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 ENOG4105C0F tryptophanase EC 4.1.99.1 0.028355
2 ENOG4105CTK cobaltochelatase, cobn subunit 0.017394
3 ENOG4105CFC Transporter 0.016746
4 ENOG4108VGH Abortive infection bacteriophage resistance protein -0.014897
5 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase 0.014055
6 ENOG4107RY0 Catalyzes the conversion of dihydroorotate to orotate (By similarity) 0.013157
7 ENOG4105D4H Membrane 0.012713
8 ENOG4108DBC nitroreductase -0.012266
9 ENOG4105CI2 imidazolone-5-propionate hydrolase 0.012180
10 ENOG4108SJ1 MotA TolQ exbB proton channel 0.012011
11 ENOG4106N3A copper homeostasis protein cutc 0.011735
12 ENOG4105D6N CoA-transferase, subunit a 0.011549
13 ENOG4105CEM UPF0597 protein 0.011532
14 ENOG41067MG lrgb family 0.011418
15 ENOG4105CER acetyl-CoA carboxylase biotin carboxylase -0.011109
16 ENOG4108VJJ Nitroreductase -0.010895
17 ENOG4105CHY citrate lyase, alpha 0.010520
18 ENOG41076B7 NA 0.010499
19 ENOG4108M6Y methionine sulfoxide reductase A -0.010471
20 ENOG4108M2Y site-specific recombinase, phage integrase family 0.010449
21 ENOG4105D9Q decarboxylase (Beta subunit) 0.010327
22 ENOG4105ZR0 NA 0.010245
23 ENOG4105KWZ Uncharacterized conserved protein (DUF2149) 0.010242
24 ENOG4105DGA Diaminopimelate dehydrogenase 0.009998
25 ENOG4106KSD NA 0.009727
26 ENOG4105CQB FAD linked oxidase domain protein 0.009670
27 ENOG4108KG1 NA -0.009637
28 ENOG4105D1M ATP-dependent endonuclease of the OLD 0.009568
29 ENOG4108SX0 NA 0.009542
30 ENOG4105VVY Addiction module antitoxin, RelB DinJ family 0.009443
31 ENOG4106UAC NA 0.009431
32 ENOG4105PIX NA 0.009217
33 ENOG4105MN9 B3 4 domain protein -0.009212
34 ENOG4108IIH CoA-transferase subunit B 0.009211
35 ENOG4105CW3 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.009186
36 ENOG4105CK3 Lysine 2,3-aminomutase YodO family protein 0.009118
37 ENOG4106CPW NA 0.009063
38 ENOG4105GWS NA 0.009041
39 ENOG4105ZMU T5orf172 domain -0.008944
40 ENOG4105HFB acetyltransferase -0.008944
41 ENOG4105CZM Major Facilitator -0.008923
42 ENOG4105CGP Urocanate hydratase 0.008903
43 ENOG4105CH6 catalase 0.008863
44 ENOG4105DA0 Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity) -0.008819
45 ENOG4107UA6 flavin reductase domain protein 0.008809
46 ENOG4105DZB Electron transport complex 0.008745
47 ENOG4105C6Z Gluconate 0.008666
48 ENOG4108UYI beta-alanyl-CoA ammonia lyase 0.008650
49 ENOG4108Z7F N-acetyltransferase -0.008648
50 ENOG4105C8I hydrolase, family 38 0.008631
51 ENOG4107JQS NA -0.008580
52 ENOG4105PV1 biotin lipoyl attachment domaiN-containing protein 0.008579
53 ENOG4106QH1 NA 0.008578
54 ENOG4107I3M NA 0.008519
55 ENOG4107STF Involved in phosphonate degradation (By similarity) -0.008502
56 ENOG41077EP Pfam:DUF2174 -0.008444
57 ENOG4108KAZ Involved in phosphonate degradation (By similarity) -0.008417
58 ENOG4107RN2 Peptidase family S49 0.008415
59 ENOG4105NBR Pectinesterase 0.008393
60 ENOG4108V4B ThiJ pfpI -0.008389
61 ENOG4105X44 SMC domain protein -0.008377
62 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.008354
63 ENOG4108W2Y isochorismatase -0.008329
64 ENOG4105CGZ zinc metallopeptidase 0.008318
65 ENOG4105C0R drug resistance transporter emrb qaca subfamily -0.008308
66 ENOG4105K8R UPF0145 protein -0.008300
67 ENOG4106ACC NA 0.008299
68 ENOG4106YRZ NA -0.008283
69 ENOG4108IAB Phoh family 0.008259
70 ENOG4107RV5 Glycosyl hydrolase family 3 N-terminal domain protein -0.008246
71 ENOG4105DEG Vwa containing coxe family protein 0.004110
71 ENOG4105KKX ATPase associated with various cellular activities aaa_5 0.004110
72 ENOG41070HS NA -0.008219
73 ENOG4107U80 Thioredoxin family -0.008151
74 ENOG4105CVR type I restriction-modification system 0.008136
75 ENOG4105CDB Required for chromosome condensation and partitioning (By similarity) -0.008114
76 ENOG4107U79 DNA Methylase -0.008072
77 ENOG4106CA4 NA 0.008061
78 ENOG4105C84 Histidine ammonia-lyase 0.008059
79 ENOG4107V9B Eco57I restriction-modification methylase -0.008008
80 ENOG4105CCS Glutamate formiminotransferase 0.008006
81 ENOG4105C71 hydrolase family 65, central catalytic 0.008000
82 ENOG4105FFF abc transporter permease protein -0.007984
83 ENOG4105E9H Lytic Murein transglycosylase 0.007980
84 ENOG4108Z7W HD Domain -0.007979
85 ENOG4107TY6 Acylneuraminate cytidylyltransferase 0.007949
86 ENOG4105FKQ transcriptional regulator 0.007947
87 ENOG4105DCT glycerol dehydrogenase 0.007923
88 ENOG4108IMY Transcriptional regulator -0.007909
89 ENOG4107RB3 L-asparaginase 0.007895
90 ENOG4108KGY deoR family transcriptional regulator -0.007806
91 ENOG4105CVM Molybdenum cofactor synthesis domain protein -0.007801
92 ENOG4108BUH NA 0.007790
93 ENOG4105CSQ Nitroreductase -0.007756
94 ENOG4105WMR Protein CrcB homolog -0.007742
95 ENOG4105CYX Short-chain dehydrogenase reductase Sdr -0.007698
96 ENOG4107M0B NA 0.007651
97 ENOG4105D19 Role in flagellar biosynthesis (By similarity) 0.007631
98 ENOG4105VXN addiction module toxin, RelE StbE family -0.007628
99 ENOG4105RC2 conjugative transposon protein TraQ 0.007628
100 ENOG4105EQ5 D-Lysine 5,6-aminomutase alpha subunit 0.001904
100 ENOG4105FRY Dehydrogenase 0.001904
100 ENOG4107CHF 5,6-aminomutase beta subunit 0.001904
100 ENOG4108S6F NA 0.001904
101 ENOG41069WJ NA -0.007613
102 ENOG4105QGI NA -0.007588
103 ENOG4108R3E Dna-3-methyladenine glycosylase i 0.007572
104 ENOG4106PZ2 NA 0.007549
105 ENOG4105FBU hydrolase family 16 -0.007516
106 ENOG41082S2 lipolytic protein G-D-S-L family 0.007513
107 ENOG4105CWI transcriptional regulator 0.007489
108 ENOG4105DU0 nucleoside hydrolase 0.007466
109 ENOG4105NEF Nucleotidyl transferase of unknown function (DUF1814) -0.007457
110 ENOG4108JJ8 (ABC) transporter 0.007417
111 ENOG410833S tail length tape measure 0.007408
112 ENOG4105C2J ABC transporter 0.007382
113 ENOG4105DWW P-loop domain protein -0.007373
114 ENOG4107T5D Carbon starvation protein CstA 0.007368
115 ENOG410650M NA 0.007364
116 ENOG4105JXU Histidine kinase 0.007361
117 ENOG4105EE0 oxidoreductase -0.007342
118 ENOG4105DKT Transcriptional regulator 0.007336
119 ENOG4108Z5K methylglyoxal synthase 0.007334
120 ENOG4108HIX NA -0.007308
121 ENOG4107QNI mechanosensitive ion channel 0.007304
122 ENOG4105CCP Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC) -0.007297
123 ENOG4105EAU Plays a role in nitrite reduction (By similarity) 0.007267
124 ENOG4108DAR Divergent AAA domain protein -0.007250
125 ENOG4105C5A transporter 0.007234
126 ENOG4107MU6 NA 0.007221
127 ENOG4105C0N N-acetylglutamate semialdehyde dehydrogenase -0.007214
128 ENOG4108JJ9 ABC, transporter 0.007209
129 ENOG4108JKK conserved domain protein -0.007190
130 ENOG4106MY0 NA 0.007183
131 ENOG4107581 Glycosyl transferase (Group 1 -0.007175
132 ENOG4108IAJ Nad-dependent epimerase dehydratase -0.007148
133 ENOG4105D7J NA 0.007148
134 ENOG4105C28 cystathionine 0.007140
135 ENOG4105D6J arsenicaL-resistance protein 0.007138
136 ENOG4107YAU phenylacetic acid degradation protein 0.007108
137 ENOG4105C5T Phosphoribosyl pyrophosphate synthase -0.007104
138 ENOG4108V06 Glutathione peroxidase 0.007078
139 ENOG4107C2P NA 0.007077
140 ENOG4107SQ3 mannitol-1-phosphate 5-dehydrogenase 0.007073
141 ENOG4106M5N fibronectin type III domain protein 0.007056
142 ENOG4105CK6 Two component transcriptional regulator (Winged helix family -0.007050
143 ENOG4105C1G acyl-Coa dehydrogenase 0.007031
144 ENOG4106TGT NA 0.007027
145 ENOG4106FPP NA 0.007014
146 ENOG4106DVY NA -0.007012
147 ENOG4105EX2 Binding-protein-dependent transport systems, inner membrane component -0.006992
148 ENOG4106FV1 Transcriptional regulator 0.006987
149 ENOG4105ED7 Catalyzes the specific phosphorylation of 1,6-anhydro-N- acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling (By similarity) 0.006977
150 ENOG4107XX8 ABC transporter substrate-binding protein 0.006974
151 ENOG4107R2F nlpC P60 family protein -0.006963
152 ENOG4105K7V reductase -0.006960
153 ENOG4105RWP NA -0.006959
154 ENOG410689R PemK-like protein 0.006956
155 ENOG4107QX6 helicase -0.006953
156 ENOG4106YKZ NA 0.006950
157 ENOG4105C3K feS assembly ATPase SufC -0.006915
158 ENOG4108REF Sporulation integral membrane protein ytvi 0.006909
159 ENOG4106H4B NA -0.006905
160 ENOG4105F0U glutamate mutase, mutL 0.006900
161 ENOG4105C7H Helicase, RecD TraA family -0.006895
162 ENOG4107R2P Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.006884
163 ENOG41060EM NA 0.006878
164 ENOG4108R2Q Transcriptional regulator (AraC family) -0.006871
165 ENOG4107SP0 drug resistance transporter, EmrB QacA subfamily 0.006859
166 ENOG4105C01 Dihydroxy-acid dehydratase -0.006855
167 ENOG4105E44 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.006847
168 ENOG4108H1H hydrogenase) (Fe-only 0.006847
169 ENOG4108IQD Involved in the biosynthesis of D-alanyl-lipoteichoic acid (LTA). Catalyzes an ATP-dependent two-step reaction where it forms a high energy D-alanyl AMP intermediate and transfers the alanyl residues from AMP to Dcp (By similarity) -0.006843
170 ENOG4108Z0A Cupin 2, conserved barrel domain protein -0.006841
171 ENOG4107DHT NA -0.006828
172 ENOG4105K85 Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) in DNA. Repairs alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated (By similarity) -0.006825
173 ENOG4106HBE NA -0.006818
174 ENOG4105E05 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.006813
175 ENOG4108YSM NA 0.006803
176 ENOG4107UBS Transcriptional regulator 0.006802
177 ENOG4105ECQ AraC Family Transcriptional Regulator -0.006789
178 ENOG4105WBM Protein of unknown function (DUF1232) -0.006788
179 ENOG4108V3W Chemotaxis protein, CheW 0.006786
180 ENOG4107HY1 Dehydrogenase 0.006786
181 ENOG4105C5R Aminotransferase 0.006782
182 ENOG4105EW9 transcriptional regulator AsnC family -0.006779
183 ENOG4107TCD 2',3'-cyclic-nucleotide 2'-phosphodiesterase EC 3.1.4.16 0.006779
184 ENOG4105EHA HipA domain protein -0.006777
185 ENOG4105XGS Covalent carrier of the coenzyme of citrate lyase (By similarity) 0.006764
186 ENOG4108PAV RagB SusD domain protein 0.006764
187 ENOG4105KFT NA 0.006752
188 ENOG4107WFU Glutamate mutase subunit sigma 0.006752
189 ENOG41062DB NA 0.006741
190 ENOG4108M9E kinase (PfkB family -0.006739
191 ENOG4107RW8 Mate efflux family protein 0.006738
192 ENOG4105F8D glycoside hydrolase family 4 0.006722
193 ENOG41090EA NA 0.006716
194 ENOG41078E6 NA 0.006714
195 ENOG4107QWM hydrolase family, 3 0.006707
196 ENOG4106P60 NA 0.006702
197 ENOG4105VMP Transcriptional regulator 0.006692
198 ENOG4107S7X sodium dicarboxylate symporter 0.006691
199 ENOG4105F1F Uncharacterized protein conserved in bacteria (DUF2130) -0.006688
200 ENOG41088BK DNA mismatch repair protein muts 0.006684
201 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.006667
202 ENOG4108INR phosphoesterase PA-phosphatase related protein 0.006665
203 ENOG4107R7P Potassium proton antiporter 0.006665
204 ENOG410683M YopX protein -0.006643
205 ENOG4105CD5 CoA-binding domain protein 0.006642
206 ENOG4105DWK Membrane 0.006640
207 ENOG4105VS8 Flagellar biosynthetic protein fliq 0.006615
208 ENOG4106J3Y transposon protein 0.006593
209 ENOG4108TBP Cytochrome c biogenesis protein 0.006588
210 ENOG4106TQC conserved domain protein -0.006586
211 ENOG4105EF1 ribulokinase 0.006584
212 ENOG4105VAW lrga family 0.006579
213 ENOG4105CI0 Citrate lyase 0.006578
214 ENOG4106U0Q NA -0.006565
215 ENOG4106MX1 Homologues of TraJ from Bacteroides conjugative transposon 0.006558
216 ENOG4105CJS Phosphopantothenoylcysteine decarboxylase -0.006557
217 ENOG4106104 NA -0.006541
218 ENOG41066BJ NA 0.006523
219 ENOG4105D7B Flagellar biosynthesis protein flha 0.006512
220 ENOG4106KDT NA -0.006508
221 ENOG4108MR7 Arylsulfotransferase 0.006507
222 ENOG4108U8Y Vitamin K epoxide reductase -0.006506
223 ENOG4105CG6 trap dicarboxylate transporter dctm subunit 0.006504
224 ENOG4105KT5 UmuD protein -0.006504
225 ENOG410839M 5-formyltetrahydrofolate cyclo-ligase 0.006491
226 ENOG4106FJK TonB family domain protein 0.006487
227 ENOG4106G3F Orthopoxvirus protein of unknown function (DUF830) 0.006481
228 ENOG4105EIZ Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) 0.006481
229 ENOG4105KTH gatB Yqey -0.006480
230 ENOG4106K9S NA 0.006465
231 ENOG4105C7E Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA) (By similarity) 0.006455
232 ENOG4108CK8 Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division (By similarity) 0.006437
233 ENOG4105G9B Transcriptional regulator 0.006415
234 ENOG4105CYC Transferase 0.006410
235 ENOG4108R3F Nudix family -0.006405
236 ENOG41085JV Type II DNA modification methyltransferase 0.006398
237 ENOG4105D6A Electron transport complex 0.006391
238 ENOG4105KI2 Urea amidohydrolase subunit beta 0.006389
239 ENOG4105WBZ acetyltransferase, (GNAT) family -0.006381
240 ENOG4105DPC Ragb susd domain-containing protein -0.006374
241 ENOG4105CEP NADH dehydrogenase -0.006357
242 ENOG4105CHT Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity) -0.006355
243 ENOG4107QMH DNA methylase -0.006340
244 ENOG4108PFF ethanolamine utilization cobalamin adenosyltransferase 0.006334
245 ENOG4106IVS NA 0.006333
246 ENOG4105HQ8 Uncharacterized protein conserved in bacteria (DUF2186) -0.006330