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 ENOG4107V1M polysaccharide export protein 0.005889
2 ENOG4106CD9 glycosyl transferase group 1 0.005665
3 ENOG4107KMK NA 0.005512
4 ENOG4107RTG Major Facilitator superfamily 0.005474
5 ENOG41072GB extracellular solute-binding protein 0.005359
6 ENOG4107QJ7 formate dehydrogenase alpha subunit 0.005337
7 ENOG4105C80 Catalyzes the reversible oxidation of malate to oxaloacetate (By similarity) -0.005268
8 ENOG4105C18 Uncharacterized protein conserved in bacteria (DUF2252) 0.005141
9 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic -0.005096
10 ENOG4105M7P phage repressor 0.005061
11 ENOG4108SXM bacteriophage DNA transposition B protein 0.004909
12 ENOG4108Y1E p-loop domain protein 0.004898
13 ENOG410907F phage protein 0.004853
14 ENOG41068IX NA 0.004745
15 ENOG4108W8P Diguanylate cyclase with PAS PAC sensor 0.004713
16 ENOG4105CSD Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) (By similarity) 0.004712
17 ENOG4108TEZ Pfam:DUF847 0.004698
18 ENOG4108ZQX ybak prolyl-trna synthetase 0.004676
19 ENOG4108V0P LemA family -0.004649
20 ENOG4105FCD Major Facilitator 0.004627
21 ENOG4108R3F Nudix family -0.004626
22 ENOG4108MVM Transposase 0.004620
23 ENOG4105C47 NADH ubiquinone oxidoreductase 20 kda subunit 0.004589
24 ENOG4108NFT Short-chain dehydrogenase reductase Sdr 0.004571
25 ENOG41090BB DNA mismatch endonuclease (vsr) 0.004564
26 ENOG4105CA0 peroxidase 0.004535
27 ENOG4107QKC Oxidoreductase alpha (molybdopterin) subunit -0.004533
28 ENOG4108JKD thiamine biosynthesis protein this 0.004522
29 ENOG4105EXC Acyl-transferase -0.004517
30 ENOG410830X 'Cold-shock' DNA-binding domain protein -0.004490
31 ENOG4105WPP transcriptional regulator, MarR family 0.004474
32 ENOG4108V6X -acetyltransferase 0.004426
33 ENOG4107QW8 radical SAM domain protein 0.004408
34 ENOG4105EJ9 Membrane 0.004367
35 ENOG4105C1X Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity (By similarity) 0.004359
36 ENOG4108IYT Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity) -0.004354
37 ENOG4105ZWK Inherit from COG: Low-potential electron donor to a number of redox enzymes (By similarity) 0.004322
38 ENOG4105F4F gtp-binding protein 0.004318
39 ENOG41076CE NA 0.004309
40 ENOG4107R30 NADH dehydrogenase 0.004283
41 ENOG4105UBT PAS PAC sensor protein 0.004238
42 ENOG4108ZJ4 polysaccharide deacetylase 0.004201
43 ENOG4105W29 tail protein 0.004195
44 ENOG4107ZRM mutt nudix family protein 0.004189
45 ENOG4105DZS Phenylacetate-CoA ligase 0.004186
46 ENOG4105HMK Bacterial inner membrane protein 0.004183
47 ENOG4107QT1 Phenylacetate-CoA ligase 0.004151
48 ENOG4105DSW Fusaric acid resistance protein -0.004146
49 ENOG4108RG7 formate hydrogenlyase complex iron-sulfur subunit 0.004142
50 ENOG4105FDF Could be involved in DNA repair (By similarity) -0.004123
51 ENOG4105CZM Major Facilitator 0.004118
52 ENOG4105VB8 Regulatory protein, FmdB family 0.004116
53 ENOG41084CK capsule polysaccharide 0.004114
54 ENOG4105PNG tpr repeat-containing protein 0.004106
55 ENOG4105EUZ Beta-lactamase domain protein 0.004105
56 ENOG4105D75 Capsular exopolysaccharide family -0.004089
57 ENOG4105VCQ rubredoxin 0.004052
58 ENOG4105EHH Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue (By similarity) 0.004051
59 ENOG4106000 NA 0.004045
60 ENOG4108EXR Transporter associated domain 0.004043
61 ENOG4108IY1 (ABC) transporter -0.004039
62 ENOG4108JU5 Magnesium and cobalt efflux protein -0.004039
63 ENOG4108K45 Phage plasmid-related protein TIGR03299 0.004038
64 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase 0.004032
65 ENOG4107EGH tail fiber protein 0.004026
66 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) -0.004020
67 ENOG4107QPK )-transporter -0.004006
68 ENOG4105CK2 sodium dicarboxylate symporter 0.003977
69 ENOG4106VWN NA 0.003950
70 ENOG4108XTN Peptidoglycan binding domain-containing protein 0.003946
71 ENOG4105VEC DNA binding domain protein, excisionase family 0.003937
72 ENOG4105EKV Phosphonate metabolism protein 0.000981
72 ENOG4105ENV phosphonate C-P lyase system protein PhnK 0.000981
72 ENOG4105FT8 Phosphonate metabolism 0.000981
72 ENOG4105HRV phosphonate c-p lyase system protein phnl 0.000981
73 ENOG4107YPI Stage V sporulation protein B 0.003922
74 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.003890
75 ENOG4106R7S Major Facilitator Superfamily 0.003879
76 ENOG4105U44 Prophage membrane protein 0.003879
77 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase 0.003874
78 ENOG4107QVN Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) 0.003868
79 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) 0.003868
80 ENOG4108ZWN Nitroreductase 0.003866
81 ENOG41069ZS flagellar protein 0.003866
82 ENOG4105VYW UPF0251 protein 0.003858
83 ENOG41090IX small terminase subunit 0.003848
84 ENOG4105KRJ gCN5-related N-acetyltransferase 0.003845
85 ENOG4105YUM phage-related transmembrane protein 0.003843
86 ENOG4105FD8 phosphonate metabolism protein PhnM 0.003823
87 ENOG4108UV6 Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) (By similarity) 0.003813
88 ENOG4107RE8 Integrase 0.003812
89 ENOG4107RC8 solute-binding protein 0.003810
90 ENOG4105Y49 secretion protein, HlyD family -0.003803
91 ENOG4107SJQ Polysulfide reductase, NrfD 0.003803
92 ENOG4107XEC aspartate racemase 0.003799
93 ENOG4105VZ8 Transcriptional regulator -0.003792
94 ENOG4108YXI Secondary thiamine-phosphate synthase enzyme 0.003780
95 ENOG4105VB6 UPF0109 protein 0.003777
96 ENOG4108EM1 reductase 0.003775
97 ENOG4105T0Q Glycosyl transferase, family 2 0.003754
98 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.003747
99 ENOG410901P UPF0249 protein 0.003742
100 ENOG4108U1C ggdef family 0.003737
101 ENOG4105NCJ NA 0.003724
102 ENOG4108RC0 Electron transport protein 0.003723
103 ENOG4105CG6 trap dicarboxylate transporter dctm subunit 0.003712
104 ENOG4107R2A decarboxylase 0.003708
105 ENOG4105C5I Dehydrogenase -0.003702
106 ENOG4107SMT L-asparaginase 0.003685
107 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) 0.003678
108 ENOG4105CA9 Pyruvate kinase -0.003665
109 ENOG4105BZS acriflavin resistance protein 0.003663
110 ENOG4105D5B Sulfite reductase, subunit A 0.003662
111 ENOG4108UJJ activator of Hsp90 ATPase 1 family protein -0.003660
112 ENOG4108RFA Membrane 0.003660
113 ENOG4108VBI AraC family transcriptional regulator 0.003654
114 ENOG4105KI2 Urea amidohydrolase subunit beta 0.003654
115 ENOG4105DQ6 Transposase 0.003653
116 ENOG4105E12 capsule polysaccharide 0.003645
117 ENOG4105D6K lipolytic protein G-D-S-L family 0.003632
118 ENOG4107Y77 TRANSCRIPTIONAl REGULATOR GntR family 0.003630
119 ENOG4107R58 glycosyl transferase group 1 0.003630
120 ENOG4106I3K domain protein 0.003630
121 ENOG4108Z1Z gCN5-related N-acetyltransferase 0.003625
122 ENOG4107QJZ Glycosyl transferase, family 2 0.003607
123 ENOG4105E0I Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of tRNA(Met), by using acetyl-CoA as an acetyl donor and ATP (or GTP) (By similarity) -0.003600
124 ENOG4107P2S Transcriptional regulator 0.003598
125 ENOG41063EF Mor transcription activator domain protein 0.003596
126 ENOG41090KH cytochrome o ubiquinol oxidase (subunit iv) -0.003574
127 ENOG4105CTR Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity) -0.003568
128 ENOG4105M3E Glyoxalase Bleomycin resistance protein (Dioxygenase -0.003550
129 ENOG4105VJZ Helix-turn-helix domain protein 0.003548
130 ENOG4105CQM Urea amidohydrolase subunit alpha 0.003539
131 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.003539
132 ENOG4105CVK Glutamate decarboxylase -0.003535
133 ENOG41066HJ ATP-dependent Clp protease, proteolytic subunit 0.003529
134 ENOG4105EF4 Pfam:DUF151 0.003524
135 ENOG4105DFW ABC transporter 0.003522
136 ENOG4107ZU8 PTS System -0.003520
137 ENOG4105EE0 oxidoreductase -0.003517
138 ENOG4105HHQ 6-phosphogluconolactonase (EC 3.1.1.31) -0.003517
139 ENOG4105ECW sulfate abc transporter -0.003505
140 ENOG4107S6Z Na H antiporter 0.003503
141 ENOG4105E89 ABC transporter 0.003502
142 ENOG4108NF7 phage-type endonuclease 0.003482
143 ENOG4108W6E Tetr family transcriptional regulator 0.003477
144 ENOG4105WAF domain protein 0.003475
145 ENOG4105PNM synthesis protein 0.003472
146 ENOG4105FE8 tRNA (Guanosine-2'-O-)-methyltransferase 0.003469
147 ENOG4107YBG Phosphate ABC transporter, permease protein 0.003448
148 ENOG4105VDM plasmid maintenance system antidote protein, xre family 0.003441
149 ENOG4105HAY sulfurtransferase -0.003438
150 ENOG4106ESY NA 0.003432
151 ENOG4107QKF NADH Ubiquinone plastoquinone (Complex I) 0.003429
152 ENOG4108STT Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans (By similarity) -0.003425
153 ENOG4108UG4 methyl-accepting chemotaxis protein 0.003419
154 ENOG4108UZ3 Transporter -0.003408
155 ENOG4105Y5J prophage protein 0.003406
156 ENOG4107UQS peptidase 0.003404
157 ENOG4105D5Q Arginine ornithine antiporter 0.003402
158 ENOG4105CPK Glycosyl transferase (Group 1 0.003397
159 ENOG4105XDZ Tripartite ATP-independent periplasmic transporter 0.003396
160 ENOG41090SZ ABC-2 type transporter 0.003396
161 ENOG4107RR9 sulfate transporter -0.003395
162 ENOG4105S2T inner membrane protein YbcI 0.003393
163 ENOG410901E Membrane 0.003393
164 ENOG4105KJP alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.003389
165 ENOG4105DNG Major Facilitator superfamily 0.003387
166 ENOG4105EFV Major head subunit 0.003387
167 ENOG41082US Major Facilitator Superfamily -0.003385
168 ENOG4105QIB mu-like prophage Flumu protein gp29 0.003372
169 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.003371
170 ENOG4108K4V NA 0.003364
171 ENOG4105XWR Phage virion morphogenesis protein 0.003360
172 ENOG4105ECX polysaccharide export 0.003347
173 ENOG41061GG NUDIX hydrolase 0.003344
174 ENOG4107QU4 malate dehydrogenase (Oxaloacetate-decarboxylating) 0.003342
175 ENOG410657F sodium sulfate symporter 0.003337
176 ENOG4107SFI Major Facilitator superfamily -0.003335
177 ENOG4105TD1 Formyl transferase 0.003333
178 ENOG4105DGU Histone deacetylase 0.003333
179 ENOG4105FDP GntR family transcriptional regulator 0.003333
180 ENOG4106G6Q Transcriptional regulator -0.003330
181 ENOG4108TFM Kinase, PfkB family -0.003329
182 ENOG4108RB3 Capsular polysaccharide biosynthesis protein -0.003317
183 ENOG4106IPD NA 0.003316
184 ENOG410810Y Sulfite reductase 0.003304
185 ENOG4105CB5 ATP-dependent DNA helicase recG -0.003299
186 ENOG4105C3U ABC transporter 0.003290
187 ENOG4105D7V transposase 0.003280
188 ENOG4105WUF NA 0.003276
189 ENOG4105K7K Transcriptional regulator -0.003268
190 ENOG4105F1A Pyruvate formate-lyase -0.003265
191 ENOG4105F8C transglutaminase domain-containing protein 0.003263
192 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) -0.003263
193 ENOG4105VFS Tripartite ATP-independent periplasmic transporter dctq component 0.003262
194 ENOG4107VHI glycoside hydrolase family protein 0.003262
195 ENOG4107UGQ permease 0.003250
196 ENOG4108KB8 LysR family transcriptional regulator -0.003248
197 ENOG4105QBX endodeoxyribonuclease RusA 0.003246
198 ENOG4108M86 NA 0.003245
199 ENOG410743V gCN5-related N-acetyltransferase 0.003244
200 ENOG4105RT9 NA 0.003244
201 ENOG4105E2S oxidase) subunit II -0.003241
202 ENOG410695M Pilus assembly protein 0.003239
203 ENOG4105CMU LysR family (Transcriptional regulator 0.003238
204 ENOG4105DE7 Sulfate ABC transporter periplasmic sulfate-binding protein -0.003237
205 ENOG4108M4E transposase 0.003236
206 ENOG4105VMP Transcriptional regulator 0.003235
207 ENOG4108JJ9 ABC, transporter -0.003229
208 ENOG4105CV5 fumarylacetoacetate (Faa) hydrolase 0.003228
209 ENOG4105MQ8 Phage virion morphogenesis protein 0.003227
210 ENOG41086BM amino acid AbC transporter -0.003226
211 ENOG4107RA5 ABC transporter substrate-binding protein -0.003226
212 ENOG4105C7E Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA) (By similarity) 0.003225
213 ENOG4108T8K Anti-repressor protein 0.003221
214 ENOG4107QUY Guanine deaminase 0.003218
215 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) -0.003207
216 ENOG4106BXS Phage conjugal plasmid C-4 type zinc finger protein, TraR family 0.003204
217 ENOG4106HS9 NA 0.001068
217 ENOG4106YZT NA 0.001068
217 ENOG4108W37 NA 0.001068
218 ENOG4108N28 NA 0.003203
219 ENOG4108UHX Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS (By similarity) 0.003202
220 ENOG4107QWS glycogen debranching enzyme glgx -0.003202
221 ENOG4107S39 endoribonuclease L-psp 0.003200
222 ENOG4105EY8 ABC transporter 0.003199
223 ENOG4105FBX amino acid AbC transporter -0.003192
224 ENOG4105MCM Baseplate Assembly protein 0.003187
225 ENOG4108XTU NA 0.003184
226 ENOG4107EA0 NA 0.003184
227 ENOG4106EHC NA 0.001592
227 ENOG4107T06 dEAD DEAH box helicase 0.001592
228 ENOG4107Y6E flavin reductase domain protein, FMN-binding 0.003184
229 ENOG41075NE NA 0.003184
230 ENOG410751M NA 0.003184
231 ENOG4108TQJ Glutathione S-transferase 0.003184
232 ENOG4107HB7 NA 0.003184
233 ENOG4107TBY Alpha beta hydrolase 0.003184
234 ENOG4105MU2 lipopolysaccharide biosynthesis protein 0.000061
234 ENOG4105MXM Lipid A 3-O-deacylase-related protein 0.000061
234 ENOG4105PB8 Diguanylate cyclase 0.000061
234 ENOG4105QQR ABC-type amino acid transport signal transduction 0.000061
234 ENOG4105V9P Domain of unknown function (DUF305) 0.000061
234 ENOG4105YXR CHAD domain-containing protein 0.000061
234 ENOG410617W NA 0.000061
234 ENOG41061E3 Acyltransferase family 0.000061
234 ENOG41063GY Phage tail fibre protein 0.000061
234 ENOG41064DU NA 0.000061
234 ENOG41066R3 NA 0.000061