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 COG2129 metallophosphoesterase -0.032979
2 COG2110 phosphatase homologous to the C-terminal domain of histone macroH2A1 0.032226
3 COG1762 phosphoenolpyruvate-dependent sugar phosphotransferase system -0.030107
4 COG1442 glycosyl transferase family 8 -0.028283
5 COG1943 Transposase 0.027982
6 COG1254 Belongs to the acylphosphatase family -0.027937
7 COG3505 Type IV secretory pathway VirD4 0.026862
8 COG0207 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis -0.026425
9 COG1934 Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane. May form a bridge between the inner membrane and the outer membrane, via interactions with LptC and LptD, thereby facilitating LPS transfer across the periplasm 0.026312
10 COG1051 belongs to the nudix hydrolase family -0.026257
11 COG0262 Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis -0.025987
12 COG3273 potassium ion transport -0.025792
13 COG1022 Amp-dependent synthetase and ligase -0.025596
14 COG2214 Heat shock protein DnaJ domain protein 0.025418
15 COG0191 fructose-bisphosphate aldolase activity -0.024929
16 COG1351 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NAD(P)H and FADH(2) as the reductant 0.024632
17 COG1292 Belongs to the BCCT transporter (TC 2.A.15) family 0.024386
18 COG3765 Modulates the polysaccharide chain length of enterobacterial common antigen (ECA) -0.024346
19 COG0644 oxidoreductase -0.024329
20 COG3949 Membrane -0.024231
21 COG5640 endopeptidase activity 0.024144
22 COG1146 Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions 0.024136
23 COG1252 NADH dehydrogenase -0.023827
24 COG3959 Transketolase, thiamine diphosphate binding domain -0.023731
25 COG2190 (PTS) system -0.023497
26 COG1518 maintenance of DNA repeat elements 0.023377
27 COG3958 Transketolase -0.023274
28 COG0581 inorganic phosphate transmembrane transporter activity 0.023211
29 COG1349 DNA-binding transcription factor activity -0.023151
30 COG0709 Synthesizes selenophosphate from selenide and ATP 0.023081
31 COG5545 protein tyrosine phosphatase activity -0.022431
32 COG1940 carbohydrate kinase activity -0.022202
33 COG1640 4-alpha-glucanotransferase -0.021831
34 COG4972 Pilus assembly protein 0.021826
35 COG1482 cell wall glycoprotein biosynthetic process -0.021814
36 32D2I 0.021711
37 COG0573 inorganic phosphate transmembrane transporter activity 0.021569
38 COG3456 conserved protein contains FHA domain 0.021531
39 COG0584 glycerophosphoryl diester phosphodiesterase -0.021371
40 COG1621 beta-fructofuranosidase activity -0.021213
41 COG5505 Protein of unknown function (DUF819) 0.021021
42 COG1038 Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second 0.020951
43 COG2234 aminopeptidase activity 0.020935
44 COG0296 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 -0.020816
45 COG2070 2-Nitropropane dioxygenase 0.020790
46 COG1737 Transcriptional regulator -0.020762
47 COG5616 cAMP biosynthetic process -0.020748
48 COG0402 S-adenosylhomocysteine deaminase activity 0.020724
49 COG2102 of PP-loop superfamily -0.020623
50 COG4123 Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC) -0.020591
51 COG0058 SHG alpha-glucan phosphorylase activity -0.020437
52 COG0248 Ppx GppA phosphatase 0.020132
53 COG1670 COG1670 acetyltransferases, including N-acetylases of ribosomal proteins -0.020126
54 COG0372 Belongs to the citrate synthase family -0.020125
55 COG2064 Type II secretion system (T2SS), protein F -0.019935
56 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity -0.019897
57 COG0712 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation -0.019845
58 COG1794 racemase activity, acting on amino acids and derivatives 0.019833
59 COG3435 Gentisate 1,2-dioxygenase -0.019823
60 COG2327 Polysaccharide pyruvyl transferase 0.019802
61 COG1738 Involved in the import of queuosine (Q) precursors, required for Q precursor salvage -0.019782
62 COG0021 Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate 0.019778
63 COG3451 type IV secretory pathway VirB4 0.019634
64 COG0715 COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components -0.019543
65 COG0003 Pfam Anion-transporting ATPase -0.019471
66 COG4604 ABC transporter, ATP-binding protein 0.019443
67 COG0794 Belongs to the SIS family. GutQ KpsF subfamily -0.019396
68 COG4962 Type ii secretion system protein e -0.019350
69 COG3707 response regulator -0.019325
70 COG1610 YqeY-like protein 0.019318
71 COG1234 tRNA 3'-trailer cleavage -0.019237
72 COG1335 isochorismatase 0.019148
73 COG2017 converts alpha-aldose to the beta-anomer -0.019080
74 COG1117 ATPase-coupled phosphate ion transmembrane transporter activity 0.019066
75 COG0351 phosphomethylpyrimidine kinase -0.019020
76 2Z7RC Glycine/sarcosine/betaine reductase component B subunits 0.018955
77 COG0348 domain, Protein 0.018741
78 33F8J 0.018675
79 COG0561 phosphatase activity -0.018662
80 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the 0.018538
81 COG0422 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 0.018536
82 COG4823 Abi-like protein 0.018535
83 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family -0.018424
84 COG2835 tetraacyldisaccharide 4'-kinase activity 0.018422
85 2ZQPU Outer membrane efflux protein 0.018358
86 COG0039 L-malate dehydrogenase activity -0.018348
87 COG1296 Branched-chain amino acid permease (Azaleucine resistance) 0.018308
88 33968 0.018308
89 COG1564 THIamine pyrophosphokinase 0.018029
90 COG0641 radical SAM -0.017922
91 COG2704 Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane -0.017893
92 COG2061 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 -0.017780
93 COG0395 ABC-type sugar transport system, permease component -0.017777
94 COG0005 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 0.017752
95 COG2337 Toxic component of a toxin-antitoxin (TA) module 0.017715
96 COG3588 fructose-bisphosphate aldolase 0.017697
97 COG2764 glyoxalase bleomycin resistance protein dioxygenase -0.017616
98 COG1328 CTP reductase activity -0.017548
99 COG1979 alcohol dehydrogenase 0.017534
100 COG2964 Protein conserved in bacteria 0.017527
101 COG4965 Type ii secretion system -0.017415
102 COG4803 membrane protein of uknown function UCP014873 0.017334
103 COG3247 response to pH -0.017324
104 32ATT 0.017307
105 COG2021 Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine -0.017213
106 COG1866 Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA -0.017192
107 COG0420 3'-5' exonuclease activity -0.017144
108 COG3295 Protein conserved in bacteria 0.017129
109 COG5424 Ring cyclization and eight-electron oxidation of 3a-(2- amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline- 7,9-dicarboxylic-acid to PQQ -0.017125
110 COG2365 Tyrosine phosphatase family -0.017090
111 COG1194 a g-specific adenine glycosylase 0.017078
112 COG2320 Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A -0.017063
113 COG1939 Involved in correct processing of both the 5' and 3' ends of 23S rRNA precursor. Processes 30S rRNA precursor transcript even in absence of ribonuclease 3 (Rnc) -0.017063
114 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.017062
115 COG0371 Dehydrogenase -0.017050
116 COG2183 response to ionizing radiation -0.017042
117 COG3577 Aspartyl protease -0.017004
118 2ZH02 Psort location CytoplasmicMembrane, score 0.016988
119 33JYB 0.016982
120 30INA 0.016936
121 COG4115 mRNA cleavage 0.016866
122 COG0413 3-methyl-2-oxobutanoate hydroxymethyltransferase activity 0.016823
123 COG2005 Transcriptional regulator 0.016799
124 COG3221 ABC-type phosphate phosphonate transport system periplasmic component 0.016798
125 COG0400 carboxylic ester hydrolase activity 0.016798
126 COG1713 HD superfamily hydrolase involved in NAD metabolism -0.016795
127 COG2135 peptidase activity 0.016759
128 COG2099 Precorrin-6x reductase -0.016726
129 COG1834 amidinotransferase 0.016711
130 COG2610 gluconate transmembrane transporter activity -0.016696
131 COG3941 tape measure -0.016694
132 COG5426 von Willebrand factor, type A -0.016691
133 COG1280 lysine exporter protein (LysE YggA) 0.016624
134 2ZB91 0.016578
135 COG0424 maF-like protein 0.016525
136 COG2200 EAL domain 0.016507
137 2Z8YX Protein of unknown function (DUF2815) -0.016471
138 COG5614 head-tail adaptor 0.016445
139 32ZB3 0.016430
140 COG1026 Peptidase M16C associated 0.016427
141 COG3217 Mosc domain protein beta barrel domain protein -0.016422
142 COG0775 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 -0.016403
143 COG2936 dipeptidyl-peptidase activity -0.016396
144 COG1942 4-Oxalocrotonate Tautomerase -0.016366
145 COG5377 YqaJ viral recombinase family 0.016360
146 COG2079 MmgE PrpD family protein 0.016351
147 COG3442 glutamine amidotransferase -0.016341
148 COG0683 leucine binding -0.016336
149 COG3643 Formiminotransferase domain 0.016286
150 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family -0.016200
151 COG4959 Type IV secretory pathway protease TraF 0.016182
152 2Z7WH CRISPR-associated protein, Csd1 family 0.016134
153 2Z82V maintenance of DNA repeat elements 0.016134
154 COG0655 NAD(P)H dehydrogenase (quinone) activity -0.016047
155 COG2932 Transcriptional regulator -0.016017
156 COG4224 UPF0291 protein -0.016013
157 COG2318 DinB family -0.016012
158 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity -0.015940
159 COG2878 Part of a membrane complex involved in electron transport 0.015930
160 313N4 Protein of unknown function (DUF4230) 0.015927
161 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.015879
162 COG5005 Phage virion morphogenesis 0.015856
163 COG1438 arginine binding -0.015845
164 COG1085 galactose-1-phosphate uridylyltransferase -0.015796
165 33Y7F 0.015735
166 COG2188 Transcriptional regulator -0.015709
167 COG1078 dGTPase activity -0.015705
168 COG1240 Involved in chlorophyll biosynthesis. Catalyzes the insertion of magnesium ion into protoporphyrin IX to yield Mg- protoporphyrin IX -0.015699
169 COG1820 Belongs to the metallo-dependent hydrolases superfamily. NagA family -0.015683
170 33AUP COG NOG23401 non supervised orthologous group 0.015672
171 COG2425 protein containing a von Willebrand factor type A (vWA) domain -0.015663
172 COG0558 Belongs to the CDP-alcohol phosphatidyltransferase class-I family -0.015597
173 COG0213 The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis -0.015578
174 COG4416 COG NOG18757 non supervised orthologous group 0.015575
175 COG1310 metal-dependent protease of the Pad1 Jab1 superfamily -0.015554
176 COG1695 Transcriptional regulator -0.015540
177 2ZAZR Sel1-like repeats. 0.015490
178 COG4456 Virulence-associated protein -0.015478
179 COG4496 protein, YerC YecD 0.015474
180 COG0075 2-aminoethylphosphonate-pyruvate transaminase activity -0.015431
181 COG3072 Adenylate cyclase -0.015425
182 COG1033 growth of symbiont in host cell 0.015419
183 2ZYY6 Bacterial regulatory proteins, tetR family -0.015399
184 COG3711 transcriptional antiterminator -0.015396
185 COG0174 glutamine synthetase -0.015388
186 COG3512 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. Involved in the integration of spacer DNA into the CRISPR cassette 0.015385
187 COG0757 Catalyzes a trans-dehydration via an enolate intermediate 0.015350
188 COG3022 response to hydroperoxide -0.015338
189 COG2862 Uncharacterized protein family, UPF0114 -0.015309
190 COG0225 Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine -0.015284
191 COG1763 Mo-molybdopterin cofactor biosynthetic process 0.015270
192 COG4487 mechanosensitive ion channel activity 0.015245
193 COG3195 allantoin biosynthetic process -0.015243
194 COG0720 synthase 0.015224
195 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis -0.015193
196 COG4536 flavin adenine dinucleotide binding -0.015193
197 COG3715 PTS system -0.015140
198 COG0598 Magnesium transport protein CorA -0.015122
199 COG2603 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA 0.015093
200 COG4285 Biotin-protein ligase, N terminal 0.015083
201 COG1954 Regulates expression of the glpD operon. In the presence of glycerol 3-phosphate (G3P) causes antitermination of transcription of glpD at the inverted repeat of the leader region to enhance its transcription. Binds and stabilizes glpD leader mRNA -0.015078
202 COG0330 HflC and HflK could -0.015065
203 COG4235 cytochrome complex assembly -0.015064
204 COG3037 sugar-specific permease SgaT UlaA -0.015060
205 31SHG 0.015052
206 COG1070 Carbohydrate kinase -0.015007
207 COG2326 polyphosphate kinase activity 0.014998
208 COG1448 Aminotransferase -0.014968
209 COG3757 hydrolase, family 25 -0.014945
210 COG2050 protein possibly involved in aromatic compounds catabolism 0.014916
211 COG0733 neurotransmitter:sodium symporter activity 0.014895
212 COG4261 Acyltransferase -0.014885
213 COG2723 6-phospho-beta-galactosidase activity -0.014863
214 COG2368 4-hydroxyphenylacetate 0.014860
215 COG0591 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.014833
216 COG4146 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.014822
217 COG3316 Transposase and inactivated derivatives -0.014800
218 COG0637 HAD-superfamily hydrolase subfamily IA, variant 3 -0.014799
219 COG0717 Belongs to the dCTP deaminase family -0.014794
220 COG4393 Membrane 0.014781
221 346DU GDSL-like Lipase/Acylhydrolase -0.014738
222 2ZUWJ 0.014727
223 COG0847 DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease -0.014705
224 COG1275 C4-dicarboxylate transporter malic acid transport protein 0.014704
225 COG3070 regulator of competence-specific genes -0.014703
226 COG0423 glycine-tRNA ligase activity -0.014666
227 COG3843 relaxase mobilization nuclease domain protein 0.014639
228 COG3238 Protein conserved in bacteria -0.014639
229 33IE2 0.014624
230 COG0362 Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH -0.014622
231 3315E 0.014613
232 COG2249 NAD(P)H dehydrogenase (quinone) activity 0.014544
233 COG1295 ribonuclease BN -0.014479
234 COG1523 belongs to the glycosyl hydrolase 13 family -0.014478
235 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) -0.014473
236 COG0760 Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation 0.014467
237 COG3276 selenocysteine insertion sequence binding 0.014454
238 32P9E Crp-like helix-turn-helix domain -0.014390
239 COG5305 Membrane -0.014360
240 COG3124 Converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP -0.014360
241 COG4766 ethanolamine catabolic process -0.014327
242 COG0448 Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans -0.014310
243 COG3383 formate dehydrogenase (NAD+) activity 0.014292
244 COG0647 UMP catabolic process -0.014261
245 COG2501 S4 domain 0.014255
246 COG2232 ATP-grasp domain 0.014238
247 32RZW 0.014231
248 32US0 Putative redox-active protein (C_GCAxxG_C_C) -0.014229
249 COG4373 Mu-like prophage FluMu protein gp28 0.014223
250 COG4643 DNA integration 0.014214