Metamenu

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 COG0270 DNA (cytosine-5-)-methyltransferase activity 0.029018
2 COG1533 DNA photolyase activity 0.024818
3 COG3568 Endonuclease Exonuclease Phosphatase 0.024758
4 COG1432 Conserved Protein 0.024721
5 COG1328 CTP reductase activity 0.024236
6 COG2184 nucleotidyltransferase activity -0.023966
7 COG3216 Uncharacterized protein conserved in bacteria (DUF2062) 0.023326
8 COG1922 lipopolysaccharide N-acetylmannosaminouronosyltransferase activity -0.023285
9 COG0368 Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate -0.023072
10 COG3886 PLD-like domain -0.022992
11 COG1744 ABC transporter substrate-binding protein PnrA-like 0.022932
12 COG3412 dihydroxyacetone kinase, phosphotransfer subunit 0.022282
13 COG1722 exodeoxyribonuclease VII activity -0.022049
14 COG3760 aminoacyl-tRNA metabolism involved in translational fidelity 0.021873
15 COG3323 Protein of unknown function (DUF1653) -0.021585
16 COG0815 Transfers the fatty acyl group on membrane lipoproteins 0.021266
17 COG2376 Dihydroxyacetone kinase 0.021205
18 COG4091 Methyl-accepting Chemotaxis protein 0.021058
19 COG2230 cyclopropane-fatty-acyl-phospholipid synthase -0.020944
20 COG1714 RDD family 0.020772
21 COG0381 UDP-N-acetylglucosamine 2-epimerase activity -0.020664
22 COG1573 uracil-dna glycosylase 0.020236
23 COG1079 Belongs to the binding-protein-dependent transport system permease family 0.020197
24 COG3550 peptidyl-serine autophosphorylation 0.019966
25 COG1652 LysM domain 0.019878
26 COG3973 AAA domain -0.019096
27 COG2038 nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity -0.018813
28 COG2367 Beta-lactamase -0.018672
29 COG2087 Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate -0.018630
30 COG4603 Belongs to the binding-protein-dependent transport system permease family 0.018551
31 COG0819 Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway -0.018482
32 COG3404 Formiminotransferase-cyclodeaminase -0.018432
33 COG1661 DNA-binding protein with PD1-like DNA-binding motif 0.018352
34 COG0392 lysyltransferase activity -0.018344
35 COG1279 arginine transmembrane transporter activity -0.018247
36 COG2059 Chromate 0.018071
37 COG1894 NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain 0.017997
38 COG1905 PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit 0.017997
39 COG2026 Addiction module toxin, RelE StbE family -0.017969
40 COG1493 Catalyzes the ATP- as well as the pyrophosphate- dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P- Ser-HPr). The two antagonistic activities of HprK P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion 0.017927
41 COG3910 aaa ATPase 0.017849
42 COG3041 Addiction module toxin RelE StbE family -0.017837
43 COG1509 lysine 2,3-aminomutase activity -0.017827
44 COG1914 H( )-stimulated, divalent metal cation uptake system -0.017563
45 COG4942 peptidase 0.017288
46 COG4713 Psort location CytoplasmicMembrane, score -0.016923
47 COG4955 Helix-turn-helix domain -0.016602
48 COG3223 Belongs to the PsiE family -0.016581
49 COG2357 RelA SpoT domain protein -0.016518
50 COG3238 Protein conserved in bacteria -0.016480
51 COG1438 arginine binding -0.016476
52 COG3467 pyridoxamine 5'-phosphate -0.016467
53 COG2327 Polysaccharide pyruvyl transferase -0.016314
54 COG3851 Histidine kinase 0.016211
55 COG2993 Cytochrome C oxidase, mono-heme subunit/FixO 0.016209
56 COG1897 L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine -0.016199
57 316Z5 Universal stress protein family -0.016119
58 COG1858 cytochrome C peroxidase 0.015976
59 COG0348 domain, Protein 0.015974
60 COG1277 ABC-type transport system involved in multi-copper enzyme maturation permease component 0.015935
61 COG2223 nitrite transmembrane transporter activity -0.015908
62 COG3275 phosphorelay sensor kinase activity -0.015894
63 COG1797 cobyrinic acid a,c-diamide synthase activity -0.015820
64 COG1904 glucuronate isomerase -0.015819
65 COG1297 OPT oligopeptide transporter protein 0.015816
66 COG3480 Lon protease (S16) C-terminal proteolytic domain -0.015783
67 COG1194 a g-specific adenine glycosylase -0.015751
68 COG1253 flavin adenine dinucleotide binding -0.015727
69 33GD9 0.015664
70 COG0406 alpha-ribazole phosphatase activity -0.015652
71 COG3619 membrane -0.015647
72 COG2020 methyltransferase activity 0.015620
73 COG4302 ethanolamine ammonia-lyase activity -0.015609
74 COG4303 Ethanolamine ammonia lyase large subunit -0.015609
75 COG4653 Phage capsid family 0.015604
76 COG0144 Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA 0.015576
77 COG0390 transport system, permease component -0.015563
78 COG0399 UDP-4-amino-4-deoxy-L-arabinose aminotransferase 0.015526
79 COG0300 oxidoreductase activity 0.015393
80 32AVZ helix_turn_helix multiple antibiotic resistance protein 0.015353
81 341CM Bacterial regulatory proteins, tetR family -0.015266
82 COG0756 dUTP diphosphatase activity -0.015241
83 COG3201 nicotinamide mononucleotide transporter -0.015186
84 342R0 Trypsin-like peptidase domain 0.015132
85 COG4757 Alpha beta hydrolase 0.015104
86 COG4506 Protein conserved in bacteria -0.015092
87 COG3192 ethanolamine utilization protein -0.015081
88 COG1647 Serine aminopeptidase, S33 0.015010
89 COG0695 Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins 0.014998
90 COG3577 Aspartyl protease 0.014878
91 COG2826 transposase and inactivated derivatives, IS30 family -0.014813
92 COG1412 self proteolysis 0.014808
93 COG0400 carboxylic ester hydrolase activity -0.014756
94 COG2210 Belongs to the sulfur carrier protein TusA family -0.014713
95 COG0235 Class ii aldolase 0.014694
96 COG0783 Belongs to the Dps family -0.014688
97 COG2182 Extracellular solute-binding protein 0.014640
98 COG3856 small basic protein -0.014603
99 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.014598
100 COG2049 5-oxoprolinase (ATP-hydrolyzing) activity -0.014597
101 COG5522 Integral membrane protein (intg_mem_TP0381) 0.014593
102 COG0394 Belongs to the low molecular weight phosphotyrosine protein phosphatase family -0.014588
103 COG0833 amino acid -0.014557
104 COG0038 chloride channel 0.014508
105 2ZSRR Psort location Cytoplasmic, score 8.87 -0.014505
106 COG0762 integral membrane protein -0.014489
107 COG3622 Belongs to the hyi family 0.014422
108 COG2985 domain, Protein 0.014411
109 COG1956 GAF domain-containing protein -0.014409
110 COG4191 Histidine kinase 0.014396
111 3172B Bacterial PH domain -0.014362
112 COG1633 Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis. Mediates the cyclase reaction, which results in the formation of divinylprotochlorophyllide (Pchlide) characteristic of all chlorophylls from magnesium-protoporphyrin IX 13-monomethyl ester (MgPMME) 0.014358
113 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding 0.014330
114 COG3681 Belongs to the UPF0597 family -0.014299
115 COG1171 Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA 0.014295
116 COG2065 Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant -0.014280
117 COG1139 Iron-sulfur cluster binding protein 0.014277
118 COG2893 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.014199
119 COG1687 branched-chain amino acid 0.014166
120 COG0321 lipoyl(octanoyl) transferase activity 0.014073
121 COG1492 cobalamin metabolic process -0.014057
122 COG4781 glycerophosphoryl diester phosphodiesterase 0.014050
123 COG1154 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) -0.014017
124 COG3634 alkyl hydroperoxide reductase activity -0.013967
125 COG0071 Belongs to the small heat shock protein (HSP20) family -0.013931
126 COG2978 secondary active p-aminobenzoyl-glutamate transmembrane transporter activity -0.013909
127 COG1518 maintenance of DNA repeat elements -0.013873
128 COG0147 Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine- binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia -0.013854
129 COG0676 glucose-6-phosphate 1-epimerase activity 0.013854
130 COG3295 Protein conserved in bacteria 0.013840
131 COG0246 Mannitol dehydrogenase 0.013783
132 COG1564 THIamine pyrophosphokinase -0.013756
133 COG3664 PFAM glycoside hydrolase family 39 0.013737
134 COG2314 TM2 domain 0.013732
135 COG1853 conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family -0.013717
136 COG4185 zeta toxin -0.013706
137 COG0852 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 0.013699
138 COG0586 Pfam SNARE associated Golgi protein -0.013697
139 COG0595 An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay -0.013682
140 COG3177 Filamentation induced by cAMP protein fic -0.013647
141 COG0128 3-phosphoshikimate 1-carboxyvinyltransferase activity -0.013634
142 COG3158 transport of potassium into the cell -0.013604
143 COG1306 Putative glycosyl hydrolase domain 0.013596
144 COG3475 LICD family -0.013517
145 COG1180 Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine 0.013485
146 COG0414 Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate 0.013482
147 COG1070 Carbohydrate kinase 0.013480
148 COG0294 Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives -0.013472
149 COG1206 Catalyzes the folate-dependent formation of 5-methyl- uridine at position 54 (M-5-U54) in all tRNAs -0.013436
150 COG3879 Bacterial protein of unknown function (DUF881) -0.013415
151 COG3956 TIGRFAM MazG family protein -0.013359
152 COG3176 hemolysin 0.013357
153 COG3976 FMN-binding domain protein -0.013351
154 COG2707 UPF0756 membrane protein -0.013338
155 COG2936 dipeptidyl-peptidase activity -0.013328
156 COG1598 PFAM Uncharacterised protein family UPF0150 -0.013327
157 COG3623 hexulose-6-phosphate isomerase 0.013320
158 COG1975 Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family 0.013275
159 COG1496 oxidoreductase activity -0.013273
160 COG0163 prenyltransferase activity 0.013272
161 COG0612 Peptidase, M16 0.013271
162 33S0I Parallel beta-helix repeats 0.013225
163 COG3162 membrane -0.013218
164 COG2962 Rard protein -0.013184
165 COG3745 Flp pilus assembly protein CpaB 0.013176
166 COG0388 Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source -0.013173
167 COG0302 gtp cyclohydrolase -0.013168
168 COG2032 superoxide dismutase activity -0.013141
169 COG1611 Belongs to the LOG family -0.013125
170 COG4671 Glycosyl Transferase 0.013109
171 COG0478 Catalyzes the ATP-dependent phosphorylation of the 3- deoxy-D-manno-octulosonic acid (Kdo) residue in Kdo-lipid IV(A) at the 4-OH position 0.013102
172 COG0605 Destroys radicals which are normally produced within the cells and which are toxic to biological systems 0.013084
173 COG1312 Catalyzes the dehydration of D-mannonate -0.013079
174 COG3448 diguanylate cyclase activity 0.013076
175 COG0384 phenazine biosynthesis protein PhzF -0.013071
176 COG0433 COG0433 Predicted ATPase 0.013068
177 COG0281 malic enzyme 0.013044
178 COG2243 precorrin-2 c20-methyltransferase -0.013028
179 COG2875 Belongs to the precorrin methyltransferase family -0.013028
180 33PN1 Protein of unknown function (DUF1460) -0.013023
181 COG1457 Belongs to the purine-cytosine permease (2.A.39) family 0.013015
182 COG1668 transmembrane transport 0.013011
183 32SQ3 GlcNAc-PI de-N-acetylase 0.013001
184 COG5473 translation initiation factor activity 0.012984
185 COG3940 Belongs to the glycosyl hydrolase 43 family -0.012976
186 COG1034 ATP synthesis coupled electron transport 0.012972
187 COG3345 alpha-galactosidase 0.012967
188 COG1696 Membrane protein involved in D-alanine export -0.012957
189 COG2966 Psort location CytoplasmicMembrane, score 0.012947
190 COG4716 Myosin-crossreactive antigen -0.012942
191 COG2234 aminopeptidase activity -0.012940
192 COG3942 CHAP domain -0.012914
193 COG1780 Probably involved in ribonucleotide reductase function -0.012912
194 COG3877 Protein conserved in bacteria 0.012899
195 COG2241 protein methyltransferase activity -0.012836
196 COG2220 Zn-dependent hydrolases of the beta-lactamase fold 0.012831
197 COG4917 ethanolamine utilization protein -0.012782
198 COG1773 rubredoxin 0.012752
199 COG0499 May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine 0.012747
200 COG3197 Cytochrome oxidase maturation protein 0.012743
201 COG3278 Belongs to the heme-copper respiratory oxidase family 0.012743
202 COG0716 FMN binding -0.012722
203 COG4118 positive regulation of growth 0.012712
204 COG2937 Belongs to the GPAT DAPAT family -0.012653
205 COG1825 This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance 0.012650
206 COG2188 Transcriptional regulator 0.012644
207 COG3247 response to pH -0.012639
208 COG3272 Protein of unknown function (DUF1722) -0.012613
209 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity 0.012597
210 COG0030 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity -0.012580
211 COG4536 flavin adenine dinucleotide binding 0.012534
212 COG5542 integral membrane protein 0.012526
213 COG4198 Conserved Protein -0.012493
214 COG3865 3-Demethylubiquinone-9 3-methyltransferase 0.012492
215 COG0174 glutamine synthetase -0.012482
216 COG4623 carbon-oxygen lyase activity, acting on polysaccharides -0.012463
217 COG3450 Protein of unknown function (DUF861) 0.012453
218 COG2179 HAD superfamily (subfamily IIIA) phosphatase, TIGR01668 -0.012446
219 33F46 0.012439
220 COG5426 von Willebrand factor, type A 0.012437
221 2Z8ZV ABC-2 family transporter protein -0.012413
222 COG3689 TIGRFAM TIGR03943 family protein -0.012412
223 COG0043 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity 0.012396
224 COG5414 chromosome segregation 0.012346
225 COG0426 domain, Protein -0.012330
226 COG1877 trehalose-phosphatase activity -0.012311
227 COG2337 Toxic component of a toxin-antitoxin (TA) module 0.012291
228 COG0631 protein serine/threonine phosphatase activity -0.012282
229 COG2334 A protein kinase that phosphorylates Ser and Thr residues. Probably acts to suppress the effects of stress linked to accumulation of reactive oxygen species. Probably involved in the extracytoplasmic stress response 0.012266
230 COG0733 neurotransmitter:sodium symporter activity 0.012243
231 COG0386 Belongs to the glutathione peroxidase family -0.012228
232 COG1228 amidohydrolase -0.012191
233 COG2802 ATP-dependent protease La (LON) substrate-binding domain 0.012180
234 COG3672 Periplasmic Protein 0.012180
235 COG4318 ParB-like nuclease 0.012180
236 COG4764 Protein conserved in bacteria 0.012180
237 COG0543 2 iron, 2 sulfur cluster binding -0.012160
238 COG0801 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase -0.012147
239 COG2268 Band 7 protein -0.012147
240 30J72 Pathogenicity locus 0.012097
241 32Y3S ABC-2 family transporter protein 0.012096
242 COG4143 (ABC) transporter 0.012091
243 COG0269 3-dehydro-L-gulonate-6-phosphate decarboxylase activity 0.012062
244 COG0171 NAD+ synthase (glutamine-hydrolyzing) activity -0.012037
245 COG3458 cephalosporin-C deacetylase activity 0.012026
246 COG4565 transcriptional regulatory protein -0.012017
247 COG4822 anaerobic cobalamin biosynthetic process -0.011994
248 COG1770 oligopeptidase -0.011988
249 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid 0.011978
250 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.011927