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 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family 0.061303
2 2ZSRR Psort location Cytoplasmic, score 8.87 0.060296
3 COG2116 formate transmembrane transporter activity 0.058618
4 COG2936 dipeptidyl-peptidase activity 0.056803
5 COG2239 Acts as a magnesium transporter -0.055255
6 COG2856 Zn peptidase -0.054685
7 COG2453 phosphatase 0.052367
8 COG1960 acyl-CoA dehydrogenase activity -0.051899
9 COG4100 CystaTHIonine beta-lyase family protein involved in aluminum resistance -0.049652
10 COG2610 gluconate transmembrane transporter activity 0.049405
11 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding -0.048939
12 COG0615 ADP-L-glycero-beta-D-manno-heptose biosynthetic process -0.048764
13 COG3919 ATP-grasp -0.048424
14 COG1328 CTP reductase activity -0.048295
15 COG0793 Belongs to the peptidase S41A family -0.048037
16 COG5360 Heparinase II/III-like protein 0.047496
17 COG0379 Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate 0.046869
18 COG0420 3'-5' exonuclease activity -0.045425
19 COG3602 ACT domain 0.044991
20 COG1683 Conserved Protein -0.044783
21 COG4277 radical SAM -0.044492
22 32TBR Protein of unknown function (DUF2974) 0.044400
23 COG4652 0.044370
24 COG1435 thymidine kinase activity -0.044276
25 COG3886 PLD-like domain 0.044192
26 COG0509 glycine decarboxylation via glycine cleavage system 0.043420
27 32G2Z Lysin motif 0.043081
28 COG1554 hydrolase, family 65, central catalytic 0.043012
29 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 0.042915
30 COG0663 COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily -0.042765
31 COG4709 membrane 0.042682
32 COG2918 glutathione biosynthetic process 0.042672
33 COG2160 L-arabinose isomerase activity 0.042598
34 COG0790 COG0790 FOG TPR repeat, SEL1 subfamily 0.042054
35 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family 0.042053
36 COG3208 Thioesterase involved in non-ribosomal peptide biosynthesis 0.042019
37 COG1168 Bifunctional PLP-dependent enzyme with beta-cystaTHIonase and maltose regulon repressor activities -0.041588
38 COG3320 Male sterility 0.041571
39 COG3967 Belongs to the short-chain dehydrogenases reductases (SDR) family -0.041571
40 COG1220 this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis -0.041542
41 COG0562 UDP-galactopyranose mutase -0.041222
42 COG0801 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.041042
43 COG4679 PFAM Phage derived protein Gp49-like (DUF891) -0.040725
44 COG1459 type II secretion system -0.040180
45 COG3542 PFAM Cupin superfamily (DUF985) 0.039875
46 COG0754 glutathionylspermidine amidase activity 0.039800
47 COG3194 Catalyzes the catabolism of the allantoin degradation intermediate (S)-ureidoglycolate, generating urea and glyoxylate. Involved in the utilization of allantoin as nitrogen source 0.039706
48 COG3871 stress protein (general stress protein 26) -0.039659
49 COG0427 acetyl-CoA hydrolase -0.039376
50 COG4521 taurine ABC transporter 0.039349
51 COG1064 alcohol dehydrogenase 0.039324
52 COG3195 allantoin biosynthetic process 0.039072
53 31EGY 0.039041
54 329A3 Psort location CytoplasmicMembrane, score 0.038987
55 31PIN 0.038693
56 COG3942 CHAP domain 0.038656
57 COG0785 Cytochrome C biogenesis protein -0.038421
58 32RPD Erf family 0.038181
59 COG2351 hydroxyisourate hydrolase activity 0.038050
60 COG0477 Major facilitator Superfamily 0.037850
61 COG3480 Lon protease (S16) C-terminal proteolytic domain 0.037603
62 COG0716 FMN binding -0.037412
63 COG0239 Important for reducing fluoride concentration in the cell, thus reducing its toxicity -0.037167
64 COG2089 acid synthase -0.037114
65 334W6 Novel toxin 15 -0.037057
66 COG0731 radical SAM domain protein -0.037043
67 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component -0.036902
68 COG0471 metal ion transport -0.036836
69 COG4587 transport system, permease component 0.036768
70 COG1636 Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr) -0.036423
71 32SUJ Domain of unknown function (DUF3560) 0.036409
72 COG5350 Protein tyrosine phosphatase 0.036374
73 COG0626 cystathionine gamma-synthase activity 0.036275
74 COG2425 protein containing a von Willebrand factor type A (vWA) domain 0.036255
75 COG1233 COG1233 Phytoene dehydrogenase and related -0.036205
76 COG0482 sulfurtransferase activity -0.036144
77 COG3459 Glycosyltransferase 36 associated 0.036136
78 COG3290 protein histidine kinase activity 0.036084
79 COG1116 anion transmembrane transporter activity 0.036030
80 338TK 0.035981
81 COG3738 Protein conserved in bacteria 0.035954
82 COG1887 Glycosyl glycerophosphate transferases involved in teichoic acid biosynthesis TagF TagB EpsJ RodC -0.035886
83 COG1963 PFAM Acid phosphatase vanadium-dependent haloperoxidase related -0.035788
84 COG4630 Xanthine dehydrogenase iron-sulfur cluster and FAD-binding subunit A 0.035671
85 2ZF6Z Tautomerase enzyme 0.035502
86 2ZY3R integral membrane protein -0.035399
87 COG0641 radical SAM -0.035354
88 COG5278 phosphoserine phosphatase activity 0.035248
89 COG0846 NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form -0.035188
90 COG0372 Belongs to the citrate synthase family -0.035091
91 COG0715 COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components 0.035045
92 COG4703 Protein of unknown function (DUF1797) 0.035032
93 COG3698 Phosphodiester glycosidase 0.034963
94 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein -0.034955
95 COG3225 cell adhesion 0.034873
96 COG2133 pyrroloquinoline quinone binding 0.034774
97 COG3463 Predicted membrane protein (DUF2079) -0.034674
98 COG1720 tRNA m6t6A37 methyltransferase activity 0.034552
99 COG2872 Ser-tRNA(Ala) hydrolase activity -0.034317
100 COG1943 Transposase 0.034301
101 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 0.034220
102 33F9N -0.033974
103 COG5586 Nucleotidyl transferase AbiEii toxin, Type IV TA system -0.033874
104 COG1883 Na -transporting methylmalonyl-CoA oxaloacetate decarboxylase, beta subunit 0.033862
105 COG1072 (Pantothenic acid kinase)) -0.033714
106 COG1278 Cold shock -0.033621
107 COG0704 Plays a role in the regulation of phosphate uptake 0.033508
108 COG1930 Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import -0.033423
109 COG2087 Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate 0.033384
110 COG0210 DNA helicase 0.033382
111 COG2071 gamma-glutamyl-gamma-aminobutyrate hydrolase activity 0.033356
112 COG0205 6-phosphofructokinase activity -0.033262
113 COG4720 Psort location CytoplasmicMembrane, score 0.033189
114 COG0327 Belongs to the GTP cyclohydrolase I type 2 NIF3 family 0.033018
115 COG2832 Protein of unknown function (DUF454) 0.032743
116 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the -0.032730
117 COG0572 uridine kinase -0.032685
118 COG1970 mechanosensitive ion channel activity -0.032673
119 COG3428 Bacterial PH domain -0.032607
120 COG4642 MORN repeat 0.032594
121 COG4545 Glutaredoxin-related protein -0.032587
122 COG2038 nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity 0.032554
123 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity -0.032421
124 COG0645 Protein conserved in bacteria 0.032405
125 32AT1 -0.032241
126 COG1169 isochorismate synthase -0.032212
127 COG5006 permease, DMT superfamily -0.032152
128 COG1454 alcohol dehydrogenase 0.032072
129 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 -0.032004
130 COG3645 SOS response -0.031997
131 COG0674 pyruvate-flavodoxin oxidoreductase activity -0.031974
132 COG3633 Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system) 0.031962
133 32T5K COG0810 Periplasmic protein TonB links inner and outer membranes 0.031945
134 COG1803 Methylglyoxal synthase -0.031856
135 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 -0.031819
136 COG4770 biotin carboxylase activity 0.031795
137 COG1748 Saccharopine dehydrogenase 0.031780
138 33CYH ParB-like nuclease domain 0.031732
139 COG0667 Aldo Keto reductase 0.031685
140 COG4302 ethanolamine ammonia-lyase activity 0.031670
141 2Z7KY Protein of unknown function (DUF4256) 0.031656
142 COG3959 Transketolase, thiamine diphosphate binding domain -0.031586
143 31R8Y 0.031447
144 COG3707 response regulator 0.031417
145 COG1055 Involved in arsenical resistance. Thought to form the channel of an arsenite pump 0.031293
146 COG2964 Protein conserved in bacteria 0.031273
147 2Z7PD Psort location CytoplasmicMembrane, score 0.031188
148 COG2001 Belongs to the MraZ family -0.031096
149 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 0.031065
150 32Y3S ABC-2 family transporter protein -0.031044
151 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 -0.031009
152 COG2509 5-formyltetrahydrofolate cyclo-ligase activity -0.030941
153 COG1832 CoA-binding protein 0.030910
154 COG2804 Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB -0.030858
155 COG1598 PFAM Uncharacterised protein family UPF0150 0.030823
156 COG2348 transferase activity, transferring amino-acyl groups 0.030771
157 COG4409 exo-alpha-(2->6)-sialidase activity 0.030759
158 COG3189 MarR family transcriptional regulator -0.030706
159 COG1708 protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity 0.030564
160 COG3576 pyridoxamine 5-phosphate 0.030514
161 COG5283 actin binding -0.030476
162 COG5658 integral membrane protein 0.030465
163 COG2018 Roadblock/LC7 domain 0.030410
164 COG4487 mechanosensitive ion channel activity 0.030395
165 2Z9EN PDDEXK-like domain of unknown function (DUF3799) 0.030377
166 COG1253 flavin adenine dinucleotide binding 0.030314
167 COG5620 Psort location Cytoplasmic, score -0.030288
168 COG0655 NAD(P)H dehydrogenase (quinone) activity 0.030121
169 COG3639 organic phosphonate transmembrane transporter activity -0.030047
170 COG1989 Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue -0.030032
171 COG4303 Ethanolamine ammonia lyase large subunit 0.029952
172 COG1594 Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and or for immediate growth after restoration of oxygen 0.029930
173 COG3201 nicotinamide mononucleotide transporter 0.029798
174 COG4796 Type ii and iii secretion system protein -0.029782
175 COG0513 Belongs to the DEAD box helicase family -0.029782
176 COG0512 Glutamine amidotransferase of anthranilate synthase -0.029745
177 2ZM0Q NUDIX domain -0.029723
178 COG3442 glutamine amidotransferase 0.029693
179 COG5405 Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery -0.029655
180 COG4894 glucomannan catabolic process 0.029622
181 COG4262 Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine 0.029510
182 COG4405 Protein conserved in bacteria 0.029488
183 COG0518 GMP synthase (glutamine-hydrolyzing) activity 0.029471
184 COG4121 Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34 -0.029398
185 2ZT9T -0.029379
186 COG1179 involved in molybdopterin and THIamine biosynthesis family 1 -0.029378
187 COG1451 nucleotide metabolic process -0.029319
188 COG0604 alcohol dehydrogenase 0.029216
189 COG0722 Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP) 0.029106
190 COG1513 Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide 0.029091
191 COG0779 Required for maturation of 30S ribosomal subunits -0.029072
192 32W8Q -0.028991
193 COG3680 regulation of methylation-dependent chromatin silencing 0.028984
194 COG2608 mercury ion transmembrane transporter activity -0.028914
195 COG2062 phosphohistidine phosphatase, SixA 0.028913
196 COG4186 nucleotidyltransferase activity 0.028899
197 COG4257 antibiotic catabolic process 0.028894
198 COG2998 abc-type tungstate transport system, permease component 0.028884
199 COG3584 3D domain protein -0.028857
200 COG1444 tRNA N-acetyltransferase activity 0.028839
201 COG0189 ligase activity -0.028685
202 318XJ Psort location CytoplasmicMembrane, score 0.028667
203 COG3469 chitinase activity 0.028597
204 COG2966 Psort location CytoplasmicMembrane, score -0.028557
205 COG0600 ABC-type nitrate sulfonate bicarbonate transport system permease component 0.028551
206 31TB7 0.028540
207 COG4585 Histidine kinase -0.028397
208 COG1766 The M ring may be actively involved in energy transduction -0.028329
209 33NZ3 Domain of unknown function (DUF4368) -0.028276
210 COG1794 racemase activity, acting on amino acids and derivatives -0.028229
211 COG4320 Protein conserved in bacteria 0.028187
212 COG2723 6-phospho-beta-galactosidase activity 0.028139
213 COG0328 RNA-DNA hybrid ribonuclease activity 0.028115
214 340N5 0.028096
215 COG1763 Mo-molybdopterin cofactor biosynthetic process -0.028047
216 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 0.027987
217 COG4185 zeta toxin 0.027972
218 32T6S TPM domain 0.027923
219 30XWW -0.027889
220 COG0026 Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR) 0.027872
221 307WW 0.027829
222 COG0095 Lipoate-protein ligase 0.027817
223 COG1206 Catalyzes the folate-dependent formation of 5-methyl- uridine at position 54 (M-5-U54) in all tRNAs -0.027797
224 COG3257 ureidoglycine aminohydrolase activity 0.027796
225 COG3526 Rdx family 0.027759
226 COG1721 protein (some members contain a von Willebrand factor type A (vWA) domain 0.027759
227 COG1134 teichoic acid transport -0.027738
228 33BGI Parallel beta-helix repeats 0.027674
229 COG0334 Belongs to the Glu Leu Phe Val dehydrogenases family 0.027653
230 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 -0.027574
231 COG4478 integral membrane protein -0.027551
232 COG0068 Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of NiFe -hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide 0.027502
233 COG3559 Exporter of polyketide antibiotics -0.027436
234 COG1292 Belongs to the BCCT transporter (TC 2.A.15) family -0.027433
235 COG4096 Type I site-specific restriction-modification system, R (Restriction) subunit and related -0.027423
236 COG1167 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs 0.027414
237 2ZBRM Accessory Sec system protein Asp1 0.027393
238 COG2030 dehydratase -0.027380
239 COG0114 fumarate hydratase activity -0.027339
240 33AWG Helix-turn-helix domain 0.027202
241 32H4Q Bacterial regulatory proteins, tetR family 0.027197
242 COG2326 polyphosphate kinase activity 0.027150
243 33VMR -0.027103
244 2Z7TS Domain of unknown function (DUF4317) 0.027074
245 COG1240 Involved in chlorophyll biosynthesis. Catalyzes the insertion of magnesium ion into protoporphyrin IX to yield Mg- protoporphyrin IX 0.027054
246 33BRY 0.027046
247 COG1230 cation diffusion facilitator family transporter 0.026911
248 COG3876 Protein conserved in bacteria -0.026894
249 33A7N Cysteine-rich CWC 0.026863
250 COG0786 glutamate:sodium symporter activity 0.026816