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 ENOG4108MIC Mg-protoporphyrin IX methyl transferase 0.012475
2 ENOG4105C78 Uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent (By similarity) 0.006055
2 ENOG4105EVY Uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent (By similarity) 0.006055
3 ENOG4105DB3 bacteriochlorophyll chlorophyll a synthase 0.012031
4 ENOG4105XCI PucC protein 0.011777
5 ENOG4105D61 protein, conserved in bacteria 0.011435
6 ENOG4105EET magnesium chelatase 0.011309
7 ENOG4105C0I Conserved Protein 0.011003
8 ENOG4105DSM The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components the iron protein and the molybdenum-iron protein (By similarity) 0.010243
9 ENOG4105CTK cobaltochelatase, cobn subunit 0.009813
10 ENOG4105ETK chlorophyllide reductase subunit Z 0.002413
10 ENOG41060GA Chlorophyllide reductase subunit Y 0.002413
10 ENOG4107XHQ chlorophyll synthesis pathway, bchC 0.002413
10 ENOG4108VJI 2-vinyl bacteriochlorophyllide hydratase 0.002413
11 ENOG4105FE1 phytoene synthase 0.008878
12 ENOG4105I29 Bacteriochlorophyll 4-vinyl reductase 0.008674
13 ENOG4105FBB Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis. Mediates the cyclase reaction, which results in the formation of divinylprotochlorophyllide (Pchlide) characteristic of all chlorophylls from magnesium-protoporphyrin IX 13-monomethyl ester (MgPMME) (By similarity) 0.008649
14 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.008391
15 ENOG4105CIA precorrin-4 C(11)-methyltransferase 0.008183
16 ENOG4105DVK Precorrin-2 c20-methyltransferase 0.008181
17 ENOG4105EXX Deoxyribodipyrimidine photolyase-related protein 0.007979
18 ENOG4105E00 20S proteasome, A and B subunits 0.007840
19 ENOG4105CC5 ABC transporter 0.007604
20 ENOG4105EGS Mechanosensitive ion channel 0.007520
21 ENOG4107QKW extracellular solute-binding protein family 1 0.007444
22 ENOG4105DSX permease 0.007442
23 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 0.007424
24 ENOG4105D4D transcriptional regulator 0.007119
25 ENOG4105DH2 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group (By similarity) 0.007087
26 ENOG4107S75 HAD-superfamily hydrolase subfamily IA variant 3 0.007056
27 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) 0.006983
28 ENOG4106I2R Coenzyme F420 hydrogenase dehydrogenase, beta 0.006960
29 ENOG4106ER4 transglutaminase domain protein 0.006848
30 ENOG4107SM9 geranylgeranyl reductase 0.006817
31 ENOG4107R94 photosynthetic reaction center, M subunit 0.003408
31 ENOG4108TF2 Photosynthetic complex assembly protein 2 0.003408
32 ENOG41081F0 Precorrin-8x methylmutase 0.006779
33 ENOG4105DEU major facilitator superfamily 0.006732
34 ENOG4105CQX Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.006711
35 ENOG4108IPT Naphthoate synthase 0.006675
36 ENOG4105EPH radical SAM domain protein 0.006643
37 ENOG4105QNF Outer membrane lipoprotein 0.006622
38 ENOG4105CX4 Precorrin-6y C5,15-methyltransferase 0.006617
39 ENOG4108JJB ABC transporter 0.006575
40 ENOG4105HZ2 Diguanylate cyclase 0.006518
41 ENOG4105D37 Low-affinity potassium transport system. Interacts with Trk system potassium uptake protein TrkA (By similarity) -0.006486
42 ENOG4108H18 Polysaccharide biosynthesis protein 0.006413
43 ENOG4105C30 Nad-dependent epimerase dehydratase 0.006402
44 ENOG41068B1 Cob-I-yrinic acid a,c-diamide adenosyltransferase 0.006394
45 ENOG4105FEU K -dependent Na -Ca exchanger 0.006384
46 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) 0.006294
47 ENOG4105RGU S-isoprenylcysteine methyltransferase-like protein 0.006216
48 ENOG4105PGM cation diffusion facilitator family transporter -0.006196
49 ENOG4105DE9 3-keto-5-aminohexanoate cleavage enzyme 0.006109
50 ENOG4105E99 Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP) (By similarity) 0.006073
51 ENOG4105C7Z Conserved Protein -0.006039
52 ENOG410900A Domain of unknown function (DUF427) 0.006021
53 ENOG4107QZT geranylgeranyl reductase 0.006011
54 ENOG4105C3U ABC transporter 0.006006
55 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) 0.006003
56 ENOG41067U9 conserved protein UCP037205 0.005847
57 ENOG4105CH2 amidohydrolase 0.005802
58 ENOG4105DWH electron transfer flavoprotein-ubiquinone oxidoreductase 0.005729
59 ENOG4105CGY Dna recombination protein 0.005719
60 ENOG4105XUR ABC-1 domain protein 0.005713
61 ENOG4105CA0 peroxidase -0.005686
62 ENOG4105SS7 PucC protein 0.001886
62 ENOG4105VGZ photosynthetic reaction center L subunit 0.001886
62 ENOG4108S36 Photosynthetic reaction center 0.001886
63 ENOG41082A2 Alpha beta hydrolase 0.005658
64 ENOG4108UHF Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin) (By similarity) 0.005655
65 ENOG4105EV8 ectoine hydroxylase -0.005605
66 ENOG4107QRP cobalamin biosynthesis protein CobW 0.005585
67 ENOG4108PZJ hydroxyneurosporene synthase 0.005576
68 ENOG4107EPK O-methyltransferase, family 2 0.005528
69 ENOG4107SV1 subunit D 0.005508
70 ENOG4107QVT Binding-protein-dependent transport systems, inner membrane component 0.005506
71 ENOG4107WT5 transcriptional regulator (NifA 0.005491
72 ENOG4105CY9 nitrogenase molybdenum-iron protein beta chain 0.005455
73 ENOG4108X7V cobyrinic Acid a,c-diamide synthase -0.005428
74 ENOG4105C4A Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate (SEPHCHC) (By similarity) 0.005427
75 ENOG4105E78 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity) -0.005425
76 ENOG4107REA Phosphoglucomutase (EC 5.4.2.2 0.005420
77 ENOG4105CXW Synthesizes alpha-1,4-glucan chains using ADP-glucose (By similarity) 0.005409
78 ENOG4105D0B Nitrogenase protein alpha chain 0.005391
79 ENOG4107QZF nitrite reductase NADPH large subunit -0.005380
80 ENOG4105E4F Isochorismate synthase 0.005374
81 ENOG4105CZF Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism (By similarity) -0.005364
82 ENOG4105X44 SMC domain protein 0.005332
83 ENOG4105KAV tspo and mbr like protein 0.005330
84 ENOG4108YXX Photosynthetic complex assembly protein 0.005304
85 ENOG41082JE Phosphoribosylformylglycinamidine synthase, purS 0.005297
86 ENOG4105E1N methyl-accepting chemotaxis 0.005288
87 ENOG4108VFZ ribulose bisphosphate carboxylase, small 0.005287
88 ENOG4105VGV redox-active disulfide protein 2 0.005285
89 ENOG4107QKD faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.005251
90 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) 0.005249
91 ENOG4108V1U phospholipid-binding protein -0.005247
92 ENOG4105ECP epimerase 0.005221
93 ENOG4107VFM Dehydrogenase 0.005214
94 ENOG4105ES7 radical SAM domain protein 0.005190
95 ENOG41068GY Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers (By similarity) 0.005181
96 ENOG4105D7B Flagellar biosynthesis protein flha -0.005162
97 ENOG4105C1A potassium transporter peripheral membrane -0.005154
98 ENOG4105CG3 alpha amylase, catalytic region 0.005148
99 ENOG4107VTY Mg-protoporphyrin IX monomethyl ester oxidative cyclase 66 kD subunit 0.005146
100 ENOG4105BZH Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.005126
101 ENOG4105EWK phytoene 0.005120
102 ENOG4108Z9Z response to DNA damage stimulus 0.005103
103 ENOG4105KPV Transcriptional regulator -0.005080
104 ENOG4106KXR thiamine pyrophosphate protein (EC 2.2.1.6) 0.005072
105 ENOG4107RDR Peptidase S9 prolyl oligopeptidase active site 0.005049
106 ENOG41080IW Transcriptional regulator, ARSR family 0.005049
107 ENOG4105E5N succinylglutamate desuccinylase aspartoacylase 0.005049
108 ENOG4105F7Z ABC transporter 0.005047
109 ENOG4105CGC Nitrogenase cofactor biosynthesis protein NifB 0.005036
110 ENOG4107R60 Aldo/keto reductase family -0.005033
111 ENOG4105WH1 Two component transcriptional regulator luxr family -0.005029
112 ENOG4105CBM Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12 (By similarity) 0.005027
113 ENOG4107S5T Carbohydrate kinase 0.005026
114 ENOG4108Z1W Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD) (By similarity) -0.005025
115 ENOG4105CVP deoxyribo-dipyrimidine photolyase 0.004998
116 ENOG4105EHU Circadian clock protein KaiC 0.004990
117 ENOG4107U4C Rhomboid family 0.004989
118 ENOG4105CBS Chea signal transduction histidine kinase 0.004988
119 ENOG4105DIK (ABC) transporter 0.004984
120 ENOG4107RHB Catalyzes the reversible phosphorylation of S-methyl-5'- thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. Involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. Responsible for the first step in the methionine salvage pathway after MTA has been generated from S- adenosylmethionine. Has broad substrate specificity with 6- aminopurine nucleosides as preferred substrates (By similarity) 0.004977
121 ENOG4107QP8 phosphohexose isomerase 0.004963
122 ENOG41090BB DNA mismatch endonuclease (vsr) 0.004952
123 ENOG4105KJR deoxyribo-dipyrimidine photolyase 0.004951
124 ENOG4106A79 NA 0.004935
125 ENOG4107YWI protein tyrosine phosphatase 0.004929
126 ENOG4105EWN Heme oxygenase 0.004915
127 ENOG4106194 Phospholipase Carboxylesterase 0.004911
128 ENOG4107QIM DNA ligase 0.004911
129 ENOG4105ESY DevC protein 0.004889
130 ENOG4107QPN acyl-Coa dehydrogenase -0.004872
131 ENOG4105D2N Aldolase 0.004856
132 ENOG4107RCP Multicopper oxidase -0.004834
133 ENOG4105CTX dehydratase -0.004833
134 ENOG4107EES Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide the precursor of murein (By similarity) 0.004825
135 ENOG4105CHC glucokinase (EC 2.7.1.2) 0.004813
136 ENOG4107SIN Na H antiporter 0.004811
137 ENOG4107QZ0 cation diffusion facilitator family transporter 0.004809
138 ENOG4106FSN Antenna complexes are light-harvesting systems, which transfer the excitation energy to the reaction centers 0.004806
139 ENOG4108VQJ O-methyltransferase -0.004804
140 ENOG4105FP9 thiamine pyrophosphate -0.004793
141 ENOG4105K78 MarR family Transcriptional regulator -0.004790
142 ENOG4108KMD Alpha Beta Hydrolase 0.004770
143 ENOG4108JQ7 (ABC) transporter 0.004763
144 ENOG4107A9P Membrane 0.004745
145 ENOG4106P19 photosystem i assembly btpa 0.004737
146 ENOG4105CY3 ABC transporter, permease 0.004730
147 ENOG4107QRH Arylsulfatase (Ec 3.1.6.1) -0.004729
148 ENOG4108PM7 NA 0.004715
149 ENOG4105KK9 This protein binds to 23S rRNA in the presence of protein L20 (By similarity) -0.004714
150 ENOG4105VXP Protein of unknown function DUF86 0.004713
151 ENOG4105K89 arsenate reductase -0.004711
152 ENOG4105C7W Xanthine dehydrogenase -0.004704
153 ENOG4107R37 Glutamate dehydrogenase -0.004703
154 ENOG4106PT6 cdpdiacylglycerol-serine O-phosphatidyltransferase -0.004694
155 ENOG4105CNZ decarboxylase family 0.004678
156 ENOG4108V3W Chemotaxis protein, CheW 0.004672
157 ENOG4105RE0 Asp Glu hydantoin racemase -0.004669
158 ENOG4108P7Y NA 0.004662
159 ENOG41062WV short-chain dehydrogenase reductase 0.004658
160 ENOG4105G1G alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen -0.004649
161 ENOG4108UNH dienelactone hydrolase -0.004641
162 ENOG4105DDZ Methyltransferase required for the conversion of demethylmenaquinone (DMKH2) to menaquinone (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) (By similarity) -0.004628
163 ENOG4105M0E Domain of unknown function (DUF1818) 0.001156
163 ENOG4105SZD Inherit from COG: Divisome component that associates with the complex late in its assembly, after the Z-ring is formed, and is dependent on DivIC and PBP2B for its recruitment to the divisome. Together with EzrA, is a key component of the system that regulates PBP1 localization during cell cycle progression. Its main role could be the removal of PBP1 from the cell pole after pole maturation is completed. Also contributes to the recruitment of PBP1 to the division complex. Not essential for septum formation (By similarity) 0.001156
163 ENOG410689D This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity) 0.001156
163 ENOG41084GG 50S ribosomal protein L33 0.001156
164 ENOG4108SEI SOUL heme-binding protein 0.004617
165 ENOG4105C48 Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (By similarity) -0.004611
166 ENOG4105C9X ppx gppa phosphatase 0.004610
167 ENOG4107RDB Major Facilitator -0.004608
168 ENOG4105CJX Molecular chaperone. Has ATPase activity (By similarity) 0.004604
169 ENOG4108Z4W Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis (By similarity) 0.004593
170 ENOG4105K6V RNA polymerase 0.004574
171 ENOG4105CP5 Pfam:DUF88 0.004569
172 ENOG4107PU6 Membrane -0.004558
173 ENOG410906A Beta-Ig-H3 fasciclin 0.004557
174 ENOG4105VKA DNA Polymerase Beta Domain Protein Region 0.004522
175 ENOG4105DHJ ABC, transporter 0.004517
176 ENOG4105DN2 repeat protein -0.004515
177 ENOG4108Z4T Peptidase M50 -0.004492
178 ENOG4108VX5 3-methyladenine DNA glycosylase 0.004487
179 ENOG4105ES5 Histidine kinase -0.004476
180 ENOG4105CNW domain protein 0.004471
181 ENOG4105D9I Responsible for the addition of glutamate residues to the C-terminus of ribosomal protein S6 (By similarity) 0.004468
182 ENOG4107QWV solute symporter 0.004459
183 ENOG4107ZJ0 Nad-dependent epimerase dehydratase 0.004453
184 ENOG4105D1U peptidase U62 modulator of DNA gyrase -0.004436
185 ENOG4105EYU Glutamine amido-transferase -0.004432
186 ENOG4108ZA0 Protein of unknown function (DUF779) -0.004411
187 ENOG4105JZI cytochrome P450 0.004410
188 ENOG4105ECK Fatty Acid Desaturase 0.004403
189 ENOG4105CYC Transferase 0.004384
190 ENOG4107QRX oxidoreductase 0.004376
191 ENOG4105CF4 DegT DnrJ EryC1 StrS aminotransferase 0.004376
192 ENOG4108YZT Adenosylcobinamide kinase 0.004375
193 ENOG4106J9T SpoIID LytB domain protein 0.004371
194 ENOG4105MNW Protein of unknown function (DUF971) -0.004354
195 ENOG4105M7G exopolysaccharide synthesis 0.004345
196 ENOG4108M8W Monooxygenase -0.004335
197 ENOG4108V61 Thiopurine S-methyltransferase 0.004323
198 ENOG4105G8W NA -0.004323
199 ENOG4105C6Y Udp-glucose 6-dehydrogenase 0.004321
200 ENOG4108IAJ Nad-dependent epimerase dehydratase -0.004320
201 ENOG4105DK4 Major Facilitator superfamily 0.004307
202 ENOG4105DMT epimerase dehydratase -0.004304
203 ENOG4105C35 Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P) (By similarity) 0.004298
204 ENOG4105D8E domain protein 0.004296
205 ENOG4105EXC Acyl-transferase 0.004291
206 ENOG4105YB8 TM2 domain containing protein 0.004285
207 ENOG4105F6N Nad-dependent epimerase dehydratase -0.004275
208 ENOG4105DQQ Major facilitator superfamily MFS_1 -0.004274
209 ENOG410813D RNA Polymerase 0.004256
210 ENOG4105M24 Pfam:DUF2241 0.004256
211 ENOG4108S1A Glycosyl transferase (Group 1 0.004240
212 ENOG41080ME methyltransferase 0.004231
213 ENOG4108QTX prolyl 4-hydroxylase subunit alpha 0.004227
214 ENOG4107S9Z membrane protein involved in aromatic hydrocarbon degradation 0.004227
215 ENOG4105C3B Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins (By similarity) 0.004220
216 ENOG4105UIB (ABC) transporter 0.004219
217 ENOG4105Y5C oxidoreductase 0.004217
218 ENOG41087YS Phage shock protein A 0.004209
219 ENOG4105E0A ABC, transporter 0.004209
220 ENOG4108QDN Signal transduction histidine kinase 0.004206
221 ENOG41090G6 cupin superfamily protein 0.004206
222 ENOG4105CKI cobalamin synthesis protein 0.004201
223 ENOG4105C0K Gdp-mannose 4,6-dehydratase 0.004199
224 ENOG4105EKE dihydroorotase 0.004196
225 ENOG4108XDX Phospholipase Carboxylesterase -0.004192
226 ENOG4107QXS (Na H) antiporter 0.004186
227 ENOG4107U5K NmrA family 0.004185
228 ENOG4105CQR helicase 0.001394
228 ENOG4107S30 sirohydrochlorin cobaltochelatase 0.001394
228 ENOG410828I precorrin-6x reductase 0.001394
229 ENOG4105KUG anti-sigma K factor Rska 0.004176
230 ENOG4108SQH Phage-related protein -0.004176
231 ENOG4105E21 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity) -0.004174
232 ENOG4105CG4 gCN5-related N-acetyltransferase 0.004171
233 ENOG41061GT Aldolase 0.004170
234 ENOG4105CK0 Membrane bOund o-acyl transferase mboat family protein -0.004168
235 ENOG4105CEN a g-specific adenine glycosylase 0.004162
236 ENOG4107RGG Peroxiredoxin 0.004160
237 ENOG4105CVN desaturase 0.004158
238 ENOG4105KK4 UPF0060 membrane protein -0.004142