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 ENOG4107RSS Hydrogenase accessory protein HypB 0.014344
2 ENOG4105C8H hydrogenase maturation protein Hypf 0.006028
2 ENOG4105CQS hydrogenase expression formation protein HypD 0.006028
3 ENOG4106KUD Membrane -0.011679
4 ENOG4105C45 hydrogenase expression formation protein (HypE) 0.011395
5 ENOG4105DPX Hydrogenase, large subunit 0.011051
6 ENOG4105E3S small subunit 0.011039
7 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit 0.010294
8 ENOG4105C5R Aminotransferase 0.010216
9 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase -0.010210
10 ENOG4108USZ hydrogenase 0.010161
11 ENOG4105DT1 RuBisCO catalyzes two reactions the carboxylation of D- ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate 0.010123
12 ENOG4105X7T Ni Fe-hydrogenase, b-type cytochrome subunit 0.009763
13 ENOG4105DUM transcriptional regulator, lysR family 0.009549
14 ENOG4105BZ9 Cytochrome C oxidase, subunit I -0.009172
15 ENOG4108VFZ ribulose bisphosphate carboxylase, small 0.008707
16 ENOG4105FR1 rard protein -0.008492
17 ENOG4105EE0 oxidoreductase -0.008412
18 ENOG4105CK7 Sodium proline symporter -0.008384
19 ENOG4106855 Competence protein -0.008249
20 ENOG4105C84 Histidine ammonia-lyase -0.008218
21 ENOG4105C5S asparaginyl-tRNA synthetase -0.008120
22 ENOG4105CZ5 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate (By similarity) -0.007912
23 ENOG41071I4 Phosphatidylserine decarboxylase proenzyme 0.007877
24 ENOG4105DB9 Binding-protein-dependent transport systems inner membrane component -0.007828
25 ENOG4108YXA Membrane 0.007731
26 ENOG4105C1B dTDP-glucose 4-6-dehydratase 0.007716
27 ENOG4105EVN Prephenate dehydrogenase 0.007677
28 ENOG4105W7A Protein of unknown function (DUF503) 0.007644
29 ENOG410814C multidrug resistance protein 0.007642
30 ENOG4105E09 nadh pyrophosphatase -0.007614
31 ENOG4108HNZ carboxyl transferase -0.007581
32 ENOG4105CXW Synthesizes alpha-1,4-glucan chains using ADP-glucose (By similarity) 0.007538
33 ENOG4105D3H Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol (By similarity) 0.007417
34 ENOG4107QU1 polyA polymerase 0.007329
35 ENOG4105DQX Zinc finger domain -0.007277
36 ENOG410835K Tripartite ATP-Independent Periplasmic transporter DctQ -0.007201
37 ENOG4105D5B Sulfite reductase, subunit A 0.007190
38 ENOG4108HMW glycyl-tRNA synthetase, alpha subunit 0.007178
39 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.007175
40 ENOG4105C3K feS assembly ATPase SufC -0.007158
41 ENOG4105C9B Cysteine desulfurase -0.007100
42 ENOG4107R91 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position (By similarity) 0.007037
43 ENOG4105DG4 malate L-lactate dehydrogenase -0.007020
44 ENOG4105DSS Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.006967
45 ENOG4108V4Y Phosphoribosyltransferase 0.006950
46 ENOG4108R99 pseudouridine synthase -0.006897
47 ENOG4105C93 Xylose Isomerase -0.006881
48 ENOG4105DSE periplasmic solute binding protein 0.006876
49 ENOG4105D53 Catalyzes the hydrolysis of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil (By similarity) -0.006861
50 ENOG4108KHX Diguanylate cyclase -0.006838
51 ENOG4108ZGC gaf domain protein -0.006815
52 ENOG41086B8 CoB-CoM heterodisulfide reductase 0.006799
53 ENOG4105DHC Aminoglycoside phosphotransferase 0.006794
54 ENOG4105CI2 imidazolone-5-propionate hydrolase -0.006781
55 ENOG4105E6N shikimate quinate 5-dehydrogenase 0.006771
56 ENOG4105EFC phage portal protein HK97 family -0.006769
57 ENOG4107QN8 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA (By similarity) 0.006757
58 ENOG4105ES3 NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) 0.006739
59 ENOG4107SD2 Methylenetetrahydrofolate reductase -0.006709
60 ENOG4105N2T Domain of unknown function DUF302 -0.006703
61 ENOG4105ZIE Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides (By similarity) -0.006652
62 ENOG41089BK Glutamine amido-transferase 0.006643
63 ENOG4108UN4 phage SPO1 DNA polymerase-related protein 0.006641
64 ENOG4105CMQ Chloride channel -0.006632
65 ENOG4108R5P Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery (By similarity) 0.006619
66 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) 0.006585
67 ENOG4105D82 Glutamate dehydrogenase -0.006568
68 ENOG4105CH6 catalase -0.006529
69 ENOG4105EJ5 oxidoreductase gamma subunit 0.006528
70 ENOG4105FKQ transcriptional regulator -0.006487
71 ENOG4105D42 Cleaves the N-terminal amino acid of tripeptides (By similarity) -0.006453
72 ENOG4105F97 virion core protein (Lumpy skin disease -0.006433
73 ENOG4105CD9 Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring (By similarity) -0.006408
74 ENOG4105EU8 FAD linked oxidase domain protein 0.006373
75 ENOG4108IYT Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity) -0.006356
76 ENOG4105BZP glycoside hydrolase 15-related 0.006355
77 ENOG4105E0F Histidine kinase -0.006340
78 ENOG4105CS2 ec 3.2.1.21 -0.006315
79 ENOG4105C8M UPF0272 protein 0.006314
80 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase 0.006304
81 ENOG4105C9X ppx gppa phosphatase 0.006291
82 ENOG4105BZF Glycosyl transferase (Group 1 0.006280
83 ENOG4105RIJ domain protein -0.006272
84 ENOG4108V4M Cobalt abc transporter 0.006270
85 ENOG4105CGP Urocanate hydratase -0.006268
86 ENOG4105CFT Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) 0.006217
87 ENOG4105C72 UPF0176 protein -0.006209
88 ENOG4106EG9 Catalyzes the decarboxylation of orotidine 5'- monophosphate (OMP) to uridine 5'-monophosphate (UMP) (By similarity) 0.006156
89 ENOG4105C28 cystathionine -0.006152
90 ENOG4105C1K alpha-alpha-trehalose-phosphate synthase 0.006152
91 ENOG4105DDK oxidoreductase, beta subunit 0.006107
92 ENOG4108UVN methyltransferase 0.006084
93 ENOG4105EJQ L-serine dehydratase -0.006080
94 ENOG4105CJE phosphoribulokinase (EC 2.7.1.19) 0.006075
95 ENOG4105E9Q Acyl-transferase 0.006003
96 ENOG4108UKM mov34 mpn pad-1 family protein -0.005997
97 ENOG4107R0I Cell wall formation (By similarity) -0.005980
98 ENOG4107QR9 Iron-sulfur cluster binding protein -0.005948
99 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) 0.005934
100 ENOG4107QRG dna polymerase iii -0.005896
101 ENOG4105D7W serine acetyltransferase 0.005892
102 ENOG4105EET magnesium chelatase 0.005890
103 ENOG4105EXU Membrane -0.005889
104 ENOG4108ZGN Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-non-specific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it decreases the phosphorylation status of KaiC. It has no effect on KaiC by itself, but instead needs the presence of both KaiA and KaiC, suggesting that it acts by antagonizing the interaction between KaiA and KaiC (By similarity) 0.005872
105 ENOG4107SSC biotin acetyl-CoA-carboxylase ligase 0.005843
106 ENOG4105D44 asparaginase 0.005843
107 ENOG4105D9N nucleoside -0.005842
108 ENOG4107S75 HAD-superfamily hydrolase subfamily IA variant 3 0.005829
109 ENOG4108IJ1 Dehydrogenase -0.005812
110 ENOG4105D9I Responsible for the addition of glutamate residues to the C-terminus of ribosomal protein S6 (By similarity) -0.005806
111 ENOG4105CRE cytochrome C 0.005802
112 ENOG4105DUX Transporter -0.005802
113 ENOG4105MZG transcriptional modulator of maze toxin, mazf 0.005795
114 ENOG41090K7 metallophosphoesterase 0.005792
115 ENOG4108S93 Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate (By similarity) 0.005780
116 ENOG4105DU1 integral membrane protein, terc -0.005773
117 ENOG4105DSX permease 0.005750
118 ENOG4105DCT glycerol dehydrogenase 0.005737
119 ENOG4107SP1 IroN-sulfur binding 0.005731
120 ENOG41082YV Hydrogenase assembly chaperone hypC hupF 0.005730
121 ENOG4105M7V 2'-5' rna ligase 0.005726
122 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.005724
123 ENOG4105CV9 cyclopropane-fatty-acyl-phospholipid synthase 0.005708
124 ENOG41060TV EF hand domain protein -0.005704
125 ENOG4107QPR SAICAR synthetase 0.005703
126 ENOG4105EJ9 Membrane -0.005697
127 ENOG4105EPU Molybdenum cofactor synthesis domain protein 0.005685
128 ENOG4107UR6 Protein of unknown function DUF72 0.005685
129 ENOG4105CSJ Enoyl- acyl-carrier-protein reductase NADH 0.005680
130 ENOG4105C8W ABC transporter -0.005673
131 ENOG4105C6K Malic enzyme -0.005672
132 ENOG410842U beta-lactamase domain protein 0.005664
133 ENOG4107EF8 Glycosyl transferase (Group 1 0.005660
134 ENOG4105KTQ flagellar basal-body rod protein 0.005655
135 ENOG4108PXT Sensor hybrid histidine kinase -0.005654
136 ENOG4105F7Z ABC transporter 0.005638
137 ENOG4107XTC May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins 0.005636
138 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase 0.005612
139 ENOG4105JAS Dephosphorylates 2-hydroxy-3-keto-5-methylthiopentenyl- 1-phosphate (HK-MTPenyl-1-P) yielding 1,2-dihydroxy-3-keto-5- methylthiopentene (DHK-MTPene) (By similarity) -0.005604
140 ENOG4105EST Metal Dependent Phosphohydrolase -0.005534
141 ENOG4107645 peptidase M23 -0.005525
142 ENOG4106538 saf domain-containing protein 0.005520
143 ENOG4107QXG alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen -0.005517
144 ENOG4105ENJ RND efflux system, outer membrane lipoprotein 0.005512
145 ENOG4105CY9 nitrogenase molybdenum-iron protein beta chain 0.005506
146 ENOG4105CZI D-fructose-1,6-bisphosphate 1-phosphohydrolase class 1 0.005492
147 ENOG4105EZI multiple antibiotic resistance (MarC)-related protein -0.005489
148 ENOG4105E2R ROK family -0.005473
149 ENOG4105D5P Methylmalonyl-coA mutase -0.005465
150 ENOG4107T1I Endonuclease Exonuclease phosphatase -0.005464
151 ENOG4105DTT CRISPR-associated helicase, cas3 0.005462
152 ENOG4105DA5 (ABC) transporter -0.005439
153 ENOG4108IJ7 Glycine betaine -0.005405
154 ENOG4105C3R Methionine synthase 0.005405
155 ENOG4108Z0N nerd domain protein 0.005404
156 ENOG4108Q5A pega domain protein -0.005402
157 ENOG4105EHA HipA domain protein -0.005397
158 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) 0.005396
159 ENOG4105DQ9 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.005391
160 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.005381
161 ENOG4105C5W Aldolase -0.005376
162 ENOG4105DJ5 Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis (By similarity) 0.005358
163 ENOG4105I29 Bacteriochlorophyll 4-vinyl reductase 0.005322
164 ENOG4107TGU Thiamine biosynthesis protein ThiF -0.005319
165 ENOG4105C3D Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA (By similarity) -0.005311
166 ENOG4105W4R Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) 0.005304
167 ENOG4105D8V Glucose sorbosone dehydrogenase 0.005293
168 ENOG4108UNV SUF system FeS assembly protein, NifU family -0.005290
169 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase 0.005285
170 ENOG4105DGU Histone deacetylase 0.005278
171 ENOG4108ZQD Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A (By similarity) 0.005272
172 ENOG4105C5V Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate (By similarity) 0.005259
173 ENOG4105CU6 carbamoyl-phosphate synthetase ammonia chain 0.005245
174 ENOG4105D9H Catalyzes the attachment of glycine to tRNA(Gly) (By similarity) -0.005245
175 ENOG4108UHX Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS (By similarity) -0.005244
176 ENOG4107QZ6 oxidoreductase -0.005244
177 ENOG4105C1M carbamoyl-phosphate synthetase glutamine chain 0.005236
178 ENOG4108Z9K Osmotically inducible protein -0.005233
179 ENOG4105D58 Diguanylate phosphodiesterase -0.005232
180 ENOG4107QMS site-determining protein 0.005231
181 ENOG4107Z04 HAD-superfamily hydrolase subfamily IA 0.005228
182 ENOG4105C35 Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P) (By similarity) 0.005215
183 ENOG4106001 sulfur oxidation protein SoxZ 0.005215
184 ENOG41063N7 cyclase, family 0.005211
185 ENOG4107QKW extracellular solute-binding protein family 1 0.005208
186 ENOG4105CHG glycolate oxidase (iron-sulfur subunit) 0.005202
187 ENOG4108RJ9 Glycosyl transferase, family 2 -0.005200
188 ENOG4108ENK Aamy 0.005195
189 ENOG4105ESV Glycosyl transferase, family 4 -0.005181
190 ENOG4105D4F Synthesizes selenophosphate from selenide and ATP (By similarity) 0.005178
191 ENOG4105CKI cobalamin synthesis protein 0.005175
192 ENOG4107U2G Methylenetetrahydrofolate reductase 0.005166
193 ENOG4105C0R drug resistance transporter emrb qaca subfamily 0.005157
194 ENOG4107R26 Methyl-accepting chemotaxis sensory transducer 0.005156
195 ENOG4107RMP Alcohol dehydrogenase GroES-like domain -0.005136
196 ENOG4108IJ6 ABC transporter 0.005133
197 ENOG4107R76 Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) 0.005130
198 ENOG4105D3R alkyl hydroperoxide reductase 0.005130
199 ENOG4107R69 radical SAM domain protein 0.005126
200 ENOG4105KJJ Uncharacterized ACR, COG1993 0.005124
201 ENOG4105FAE von Willebrand factor, type A 0.005123
202 ENOG4105WPN DNA integration recombination invertion protein 0.005110
203 ENOG4105CSZ Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate (By similarity) 0.005100
204 ENOG4108K4B hydrolase -0.005099
205 ENOG4105CNW domain protein 0.005099
206 ENOG4107RIQ Sulfate adenylate transferase 0.005099
207 ENOG4108C33 Resolvase -0.005087
208 ENOG4108RW0 Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid (By similarity) 0.005081
209 ENOG4107UZ3 Sulfatase -0.005073
210 ENOG4108Z7R Chaperone CsaA -0.005069
211 ENOG4107R5I Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine (By similarity) 0.005067
212 ENOG4105DJT lAO AO transport system ATPase -0.005066
213 ENOG4105D1Z hydroxypyruvate reductase 0.005064
214 ENOG4105C2Y STE24 endopeptidase EC 3.4.24.84 0.005059
215 ENOG41073TP transcriptional regulator -0.005059
216 ENOG4107QMH DNA methylase -0.005057
217 ENOG4105J4Q Transcriptional regulator 0.005037
218 ENOG4105JRK feS assembly protein SufD -0.005030
219 ENOG4105EIZ Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) -0.005028
220 ENOG4108HWX NADH flavin oxidoreductase, NADH oxidase -0.005020
221 ENOG4105EMN RNA polymerase sigma factor -0.005012
222 ENOG4107QIR type iii restriction protein res subunit -0.005006
223 ENOG4105WH1 Two component transcriptional regulator luxr family -0.005004
224 ENOG4105CPP Dehydrogenase, E1 component -0.005004
225 ENOG4105D0U Arsenite-activated ATPase (ArsA) 0.005001
226 ENOG4105CYU NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain 0.004995
227 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) 0.004995
228 ENOG4107S73 homocitrate synthase 0.004991
229 ENOG4105DIW FeS assembly protein SUFB -0.004975
230 ENOG4105CTK cobaltochelatase, cobn subunit 0.004974
231 ENOG4105VFF UPF0102 protein 0.004966
232 ENOG4105C1S aspic unbv domain protein -0.004965
233 ENOG4105ET9 ABC transporter substrate-binding protein 0.004961
234 ENOG4105CY1 sulfite reductase, dissimilatory-type alpha subunit 0.001648
234 ENOG4105PJW Sulfite reductase dissimilatory-type beta subunit 0.001648
234 ENOG4107EAK nitrate reductase, gamma subunit 0.001648
235 ENOG4108JIJ Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second (By similarity) -0.004943
236 ENOG4107ZBE zinc-finger protein 0.004943
237 ENOG4107R3N Filamentation induced by cAMP protein fic 0.004943
238 ENOG4105CSR polyphosphate kinase 2 0.004941
239 ENOG4105DZR Type I site-specific deoxyribonuclease 0.004932
240 ENOG4108U78 Glutathione S-transferase 0.004918
241 ENOG4107RAB Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA (By similarity) 0.004912
242 ENOG4107QTG Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA (By similarity) 0.004911
243 ENOG4108ZT0 50S ribosomal protein l17 0.004907
244 ENOG4105VM1 flagellar 0.004901
245 ENOG4108YXD 3-demethylubiquinone-9 3-methyltransferase 0.004899
246 ENOG4105C4B ABC transporter, permease 0.004874
247 ENOG4105KHV Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate (By similarity) 0.004873