase 0.010644
88 ENOG4105D5S Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity) 0.010638
89 ENOG4105PMB Cupin 2, conserved barrel domain protein 0.010621
90 ENOG4108M6Y methionine sulfoxide reductase A -0.010614
91 ENOG4108IB8 reductase 0.010596
92 ENOG4105E1R phage tail tape measure protein 0.010574
93 ENOG4105EE6 Alcohol dehydrogenase zinc-binding domain protein 0.010558
94 ENOG4106CWA Signal peptidase i 0.010551
95 ENOG4105CJZ response regulator 0.010542
96 ENOG4105CTH Magnesium or manganese-dependent protein phosphatase 0.010540
97 ENOG41088ZU repeat-containing protein 0.010519
98 ENOG4107QTZ amino acid 0.010512
99 ENOG4107UTF regulatoR 0.010504
100 ENOG4106RTH Histidine kinase 0.010496
101 ENOG4108V0P LemA family -0.010454
102 ENOG4106299 Transcriptional regulator 0.010432
103 ENOG4105R00 Two-component system sensor kinase 0.010416
104 ENOG4105K5C Phosphonate degradation operons associated HDIG domain protein 0.010411
105 ENOG41074RY transcriptional regulator 0.010405
106 ENOG4108NJZ Sensory box GGDEF EAL domain protein -0.010405
107 ENOG4105F0V Cell wall hydrolase 0.010402
108 ENOG4105MCT stage V sporulation protein S 0.010400
109 ENOG4105DQ6 Transposase 0.010396
110 ENOG4108R7T extracellular solute-binding protein family 1 0.010390
111 ENOG4105WZK nitrite reductase NADPH small subunit 0.010373
112 ENOG4107FPT Cell surface receptor IPT TIG domain protein 0.010372
113 ENOG4105NCB laci family transcriptional regulator 0.010371
114 ENOG4105NUB Transmembrane transport protein 0.010356
115 ENOG4108Z52 Appr-1-p processing domain protein 0.010354
116 ENOG4108Y5P NmrA family 0.010325
117 ENOG41075UX NA 0.010287
118 ENOG410826A Transcriptional regulator, MarR family 0.010273
119 ENOG410622R NA 0.010265
120 ENOG4108SQ9 flavin reductase domain protein, FMN-binding 0.010264
121 ENOG4105VGV redox-active disulfide protein 2 -0.010254
122 ENOG4105MNF NA 0.010245
123 ENOG410648D Yip1 domain 0.010234
124 ENOG4105RGJ gCN5-related N-acetyltransferase 0.010220
125 ENOG4106ZVH Domain of unknown function (DUF1877) 0.010208
126 ENOG41072WX NA 0.010207
127 ENOG4106HAF NA 0.010196
128 ENOG4105P5Y Spherulation-specific family 4 0.010195
129 ENOG41060P0 NA 0.010191
130 ENOG4107PU6 Membrane 0.010186
131 ENOG4106BK4 NA 0.010186
132 ENOG4105BZK Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity) 0.010177
133 ENOG4107D81 Domain of unknown function DUF20 0.010174
134 ENOG4106CYJ NA 0.010168
135 ENOG4108VPS metallophosphoesterase 0.010161
136 ENOG4106A1X NA 0.010157
137 ENOG41067CN Transcriptional regulator, TetR family 0.010157
138 ENOG4107PQ7 NA 0.010157
139 ENOG41071FA Magnesium or manganese-dependent protein phosphatase 0.010123
140 ENOG41073TT NA 0.010110
141 ENOG4108W3M isochorismatase hydrolase 0.010109
142 ENOG4106GHR FtsX-like permease family 0.010076
143 ENOG4106R72 Endonuclease Exonuclease phosphatase 0.010074
144 ENOG41090H6 Peptidyl-prolyl cis-trans isomerase 0.010063
145 ENOG4105CM2 brancheD-chain amino acid aminotransferase -0.010047
146 ENOG4105WSM Anti-sigma-factor antagonist 0.010029
147 ENOG41064C4 transposase, IS3 IS911 family protein 0.010015
148 ENOG4107DUC NA 0.010004
149 ENOG4105C26 Dehydrogenase 0.010003
150 ENOG4108VVV Transcriptional factor involved in regulation of membrane lipid biosynthesis by repressing genes involved in fatty acid and phospholipid metabolism (By similarity) 0.009996
151 ENOG4107RR1 TRANSCRIPTIONal 0.009995
152 ENOG4105WE1 Transcriptional regulator 0.009964
153 ENOG41090R7 Ferric uptake 0.009953
154 ENOG41084D2 2-phosphosulfolactate phosphatase 0.009929
155 ENOG4108XUF NA 0.009908
156 ENOG4105KUR CAAX amino terminal protease family protein -0.009892
157 ENOG4105Z5P Transposase 0.009882
158 ENOG4108VPX Involved in 1,2-propanediol (1,2-PD) degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate (By similarity) 0.009874
159 ENOG4105DN8 K05989 alpha-L-rhamnosidase EC 3.2.1.40 0.009855
160 ENOG4105FXU 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) 0.009849
161 ENOG4105E1G Band 7 protein 0.009839
162 ENOG4105CNE Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane (By similarity) 0.009835
163 ENOG4105CKI cobalamin synthesis protein 0.009829
164 ENOG4105VBN Might take part in the signal recognition particle (SRP) pathway. This is inferred from the conservation of its genetic proximity to ftsY ffh. May be a regulatory protein (By similarity) 0.009797
165 ENOG410670M Protein of unknown function (DUF2716) 0.009777
166 ENOG4108UT2 hemolysin iii 0.009770
167 ENOG4108NAU Short-chain dehydrogenase reductase sdr 0.009766
168 ENOG4108QUI NA 0.009762
169 ENOG4105DEK Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.009730
170 ENOG4105H80 Tetr family transcriptional regulator 0.009700
171 ENOG4105KWY NA 0.009675
172 ENOG4105E35 Dipicolinate synthase subunit A 0.009662
173 ENOG4105EFS Binding-protein-dependent transport systems, inner membrane component 0.009642
174 ENOG4105EWD stage III sporulation protein ae 0.009639
175 ENOG4105VMP Transcriptional regulator 0.009634
176 ENOG4105ZYM Protein of unknown function (DUF2809) 0.009622
177 ENOG4107SVN transposase 0.009600
178 ENOG4108XBD Inherit from COG: peptidase 0.009564
179 ENOG4108N6Q NA 0.009564
180 ENOG4105C9F isomerase 0.009501
181 ENOG4107QW4 alcohol dehydrogenase 0.009491
182 ENOG4105XFA sporulation peptidase YabG 0.009490
183 ENOG4108I0Z Aconitate hydratase 0.009472
184 ENOG4107FI8 stage II sporulation protein 0.009455
185 ENOG4105C30 Nad-dependent epimerase dehydratase -0.009451
186 ENOG4105T5D Inherit from COG: O-methyltransferase 0.009442
187 ENOG4107S0Q Acyl-CoA dehydrogenase N terminal 0.009434
188 ENOG4106RBQ NA 0.009374
189 ENOG4105GKH Zn-finger in ubiquitin-hydrolases and other protein 0.009365
190 ENOG4105VAT metal-binding protein 0.009361
191 ENOG4105C02 permease 0.009353
192 ENOG4107QR7 peptidase S8 and S53, subtilisin, kexin, sedolisin 0.009352
193 ENOG4108PHQ Alcohol dehydrogenase zinc-binding domain protein 0.009313
194 ENOG4105CNB Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans (By similarity) -0.009306
195 ENOG4105TDY Methyltransferase 0.009279
196 ENOG41084AF NA 0.009267
197 ENOG4108R94 NA 0.009265
198 ENOG4105EXQ uroporphyrinogen iii synthase hem4 0.009256
199 ENOG4105CIK Amidinotransferase 0.009253
200 ENOG4107YA8 d-alanyl-d-alanine carboxypeptidase 0.009251
201 ENOG4107SFG aldo keto reductase 0.009249
202 ENOG4105CYN Serine protein kinase 0.009244
203 ENOG4107R83 hydrolase family 3 0.009241
204 ENOG4108ZC3 AsnC family transcriptional regulator 0.009227
205 ENOG4105Y4N flagellar 0.009199
206 ENOG4108R3F Nudix family 0.009196
207 ENOG4105CVM Molybdenum cofactor synthesis domain protein -0.009191
208 ENOG4105CRR lysr family transcriptional regulator 0.009172
209 ENOG4105D4K integrase catalytic 0.009160
210 ENOG4105M4F hydrolase 0.009146
211 ENOG4107V80 epimerase dehydratase 0.009144
212 ENOG4105DI2 Pyruvate flavodoxin ferredoxin oxidoreductase domain protein 0.009122
213 ENOG4105D6W Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps (By similarity) 0.009116
214 ENOG4105NI1 DNA-binding protein with PD1-like DNA-binding motif 0.009086
215 ENOG4108V00 Short chain dehydrogenase 0.009078
216 ENOG4105ERH Fumarylacetoacetate hydrolase -0.009075
217 ENOG4108VPT UPF0234 protein 0.009065
218 ENOG4107TXC Transcriptional regulator 0.009049
219 ENOG4108KTG Membrane protein, drug metabolite transporter 0.009029
220 ENOG4108Z0R Transferase -0.009023
221 ENOG4106AKX UPF0229 protein 0.009017
222 ENOG4105KRN Transcriptional regulator, abrb family 0.009001
223 ENOG4105CEV competence damage-inducible protein 0.008996
224 ENOG41082AN stage II sporulation protein 0.008992
225 ENOG41068Z3 NA 0.008966
226 ENOG4105FZW flagellar biosynthesis regulator FlhF 0.008959
227 ENOG4108RD3 chew protein 0.008957
228 ENOG4107ZUK LysR family Transcriptional regulator 0.008956
229 ENOG4108ZA0 Protein of unknown function (DUF779) 0.008941
230 ENOG4105VXP Protein of unknown function DUF86 -0.008938
231 ENOG41085V3 Aldo Keto reductase 0.008937
232 ENOG4105CK7 Sodium proline symporter -0.008893
233 ENOG4106I03 Sporulation stage 0, Spo0E-like 0.008843
234 ENOG4108RF1 Protein of unknown function DUF2625 0.008825
235 ENOG4105CVG Homoserine O-transsuccinylase 0.008789
236 ENOG4105G6Z alkaline phosphatase 0.008789
237 ENOG4107RFQ Polyprenyl synthetase 0.008787
238 ENOG4105DU1 integral membrane protein, terc 0.008734
239 ENOG4108T4I phosphoglycerate mutase 0.008675
240 ENOG4105W7S Spore coat peptide assembly protein 0.008614
241 ENOG4105KD7 acetyltransferase 0.008614
242 ENOG4106BHC NA 0.008613
243 ENOG4107QZF nitrite reductase NADPH large subunit 0.008597
244 ENOG4107EQ4 Pfam:DUF2078 -0.008593
245 ENOG4105XX2 phosphoglycerate mutase family protein 0.008586
246 ENOG41068BZ NA 0.008584
247 ENOG4107Y2H ErfK ybiS ycfS ynhG family protein 0.008555
248 ENOG41081C9 Peptidase M50 0.008550
249 ENOG4105C7P 2-oxoglutarate dehydrogenase, E1 0.008541
250 ENOG4105PMW Domain of unknown function (DUF1990) 0.008508