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 ENOG4107FQX Alpha-acetolactate decarboxylase 0.021897
2 ENOG4107R63 acetolactate synthase 0.019237
3 ENOG4105W1V general stress protein 0.015836
4 ENOG4108C3H Magnesium-importing ATPase -0.015469
5 ENOG4108RS6 transposase 0.014817
6 ENOG4105C2C drug resistance transporter, Bcr CflA 0.014689
7 ENOG4105E5D amino acid -0.014343
8 ENOG4108VUZ Protein of unknown function (DUF1722) -0.013960
9 ENOG4108I66 PTS System 0.013931
10 ENOG4106A8V Protein CrcB homolog -0.013511
11 ENOG4108HRK Histidine kinase 0.013491
12 ENOG4105D1W Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate (By similarity) 0.013413
13 ENOG4107XDY Nicotinamide Mononucleotide Transporter -0.013230
14 ENOG4105DIM ABC transporter -0.012618
15 ENOG4105C0D helicase 0.012595
16 ENOG4105DY9 regulatoR 0.012575
17 ENOG41062IX FMN_bind -0.012476
18 ENOG410667J hydrolase 0.012418
19 ENOG4107SSC biotin acetyl-CoA-carboxylase ligase 0.012408
20 ENOG4105CJQ hydrolase, family 31 -0.012225
21 ENOG41062A2 Membrane -0.012076
22 ENOG4108IIH CoA-transferase subunit B -0.011923
23 ENOG4108HKT sucrose-6-phosphate hydrolase 0.011770
24 ENOG4105KRF dihydroneopterin aldolase 0.011701
25 ENOG4105DRQ Conserved Protein -0.011688
26 ENOG4105CDP Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA) (By similarity) 0.011657
27 ENOG4105NJS thiw protein -0.011542
28 ENOG4105CUR 5'-nucleotidase, lipoprotein e(p4) family 0.011517
29 ENOG4108ZIV NA 0.011511
30 ENOG4105WCN acetyltransferase 0.011439
31 ENOG4105GVB Replication Protein 0.011434
32 ENOG41064HB NA -0.011404
33 ENOG4107QYE Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.011360
34 ENOG4105C57 major facilitator superfamily 0.011334
35 ENOG4105CH2 amidohydrolase 0.011283
36 ENOG4105CID antiterminator 0.011121
37 ENOG4108HMR Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) -0.011115
38 ENOG4105K7K Transcriptional regulator -0.011031
39 ENOG41080DN Telomere recombination -0.011000
40 ENOG4107414 GntR family transcriptional regulator 0.010910
41 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.010868
42 ENOG4107VZS Nicotinamide-nucleotide adenylyltransferase -0.010849
43 ENOG4108CRR NA -0.010803
44 ENOG4108W7F transporter, permease -0.010669
45 ENOG410760G Gram positive anchor 0.010556
46 ENOG4106DR7 MORN repeat protein 0.010551
47 ENOG410907G NA -0.010487
48 ENOG4106EIX NA 0.010457
49 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) -0.010415
50 ENOG4105C2T Binding-protein-dependent transport systems, inner membrane component 0.010409
51 ENOG4105HJX Biotin- acetyl-CoA-carboxylase ligase -0.010350
52 ENOG4107S33 PTS System 0.010347
53 ENOG4107RZ4 Methionine synthase 0.010336
54 ENOG4108VR6 peptidoglycan binding protein 0.010331
55 ENOG4106VPC NA -0.010304
56 ENOG410813P histidinol phosphate phosphatase hisj family 0.010285
57 ENOG4105C3S Mate efflux family protein 0.010272
58 ENOG4105ICD Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.010264
59 ENOG410631I Domain of unknown function (DUF3173) 0.010234
60 ENOG4105EBR Carboxylesterase 0.010232
61 ENOG4108SSE Transposase -0.010158
62 ENOG4106VSS Membrane 0.010097
63 ENOG4105CFH Aspartokinase 0.010043
64 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.010010
65 ENOG4107ZGM malolactic fermentation system -0.009983
66 ENOG4108DKJ flavin oxidoreductase -0.009933
67 ENOG4105V9V Short-chain dehydrogenase reductase Sdr -0.009933
68 ENOG4108KMV Glycosyl transferase (Group 1 0.009923
69 ENOG4107SHI hydrolase, CocE NonD family protein 0.009849
70 ENOG4107WM1 Major Intrinsic Protein -0.009848
71 ENOG41083K5 isomerase -0.009805
72 ENOG4106CKA Bacteriocin transport accessory protein 0.009776
73 ENOG410820V NA -0.009751
74 ENOG4105WHA Protein of unknown function, DUF624 -0.009726
75 ENOG4105S04 Abi-like protein 0.009690
76 ENOG4107GDW Glucan-binding protein C 0.009661
77 ENOG4105CX7 Alpha-L-fucosidase -0.009622
78 ENOG4105KQV Binds directly to 16S ribosomal RNA (By similarity) -0.009610
79 ENOG4108S01 response regulator 0.009586
80 ENOG4107YCK Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity (By similarity) 0.009571
81 ENOG4106S0T transcriptional regulator 0.009558
82 ENOG4108601 Binds directly to 16S ribosomal RNA (By similarity) 0.009500
83 ENOG4108MW7 phage capsid family -0.009482
84 ENOG4106P1G NA -0.009480
85 ENOG4106NF0 Phage nucleotide-binding protein -0.009411
86 ENOG41081F0 Precorrin-8x methylmutase -0.009358
87 ENOG4105E8A Alpha-L-fucosidase -0.009355
88 ENOG4105CT5 Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate (By similarity) 0.009342
89 ENOG4105DC8 reductase 0.009336
90 ENOG4105CSV Glutaminase 0.009331
91 ENOG4105VHW Transcriptional regulator 0.009306
92 ENOG4105MYU Immunoglobulin A1 protease -0.009186
93 ENOG4108WA6 metallo-beta-lactamase superfamily protein 0.009162
94 ENOG4108FKQ FMN_bind 0.009160
95 ENOG4108Z0A Cupin 2, conserved barrel domain protein 0.009153
96 ENOG4105CJA serine threonine protein kinase 0.009152
97 ENOG4105XX2 phosphoglycerate mutase family protein -0.009144
98 ENOG4105MU9 integral membrane protein 0.009134
99 ENOG4105DA5 (ABC) transporter -0.009133
100 ENOG4108X4Z NA 0.009104
101 ENOG4106ETB IIa component -0.009096
102 ENOG4108HH2 Major Facilitator superfamily 0.009080
103 ENOG41075AB NA 0.009062
104 ENOG4105CPU Monooxygenase 0.009060
105 ENOG4108VCN amino acid 0.009059
106 ENOG4107RA1 nh(3)-dependent nad( ) synthetase 0.009041
107 ENOG4105RHA ABC transporter, permease -0.009022
108 ENOG4105EY8 ABC transporter 0.009012
109 ENOG41083BE Competence protein 0.009012
110 ENOG4106KIF Gram positive anchor 0.009007
111 ENOG4108X4Q Hydrolase 0.009001
112 ENOG4106FTB Protein of unknwon function (DUF3310) 0.008995
113 ENOG4105E4R Precorrin-3B C17-methyltransferase -0.008964
114 ENOG4105VPX protein, conserved in bacteria 0.008913
115 ENOG4105CHF Glutathione S-transferase 0.008904
116 ENOG4107QW5 hydrolase, family 20 -0.008896
117 ENOG4105D9M gamma-glutamylcysteine synthetase 0.008884
118 ENOG4105CIA precorrin-4 C(11)-methyltransferase -0.008876
119 ENOG4108FPF anti-repressor 0.008831
120 ENOG4108YZT Adenosylcobinamide kinase -0.008829
121 ENOG4105PXR Erf family 0.008810
122 ENOG4108Z3A general stress protein 0.008802
123 ENOG4105C6N Formate acetyltransferase 0.008796
124 ENOG4108JTV Nad-dependent epimerase dehydratase 0.008789
125 ENOG4105D0M Protease HtpX homolog -0.008787
126 ENOG4108W89 Membrane -0.008782
127 ENOG4108XI2 Domain of unknown function (DUF1963) 0.008780
128 ENOG4105DR4 Methyltransferase 0.008720
129 ENOG4105DH2 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group (By similarity) -0.008718
130 ENOG4108V06 Glutathione peroxidase -0.008705
131 ENOG4105HWQ Monooxygenase 0.008698
132 ENOG4105I1K ABC transporter -0.008682
133 ENOG4105E1R phage tail tape measure protein 0.008669
134 ENOG4106RAR accessory protein CadX -0.008645
135 ENOG4107WD8 ABC transporter, permease -0.008644
136 ENOG4108IQI permease 0.008643
137 ENOG4108Z3Y Protein of unknown function (DUF664) 0.008639
138 ENOG4105EB3 Histidine kinase -0.008622
139 ENOG4105EST Metal Dependent Phosphohydrolase 0.008608
140 ENOG4107RGR short-chain dehydrogenase reductase 0.008598
141 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) -0.008570
142 ENOG4105C88 aminopeptidase 0.008550
143 ENOG41085S6 NA 0.008539
144 ENOG4105S0B NA 0.008484
145 ENOG4108Z3G 3H domain protein 0.008482
146 ENOG4105CPD ethanolamine ammonia-lyase -0.008436
147 ENOG41068AU NA 0.008434
148 ENOG4105M4B Catalyzes the transfer of an acetyl group from acetyl- CoA to the 6'-amino group of aminoglycoside molecules conferring resistance to antibiotics containing the purpurosamine ring (By similarity) 0.008406
149 ENOG4105EIM ABC transporter, permease -0.008399
150 ENOG4105MXP polysaccharide deacetylase 0.008395
151 ENOG4106HC3 Membrane 0.008379
152 ENOG4105CNB Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans (By similarity) 0.008366
153 ENOG4105CBZ Short-chain dehydrogenase reductase Sdr 0.008365
154 ENOG4105D6E homoserine dehydrogenase 0.008359
155 ENOG4105CNT hydrolase family 2 -0.008349
156 ENOG4105EP4 Histidine kinase -0.008342
157 ENOG4105KZ5 Nudix family -0.008333
158 ENOG4107F8Z Inherit from COG: -acetyltransferase -0.004156
158 ENOG4108HF9 COF family -0.004156
159 ENOG4108M15 ABC transporter 0.008307
160 ENOG4105ETW Luciferase-like -0.008304
161 ENOG4108I3C Pfam:DapD_N 0.008291
162 ENOG4108ZGX Histidine kinase 0.008281
163 ENOG4107FQ9 ethanolamine ammonia-lyase -0.008278
164 ENOG4105CD1 Uncharacterized conserved protein (DUF2075) -0.008274
165 ENOG4105DUX Transporter 0.008255
166 ENOG4108RPX mosc domain containing protein 0.008252
167 ENOG4107U9U function transcriptional attenuator common domain protein 0.008249
168 ENOG4106H2A Pfam:PhdYeFM -0.008239
169 ENOG4107RK0 Sucrose phosphorylase -0.008233
170 ENOG4108RQ1 single-stranded DNA-binding protein 0.008229
171 ENOG4108SAI NA -0.008225
172 ENOG4108S7C NA 0.008196
173 ENOG4105FI1 (CBS) domain 0.008196
174 ENOG4108IMN Transcriptional regulator 0.008195
175 ENOG4105E4Z Catalyzes the stereoinversion of LL-2,6- diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso- DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan (By similarity) 0.008188
176 ENOG4105BZH Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.008182
177 ENOG4109054 NA 0.008143
178 ENOG4107T99 Guanine deaminase -0.008137
179 ENOG4105DV8 filamentation induced by cAMP protein Fic 0.008129
180 ENOG4107TG2 phosphoenolpyruvate carboxykinase 0.008128
181 ENOG4105DEF Extracellular solute-binding protein, family 5 0.008104
182 ENOG4105DFF Rod shape-determining protein mreb -0.008102
183 ENOG4107Z7N decarboxylase 0.008096
184 ENOG4105UD4 alkylmercury lyase -0.008096
185 ENOG4107QZ7 Cellulose synthase catalytic subunit 0.008090
186 ENOG4105KY0 addiction module toxin, Txe YoeB family -0.008083
187 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.008082
188 ENOG4106GBV NA -0.008080
189 ENOG4105EZD ABC transporter, permease -0.008079
190 ENOG4107UV0 Alcohol dehydrogenase zinc-binding domain protein -0.008079
191 ENOG4105D5G Transposase -0.008077
192 ENOG4108UTT Catalyzes the formation of 6,7-dimethyl-8- ribityllumazine by condensation of 5-amino-6-(D- ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin (By similarity) 0.008070
193 ENOG4105CEP NADH dehydrogenase 0.008058
194 ENOG4108EQA pts system -0.008040
195 ENOG4105FR1 rard protein 0.008012
196 ENOG4105CRW Short chain fatty acid transporter -0.007997
197 ENOG4105DYN 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) -0.007997
198 ENOG4105QZP Uncharacterized protein conserved in bacteria (DUF2140) 0.007995
199 ENOG4105CI1 PTS System 0.007984
200 ENOG4108NNR transporter substrate-binding protein 0.007972
201 ENOG4105VC3 hydrocarbon binding protein -0.007949
202 ENOG410849E Transcriptional regulator -0.007948
203 ENOG4107QP7 CoA-transferase subunit A -0.007946
204 ENOG4106762 Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5- dihydroxy-2,3-pentadione (DPD) (By similarity) 0.007941
205 ENOG4106TCU acyl-CoA thioesterase -0.007931
206 ENOG41067S9 phage shock protein C, PspC 0.007925
207 ENOG4106DSX CsbD-like -0.007925
208 ENOG4105ERC PTS System 0.007924
209 ENOG4107ST3 ABC transporter 0.007919
210 ENOG4107TQF DNA primase -0.007918
211 ENOG41078A3 NA 0.007916
212 ENOG4107QRI Phosphoketolase -0.007905
213 ENOG4105EGK Proline imino-peptidase -0.007902
214 ENOG4105EYF MMPL domain protein 0.007872
215 ENOG4105D2M Aldolase 0.007871
216 ENOG41067YF Family Transcriptional Regulator 0.007864
217 ENOG4105EH1 NA 0.007860
218 ENOG4108KDH PTS System 0.007858
219 ENOG4105GH9 galactofuranosyltransferase 0.007848
220 ENOG410686K NA -0.007838
221 ENOG4105KVJ Periplasmic binding protein 0.007836
222 ENOG4106EWJ Major tail protein 0.007829
223 ENOG4108IMX DNA-binding helix-turn-helix protein 0.007828
224 ENOG41082Q3 Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity) 0.007823
225 ENOG4108IQK o-acetylhomoserine -0.007803
226 ENOG4105NFQ Nudix family -0.007799
227 ENOG4105Z7E Protein of unknown function (DUF968) 0.007795
228 ENOG4105CI2 imidazolone-5-propionate hydrolase -0.007786
229 ENOG41061AM NA -0.007767
230 ENOG41069UX Beta-N-acetyl-hexosaminidase -0.007747
231 ENOG4107YBY Hydrolase 0.007747
232 ENOG4108WBT adenosyltransferase -0.007747
233 ENOG4105DKM CRISPR-Associated Helicase Cas3 -0.007741
234 ENOG4106659 NA 0.007739
235 ENOG4108TFM Kinase, PfkB family -0.007720
236 ENOG4106TGK NA 0.007706
237 ENOG4105MN5 HAD-superfamily hydrolase subfamily IA variant 3 -0.007697
238 ENOG4105NNT Acetyltransferase GNAT Family -0.007686
239 ENOG4105W2A integral membrane protein 0.007684
240 ENOG4105M9K secreted protein containing plastocyanin domain -0.007683
241 ENOG41083N9 Membrane 0.007673
242 ENOG4105F35 Catalyzes the NAD( )-dependent oxidation of L-carnitine to 3-dehydrocarnitine (By similarity) -0.007671
243 ENOG4108K05 Pyridoxal kinase -0.007659
244 ENOG4108SCW hydrolase -0.007626
245 ENOG4105CM4 permease protein 0.003801
245 ENOG4108IPW abc transporter atp-binding protein 0.003801
246 ENOG4106SVQ Phi ETA orf 55-like protein -0.007598
247 ENOG4107VBZ Transaldolase -0.007597
248 ENOG4108WCS YbbR-like protein -0.007572