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 ENOG4107R0D fad dependent oxidoreductase 0.012397
2 ENOG4105E15 Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate 0.011508
3 ENOG4106KNT transcriptional regulator 0.011195
4 ENOG4108UMB Flavodoxin 0.011016
5 ENOG410816S Transcriptional regulator -0.010806
6 ENOG4105EY8 ABC transporter -0.010745
7 ENOG4105F1A Pyruvate formate-lyase 0.010731
8 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) -0.010641
9 ENOG4108ZMD Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) -0.010510
10 ENOG41064WA Binding-protein-dependent transport systems, inner membrane component -0.010413
11 ENOG4105CG5 Glycosyl transferase (Group 1 0.010377
12 ENOG4108JQ1 Dehydrogenase -0.010337
13 ENOG4107QZB decarboxylase -0.010286
14 ENOG4105XBY Regulates arginine biosynthesis genes (By similarity) 0.009948
15 ENOG4105FKQ transcriptional regulator 0.009749
16 ENOG4105EZR dyp-type peroxidase family protein 0.009733
17 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) 0.009436
18 ENOG4105FD2 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) -0.009423
19 ENOG4105FDK ABC transporter 0.009399
20 ENOG4105F6E Acyl-transferase 0.009393
21 ENOG4105BZY Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system (By similarity) -0.009264
22 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) -0.009205
23 ENOG4105C1G acyl-Coa dehydrogenase -0.009172
24 ENOG4108ZK7 protein family UPF0029, Impact, N-terminal protein 0.009161
25 ENOG4105MEV Acyl-transferase -0.009081
26 ENOG4105ZWK Inherit from COG: Low-potential electron donor to a number of redox enzymes (By similarity) -0.008997
27 ENOG4105CSX c4-dicarboxylate anaerobic carrier 0.008969
28 ENOG4108IQF Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA (By similarity) -0.008957
29 ENOG4105RIJ domain protein -0.008945
30 ENOG4108UIC UPF0340 protein 0.008938
31 ENOG4105C26 Dehydrogenase -0.008925
32 ENOG4105D7A ATP-binding protein -0.008886
33 ENOG4105D9M gamma-glutamylcysteine synthetase -0.008874
34 ENOG4105DZS Phenylacetate-CoA ligase -0.008868
35 ENOG4105C3E May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine (By similarity) -0.008819
36 ENOG4108VW9 Membrane -0.008816
37 ENOG4105E39 Enoyl-CoA hydratase -0.008721
38 ENOG4105UQX Mate efflux family protein 0.008683
39 ENOG4107Y9E nuclease -0.008660
40 ENOG4105C6N Formate acetyltransferase 0.008634
41 ENOG4108UHU Aldolase 0.008628
42 ENOG4105C1I TRANSCRIPTIONAl REGULATOR GntR family 0.008625
43 ENOG4105VSH 4-oxalocrotonate tautomerase -0.008581
44 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase -0.008559
45 ENOG4108HCJ Hydrolase 0.008509
46 ENOG4105KPE licD family 0.008503
47 ENOG4105X1V 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) -0.008467
48 ENOG4105IXE Abortive infection protein 0.008428
49 ENOG4105D42 Cleaves the N-terminal amino acid of tripeptides (By similarity) 0.008400
50 ENOG4105EHA HipA domain protein -0.008347
51 ENOG4107R5U Periplasmic binding protein LacI transcriptional regulator 0.008346
52 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.008325
53 ENOG4105WS8 NA -0.008315
54 ENOG4107QSV RmuC domain protein 0.008295
55 ENOG4105C6Y Udp-glucose 6-dehydrogenase -0.008275
56 ENOG41068PG O-Antigen polymerase 0.008209
57 ENOG4105DMF Dehydrogenase -0.008201
58 ENOG4105K9X Membrane 0.008166
59 ENOG4105X0I Fimbrial 0.008098
60 ENOG4105CT4 transporter 0.008097
61 ENOG4105CAS nag kinase -0.008072
62 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) 0.008069
63 ENOG4107RQ4 Aldolase 0.008039
64 ENOG4107VDP teichoic acid biosynthesis -0.007996
65 ENOG4105C4C beta-galactosidase 0.007991
66 ENOG4105E2Z phosphate ABC transporter (Permease -0.007981
67 ENOG4107QSK Phage infection protein 0.007973
68 ENOG41076HS cation diffusion facilitator family transporter -0.007956
69 ENOG41062B0 ABC transporter, permease 0.007955
70 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin -0.007954
71 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) -0.007935
72 ENOG4105BZP glycoside hydrolase 15-related -0.007889
73 ENOG4105DJR solute-binding protein 0.007876
74 ENOG4107X4A ABC-2 type transporter 0.007867
75 ENOG4105NUU permease -0.007860
76 ENOG4105DQU oxidoreductase, subunit beta -0.007840
77 ENOG4105W1N transcriptional regulator -0.007839
78 ENOG4105KVH Transcriptional regulator 0.007822
79 ENOG4105CF8 branched-chain amino acid ABC transporter, permease 0.007815
80 ENOG4105C2X Arabinose 5-phosphate isomerase 0.007799
81 ENOG4106554 NA -0.007798
82 ENOG4105C7W Xanthine dehydrogenase -0.007788
83 ENOG4105C0V Provides the sole de novo source of dTMP for DNA biosynthesis (By similarity) 0.007780
84 ENOG4105CRD Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) (By similarity) 0.007759
85 ENOG41081B2 Reverse transcriptase -0.007739
86 ENOG4108EQA pts system 0.007712
87 ENOG4107U7Y Peptidase M48, Ste24p -0.007696
88 ENOG4105EE0 oxidoreductase 0.007676
89 ENOG4105CV2 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates (By similarity) -0.007650
90 ENOG4105CE4 GlcNAc 6-P deacetylase 0.007641
91 ENOG4108Z0Z intracellular protease Pfpi family 0.007615
92 ENOG4107RW9 nh(3)-dependent nad( ) synthetase -0.007594
93 ENOG4105VJG Transcriptional regulator -0.007593
94 ENOG4108IY1 (ABC) transporter 0.007587
95 ENOG4105D8A 3-Deoxy-D-manno-octulosonic-acid transferase 0.007572
96 ENOG4105FB9 CRISPR-associated protein -0.007553
97 ENOG4105KCF 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) -0.007553
98 ENOG4105XCU O-antigen ligase -0.007544
99 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) 0.007529
100 ENOG4105QIR divalent ion tolerance protein -0.007521
101 ENOG4108KE5 Membrane -0.007495
102 ENOG4105EJ5 oxidoreductase gamma subunit -0.007483
103 ENOG4107R9N ABC transporter 0.007431
104 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) -0.007424
105 ENOG4105DWY Agmatine deiminase -0.007417
106 ENOG4105CG2 Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1 (By similarity) -0.007392
107 ENOG4106CD9 glycosyl transferase group 1 -0.007389
108 ENOG4108MUS ABC-2 type transporter 0.007388
109 ENOG4105D3Q Sugar transferase -0.007372
110 ENOG4105C35 Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P) (By similarity) -0.007325
111 ENOG4105MXH Transcriptional Regulator, LuxR family -0.007314
112 ENOG4105CMT Dihydroxyacetone kinase 0.007311
113 ENOG4108KYP polysaccharide deacetylase -0.007307
114 ENOG4105CXR Phospho-2-dehydro-3-deoxyoctonate aldolase 0.007280
115 ENOG4105CH2 amidohydrolase 0.007268
116 ENOG4108RAV Conserved protein -0.007266
117 ENOG4105F9F transposase 0.007233
118 ENOG4105ECW sulfate abc transporter 0.007231
119 ENOG4107QW9 peptidase, M24 -0.007230
120 ENOG4105DWJ CRISPR-Associated Protein -0.007203
121 ENOG4108YYQ gCN5-related N-acetyltransferase -0.007202
122 ENOG4105XWR Phage virion morphogenesis protein -0.007182
123 ENOG4108MVM Transposase -0.007174
124 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase -0.007163
125 ENOG4105DQ6 Transposase -0.007145
126 ENOG4105FJP NA -0.007139
127 ENOG4106EI2 helix-turn-helix domain protein -0.007113
128 ENOG4107SW2 integral membrane protein 0.007096
129 ENOG4108ZJ4 polysaccharide deacetylase 0.007093
130 ENOG4105DHW Required for the insertion and or proper folding and or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins 0.007088
131 ENOG4105S10 periplasmic binding protein -0.007080
132 ENOG4105XV2 secreted protein 0.007067
133 ENOG4105E12 capsule polysaccharide -0.007063
134 ENOG4105FDR Membrane -0.007058
135 ENOG4105CPZ Transcriptional regulator, rpir family -0.007039
136 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase -0.007026
137 ENOG4107QZW Altronate oxidoreductase 0.007025
138 ENOG4105DG6 mannose-6-phosphate isomerase 0.007022
139 ENOG410695M Pilus assembly protein -0.007009
140 ENOG4108QD1 Membrane -0.006995
141 ENOG4105FAZ Membrane 0.006979
142 ENOG4105D9R oxidoreductase 0.006971
143 ENOG410694F NA -0.006969
144 ENOG4105VXR cytoplasmic protein -0.006961
145 ENOG4108HUF Transporter -0.006959
146 ENOG4105C6M Alpha-keto-beta-hydroxylacyl reductoisomerase -0.006932
147 ENOG4105CS2 ec 3.2.1.21 0.006928
148 ENOG4105C5N The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination 0.006912
149 ENOG4105C8U phosphate abc transporter -0.006908
150 ENOG41063RB Lysine exporter protein (Lyse ygga) -0.006903
151 ENOG4107EMB crispr-associated protein -0.006896
152 ENOG4105KUR CAAX amino terminal protease family protein -0.006891
153 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 0.006886
154 ENOG4108U1C ggdef family -0.006883
155 ENOG4105GHK Carboxymethylenebutenolidase-related protein -0.006878
156 ENOG4108JJA ABC, transporter 0.006877
157 ENOG4105CEU Arginine dihydrolase 0.006864
158 ENOG4105C5Y PTS System 0.006849
159 ENOG4105ECX polysaccharide export -0.006848
160 ENOG4105X1N Glycosyl transferase family 8 -0.006835
161 ENOG4105DCH radical SAM domain protein -0.006828
162 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) 0.006819
163 ENOG4108VPX Involved in 1,2-propanediol (1,2-PD) degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate (By similarity) 0.006811
164 ENOG4105C5E polysaccharide biosynthesis protein -0.006806
165 ENOG4105DPH UPF0371 protein 0.006806
166 ENOG4105DZC cytosine deaminase -0.006797
167 ENOG4107QJT sodium dicarboxylate symporter -0.006789
168 ENOG4105KNY Microcompartments protein 0.006741
169 ENOG4108IQK o-acetylhomoserine -0.006741
170 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.006727
171 ENOG4108Z66 YbaK ebsC protein 0.006711
172 ENOG4105TFI NA -0.006701
173 ENOG4105MF8 Membrane -0.006701
174 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.006670
175 ENOG4105QNR S1 RNA binding domain protein 0.006669
176 ENOG4108VSY crispr-associated protein Cas4 -0.006656
177 ENOG4105CJW magnesium transporter 0.006651
178 ENOG4105KQV Binds directly to 16S ribosomal RNA (By similarity) 0.006643
179 ENOG4108XMW Membrane 0.006638
180 ENOG4108K6U Transcriptional regulator, TetR family 0.006636
181 ENOG4108WWJ NA -0.006614
182 ENOG4107WUI DNA Methylase -0.006604
183 ENOG4105EAM Na Pi-cotransporter -0.006603
184 ENOG4105DU0 nucleoside hydrolase 0.006590
185 ENOG4108N7Z 5-bromo-4-chloroindolyl phosphate hydrolysis protein -0.006580
186 ENOG4109066 lysm domain bon superfamily protein -0.006579
187 ENOG4105DDQ anthranilate synthase -0.006574
188 ENOG4108ZG8 Gcn5-related n-acetyltransferase -0.006574
189 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) 0.006537
190 ENOG4105DE7 Sulfate ABC transporter periplasmic sulfate-binding protein 0.006535
191 ENOG4107EES Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide the precursor of murein (By similarity) 0.006522
192 ENOG4108Z73 Siroheme synthase -0.006507
193 ENOG4107SPW HsdM N-terminal domain -0.006498
194 ENOG4107QYE Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.006483
195 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase 0.006478
196 ENOG4108UJJ activator of Hsp90 ATPase 1 family protein 0.006475
197 ENOG4105GQR Chaperone 0.006472
198 ENOG4105JHF YheO-like PAS domain -0.006463
199 ENOG4108JPX Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor (By similarity) -0.006459
200 ENOG4105CWI transcriptional regulator 0.006458
201 ENOG4105CI2 imidazolone-5-propionate hydrolase -0.006443
202 ENOG4106FEU of the drug metabolite transporter, DMT superfamily -0.006436
203 ENOG4108JJB ABC transporter 0.006435
204 ENOG4105DHU Bile acid 0.006414
205 ENOG4107T6Z Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (By similarity) 0.006413
206 ENOG4107KGK dmso reductase anchor subunit 0.006404
207 ENOG4105HJX Biotin- acetyl-CoA-carboxylase ligase 0.006398
208 ENOG4108Q00 Domain of unknown function (DUF1794) -0.006391
209 ENOG4106AKC NA -0.006366
210 ENOG4105MQR ankyrin repeat-containing protein -0.006362
211 ENOG4105DR5 peptidase 0.006356
212 ENOG4105EYF MMPL domain protein -0.006344
213 ENOG4107AR0 NA -0.006323
214 ENOG4107WEC Periplasmic Protein -0.006315
215 ENOG4106KH4 NA 0.006301
216 ENOG4105X6M response regulator -0.006299
217 ENOG4105DSS Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) -0.006298
218 ENOG4108UMN azlc family -0.006296
219 ENOG4107RW8 Mate efflux family protein -0.006292
220 ENOG4108I2M methyltransferase -0.006291
221 ENOG4105ECR NmrA family -0.006289
222 ENOG41069R5 rhs family -0.006282
223 ENOG4108ZHB oxidoreductase -0.006278
224 ENOG4107C7S NA -0.006278
225 ENOG4105UKW Inherit from COG: PAAR repeat-containing protein -0.006277
226 ENOG4105CAX The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system (By similarity) 0.006273
227 ENOG4107QR9 Iron-sulfur cluster binding protein 0.006271
228 ENOG4105CB6 ATPase associated with various cellular activities aaa_5 -0.006266
229 ENOG4105DK0 Indole-3-glycerol phosphate synthase -0.006252
230 ENOG41080E8 Transcriptional regulator, Spx MgsR family 0.006250
231 ENOG4105CUW cytochrome C-TYPE protein -0.006247
232 ENOG4105CGP Urocanate hydratase -0.006227
233 ENOG4105X2Z NA -0.006214
234 ENOG4105CVX Polysaccharide Biosynthesis Protein -0.006212
235 ENOG4107QWS glycogen debranching enzyme glgx 0.006211
236 ENOG4108ZKG OsmC family 0.006207
237 ENOG4106929 Transcriptional regulator -0.006191
238 ENOG4105CR7 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA (By similarity) -0.006174
239 ENOG4107DYY NA -0.006168
240 ENOG4107RDF Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate (By similarity) -0.006166
241 ENOG4105DKM CRISPR-Associated Helicase Cas3 -0.006166
242 ENOG4108Z8I decarboxylase 0.006163
243 ENOG4105F1S paraquat-inducible protein a 0.006160
244 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.006154
245 ENOG4105F1K Glutamine amidotransferase 0.006154
246 ENOG41080QF Protein of unknown function (DUF1320) -0.006152
247 ENOG4108Z1W Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD) (By similarity) 0.006135
248 ENOG4108RUW Hydrolase -0.006131
249 ENOG4105CND Glycosyl transferase, family 2 -0.006127
250 ENOG4107QPG succinate dehydrogenase, flavoprotein subunit 0.006119