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 ENOG4105C94 Transporter 0.012118
2 ENOG4105KZE Death-On-Curing Family -0.010563
3 ENOG4107XEC aspartate racemase 0.010411
4 ENOG4105E4N tonB-dependent Receptor 0.010248
5 ENOG41067QG Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides (By similarity) -0.010238
6 ENOG4108K88 Membrane -0.010005
7 ENOG4105QB7 gCN5-related N-acetyltransferase 0.009956
8 ENOG4105IGJ Zn-dependent Hydrolase of the beta-lactamase fold protein -0.009948
9 ENOG4105E98 transcriptional regulator DeoR family -0.009898
10 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) -0.009686
11 ENOG4105CI1 PTS System -0.009570
12 ENOG4108IA5 tonB-dependent Receptor 0.009514
13 ENOG4105CE4 GlcNAc 6-P deacetylase -0.009477
14 ENOG4107QQN Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) -0.009430
15 ENOG4105C0V Provides the sole de novo source of dTMP for DNA biosynthesis (By similarity) -0.009309
16 ENOG4108ZHB oxidoreductase 0.009296
17 ENOG41087GE Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate (By similarity) 0.009263
18 ENOG4105EFR glucose-1-phosphate adenylyltransferase, glgd subunit -0.009137
19 ENOG4105WQ5 TonB family 0.009132
20 ENOG4107VS1 KR domain -0.009009
21 ENOG4105CNB Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans (By similarity) -0.008996
22 ENOG4106CVF DNA replication protein 0.008904
23 ENOG4107P0H HTH_XRE 0.008889
24 ENOG4108RCY Nadph-dependent fmn reductase -0.008862
25 ENOG4105EE0 oxidoreductase -0.008770
26 ENOG4105CBF Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction (By similarity) 0.008695
27 ENOG4105D2N Aldolase -0.008604
28 ENOG4105VNF NA -0.008591
29 ENOG4105D64 Mechanosensitive ion channel -0.008544
30 ENOG4105D4F Synthesizes selenophosphate from selenide and ATP (By similarity) 0.008528
31 ENOG4106UX7 integral membrane protein 0.008525
32 ENOG4105BZM domain protein -0.008504
33 ENOG4108R5D Transcriptional regulator, TetR family 0.008447
34 ENOG4105CXW Synthesizes alpha-1,4-glucan chains using ADP-glucose (By similarity) -0.008322
35 ENOG4105ENN converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity) -0.008256
36 ENOG4105D15 transcriptional regulator protein-like protein 0.008247
37 ENOG41086HC OstA-like protein 0.008199
38 ENOG4107SPW HsdM N-terminal domain 0.008151
39 ENOG4105DKQ ROK family -0.008147
40 ENOG4107QRM domain protein -0.008144
41 ENOG4107VXF methyltransferase -0.008127
42 ENOG4105MXV Polyketide cyclase / dehydrase and lipid transport 0.008082
43 ENOG4108EQX TonB family 0.008068
44 ENOG4105CKT filamentous hemagglutinin -0.008053
45 ENOG4107EV7 Domain-Containing protein -0.008034
46 ENOG4108KE5 Membrane 0.008008
47 ENOG4107TKC )-transporter -0.007999
48 ENOG4105WKZ 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). Functions as a ssRNA-specific endoribonuclease (By similarity) 0.007989
49 ENOG4107TFP succinylglutamate desuccinylase aspartoacylase 0.007988
50 ENOG4107QQG Dehydrogenase 0.007962
51 ENOG4105HMI Membrane 0.007937
52 ENOG41089BK Glutamine amido-transferase -0.007934
53 ENOG4105CEP NADH dehydrogenase -0.007930
54 ENOG4105HYQ NA -0.007907
55 ENOG4105ITI NA -0.007901
56 ENOG41066AA NA 0.007883
57 ENOG4105D5K Hemolysin activator protein -0.007825
58 ENOG4108ZMD Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) 0.007789
59 ENOG4108Z0Z intracellular protease Pfpi family -0.007716
60 ENOG4108NF7 phage-type endonuclease 0.007677
61 ENOG4105GA3 phage protein -0.007621
62 ENOG4105M18 -acetyltransferase 0.007568
63 ENOG4107T8J thymidine kinase 0.007522
64 ENOG4107S4Y M20 DapE family protein YgeY -0.007480
65 ENOG4105MN5 HAD-superfamily hydrolase subfamily IA variant 3 -0.007460
66 ENOG4107SFZ crispr-associated protein 0.007453
67 ENOG4105D41 biosynthesis protein thiH 0.007451
68 ENOG410908R Methenyltetrahydrofolate cyclohydrolase 0.007449
69 ENOG4105C5N The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination -0.007439
70 ENOG410878U Protein of unknown function (DUF805) -0.007386
71 ENOG4107Y03 Nitroreductase 0.007372
72 ENOG4107R2A decarboxylase -0.007362
73 ENOG4108K3K sigma-70, region 4 0.007353
74 ENOG4107QW4 alcohol dehydrogenase 0.007324
75 ENOG41064IQ NA 0.007308
76 ENOG4105CF9 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation dephosphorylation (By similarity) 0.007298
77 ENOG4108JKD thiamine biosynthesis protein this 0.007286
78 ENOG4108Y76 addiction module toxin, RelE StbE family 0.007262
79 ENOG4106G39 TonB family -0.007257
80 ENOG4105CHR reductase 0.007223
81 ENOG4105WXW Antirepressor 0.007154
82 ENOG4105DKJ Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate (By similarity) -0.007140
83 ENOG4108HHA Transketolase -0.007135
84 ENOG4107R09 zinc metalloprotease 0.007113
85 ENOG4107EEK Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide (By similarity) 0.007111
86 ENOG4107RW8 Mate efflux family protein 0.007097
87 ENOG4105KII Roadblock lc7 family protein 0.001180
87 ENOG4105SFR NA 0.001180
87 ENOG41062AG NA 0.001180
87 ENOG4106BCM NA 0.001180
87 ENOG4107NUR NA 0.001180
87 ENOG4108EJ4 Histidine kinase 0.001180
88 ENOG4106X27 NA 0.007078
89 ENOG4106QDD NA 0.007078
90 ENOG4107Y5R fatty acid desaturase 0.007078
91 ENOG4106IPP NA 0.007078
92 ENOG41086Z6 DivIVA protein 0.007078
93 ENOG4105GC9 Xylose isomerase domain protein TIM barrel 0.007078
94 ENOG41075T7 Spore coat associated protein JA (CotJA) 0.007078
95 ENOG4106N2A TonB-dependent receptor Plug 0.007078
96 ENOG41067QU NA 0.007078
97 ENOG4107WPE MA 0.007078
98 ENOG4107ZBX NA 0.007078
99 ENOG4106D74 NA 0.007078
100 ENOG4108QHC Crispr-associated ramp protein 0.007078
101 ENOG4105TNN Biopolymer transport protein exbD tolR 0.007078
102 ENOG4105JEP uroporphyrinogen iii synthase hem4 0.007077
103 ENOG4105C8U phosphate abc transporter 0.007065
104 ENOG410677E NA 0.007065
105 ENOG41070GX Possible hemagglutinin (DUF637) -0.007053
106 ENOG4108ZWD selenium metabolism protein yedf 0.007053
107 ENOG4105W61 NA 0.007037
108 ENOG4105YNV CRISPR-associated protein cas6 0.007036
109 ENOG4105C4J Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits (By similarity) -0.007030
110 ENOG4105J80 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex (By similarity) -0.007030
111 ENOG4107ZU8 PTS System -0.007030
112 ENOG4105GT6 DNA polymerase -0.007024
113 ENOG41082FC Fimbrial assembly family protein 0.007012
114 ENOG4105H2V Virulence-associated protein e -0.007010
115 ENOG4105D0S secretion protein (HlyD 0.006996
116 ENOG4105F1A Pyruvate formate-lyase -0.006982
117 ENOG4108QDY Endonuclease Exonuclease phosphatase 0.006969
118 ENOG410905Q NA 0.006945
119 ENOG4108845 Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides (By similarity) 0.006927
120 ENOG4108P5J Membrane 0.006921
121 ENOG4105CV8 reductase -0.006917
122 ENOG4105VXX VRR-NUC domain protein -0.006911
123 ENOG4107EE0 NA 0.006908
124 ENOG4108MYT crispr-associated protein 0.006896
125 ENOG4108M7W NA 0.003448
125 ENOG4108N8P Crispr-associated ramp protein 0.003448
126 ENOG4108F0A ErfK ybiS ycfS ynhG family 0.006896
127 ENOG4107VAQ metallophosphoesterase 0.006891
128 ENOG4105BZN citrate synthase -0.006891
129 ENOG4105GH4 LemA family -0.006874
130 ENOG4105C7F AcnD-accessory protein PrpF 0.006870
131 ENOG4107JEM NA 0.006854
132 ENOG4106758 NA 0.006840
133 ENOG4108ZN0 Chromate transport protein 0.006822
134 ENOG4106036 Protein of unknown function (DUF2953) 0.006820
135 ENOG4105EH4 helicase 0.006801
136 ENOG4107UDJ Inherit from COG: helicase 0.006773
137 ENOG4107QQI Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity) -0.006768
138 ENOG410814C multidrug resistance protein -0.006750
139 ENOG4107STB Periplasmic binding protein 0.006749
140 ENOG41085NV Membrane -0.006725
141 ENOG4108CH9 N-6 DNA Methylase -0.006715
142 ENOG4108UEI NA 0.006706
143 ENOG4108RAS NA 0.006701
144 ENOG4105EYH Exonuclease -0.006701
145 ENOG4108JPX Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor (By similarity) 0.006700
146 ENOG4107RAW 3-carboxy-cis-cis-muconate cycloisomerase 0.006697
147 ENOG4107R4E Membrane 0.006648
148 ENOG4108Z4T Peptidase M50 0.006643
149 ENOG4105CV1 Transketolase (EC 2.2.1.1) 0.006629
150 ENOG4107XFU Chromate transport protein 0.006618
151 ENOG4108E0S reductase 0.006603
152 ENOG4105C7Q Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity) -0.006591
153 ENOG4105RV9 Transcriptional regulator 0.006576
154 ENOG4105WCM NA 0.006573
155 ENOG4108I6V XRE family Transcriptional regulator 0.006563
156 ENOG4105VDH Dihydroxyacetone kinase -0.006560
157 ENOG4105DM4 PTS System -0.006541
158 ENOG41068W6 Capsular polysaccharide biosynthesis protein -0.006536
159 ENOG410642B Protein of unknown function (DUF805) 0.006531
160 ENOG4105DDZ Methyltransferase required for the conversion of demethylmenaquinone (DMKH2) to menaquinone (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) (By similarity) 0.006527
161 ENOG4107QZB decarboxylase 0.006523
162 ENOG4105ENJ RND efflux system, outer membrane lipoprotein 0.006494
163 ENOG4105CZC PTS system ascorbate-specific transporter subunit IIC -0.006485
164 ENOG4105DWY Agmatine deiminase 0.006484
165 ENOG4106IIY NA 0.006480
166 ENOG4105VEC DNA binding domain protein, excisionase family 0.006479
167 ENOG4108QY0 Membrane -0.006465
168 ENOG4107HQM Transposase, Mutator family -0.006464
169 ENOG4107XK1 Protein of unknown function (DUF421) 0.006460
170 ENOG4107ZNW DNA protecting protein DprA 0.006459
171 ENOG4108TKT Luciferase-like monooxygenase 0.006459
172 ENOG4105CDG Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit (By similarity) -0.006455
173 ENOG4107RA0 type I restriction modification 0.006452
174 ENOG4105D7Q type ii secretion system 0.006449
175 ENOG41063JJ Phage derived protein Gp49-like (DUF891) -0.006448
176 ENOG4106FUX Inherit from NOG: transposase -0.006444
177 ENOG4108YY9 U mismatch-specific DNA glycosylase 0.006444
178 ENOG4107S0N DJ-1 family 0.006429
179 ENOG4107KVK NA -0.006427
180 ENOG4105EN2 IstB domain-containing protein ATP-binding protein -0.006425
181 ENOG4105F1K Glutamine amidotransferase -0.006414
182 ENOG4109051 YadA domain protein 0.006410
183 ENOG4105PAC Elongation factor Tu GTP binding domain 0.006410
184 ENOG4105C4B ABC transporter, permease 0.006404
185 ENOG4106X1X NA -0.006385
186 ENOG410859T Inherit from COG: Thioredoxin -0.006385
187 ENOG41060U7 NA -0.006385
188 ENOG41068F2 Conserved hypothetical, protein -0.006385
189 ENOG4106KJE Pfam:HIM -0.006385
190 ENOG4108IMM HTH_XRE -0.006385
191 ENOG41075SE NA -0.006385
192 ENOG4106XVW NA -0.006385
193 ENOG4107PQW transporter major facilitator family protein -0.006385
194 ENOG4107RW9 nh(3)-dependent nad( ) synthetase 0.006383
195 ENOG4108QF3 pyruvate flavodoxin ferredoxin oxidoreductase 0.006374
196 ENOG4108R96 Methyltransferase, YaeB family -0.006355
197 ENOG4105F4F gtp-binding protein 0.006354
198 ENOG41066YZ NA 0.006342
199 ENOG4107TPK Base excision DNA repair protein, HhH-GPD family 0.006311
200 ENOG4105DG6 mannose-6-phosphate isomerase -0.006307
201 ENOG4105EMU Dehydrogenase 0.006295
202 ENOG41076HS cation diffusion facilitator family transporter 0.006274
203 ENOG4107QW8 radical SAM domain protein 0.006272
204 ENOG4105D1Q UPF0246 protein -0.006256
205 ENOG4107TGU Thiamine biosynthesis protein ThiF 0.006238
206 ENOG4108JYN Transketolase -0.006231
207 ENOG4107SYF amidohydrolase 0.006230
208 ENOG4108X76 ATP binding protein -0.006229
209 ENOG41061NH Transcriptional regulator 0.006226
210 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) -0.006224
211 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) 0.006216
212 ENOG4105EFF NLP P60 protein 0.006212
213 ENOG4108I0Z Aconitate hydratase -0.006190
214 ENOG4105CKA Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion (By similarity) -0.006182
215 ENOG4105C1Y Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity) 0.006180
216 ENOG4108YYV Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity) -0.006177
217 ENOG4108JJA ABC, transporter 0.006169
218 ENOG4106KNT transcriptional regulator -0.006156
219 ENOG4107WRT Phage-associated protein -0.006131
220 ENOG4108VYD Bacterial mobilisation protein (MobC) 0.006125
221 ENOG4105CSD Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) (By similarity) 0.006123
222 ENOG4105EHG Permease protein 0.006118
223 ENOG4105CAG UPF0210 protein -0.006108
224 ENOG4105STC NA -0.006106
225 ENOG4105D8C Channel that permits osmotically driven movement of water in both directions. It is involved in the osmoregulation and in the maintenance of cell turgor during volume expansion in rapidly growing cells. It mediates rapid entry or exit of water in response to abrupt changes in osmolarity (By similarity) -0.006083
226 ENOG4108PI2 O-Methyltransferase 0.006083
227 ENOG4105FKQ transcriptional regulator -0.006065
228 ENOG4108ZIW QueT transporter 0.006054
229 ENOG4105CTJ Metal Dependent Phosphohydrolase 0.006040
230 ENOG4105DQB NA -0.003019
230 ENOG4105PGF domain containing) protein -0.003019
231 ENOG4107RTW Restriction modification system DNA specificity domain protein 0.006008
232 ENOG4105HJS metallophosphoesterase -0.006000
233 ENOG4105MKX n-acetylmuramoyl-l-alanine amidase 0.005990
234 ENOG4105ETZ PTS System -0.005988
235 ENOG4107XE3 adenine phosphoribosyltransferase -0.005981
236 ENOG4105HJX Biotin- acetyl-CoA-carboxylase ligase -0.005966
237 ENOG4105F59 Methylates ribosomal protein L11 (By similarity) 0.005949
238 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase -0.005945
239 ENOG4105CB8 Multifunctional enzyme that catalyzes the SAM-dependent methylation of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 and then position C-12 or C-18 to form trimethylpyrrocorphin 2. It also catalyzes the conversion of precorrin-2 into siroheme. This reaction consists of the NAD- dependent oxidation of precorrin-2 into sirohydrochlorin and its subsequent ferrochelation into siroheme (By similarity) -0.005936
240 ENOG4105C6I Resolvase 0.005936
241 ENOG4105D3A purine nucleoside phosphorylase DeoD-type -0.005936
242 ENOG4105JHY Membrane 0.005913
243 ENOG41067VY 50S ribosomal protein L32 -0.005894