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 COG1704 LemA family -0.028493
2 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.025372
3 COG0039 L-malate dehydrogenase activity -0.022584
4 COG0220 tRNA (guanine-N7-)-methyltransferase activity -0.021948
5 COG1680 COG1680 Beta-lactamase class C and other penicillin binding -0.021184
6 COG1858 cytochrome C peroxidase 0.020129
7 COG5557 Pfam Polysulphide reductase, NrfD 0.020079
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 -0.019927
9 COG4392 branched-chain amino acid 0.019853
10 COG0780 Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) 0.019239
11 2Z9UG 0.019236
12 COG3760 aminoacyl-tRNA metabolism involved in translational fidelity 0.019145
13 COG0794 Belongs to the SIS family. GutQ KpsF subfamily -0.018915
14 COG5611 PilT protein domain protein 0.018724
15 COG1671 Belongs to the UPF0178 family -0.018355
16 33HZK Putative peptidoglycan binding domain 0.018308
17 COG4320 Protein conserved in bacteria 0.018302
18 31XCZ 0.018260
19 COG0738 Major facilitator superfamily -0.018061
20 COG0469 pyruvate kinase activity -0.017969
21 COG2221 Nitrite and sulphite reductase 4Fe-4S 0.017872
22 COG1102 Psort location Cytoplasmic, score -0.017799
23 COG1297 OPT oligopeptide transporter protein -0.017614
24 COG3304 Inner membrane component domain 0.017598
25 COG1794 racemase activity, acting on amino acids and derivatives 0.017215
26 COG4928 KAP family P-loop domain 0.017155
27 COG4373 Mu-like prophage FluMu protein gp28 0.017132
28 COG0637 HAD-superfamily hydrolase subfamily IA, variant 3 -0.017074
29 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC -0.017047
30 COG4978 Transcriptional regulator -0.017040
31 COG0229 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 -0.016817
32 COG1200 Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA) -0.016809
33 COG0552 protein localization to endoplasmic reticulum -0.016638
34 COG1541 Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA) 0.016557
35 COG0588 phosphoglycerate mutase activity -0.016553
36 COG2049 5-oxoprolinase (ATP-hydrolyzing) activity -0.016365
37 COG0673 inositol 2-dehydrogenase activity -0.016307
38 COG2249 NAD(P)H dehydrogenase (quinone) activity -0.016119
39 COG1433 Dinitrogenase iron-molybdenum cofactor 0.016031
40 COG0841 Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family 0.016025
41 COG0450 alkyl hydroperoxide reductase -0.016014
42 COG1011 Hydrolase -0.016010
43 COG0076 glutamate decarboxylase activity -0.015854
44 COG0191 fructose-bisphosphate aldolase activity -0.015815
45 COG0412 Dienelactone hydrolase 0.015748
46 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) -0.015694
47 COG2908 Hydrolyzes the pyrophosphate bond of UDP-2,3- diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell -0.015638
48 COG3093 addiction module antidote protein HigA 0.015622
49 COG3872 metal-dependent enzyme 0.015535
50 COG3664 PFAM glycoside hydrolase family 39 0.015508
51 COG3022 response to hydroperoxide -0.015387
52 COG1488 Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP -0.015373
53 COG3383 formate dehydrogenase (NAD+) activity 0.015368
54 COG0752 glycyl-tRNA synthetase alpha subunit -0.015290
55 COG3624 Phosphonate C-P lyase system protein PhnG 0.015269
56 COG3625 alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity 0.015269
57 COG3626 phosphonate metabolism 0.015269
58 COG3627 carbon phosphorus lyase activity 0.015269
59 COG4107 phosphonate C-P lyase system protein PhnK 0.015269
60 COG4778 phosphonate C-P lyase system protein PhnL 0.015269
61 COG1640 4-alpha-glucanotransferase -0.015253
62 COG2818 Glycosylase -0.015235
63 COG1438 arginine binding -0.015155
64 COG0311 Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS 0.015098
65 335R8 0.015039
66 COG4803 membrane protein of uknown function UCP014873 0.015037
67 COG3454 Phosphonate metabolism 0.015029
68 COG4200 ABC-2 family transporter protein -0.014983
69 COG3371 Protein of unknown function (DUF998) 0.014943
70 COG0561 phosphatase activity -0.014924
71 COG5305 Membrane -0.014917
72 COG2331 Regulatory protein, FmdB family 0.014898
73 COG1125 glycine betaine transport -0.014857
74 COG1793 dna ligase -0.014849
75 COG0237 dephospho-CoA kinase activity -0.014841
76 33D13 0.014819
77 COG1823 symporter activity -0.014773
78 COG1002 Type II restriction enzyme, methylase subunits -0.014736
79 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 -0.014703
80 COG1975 Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family 0.014689
81 COG0755 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes 0.014586
82 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.014555
83 COG3593 DNA synthesis involved in DNA repair -0.014526
84 COG2936 dipeptidyl-peptidase activity -0.014517
85 COG1273 With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD -0.014487
86 COG2183 response to ionizing radiation -0.014427
87 COG4624 Iron only hydrogenase large subunit, C-terminal domain 0.014409
88 COG4464 protein tyrosine phosphatase activity -0.014300
89 COG3926 Glycosyl hydrolase 108 0.014179
90 COG1386 Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves -0.014171
91 COG1984 allophanate hydrolase subunit 2 -0.014121
92 COG4640 response to antibiotic -0.014095
93 COG3005 denitrification pathway 0.014079
94 COG1560 Kdo2-lipid A biosynthetic process -0.013979
95 COG1006 Multisubunit Na H antiporter MnhC subunit -0.013968
96 COG1174 glycine betaine transport -0.013937
97 COG5519 DNA primase 0.013923
98 31W2T Universal stress protein family -0.013866
99 COG4925 sulfurtransferase activity 0.013825
100 COG1479 Protein of unknown function DUF262 -0.013805
101 COG2211 Major facilitator Superfamily -0.013798
102 COG4915 5-bromo-4-chloroindolyl phosphate hydrolysis protein 0.013785
103 COG2720 vancomycin resistance protein 0.013764
104 COG5416 Lipopolysaccharide assembly protein A domain 0.013755
105 COG4285 Biotin-protein ligase, N terminal 0.013752
106 COG3605 phosphoenolpyruvate-protein phosphotransferase activity 0.013677
107 COG4988 ABC transporter -0.013677
108 COG4469 Competence protein 0.013651
109 COG0174 glutamine synthetase -0.013619
110 COG1512 COG1512 Beta-propeller domains of methanol dehydrogenase type -0.013600
111 COG2267 carboxylic ester hydrolase activity 0.013572
112 COG0717 Belongs to the dCTP deaminase family -0.013568
113 COG3707 response regulator -0.013534
114 COG0262 Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis -0.013474
115 COG4237 Hydrogenase 4 membrane 0.013384
116 COG0639 Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP -0.013323
117 COG3450 Protein of unknown function (DUF861) 0.013311
118 31PR8 0.013307
119 33C41 0.013307
120 2Z83C 0.013307
121 2ZABJ 0.013307
122 32V6V 0.013307
123 COG1310 metal-dependent protease of the Pad1 Jab1 superfamily -0.013291
124 COG2414 aldehyde ferredoxin oxidoreductase 0.013234
125 COG0735 belongs to the Fur family -0.013230
126 COG0120 Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate -0.013213
127 COG3366 ferrous iron transmembrane transporter activity 0.013210
128 COG1597 lipid kinase activity -0.013203
129 COG0575 Belongs to the CDS family -0.013163
130 COG0686 Belongs to the AlaDH PNT family 0.013090
131 COG4245 von Willebrand factor, type A 0.013088
132 COG1767 triphosphoribosyl-dephospho-CoA synthase activity -0.013023
133 COG2819 hydrolase of the alpha beta superfamily -0.013021
134 COG3498 tail tube protein 0.012968
135 COG3499 P2 GpU family protein 0.012968
136 COG1178 ABC-type Fe3 transport system permease component -0.012948
137 COG4635 menaquinone-dependent protoporphyrinogen oxidase activity -0.012934
138 COG2897 thiosulfate sulfurtransferase activity 0.012922
139 COG4927 Acyl-coenzyme A 6-aminopenicillanic acid acyl-transferase 0.012920
140 COG0123 including yeast histone deacetylase and acetoin utilization protein 0.012912
141 COG1285 pathogenesis 0.012842
142 COG2314 TM2 domain -0.012771
143 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis -0.012759
144 341CM Bacterial regulatory proteins, tetR family -0.012755
145 COG1448 Aminotransferase -0.012741
146 COG1214 PFAM Peptidase M22, glycoprotease -0.012655
147 COG3666 COG3666 Transposase and inactivated derivatives -0.012642
148 COG0067 glutamate synthase 0.012559
149 32US0 Putative redox-active protein (C_GCAxxG_C_C) -0.012508
150 COG5625 HemY protein N-terminus 0.012476
151 COG0382 Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of ubiquinone-8 (UQ-8) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB, generating the first membrane-bound Q intermediate 3- octaprenyl-4-hydroxybenzoate -0.012421
152 COG0243 molybdopterin cofactor binding 0.012417
153 COG1708 protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity 0.012396
154 COG1373 ATPase (AAA superfamily -0.012362
155 COG1526 Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH 0.012317
156 COG2421 Acetamidase/Formamidase family 0.012300
157 2Z7XJ Bacteriophage head to tail connecting protein 0.012298
158 COG2309 aminopeptidase activity -0.012261
159 COG1550 Protein conserved in bacteria 0.012239
160 COG2021 Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine -0.012214
161 COG4152 abc transporter atp-binding protein -0.012208
162 COG3830 Belongs to the UPF0237 family -0.012202
163 COG1522 sequence-specific DNA binding 0.012119
164 COG2252 PERMEase -0.012110
165 COG4540 Baseplate assembly protein 0.012107
166 33JI9 PFAM FeoA family protein -0.012088
167 COG4592 Periplasmic binding protein 0.012058
168 COG4145 pantothenate transmembrane transporter activity 0.012042
169 COG0512 Glutamine amidotransferase of anthranilate synthase -0.012035
170 COG2764 glyoxalase bleomycin resistance protein dioxygenase -0.012031
171 COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit, (S4 paralog)) -0.011999
172 33BC0 PFAM Coenzyme PQQ synthesis protein D (PqqD) 0.011997
173 COG3273 potassium ion transport -0.011989
174 COG1540 5-oxoprolinase (ATP-hydrolyzing) activity -0.011987
175 COG0336 Belongs to the RNA methyltransferase TrmD family -0.011974
176 COG0858 One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA -0.011974
177 COG0560 Phosphoserine phosphatase -0.011971
178 COG1121 (ABC) transporter -0.011929
179 30TKF 0.011922
180 COG1296 Branched-chain amino acid permease (Azaleucine resistance) 0.011911
181 COG0037 tRNA processing -0.011866
182 COG1116 anion transmembrane transporter activity -0.011863
183 COG1866 Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA -0.011761
184 COG2839 Protein conserved in bacteria 0.011761
185 COG3600 Phage-associated protein -0.011746
186 COG1434 Gram-negative-bacterium-type cell wall biogenesis -0.011735
187 COG1690 Belongs to the RtcB family -0.011732
188 COG2232 ATP-grasp domain 0.011682
189 COG3293 Transposase 0.011681
190 32YT2 Protein of unknown function (DUF2442) 0.011664
191 COG2176 DNA-directed DNA polymerase activity -0.011658
192 COG2230 cyclopropane-fatty-acyl-phospholipid synthase -0.011602
193 32TNY Domain of unknown function (DUF1992) 0.011578
194 COG0214 Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively 0.011554
195 COG1343 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 -0.011550
196 COG3811 Belongs to the UPF0386 family 0.011483
197 COG0171 NAD+ synthase (glutamine-hydrolyzing) activity -0.011478
198 COG2996 Protein conserved in bacteria -0.011442
199 COG3602 ACT domain 0.011426
200 32SGE Protein of unknown function (DUF3793) -0.011424
201 COG2510 membrane 0.011400
202 COG3641 Membrane -0.011394
203 COG0692 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine -0.011359
204 COG3862 protein with conserved CXXC pairs -0.011344
205 COG1392 Phosphate transport regulator 0.011320
206 COG0312 modulator of DNA gyrase -0.011297
207 COG3311 Transcriptional regulator 0.011273
208 COG5005 Phage virion morphogenesis 0.011263
209 COG1484 DNA-dependent DNA replication -0.011261
210 COG2173 Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide -0.011243
211 COG1764 response to oxidative stress -0.011231
212 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit -0.011206
213 COG2057 Acyl CoA acetate 3-ketoacid CoA transferase beta subunit -0.011206
214 COG0641 radical SAM -0.011189
215 COG1465 3-dehydroquinate synthase 0.011161
216 2ZK16 Histidine Phosphotransfer domain 0.011112
217 COG1225 Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.011106
218 COG1148 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.011088
219 COG3090 Trap-type c4-dicarboxylate transport system, small permease component 0.011075
220 COG5547 Small integral membrane protein -0.011054
221 COG4767 VanZ like family 0.011050
222 COG4709 membrane -0.011036
223 COG0378 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG 0.011032
224 COG1245 4Fe-4S binding domain 0.011019
225 COG1138 Cytochrome C-type biogenesis protein 0.010999
226 COG2332 Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH 0.010999
227 COG3576 pyridoxamine 5-phosphate -0.010999
228 COG2356 endonuclease I 0.010989
229 COG1063 alcohol dehydrogenase -0.010965
230 COG3344 reverse transcriptase 0.010964
231 COG0620 Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation -0.010910
232 COG4643 DNA integration 0.010905
233 COG3970 fumarylacetoacetate (FAA) hydrolase 0.010904
234 32TMV Bacterial inner membrane protein 0.010870
235 COG1830 Aldolase 0.010830
236 COG0337 Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ) -0.010811
237 COG2094 Belongs to the DNA glycosylase MPG family -0.010809
238 COG1259 PFAM Uncharacterised ACR, COG1259 0.010794
239 COG0807 Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate -0.010729
240 COG1813 peptidyl-tyrosine sulfation 0.010716
241 COG1765 OsmC-like protein 0.010701
242 COG2111 Na H antiporter -0.010691
243 COG1863 multisubunit Na H antiporter MnhE subunit -0.010691
244 COG0403 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.010625
245 COG0404 The glycine cleavage system catalyzes the degradation of glycine 0.010625
246 COG1922 lipopolysaccharide N-acetylmannosaminouronosyltransferase activity -0.010621
247 312Q2 0.010620
248 COG2816 NAD+ diphosphatase activity -0.010619
249 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family -0.010599
250 COG2912 Transglutaminase-like superfamily -0.010595