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 ENOG4107RUZ Sss sodium solute transporter superfamily -0.010088
2 ENOG4105CS1 NAD(P)H quinone oxidoreductase 0.009062
3 ENOG4105CKK Glycosyl transferase, family 2 0.008311
4 ENOG4108IJ8 ABC transporter 0.008270
5 ENOG4105DND Transcriptional regulator 0.008158
6 ENOG4105C8S subunit m 0.008021
7 ENOG410719E cytochrome p450 0.007691
8 ENOG4107R3I sulfatase-modifying factor 0.007563
9 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 0.007437
10 ENOG4105CSR polyphosphate kinase 2 0.007381
11 ENOG4105GFX Transcriptional regulator 0.007373
12 ENOG4105PMW Domain of unknown function (DUF1990) 0.007290
13 ENOG4105CZ6 Can catalyze the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine (By similarity) 0.007194
14 ENOG4105CTD carboxy-peptidase 0.007072
15 ENOG4105CHJ isochorismatase hydrolase 0.007046
16 ENOG4105KWU NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain 0.007031
17 ENOG4105CGZ zinc metallopeptidase 0.006978
18 ENOG4105Z93 Transcriptional regulator -0.006898
19 ENOG4105DR1 Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration (By similarity) 0.006895
20 ENOG41087YS Phage shock protein A 0.006878
21 ENOG4105D68 Ion transport protein -0.006851
22 ENOG4105WFK nuclease 0.006826
23 ENOG4105CSA Coproporphyrinogen iii oxidase 0.006775
24 ENOG4108VPT UPF0234 protein 0.006759
25 ENOG4105UQX Mate efflux family protein 0.006749
26 ENOG4105CQV 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) 0.006731
27 ENOG4107U8N MATE efflux family protein 0.006670
28 ENOG4105C3V 40-residue yvtn family beta-propeller repeat protein 0.006669
29 ENOG4105KGF protein, YerC YecD -0.006656
30 ENOG41068KN TraR DksA family transcriptional regulator 0.006641
31 ENOG4107RMT Osmosensitive K channel His kinase sensor 0.006627
32 ENOG4105XJC Two component transcriptional regulator (Winged helix family 0.006621
33 ENOG4105FQP Beta-lactamase -0.006579
34 ENOG4105CNR 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) 0.006571
35 ENOG4107RIM Dehydrogenase 0.006552
36 ENOG4105CNZ decarboxylase family 0.006549
37 ENOG4105D7A ATP-binding protein 0.006457
38 ENOG4105D65 subunit l 0.006388
39 ENOG4105CIY formyltetrahydrofolate deformylase 0.006367
40 ENOG4105CMM transposase 0.006352
41 ENOG4108YBP pseudouridine synthase 0.006343
42 ENOG4105C0K Gdp-mannose 4,6-dehydratase 0.006327
43 ENOG4105CJH Alcohol dehydrogenase zinc-binding domain protein 0.006322
44 ENOG4105MZS Rubredoxin-like zinc ribbon domain (DUF35_N) 0.006320
45 ENOG4105CMZ 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. This subunit may bind ubiquinone (By similarity) 0.006290
46 ENOG4107W64 Pyruvate phosphate dikinase, PEP/pyruvate binding domain 0.006287
47 ENOG4105CNA YD repeat protein 0.006274
48 ENOG4108STC Methyltransferase 0.006263
49 ENOG4105WD1 Membrane 0.006212
50 ENOG4105H9W Short-chain dehydrogenase reductase Sdr 0.006208
51 ENOG4105EWU Squalene--hopene cyclase 0.006146
52 ENOG4105CKW Inner membrane protein yedI 0.006138
53 ENOG4107WN2 Aminotransferase class IV -0.006114
54 ENOG4105F0M Aldo Keto reductase 0.006067
55 ENOG4107T2R (twin-arginine translocation) pathway signal -0.006065
56 ENOG4105E0X reductase 0.006059
57 ENOG4108IEH NADH dehydrogenase subunit g 0.006013
58 ENOG4105C7W Xanthine dehydrogenase 0.006001
59 ENOG4107RAD Sodium hydrogen exchanger 0.005974
60 ENOG4108WZW RNA polymerase sigma 0.005963
61 ENOG4108H18 Polysaccharide biosynthesis protein 0.005963
62 ENOG4108VHC Short-chain dehydrogenase reductase Sdr 0.005957
63 ENOG4108RKB methyltransferase -0.005949
64 ENOG4107QMK Protein of unknown function (DUF1800) -0.005932
65 ENOG4107UZB amidohydrolase 0.005924
66 ENOG4105CPP Dehydrogenase, E1 component 0.005921
67 ENOG41060B1 NA 0.005905
68 ENOG4105E9Z Nad-dependent epimerase dehydratase 0.005889
69 ENOG4108MUX N-hydroxyarylamine O-acetyltransferase 0.005869
70 ENOG4108P9D Alpha beta hydrolase 0.005867
71 ENOG4105C0W non-ribosomal peptide synthetase 0.005851
72 ENOG4108DZJ FAD binding domain 0.005820
73 ENOG4107XX8 ABC transporter substrate-binding protein 0.005817
74 ENOG4105P3U 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) 0.005815
75 ENOG4105DRP amino acid AbC transporter 0.005814
76 ENOG4105C3I Nad-dependent epimerase dehydratase 0.005791
77 ENOG4105CVR type I restriction-modification system -0.005783
78 ENOG4105EAC phosphoserine phosphatase 0.005768
79 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) 0.005744
80 ENOG4105EUN Transposase -0.005731
81 ENOG4105D22 carbon starvation protein -0.005726
82 ENOG4108ZP8 Acetolactate synthase small subunit 0.005719
83 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) 0.005683
84 ENOG4105VS8 Flagellar biosynthetic protein fliq -0.005678
85 ENOG4107R8Z faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.005666
86 ENOG4107SK2 acrb acrd acrf family 0.005651
87 ENOG4108ID9 lipid-transfer protein 0.005647
88 ENOG41090JB Transcriptional regulator -0.005617
89 ENOG4106A3M Cytochrome p-450 0.005616
90 ENOG4108UW5 maltose o-acetyltransferase -0.005580
91 ENOG4106EDJ NA -0.005554
92 ENOG4105DRY peptidase s9 prolyl oligopeptidase active site domain protein -0.005515
93 ENOG41066Z3 extracellular ligand-binding receptor -0.005514
94 ENOG4105G7N Transposase -0.005506
95 ENOG4105EKU Uncharacterized protein conserved in bacteria (DUF2236) 0.005498
96 ENOG4105GKE subunit e 0.005488
97 ENOG4108RPX mosc domain containing protein 0.005483
98 ENOG4105YHC Rod shape-determining protein MreD 0.005475
99 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) 0.005473
100 ENOG4105FD2 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) -0.005459
101 ENOG4107VFA NA 0.005459
102 ENOG4105PA7 Protein of unknown function, DUF485 0.005455
103 ENOG4105IN9 MaoC domain protein dehydratase -0.005446
104 ENOG410711E Putative papain-like cysteine peptidase (DUF1796) 0.005440
105 ENOG4107RBX acriflavin resistance protein -0.005439
106 ENOG41061DV MutT NUDIX family protein 0.005429
107 ENOG4108IJ9 (ABC) transporter -0.005425
108 ENOG4105EGG ABC transporter 0.005417
109 ENOG4105WJ1 SnoaL-like polyketide cyclase 0.005414
110 ENOG4108KU9 integrase family -0.005410
111 ENOG4105C6Y Udp-glucose 6-dehydrogenase 0.005408
112 ENOG4105EZY Pyrroloquinoline quinone biosynthesis protein E 0.005385
113 ENOG4105DVW rieske (2Fe-2S) 0.005380
114 ENOG4105MYW Pentapeptide repeat protein -0.005374
115 ENOG4105CZ5 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate (By similarity) 0.005374
116 ENOG4105P1X NA -0.005371
117 ENOG4107TKX transglutaminase -0.005371
118 ENOG4107Y2X deaminase 0.005359
119 ENOG4106BP7 NA -0.005356
120 ENOG4105EVH UPF0753 protein 0.005341
121 ENOG4108SRX Protein of unknown function 0.005287
122 ENOG4107K5X Membrane-bound metal-dependent hydrolase -0.005286
123 ENOG4108YYH Nadph-dependent fmn reductase 0.005284
124 ENOG4107E9N Protein of unknown function DUF262 -0.005283
125 ENOG4105F55 Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate (By similarity) 0.005280
126 ENOG4106F7M NA 0.005273
127 ENOG41068MP NA 0.005270
128 ENOG4107YID Cadmium efflux system accessory protein -0.005247
129 ENOG4105EJB Short-chain dehydrogenase reductase Sdr 0.005246
130 ENOG4105DEU major facilitator superfamily 0.005226
131 ENOG4108K88 Membrane 0.005223
132 ENOG4107QZF nitrite reductase NADPH large subunit 0.005203
133 ENOG4108YYX Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome (By similarity) -0.005203
134 ENOG4105XRQ Xanthine dehydrogenase accessory factor 0.005201
135 ENOG41067TZ transcriptional regulator, MarR family 0.005193
136 ENOG4106YZW NA 0.005179
137 ENOG4105CMW The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity) 0.005169
138 ENOG4105M4M NA 0.005146
139 ENOG4107RNS bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase 3'-nucleotidase periplasmic 0.005143
140 ENOG4105DTJ flagellar hook-associated protein -0.005132
141 ENOG4107S4F acyltransferase, ws dgat mgat 0.005125
142 ENOG4107R1I NAD-dependent malic enzyme 0.005123
143 ENOG4105HA6 Glycosyl transferase, family 2 0.005122
144 ENOG4105CAR Terminase, large subunit 0.005110
145 ENOG4107Z7P Ferredoxin 0.005103
146 ENOG41074CT NA 0.005083
147 ENOG4107R21 site-determining protein -0.005053
148 ENOG4105D13 transposase -0.005040
149 ENOG4105G3W transcriptional regulator MERR family 0.005032
150 ENOG4105KAG DsrE/DsrF-like family -0.005031
151 ENOG4108RK9 3-hydroxyacyl-CoA dehydrogenase -0.005029
152 ENOG4105DUQ Amp-dependent synthetase and ligase 0.005021
153 ENOG4105VEQ Cold shock protein 0.005016
154 ENOG4106166 NA -0.005011
155 ENOG4105ECR NmrA family 0.005005
156 ENOG4105TMB Formate nitrite transporter 0.005003
157 ENOG4108SR5 Transcriptional regulator, TetR family -0.004992
158 ENOG4105EDW glycosyl transferase, family 39 0.004985
159 ENOG4106ER4 transglutaminase domain protein 0.004985
160 ENOG4105M8H Phospholipid N-methyltransferase 0.004984
161 ENOG4105MT7 Arsenical resistance operon tranS-acting repressor -0.004978
162 ENOG4107S9F NmrA family -0.004973
163 ENOG4108VR9 Methyltransferase, type 11 0.004973
164 ENOG4105XG8 Glutathione-dependent formaldehyde-activating Gfa 0.004971
165 ENOG4105C35 Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P) (By similarity) 0.004967
166 ENOG4107PQI Flavin containing amine oxidoreductase 0.004962
167 ENOG4105ZX3 Transcriptional regulator, TetR family 0.004939
168 ENOG4108IPS beta-lactamase 0.004938
169 ENOG4105KA0 thioesterase Superfamily protein 0.004927
170 ENOG4105DGU Histone deacetylase 0.004919
171 ENOG4105D4R Catalyzes the desulfonation of aliphatic sulfonates (By similarity) 0.004909
172 ENOG4107RXS secreted protein -0.004906
173 ENOG4105CZJ Aldehyde dehydrogenase 0.004905
174 ENOG4105QYP Transcriptional regulator -0.004896
175 ENOG4107RK1 peptidase 0.004891
176 ENOG4105WJF NA 0.004884
177 ENOG4107UM8 polysaccharide deacetylase 0.004884
178 ENOG41089H9 NA 0.004874
179 ENOG4108MMT Histidine kinase 0.004873
180 ENOG4108R39 pyridoxamine 5'-phosphate 0.004868
181 ENOG4105HM6 Rod shape-determining protein MreD -0.004860
182 ENOG4105KH3 nitrite reductase (NAD(P)h) small subunit 0.004842
183 ENOG4105D2Y Vwa containing coxe family protein 0.004840
184 ENOG41067U0 -acetyltransferase -0.004827
185 ENOG4106571 Short-chain dehydrogenase reductase Sdr 0.004823
186 ENOG4108U4M Alpha beta hydrolase fold -0.004817
187 ENOG4106CR2 Protein of unknown function (DUF2891) 0.004813
188 ENOG4108FPN Integrase -0.004808
189 ENOG4105DC6 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex (By similarity) 0.004804
190 ENOG4108R87 pep phosphonomutase -0.004788
191 ENOG4108PHQ Alcohol dehydrogenase zinc-binding domain protein 0.004777
192 ENOG4108EV1 Haloalkane dehalogenase 0.004767
193 ENOG4108IF1 Methyl-accepting chemotaxis -0.004756
194 ENOG4107ZYZ transcriptional regulator 0.004753
195 ENOG4105YSQ chromosome segregation ATPase-like protein -0.004753
196 ENOG4105E4I Glycoside hydrolase family 28 0.004732
197 ENOG4105D19 Role in flagellar biosynthesis (By similarity) -0.004731
198 ENOG4107QJZ Glycosyl transferase, family 2 -0.004729
199 ENOG4107C7A NA -0.004725
200 ENOG4108S5D Inherit from COG: oxygenase 0.004725
201 ENOG4108SGY acetyltransferase 0.004722
202 ENOG4108ZXM Esterase 0.004721
203 ENOG4107T44 YD repeat protein -0.004701
204 ENOG4108Z9J NA -0.004700
205 ENOG4105ZNY NA 0.004698
206 ENOG4108Z8I decarboxylase 0.004696
207 ENOG4106EII NA -0.004692
208 ENOG4107Y9E nuclease -0.004690
209 ENOG4105C2J ABC transporter 0.004690
210 ENOG4108IMY Transcriptional regulator 0.004678
211 ENOG4107MZD HTH_XRE 0.004675
212 ENOG4105C7Z Conserved Protein 0.004661
213 ENOG4105XYF acetyltransferase 0.004661
214 ENOG4105VCQ rubredoxin 0.004641
215 ENOG4105CPK Glycosyl transferase (Group 1 0.004640
216 ENOG4105MIV NA 0.004638
217 ENOG4108DIY NA -0.004638
218 ENOG4108XM1 transcriptional regulator AsnC family 0.004638
219 ENOG4105X2W Coenzyme PQQ synthesis protein D (PqqD) 0.004632
220 ENOG4105QPS Monooxygenase 0.004624
221 ENOG41060TR NA -0.004623
222 ENOG4107RFM alcohol dehydrogenase 0.004614
223 ENOG41082FT major facilitator superfamily MFS_1 0.004613
224 ENOG4106J52 helicase -0.001537
224 ENOG4107EFI NA -0.001537
224 ENOG4108D2U NA -0.001537
225 ENOG4108Z5J permease -0.004610
226 ENOG4107GI5 N-acetyltransferase -0.004599
227 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.004596
228 ENOG4105ZJE NA -0.004593
229 ENOG4108ZCE endoribonuclease L-psp -0.004589
230 ENOG4108XG0 Transcriptional regulator, TetR family 0.004589
231 ENOG4105M4P Tetr family transcriptional regulator 0.004578
232 ENOG4107V7T Dienelactone hydrolase 0.004574
233 ENOG4105ET3 Reduction of activated sulfate into sulfite (By similarity) 0.004573
234 ENOG4105DD5 Flagellar motor switch protein -0.004569
235 ENOG4105CVK Glutamate decarboxylase 0.004563
236 ENOG410652G NA -0.004562
237 ENOG4105VTJ saf domain-containing protein 0.004561
238 ENOG4105MQ3 flagellar protein FliS -0.004557
239 ENOG4107EXU Short-chain dehydrogenase reductase Sdr 0.004549
240 ENOG4105EKD Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism (By similarity) -0.004549
241 ENOG4108K5V Major Facilitator superfamily 0.004548
242 ENOG410604Q amidohydrolase 0.004547
243 ENOG4105KSC Transcriptional regulator, TraR DksA family 0.004546
244 ENOG4107QYD Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.004545
245 ENOG4105UP1 NA -0.004537
246 ENOG4107TWM deoxynucleoside kinase 0.004535
247 ENOG4106XV2 Cytochrome p-450 0.004529
248 ENOG4105RFZ Methylmalonyl-coA mutase 0.004526