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 COG5637 Cyclase dehydrase -0.035755
2 COG3011 Protein conserved in bacteria -0.031025
3 COG0641 radical SAM 0.030127
4 COG0095 Lipoate-protein ligase 0.030118
5 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 0.029903
6 COG3707 response regulator -0.029786
7 COG3608 succinylglutamate desuccinylase aspartoacylase -0.027475
8 COG1528 Iron-storage protein 0.026982
9 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 -0.026321
10 COG3655 Transcriptional regulator -0.026201
11 COG0863 Belongs to the N(4) N(6)-methyltransferase family 0.025947
12 COG0010 Belongs to the arginase family -0.025514
13 COG4308 Limonene-1,2-epoxide hydrolase catalytic domain -0.025059
14 COG5485 Ester cyclase -0.024666
15 COG4700 PFAM Protein kinase domain -0.024636
16 COG1488 Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP 0.024457
17 COG3152 Membrane 0.024271
18 COG3005 denitrification pathway 0.024075
19 COG5316 arabinan endo-1,5-alpha-L-arabinosidase activity -0.024070
20 COG2210 Belongs to the sulfur carrier protein TusA family 0.023872
21 COG1708 protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity 0.023566
22 COG3285 dna ligase -0.023071
23 COG5426 von Willebrand factor, type A -0.023047
24 COG1139 Iron-sulfur cluster binding protein 0.022823
25 COG3892 5-dehydro-2-deoxygluconokinase -0.022765
26 COG2211 Major facilitator Superfamily 0.022532
27 COG2343 Domain of unknown function (DUF427) -0.022502
28 COG4101 3-hydroxyanthranilate 3,4-dioxygenase activity -0.022401
29 COG1032 radical SAM domain protein 0.022315
30 COG3267 Type II secretory pathway component ExeA 0.022128
31 COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase -0.021988
32 COG4875 SnoaL-like domain 0.021906
33 COG0662 Cupin 2, conserved barrel domain protein -0.021694
34 COG0655 NAD(P)H dehydrogenase (quinone) activity -0.021659
35 COG3240 lipase activity 0.021625
36 COG2912 Transglutaminase-like superfamily 0.021485
37 COG0327 Belongs to the GTP cyclohydrolase I type 2 NIF3 family 0.021355
38 COG2096 Adenosyltransferase -0.021251
39 COG2357 RelA SpoT domain protein 0.021235
40 COG2910 NAD(P)H-binding 0.021191
41 COG3274 enterobacterial common antigen metabolic process 0.021090
42 COG4219 Peptidase M56 -0.021083
43 COG2095 MarC family integral membrane protein -0.020848
44 31W2T Universal stress protein family 0.020724
45 COG1513 Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide 0.020717
46 COG1075 acetyltransferases and hydrolases with the alpha beta hydrolase fold -0.020531
47 COG1451 nucleotide metabolic process 0.020438
48 COG3682 Transcriptional regulator -0.020299
49 COG3620 sequence-specific DNA binding -0.020292
50 COG5337 Spore coat protein CotH 0.020223
51 2Z9ZP Conserved TM helix -0.020219
52 COG3458 cephalosporin-C deacetylase activity -0.020012
53 COG3541 Predicted nucleotidyltransferase -0.019971
54 COG3774 pathogenesis 0.019870
55 COG1004 Belongs to the UDP-glucose GDP-mannose dehydrogenase family -0.019868
56 COG0499 May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine -0.019841
57 COG1764 response to oxidative stress -0.019822
58 COG3932 Exopolysaccharide synthesis, ExoD -0.019755
59 COG4260 virion core protein, lumpy skin disease virus -0.019603
60 COG3405 Belongs to the glycosyl hydrolase 8 (cellulase D) family -0.019509
61 COG1801 Protein of unknown function DUF72 -0.019324
62 COG1238 metal cluster binding 0.019296
63 COG3145 DNA-N1-methyladenine dioxygenase activity -0.019285
64 COG0230 Belongs to the bacterial ribosomal protein bL34 family 0.019224
65 COG5271 translation initiation factor activity 0.019182
66 COG2513 Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate -0.019153
67 COG3795 YCII-related domain -0.019147
68 339UG -0.019138
69 COG0062 Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration 0.019069
70 COG2832 Protein of unknown function (DUF454) 0.018981
71 COG3001 Fructosamine kinase 0.018853
72 COG5507 3-demethylubiquinone-9 3-methyltransferase -0.018809
73 COG5394 Polyhydroxyalkanoate synthesis repressor PhaR -0.018665
74 COG0665 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity -0.018607
75 COG1167 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs 0.018551
76 COG3144 bacterial-type flagellum assembly 0.018528
77 COG4359 Dephosphorylates 2-hydroxy-3-keto-5-methylthiopentenyl- 1-phosphate (HK-MTPenyl-1-P) yielding 1,2-dihydroxy-3-keto-5- methylthiopentene (DHK-MTPene) -0.018510
78 COG1861 Spore coat polysaccharide biosynthesis protein F CMP-KDO synthetase -0.018403
79 COG5349 Protein of unknown function (DUF983) -0.018315
80 COG3233 deacetylase 0.018219
81 COG4667 esterase of the alpha-beta hydrolase superfamily 0.018185
82 COG2124 cytochrome p450 -0.018129
83 COG1328 CTP reductase activity 0.018089
84 COG1412 self proteolysis -0.018075
85 2Z7PD Psort location CytoplasmicMembrane, score -0.018056
86 COG3129 Specifically methylates the adenine in position 1618 of 23S rRNA 0.018054
87 32VR7 Protein of unknown function (DUF2490) -0.018050
88 COG0619 Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates 0.018046
89 COG1245 4Fe-4S binding domain 0.018035
90 COG4325 translation initiation factor activity -0.018030
91 COG0648 Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin 0.017994
92 COG0174 glutamine synthetase 0.017926
93 COG0822 iron-sulfur transferase activity 0.017896
94 COG3174 membrane 0.017889
95 31SDF -0.017787
96 COG0367 asparagine synthase 0.017768
97 COG3222 Protein conserved in bacteria -0.017759
98 COG1063 alcohol dehydrogenase 0.017722
99 COG3439 Domain of unknown function DUF302 -0.017692
100 COG3602 ACT domain 0.017677
101 COG0407 Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III -0.017671
102 COG1236 Exonuclease of the beta-lactamase fold involved in RNA processing -0.017611
103 COG1122 ATPase activity 0.017499
104 COG1721 protein (some members contain a von Willebrand factor type A (vWA) domain -0.017484
105 COG1598 PFAM Uncharacterised protein family UPF0150 0.017466
106 COG2109 Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids 0.017428
107 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 -0.017390
108 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin 0.017340
109 COG4880 Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats -0.017308
110 COG4963 Pilus assembly protein 0.017303
111 COG3576 pyridoxamine 5-phosphate 0.017281
112 COG0277 FAD linked oxidase domain protein -0.017271
113 COG0654 COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases -0.017235
114 COG4845 Chloramphenicol acetyltransferase 0.017217
115 COG1821 Pfam ATP-grasp domain -0.017212
116 32Y9V Putative peptidoglycan binding domain -0.017198
117 COG4680 protein conserved in bacteria -0.017197
118 COG3424 synthase -0.017158
119 COG1477 protein flavinylation 0.017137
120 COG0375 protein maturation 0.017124
121 3172B Bacterial PH domain 0.017092
122 COG3718 enzyme involved in inositol metabolism -0.017083
123 COG1858 cytochrome C peroxidase -0.017066
124 COG1069 ribulokinase activity -0.017012
125 COG3408 Glycogen debranching enzyme -0.017000
126 COG2005 Transcriptional regulator 0.016975
127 COG0132 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring -0.016959
128 COG1289 transmembrane transporter activity 0.016953
129 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 -0.016919
130 COG3871 stress protein (general stress protein 26) -0.016916
131 COG1908 Methyl-viologen-reducing hydrogenase, delta subunit 0.016912
132 COG3619 membrane -0.016855
133 COG3703 Catalyzes the cleavage of glutathione into 5-oxo-L- proline and a Cys-Gly dipeptide. Acts specifically on glutathione, but not on other gamma-glutamyl peptides -0.016854
134 2Z9A6 Outer membrane protein SusF_SusE 0.016853
135 COG4409 exo-alpha-(2->6)-sialidase activity -0.016835
136 COG2968 Membrane -0.016818
137 COG1635 Involved in the biosynthesis of the thiazole moiety of thiamine. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylate (ADT), an adenylated thiazole intermediate, using free sulfide as a source of sulfur 0.016795
138 COG1105 Belongs to the carbohydrate kinase PfkB family -0.016660
139 COG3804 dihydrodipicolinate reductase -0.016636
140 COG0149 triose-phosphate isomerase activity 0.016630
141 COG3256 nitric oxide reductase 0.016612
142 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 0.016590
143 COG3962 Belongs to the TPP enzyme family -0.016551
144 COG0807 Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate -0.016528
145 COG2963 transposase activity -0.016493
146 COG1913 serine-type endopeptidase activity -0.016492
147 COG0753 catalase activity -0.016484
148 COG5410 chromosome segregation 0.016483
149 COG3473 Maleate cis-trans isomerase -0.016368
150 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase -0.016359
151 COG2374 Endonuclease Exonuclease Phosphatase 0.016344
152 COG2964 Protein conserved in bacteria -0.016332
153 COG5488 Integral membrane protein (DUF2244) -0.016304
154 COG3816 Protein conserved in bacteria -0.016253
155 COG1474 Belongs to the peptidase S16 family 0.016248
156 COG3428 Bacterial PH domain -0.016221
157 COG0785 Cytochrome C biogenesis protein 0.016211
158 COG3832 glyoxalase III activity -0.016177
159 COG2232 ATP-grasp domain -0.016135
160 COG3613 nucleoside 2-deoxyribosyltransferase 0.016128
161 COG2906 2 iron, 2 sulfur cluster binding 0.016111
162 COG1729 Mediates coordination of peptidoglycan synthesis and outer membrane constriction during cell division -0.016102
163 COG4894 glucomannan catabolic process 0.016101
164 COG1518 maintenance of DNA repeat elements 0.016096
165 COG1228 amidohydrolase -0.016091
166 COG2048 Heterodisulfide reductase, subunit B 0.016068
167 COG2253 Psort location Cytoplasmic, score 0.016036
168 COG3806 Anti-sigma factor -0.015981
169 COG3033 Beta-eliminating lyase 0.015955
170 COG3663 DNA glycosylase 0.015947
171 30XA9 -0.015931
172 COG5401 PFAM Sporulation and spore germination -0.015921
173 COG5580 Activator of Hsp90 ATPase -0.015852
174 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity -0.015846
175 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit -0.015838
176 COG2826 transposase and inactivated derivatives, IS30 family -0.015832
177 COG0714 Associated with various cellular activities -0.015777
178 COG0674 pyruvate-flavodoxin oxidoreductase activity 0.015744
179 COG2808 Putative FMN-binding domain -0.015741
180 COG0286 site-specific DNA-methyltransferase (adenine-specific) activity 0.015739
181 COG4877 0.015719
182 COG3062 negative regulation of establishment of protein localization 0.015717
183 COG1478 Catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives -0.015699
184 COG0344 acyl-phosphate glycerol-3-phosphate acyltransferase activity 0.015650
185 2ZCGH -0.015614
186 COG4785 May be involved in cell division 0.015613
187 COG0448 Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans 0.015576
188 COG1268 BioY protein 0.015554
189 COG2856 Zn peptidase 0.015544
190 COG5434 Belongs to the glycosyl hydrolase 28 family -0.015533
191 2ZBT9 YKOF-related Family -0.015531
192 COG1811 Na channel or pump 0.015524
193 COG4284 Utp--glucose-1-phosphate uridylyltransferase 0.015518
194 COG3243 poly(R)-hydroxyalkanoic acid synthase -0.015482
195 COG3672 Periplasmic Protein 0.015472
196 COG4577 Carbon dioxide concentrating mechanism carboxysome shell protein 0.015458
197 COG5499 transcription regulator containing HTH domain -0.015385
198 COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain -0.015361
199 COG2017 converts alpha-aldose to the beta-anomer -0.015352
200 COG3569 DNA Topoisomerase -0.015317
201 COG1666 GTP binding -0.015268
202 COG4582 Cell division factor that enhances FtsZ-ring assembly. Directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity 0.015224
203 33FR3 -0.015216
204 COG0038 chloride channel 0.015184
205 COG0282 Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction 0.015155
206 COG3425 synthase 0.015132
207 COG2853 Lipoprotein 0.015131
208 COG3295 Protein conserved in bacteria 0.015126
209 COG1773 rubredoxin 0.015035
210 COG3882 phosphopantetheine binding 0.015025
211 331UM -0.014995
212 COG3108 Peptidase M15 -0.014995
213 COG3292 Two component regulator propeller 0.014992
214 316Z5 Universal stress protein family 0.014990
215 COG4067 protein conserved in archaea -0.014973
216 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC 0.014952
217 COG2363 Small membrane protein -0.014939
218 COG2176 DNA-directed DNA polymerase activity 0.014937
219 32RVW -0.014922
220 COG3950 AAA domain, putative AbiEii toxin, Type IV TA system -0.014907
221 COG1443 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) -0.014899
222 COG4102 Protein conserved in bacteria -0.014854
223 COG3459 Glycosyltransferase 36 associated 0.014836
224 COG0573 inorganic phosphate transmembrane transporter activity 0.014789
225 COG2116 formate transmembrane transporter activity 0.014750
226 COG2768 binding domain, Protein 0.014721
227 COG0727 PFAM Uncharacterised protein family (UPF0153) 0.014718
228 COG4354 Bile acid beta-glucosidase -0.014693
229 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family -0.014691
230 COG3751 2OG-Fe(II) oxygenase superfamily -0.014673
231 30MN6 -0.014671
232 COG1496 oxidoreductase activity 0.014644
233 COG1853 conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family -0.014644
234 COG4806 L-rhamnose isomerase -0.014624
235 COG2043 Uncharacterised ArCR, COG2043 0.014592
236 COG1739 Uncharacterized protein family UPF0029 0.014572
237 COG5611 PilT protein domain protein 0.014557
238 COG1918 ferrous iron import across plasma membrane 0.014521
239 COG1550 Protein conserved in bacteria -0.014520
240 COG1324 tolerance protein 0.014459
241 COG4694 Protein conserved in bacteria 0.014452
242 2Z8Z5 -0.014436
243 COG0826 peptidase U32 0.014423
244 COG2355 Zn-dependent dipeptidase, microsomal dipeptidase -0.014412
245 COG4927 Acyl-coenzyme A 6-aminopenicillanic acid acyl-transferase -0.014409
246 COG0244 Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors 0.014387
247 33Y3A GDSL-like Lipase/Acylhydrolase -0.014354
248 COG1793 dna ligase -0.014329
249 COG0161 adenosylmethionine-8-amino-7-oxononanoate transaminase activity -0.014318
250 COG1350 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine 0.014290