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 ENOG4105Q9D Abortive infection protein AbiGI -0.013888
2 ENOG4107QW8 radical SAM domain protein 0.013324
3 ENOG4105D0I Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity) 0.013099
4 ENOG4105F2S Abortive infection protein AbiGII -0.013026
5 ENOG4108I0Z Aconitate hydratase 0.012331
6 ENOG4108IAB Phoh family 0.012272
7 ENOG4105MAP Phage prohead protease, HK97 family 0.012007
8 ENOG4105VEQ Cold shock protein -0.011846
9 ENOG4105EH4 helicase -0.011794
10 ENOG4105EHH Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue (By similarity) 0.011785
11 ENOG4105D41 biosynthesis protein thiH 0.011756
12 ENOG4107SP8 Filamentation induced by cAMP protein fic -0.011354
13 ENOG4105DIK (ABC) transporter -0.011308
14 ENOG4105D18 nicotinate-nucleotide pyrophosphorylase 0.011092
15 ENOG4105F4F gtp-binding protein 0.010960
16 ENOG4108HHA Transketolase 0.010958
17 ENOG4108XC3 NADH ubiquinone oxidoreductase 0.010912
18 ENOG4105GB1 bioY protein 0.010833
19 ENOG4107SIB radical SAM domain protein 0.010726
20 ENOG4105CAR Terminase, large subunit 0.010626
21 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.010281
22 ENOG4105DUF Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively (By similarity) -0.010268
23 ENOG41084EF Ferredoxin 0.010165
24 ENOG4108RVA ribokinase -0.010063
25 ENOG4105C26 Dehydrogenase -0.010057
26 ENOG4105CG5 Glycosyl transferase (Group 1 0.010052
27 ENOG4105CIN aminoacyl-histidine dipeptidase 0.010039
28 ENOG4108Z0Z intracellular protease Pfpi family 0.010038
29 ENOG4105C5B carbamate kinase 0.009941
30 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.009888
31 ENOG4108UMB Flavodoxin -0.009812
32 ENOG4105VF1 iron-only hydrogenase system regulator 0.009808
33 ENOG4105MZU cell filamentation protein 0.009771
34 ENOG4105DSX permease -0.009706
35 ENOG4108UK1 Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant (By similarity) 0.009637
36 ENOG4107S0U radical SAM domain protein 0.009619
37 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.009589
38 ENOG4108R8F zinc metallopeptidase 0.009528
39 ENOG4105EUD Transcriptional regulator -0.009482
40 ENOG4108SQE Helix-turn-helix -0.009429
41 ENOG410900W integral membrane protein 0.009369
42 ENOG4105C9Q fumarate hydratase class II -0.009364
43 ENOG4105DFS Conserved Protein 0.009346
44 ENOG41080E8 Transcriptional regulator, Spx MgsR family 0.009323
45 ENOG4105N1U Histidine kinase 0.009200
46 ENOG4105HMI Membrane 0.009181
47 ENOG4105EYG tyrosine recombinase. Not involved in the cutting and rejoining of the recombining DNA molecules on dif(SL) site (By similarity) -0.009099
48 ENOG4105C3M thioredoxin reductase -0.009073
49 ENOG4105C6Z Gluconate 0.009013
50 ENOG4105PJG NA 0.008957
51 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) -0.008901
52 ENOG4105BZN citrate synthase 0.008898
53 ENOG4105YED heavy metal transport detoxification protein -0.008846
54 ENOG4108E0S reductase -0.008832
55 ENOG4106F9V transposase IS116 IS110 IS902 family protein -0.008820
56 ENOG4105DSG hydrolase family 43 0.008790
57 ENOG4108XGR NA 0.008712
58 ENOG4105Z01 transcriptional regulator -0.008704
59 ENOG4108ZTW Nitrogen regulatory protein P-II 0.008681
60 ENOG4108WBT adenosyltransferase -0.008669
61 ENOG4108I66 PTS System 0.008660
62 ENOG4105GDX Domain of unknown function (DUF1877) 0.008655
63 ENOG4105D07 Signal peptide peptidase, SppA -0.008646
64 ENOG4108J59 Extracellular solute-binding protein, family 5 0.008522
65 ENOG4108VIJ Transposase -0.008516
66 ENOG4105HFZ Membrane -0.008483
67 ENOG4105N67 Proton-coupled thiamine transporter YuaJ 0.008454
68 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) -0.008439
69 ENOG4108I1J Integrase 0.008426
70 ENOG4105CWI transcriptional regulator 0.008412
71 ENOG4107QYD Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.008384
72 ENOG4105EEQ Na H antiporter -0.008341
73 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F -0.008335
74 ENOG4105CMG Carbohydrate kinase 0.008330
75 ENOG4105CI1 PTS System 0.008321
76 ENOG4105CGQ conserved protein UCP033563 0.008314
77 ENOG4108XMW Membrane 0.008282
78 ENOG4105DD5 Flagellar motor switch protein 0.008260
79 ENOG4106611 bacteriocin immunity 0.008184
80 ENOG4107UA6 flavin reductase domain protein 0.008156
81 ENOG4108T8Z NA -0.008120
82 ENOG4105P1P protein, conserved in bacteria 0.008106
83 ENOG4108R9M Involved in allosteric regulation of aspartate carbamoyltransferase (By similarity) -0.008073
84 ENOG4105VFB Binds the 23S rRNA (By similarity) 0.008071
85 ENOG4105CKP Polysaccharide Biosynthesis Protein 0.007985
86 ENOG4108IYU L-aspartate oxidase 0.007977
87 ENOG4105E0X reductase 0.007959
88 ENOG4105FWS Nadph-dependent fmn reductase 0.007956
89 ENOG4105KVA NA -0.007946
90 ENOG4105C45 hydrogenase expression formation protein (HypE) 0.007921
91 ENOG4105E0M Sulfatase -0.007919
92 ENOG4105W0D NA -0.007876
93 ENOG4105MK2 5-formyltetrahydrofolate cyclo-ligase -0.007849
94 ENOG4108MY7 Fimbrial 0.007833
95 ENOG4108UAI Histidine triad 0.007828
96 ENOG4107QNU type ii secretion system protein e 0.007820
97 ENOG4105QIV RNA polymerase 0.007756
98 ENOG4108ZBF iron (metal) dependent repressor, dtxr family -0.007752
99 ENOG4105C3R Methionine synthase 0.007715
100 ENOG4105PQ3 Radical SAM-linked protein 0.007695
101 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 0.007677
102 ENOG4105UQG NA 0.007676
103 ENOG4108SB3 DoxX Family 0.007667
104 ENOG4105C4U 4-methyl-5-beta-hydroxyethylthiazole kinase 0.007658
105 ENOG410667J hydrolase 0.007654
106 ENOG4108Z3B V-type sodium ATPase, K subunit 0.007652
107 ENOG410822I Flagellar hook capping protein 0.007622
108 ENOG4105XSR Transcriptional regulator, MarR family 0.007592
109 ENOG4107RHE UDP-glucose 6-dehydrogenase 0.007588
110 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) 0.007579
111 ENOG4108V1J Has antioxidant activity. Could remove peroxides or H(2)O(2) (By similarity) 0.007565
112 ENOG4105YU2 HNH endonuclease 0.007540
113 ENOG4107Y70 Heat shock protein -0.007529
114 ENOG4107QSV RmuC domain protein 0.007524
115 ENOG4105NI6 heptaprenyl diphosphate synthase component I 0.007520
116 ENOG4105P1U NA 0.007513
117 ENOG4107U42 phosphate 0.007507
118 ENOG4108JB8 alcohol dehydrogenase 0.007504
119 ENOG4106TNM NA -0.007489
120 ENOG4105VHM ribosomal protein 0.007483
121 ENOG4107RMW DNA Methylase 0.007472
122 ENOG4105EFS Binding-protein-dependent transport systems, inner membrane component 0.007470
123 ENOG4105VJG Transcriptional regulator 0.007447
124 ENOG4105ZMU T5orf172 domain -0.007444
125 ENOG4105G7N Transposase -0.007419
126 ENOG4105EX2 Binding-protein-dependent transport systems, inner membrane component -0.007414
127 ENOG4108TC1 Transcriptional regulator 0.007400
128 ENOG4105FV3 NA 0.007395
129 ENOG4105CTS PTS system mannitol-specific 0.007391
130 ENOG4105CN7 Flagellar biosynthetic protein FliP 0.007390
131 ENOG4105WC9 nucleotidyltransferase substrate binding protein, HI0074 family 0.007381
132 ENOG4105C93 Xylose Isomerase 0.007379
133 ENOG4107GRR phosphate transport regulator 0.007371
134 ENOG4106F1P AAA ATPase, central domain protein -0.007362
135 ENOG4108TCH flavin reductase domain protein 0.007352
136 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase 0.007339
137 ENOG4108MJM NA 0.007322
138 ENOG4107QZW Altronate oxidoreductase 0.007311
139 ENOG410757E Protein NinE homolog from lambdoid prophage DLP12 0.007294
140 ENOG41090I7 cation diffusion facilitator family transporter 0.007293
141 ENOG4105N3I Involved in formation and maintenance of cell shape (By similarity) 0.007282
142 ENOG4105CRZ Nucleotidyl transferase of unknown function (DUF1814) -0.007260
143 ENOG4108Z58 rRNA Methylase 0.007256
144 ENOG4108J2R molybdopterin oxidoreductase 0.007250
145 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.007241
146 ENOG4105NJS thiw protein 0.007229
147 ENOG4105CPK Glycosyl transferase (Group 1 -0.007208
148 ENOG4105CVM Molybdenum cofactor synthesis domain protein 0.007197
149 ENOG4105CBE radical SAM domain protein 0.007185
150 ENOG4108MR7 Arylsulfotransferase 0.007171
151 ENOG4105EFC phage portal protein HK97 family 0.007164
152 ENOG4106TCE NA 0.007144
153 ENOG410672P Plasmid recombination enzyme -0.007131
154 ENOG4107QSW The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate (By similarity) -0.007129
155 ENOG4108ESE uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center 0.007123
156 ENOG4105CQB FAD linked oxidase domain protein 0.007116
157 ENOG4108S4H thioesterase Superfamily protein -0.007108
158 ENOG4108RYC glycosyltransferase 0.007107
159 ENOG4108SDZ domain protein 0.007100
160 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) -0.007095
161 ENOG4108RCY Nadph-dependent fmn reductase 0.007083
162 ENOG4106Y6C NA 0.007079
163 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.007074
164 ENOG4108G5V Capsule synthesis protein 0.007066
165 ENOG41060V9 Cysteine-rich small domain protein 0.007058
166 ENOG4108QHG Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) -0.007045
167 ENOG4108RBF ROK family -0.007035
168 ENOG4108W76 histidinol phosphate phosphatase hisj family 0.007029
169 ENOG4105II7 pyrroline-5-carboxylate reductase 0.007014
170 ENOG4107RCJ Phage Tail Tape Measure Protein 0.007011
171 ENOG4108KFT cyclic nucleotide-binding domain protein 0.007009
172 ENOG41068W6 Capsular polysaccharide biosynthesis protein 0.007008
173 ENOG4108UIC UPF0340 protein 0.006969
174 ENOG4105DZB Electron transport complex 0.006961
175 ENOG4105HY7 NA 0.006940
176 ENOG4105CK6 Two component transcriptional regulator (Winged helix family -0.006930
177 ENOG41082M4 phosphocarrier protein hpr 0.006916
178 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) 0.006904
179 ENOG4105YNQ NA 0.006902
180 ENOG4105KKX ATPase associated with various cellular activities aaa_5 0.006902
181 ENOG4106AUB Phage head-tail adaptor 0.006901
182 ENOG4105D6A Electron transport complex 0.006891
183 ENOG4105ITW cytosolic protein 0.006890
184 ENOG41083VB Pyruvate formate lyase 0.006876
185 ENOG4107R3X Aconitase family 0.006874
186 ENOG41084KE Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity) 0.006856
187 ENOG4108I5U Uridine phosphorylase -0.006840
188 ENOG4108VGH Abortive infection bacteriophage resistance protein -0.006834
189 ENOG4106C6A Produces ATP from ADP in the presence of a proton gradient across the membrane (By similarity) -0.006833
190 ENOG4105DK2 UPF0207 protein -0.006825
191 ENOG4105EKQ RNA-directed DNA polymerase -0.006803
192 ENOG4105DR4 Methyltransferase -0.006800
193 ENOG4108F2G Chain length determinant protein 0.006796
194 ENOG4107RUW arginyl-trna synthetase 0.006790
195 ENOG4105CQS hydrogenase expression formation protein HypD 0.006775
196 ENOG41076HS cation diffusion facilitator family transporter -0.006773
197 ENOG4105DEG Vwa containing coxe family protein 0.006764
198 ENOG4105MVF Transcriptional regulator 0.006750
199 ENOG4108FT8 Transporter 0.006745
200 ENOG410801F ribosomal-protein-alanine acetyltransferase 0.006741
201 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) 0.006736
202 ENOG4105CZG Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity) 0.006723
203 ENOG4107WZ9 reductase -0.006717
204 ENOG4105C6I Resolvase -0.006712
205 ENOG4105DCU 2-hydroxyglutaryl-CoA dehydratase 0.006711
206 ENOG4105EEI dihydropteroate synthase -0.006700
207 ENOG4105CAH Chromate 0.006700
208 ENOG4105BZW Glycerate kinase -0.006699
209 ENOG4105MJ2 Competence protein 0.006693
210 ENOG4105RR0 Protein of unknown function (DUF2554) 0.006693
211 ENOG4105QTN Addiction module antitoxin, RelB DinJ family 0.006691
212 ENOG4105CHJ isochorismatase hydrolase 0.006686
213 ENOG4107SQ3 mannitol-1-phosphate 5-dehydrogenase 0.006684
214 ENOG4106TJV NA 0.006681
215 ENOG4108G4G portal protein 0.006680
216 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) 0.006679
217 ENOG41064RH membrane protein YliF 0.006660
218 ENOG4105U41 Ferric uptake regulator family 0.006660
219 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase 0.006655
220 ENOG4105E1Q flagellar hook-associated protein 0.006651
221 ENOG4107T6Z Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (By similarity) 0.006649
222 ENOG4105MFI Protein of unknown function (DUF3575) 0.006648
223 ENOG4107UNS conserved inner membrane protein 0.006636
224 ENOG4108IJY tape measure protein 0.006631
225 ENOG4105H0B Domain-Containing protein -0.006624
226 ENOG4105CH2 amidohydrolase 0.006622
227 ENOG4105J6D Fha domain 0.006610
228 ENOG4105CNN ABC, transporter 0.006609
229 ENOG41081GJ glycosyltransferase group 2 family protein -0.006605
230 ENOG4105N5T Radical SAM Protein 0.006601
231 ENOG4108V47 Antirestriction protein 0.006592
232 ENOG4105VVF NA 0.006589
233 ENOG4105W5D IS66 Orf2 family protein -0.006583
234 ENOG41082HH efflux transporter, rnd family, mfp subunit 0.006582
235 ENOG4105C9G DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks during chromosomal DNA synthesis (By similarity) -0.006579
236 ENOG4105DN4 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.006574
237 ENOG4105DIN metallophosphoesterase 0.006573
238 ENOG4107TWJ Beta-lactamase 0.006571
239 ENOG4105CDW Resistance protein -0.006534
240 ENOG41081Y5 regulator Fur family 0.006527
241 ENOG4105NN3 Response regulator of the LytR AlgR family -0.006522
242 ENOG4105E9Q Acyl-transferase 0.006510
243 ENOG4105C60 DNA-binding protein 0.006508
244 ENOG4106QS4 NA 0.006507
245 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.006504
246 ENOG4105CNH Multidrug resistance protein MdtL 0.006487
247 ENOG4105EKH ATP-grasp 0.006485
248 ENOG4105DBI uridine monophosphokinase -0.006485
249 ENOG4105CTP PilT protein domain protein 0.006478
250 ENOG4105E39 Enoyl-CoA hydratase 0.006471