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 COG1091 dTDP-4-dehydrorhamnose reductase activity 0.047065
2 COG0076 glutamate decarboxylase activity 0.046373
3 COG3560 Nitroreductase -0.043346
4 345AV Cyclic nucleotide-monophosphate binding domain 0.042154
5 2ZSRR Psort location Cytoplasmic, score 8.87 0.038051
6 COG0405 Gamma-glutamyltransferase -0.037077
7 COG0622 Phosphoesterase 0.036813
8 COG1454 alcohol dehydrogenase 0.035849
9 COG1105 Belongs to the carbohydrate kinase PfkB family -0.035077
10 COG0351 phosphomethylpyrimidine kinase 0.034195
11 COG3465 dGTPase activity -0.033730
12 COG5616 cAMP biosynthetic process 0.033292
13 COG4720 Psort location CytoplasmicMembrane, score 0.033006
14 COG0523 cobalamin synthesis protein -0.032527
15 COG1525 nuclease -0.032273
16 COG2315 Protein conserved in bacteria 0.031604
17 COG3855 fructose 1,6-bisphosphate 1-phosphatase activity 0.031396
18 COG1881 PFAM PEBP family protein 0.031382
19 COG3328 transposase activity -0.031185
20 COG4335 DNA alkylation repair 0.030334
21 COG3505 Type IV secretory pathway VirD4 0.030241
22 COG4642 MORN repeat 0.030241
23 COG1942 4-Oxalocrotonate Tautomerase -0.029971
24 COG1129 ABC transporter -0.029741
25 COG3238 Protein conserved in bacteria 0.028840
26 COG4115 mRNA cleavage 0.028827
27 COG2131 deaminase 0.028723
28 COG2162 N-hydroxyarylamine O-acetyltransferase activity -0.028635
29 COG1621 beta-fructofuranosidase activity -0.027905
30 COG2865 translation initiation factor activity 0.027810
31 COG1921 L-seryl-tRNASec selenium transferase activity 0.027730
32 COG0661 Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis 0.027676
33 COG5153 cell wall organization -0.027483
34 COG3545 Serine hydrolase -0.027397
35 COG3537 Alpha-1,2-mannosidase 0.027251
36 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding -0.027151
37 COG5430 Spore Coat -0.026853
38 COG2311 Membrane -0.026819
39 32T36 -0.026655
40 COG0286 site-specific DNA-methyltransferase (adenine-specific) activity -0.026639
41 COG5617 Psort location CytoplasmicMembrane, score -0.026573
42 COG5324 RNA ligase -0.026522
43 COG1393 Belongs to the ArsC family -0.026483
44 COG2145 Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ) 0.026476
45 2ZBPB CRISPR-associated protein Cas5 -0.026356
46 COG1914 H( )-stimulated, divalent metal cation uptake system -0.026252
47 COG4643 DNA integration 0.026199
48 COG3575 Nucleotidyltransferase 0.026094
49 30BEK CRISPR system CASCADE complex protein CasE -0.025909
50 COG2986 histidine ammonia-lyase -0.025883
51 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity -0.025850
52 COG1182 Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity -0.025830
53 303R9 -0.025681
54 COG0659 secondary active sulfate transmembrane transporter activity -0.025640
55 331W5 -0.025543
56 COG3961 Belongs to the TPP enzyme family -0.025501
57 COG2427 Protein of unknown function (DUF1641) -0.025451
58 COG0282 Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction -0.025365
59 COG2026 Addiction module toxin, RelE StbE family 0.025226
60 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine 0.025162
61 COG1754 DNA topoisomerase type I activity 0.025121
62 COG3451 type IV secretory pathway VirB4 0.024928
63 COG1249 Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family 0.024857
64 COG2972 Histidine kinase 0.024785
65 COG4213 ABC transporter substrate-binding protein -0.024625
66 COG2015 COG2015, Alkyl sulfatase and related hydrolases 0.024538
67 COG1696 Membrane protein involved in D-alanine export -0.024464
68 COG2337 Toxic component of a toxin-antitoxin (TA) module -0.024449
69 COG2514 catechol 2,3-dioxygenase activity -0.024436
70 COG2374 Endonuclease Exonuclease Phosphatase -0.024353
71 COG0334 Belongs to the Glu Leu Phe Val dehydrogenases family 0.024213
72 COG1392 Phosphate transport regulator 0.024036
73 COG1061 Type III restriction enzyme res subunit 0.023841
74 2Z7W6 CRISPR-associated protein, Cse1 -0.023794
75 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 -0.023787
76 COG1857 crispr-associated protein -0.023741
77 COG0535 radical SAM domain protein -0.023716
78 31PIN 0.023710
79 COG1172 Belongs to the binding-protein-dependent transport system permease family -0.023671
80 COG3613 nucleoside 2-deoxyribosyltransferase -0.023646
81 COG3030 protein affecting phage T7 exclusion by the F plasmid -0.023624
82 33BFA -0.023564
83 COG4651 solute:proton antiporter activity -0.023403
84 COG3402 PFAM membrane-flanked domain 0.023367
85 COG2189 Belongs to the N(4) N(6)-methyltransferase family 0.023354
86 COG3037 sugar-specific permease SgaT UlaA 0.023307
87 31EGY 0.023222
88 COG1027 Aspartate ammonia-lyase 0.023147
89 COG0110 maltose O-acetyltransferase activity -0.023069
90 COG3464 Transposase 0.023023
91 COG1438 arginine binding 0.022908
92 COG0025 NhaP-type Na H and K H 0.022879
93 COG0239 Important for reducing fluoride concentration in the cell, thus reducing its toxicity -0.022874
94 COG0788 formyltetrahydrofolate deformylase activity -0.022836
95 COG3153 acetyltransferase -0.022795
96 COG1022 Amp-dependent synthetase and ligase -0.022684
97 COG0615 ADP-L-glycero-beta-D-manno-heptose biosynthetic process -0.022549
98 COG1763 Mo-molybdopterin cofactor biosynthetic process -0.022430
99 COG2987 Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate -0.022380
100 341CT Iron-sulphur cluster biosynthesis -0.022191
101 COG4292 low temperature requirement -0.022186
102 COG0673 inositol 2-dehydrogenase activity 0.021962
103 30AT0 0.021956
104 COG3654 0.021930
105 COG2041 Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide -0.021927
106 COG1296 Branched-chain amino acid permease (Azaleucine resistance) -0.021886
107 30GDE Acetyltransferase (GNAT) domain -0.021882
108 30A3W -0.021833
109 COG1432 Conserved Protein -0.021799
110 30BKD Bacterial regulatory proteins, lacI family -0.021788
111 COG2501 S4 domain -0.021770
112 COG4277 radical SAM 0.021752
113 COG3283 Transcriptional regulator of aromatic amino acids metabolism 0.021615
114 COG3072 Adenylate cyclase -0.021538
115 2ZI4Y PAAR motif -0.021500
116 COG4147 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.021477
117 COG1487 ribonuclease activity 0.021420
118 COG0236 Carrier of the growing fatty acid chain in fatty acid biosynthesis 0.021415
119 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity 0.021405
120 COG3436 PFAM IS66 Orf2 family protein -0.021363
121 COG0500 methyltransferase 0.021361
122 COG2331 Regulatory protein, FmdB family 0.021285
123 32ZD3 lysozyme inhibitor activity 0.021239
124 33A2M Protein of unknown function (DUF2922) -0.021232
125 COG2160 L-arabinose isomerase activity 0.021221
126 COG3250 beta-galactosidase activity 0.021207
127 COG4851 CamS sex pheromone cAM373 precursor -0.021149
128 COG1088 dTDP-glucose 4,6-dehydratase activity 0.021112
129 32V5G -0.021070
130 COG1669 hydrolase activity, acting on ester bonds 0.020990
131 2ZIYW Psort location Cytoplasmic, score 0.020836
132 COG3728 DNA packaging -0.020835
133 32T1U Branched-chain amino acid transport protein (AzlD) -0.020807
134 344FT Cupin domain -0.020796
135 COG3718 enzyme involved in inositol metabolism 0.020730
136 COG1120 ATPase activity 0.020718
137 COG0608 single-stranded DNA 5'-3' exodeoxyribonuclease activity 0.020699
138 COG2945 thiolester hydrolase activity -0.020656
139 COG1742 UPF0060 membrane protein -0.020605
140 COG3818 acetyltransferase 0.020593
141 COG1447 Phosphotransferase system cellobiose-specific component IIA -0.020545
142 319WD FRG 0.020518
143 COG3835 regulator 0.020457
144 COG3077 Addiction module antitoxin, RelB DinJ family 0.020415
145 COG4803 membrane protein of uknown function UCP014873 0.020408
146 COG3081 Nucleoid-associated protein 0.020403
147 COG3039 Transposase -0.020372
148 COG2891 Involved in formation of the rod shape of the cell. May also contribute to regulation of formation of penicillin-binding proteins 0.020372
149 32UPV CRISPR system CASCADE complex protein CasB -0.020369
150 COG1448 Aminotransferase 0.020357
151 COG4248 protein with protein kinase and helix-hairpin-helix DNA-binding domains 0.020285
152 COG2361 Protein of unknown function DUF86 0.020280
153 COG1021 2,3-dihydroxybenzoate-AMP ligase 0.020274
154 COG0510 thiamine kinase activity -0.020157
155 COG4690 dipeptidase activity -0.020110
156 COG0406 alpha-ribazole phosphatase activity 0.020075
157 COG4836 Membrane -0.020031
158 COG3568 Endonuclease Exonuclease Phosphatase 0.019986
159 COG3059 membrane 0.019940
160 COG3593 DNA synthesis involved in DNA repair 0.019903
161 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the -0.019858
162 COG4421 COG4421 Capsular polysaccharide biosynthesis protein 0.019750
163 COG1015 Phosphotransfer between the C1 and C5 carbon atoms of pentose 0.019648
164 COG1506 peptidase 0.019606
165 COG2226 methyltransferase 0.019603
166 32P9E Crp-like helix-turn-helix domain -0.019600
167 COG4187 Peptidase family M20/M25/M40 -0.019592
168 COG0641 radical SAM 0.019585
169 COG1523 belongs to the glycosyl hydrolase 13 family 0.019580
170 COG4708 membrane 0.019568
171 321KG Psort location CytoplasmicMembrane, score 0.019568
172 33BPB -0.019562
173 COG2818 Glycosylase 0.019549
174 COG0039 L-malate dehydrogenase activity -0.019539
175 33A5I Psort location CytoplasmicMembrane, score 0.019466
176 COG0584 glycerophosphoryl diester phosphodiesterase -0.019451
177 COG2135 peptidase activity -0.019398
178 COG4443 Transcriptional Coactivator p15 (PC4) 0.019371
179 COG0526 COG0526, thiol-disulfide isomerase and thioredoxins 0.019263
180 COG2841 Protein conserved in bacteria -0.019230
181 33CBE Lysin motif -0.019180
182 COG3240 lipase activity -0.019161
183 2ZW9Q SEC-C motif -0.019153
184 COG3547 Transposase (IS116 IS110 IS902 family) -0.019135
185 COG0589 response to stress -0.019114
186 COG2390 Transcriptional regulator -0.019103
187 COG2978 secondary active p-aminobenzoyl-glutamate transmembrane transporter activity -0.019075
188 COG1230 cation diffusion facilitator family transporter 0.019048
189 COG2816 NAD+ diphosphatase activity 0.019035
190 33CQY -0.019027
191 COG1732 Glycine betaine -0.018987
192 COG1878 Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation -0.018983
193 COG3800 Transcriptional regulator -0.018940
194 COG0327 Belongs to the GTP cyclohydrolase I type 2 NIF3 family 0.018859
195 COG4564 Single Cache domain 2 0.018839
196 COG0695 Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins 0.018834
197 COG0246 Mannitol dehydrogenase -0.018805
198 COG5184 regulator of chromosome condensation, RCC1 -0.018766
199 COG3962 Belongs to the TPP enzyme family 0.018727
200 33FCT -0.018723
201 COG3559 Exporter of polyketide antibiotics -0.018713
202 COG1368 sulfuric ester hydrolase activity 0.018692
203 COG2912 Transglutaminase-like superfamily -0.018691
204 COG4261 Acyltransferase 0.018660
205 COG1535 isochorismatase 0.018642
206 COG3211 Phosphatase -0.018641
207 COG1784 Tripartite tricarboxylate transporter TctA family 0.018634
208 COG1112 Superfamily I DNA and RNA helicases and helicase subunits 0.018618
209 COG1947 Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol 0.018597
210 COG0498 Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine 0.018579
211 COG0388 Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source -0.018524
212 2ZMYT Psort location Cytoplasmic, score 0.018510
213 COG1546 Belongs to the CinA family 0.018510
214 COG3025 triphosphatase activity -0.018506
215 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 0.018480
216 COG4732 ThiW protein 0.018464
217 30A3B 0.018454
218 COG1054 Belongs to the UPF0176 family -0.018451
219 COG3860 Transcriptional regulator 0.018448
220 COG5642 Protein of unknown function (DUF2384) -0.018425
221 COG3616 Alanine racemase, N-terminal domain -0.018422
222 COG0600 ABC-type nitrate sulfonate bicarbonate transport system permease component 0.018298
223 COG4723 tail assembly -0.018291
224 COG3048 D-serine ammonia-lyase activity 0.018276
225 COG4388 Caudovirus prohead serine protease -0.018272
226 COG1440 protein-N(PI)-phosphohistidine-lactose phosphotransferase system transporter activity -0.018247
227 COG4715 Zinc finger, swim domain protein 0.018223
228 COG5506 Protein of unknown function (DUF1694) 0.018206
229 COG0506 proline dehydrogenase activity -0.018201
230 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis 0.018195
231 2ZHE9 Septum formation initiator -0.018187
232 COG0599 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity 0.018076
233 COG1963 PFAM Acid phosphatase vanadium-dependent haloperoxidase related -0.018064
234 COG3683 transport system, periplasmic component -0.018040
235 COG0701 Predicted permease 0.018010
236 COG4552 Acetyltransferase involved in intracellular survival and related -0.017985
237 COG4251 negative regulation of phosphorylation 0.017982
238 COG0007 Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme -0.017970
239 COG0041 Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) 0.017953
240 COG4188 dienelactone hydrolase -0.017933
241 COG1912 Pfam S-adenosyl-l-methionine hydroxide adenosyltransferase 0.017918
242 COG2084 Dehydrogenase 0.017910
243 COG4275 Chromate resistance exported protein -0.017886
244 COG4853 Protein conserved in bacteria -0.017835
245 2Z9EY WYL domain -0.017831
246 COG0169 Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA) 0.017824
247 COG1712 Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L- tetrahydrodipicolinate, to generate the meso compound, D,L-2,6- diaminopimelate 0.017808
248 COG1739 Uncharacterized protein family UPF0029 0.017773
249 COG2804 Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB -0.017744
250 33QAR Baseplate J-like protein -0.017737