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 COG0130 Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs 0.174058
2 COG1187 pseudouridine synthase activity 0.171852
3 COG0101 tRNA pseudouridine synthase activity 0.171445
4 COG0564 pseudouridine synthase activity 0.170329
5 COG0729 surface antigen 0.065328
6 COG4977 sequence-specific DNA binding 0.064866
7 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family 0.063581
8 33AGD 0.059815
9 32UTB 0.059508
10 30YFD 0.059495
11 33Z2K 0.059494
12 34AYS 0.059494
13 COG3226 Transcriptional regulator 0.055445
14 COG3590 peptidase 0.054414
15 COG1266 CAAX protease self-immunity 0.054301
16 COG1376 ErfK ybiS ycfS ynhG family protein 0.053093
17 COG1012 belongs to the aldehyde dehydrogenase family 0.037587
18 COG0596 Alpha beta hydrolase 0.036515
19 COG3239 Fatty acid desaturase 0.035138
20 COG4638 Rieske (2fe-2S) 0.034438
21 COG0625 glutathione transferase activity 0.033639
22 COG5517 Aromatic-ring-hydroxylating dioxygenase beta subunit 0.032469
23 COG4569 acetaldehyde dehydrogenase (acetylating) activity 0.032269
24 COG3971 2-oxopent-4-enoate hydratase activity 0.031984
25 COG4774 siderophore transport 0.030894
26 COG3193 protein, possibly involved in utilization of glycolate and propanediol 0.030515
27 COG0365 Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA 0.029773
28 COG3917 2-hydroxychromene-2-carboxylate isomerase 0.029734
29 COG3347 Dehydrogenase 0.027983
30 32TDU 0.027904
31 COG2146 nitrite reductase [NAD(P)H] activity 0.027709
32 COG1942 4-Oxalocrotonate Tautomerase 0.026804
33 COG0329 Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA) 0.026761
34 COG2514 catechol 2,3-dioxygenase activity 0.026442
35 COG1251 Belongs to the nitrite and sulfite reductase 4Fe-4S domain family 0.026392
36 COG5639 conserved small protein 0.026347
37 COG1995 Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP) 0.026307
38 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity 0.023312
39 COG1961 COG1961 Site-specific recombinases, DNA invertase Pin homologs 0.020947
40 COG0543 2 iron, 2 sulfur cluster binding 0.020152
41 COG1080 General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) 0.019619
42 COG2363 Small membrane protein 0.018940
43 COG0701 Predicted permease -0.018143
44 COG3604 Transcriptional regulator 0.018141
45 2ZAHD 0.017211
46 32ZT3 Thioredoxin domain -0.017137
47 COG0567 Dehydrogenase, E1 component 0.017030
48 COG2015 COG2015, Alkyl sulfatase and related hydrolases 0.016134
49 COG2910 NAD(P)H-binding 0.016127
50 COG3231 kanamycin kinase activity 0.015940
51 2ZA7W Protein of unknown function (DUF1173) 0.015932
52 COG5305 Membrane -0.015891
53 COG1592 Rubrerythrin -0.015792
54 32NDS Fibronectin type 3 domain 0.015785
55 30IXR 0.015656
56 COG0431 NADPH-dependent FMN reductase 0.015643
57 COG4185 zeta toxin 0.015515
58 31UR3 0.015496
59 31H4F Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily 0.015414
60 30WTE 0.015398
61 COG4624 Iron only hydrogenase large subunit, C-terminal domain -0.015362
62 343SX TrbC/VIRB2 family 0.015337
63 32T9Z Protein of unknown function (DUF3169) 0.015247
64 30S7A 0.015232
65 COG1331 Highly conserved protein containing a thioredoxin domain -0.015220
66 32GX3 0.015215
67 32SUJ Domain of unknown function (DUF3560) 0.015167
68 COG1070 Carbohydrate kinase -0.015088
69 345K5 0.015018
70 2ZCN5 Type IV secretion system proteins 0.015006
71 COG0613 PHP domain protein -0.014987
72 2ZXKF 0.014947
73 2ZX78 0.014932
74 2ZXYI 0.014932
75 304YF 0.014932
76 305D4 0.014932
77 30DSN 0.014932
78 31S6W 0.014932
79 31SFI 0.014932
80 32CEH 0.014932
81 32KA0 0.014932
82 32V4T 0.014932
83 33AI9 0.014932
84 3481C 0.014932
85 COG0208 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides 0.014918
86 COG3329 Na+-dependent bicarbonate transporter superfamily 0.014898
87 33DQM 0.014798
88 COG2963 transposase activity 0.014434
89 COG2826 transposase and inactivated derivatives, IS30 family 0.014308
90 COG1834 amidinotransferase 0.014290
91 COG0475 glutathione-regulated potassium exporter activity -0.014223
92 COG0411 ABC transporter -0.014201
93 32XK3 Conjugal transfer protein TraD 0.014195
94 COG2169 Transcriptional regulator 0.014187
95 COG1192 Involved in chromosome partitioning 0.014121
96 COG3564 Protein conserved in bacteria 0.014006
97 COG2162 N-hydroxyarylamine O-acetyltransferase activity 0.013908
98 COG0262 Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis 0.013821
99 COG4232 protein-disulfide reductase activity 0.013756
100 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 -0.013724
101 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC -0.013636
102 COG1072 (Pantothenic acid kinase)) 0.013633
103 COG1032 radical SAM domain protein -0.013574
104 COG4637 Psort location Cytoplasmic, score -0.013520
105 COG4962 Type ii secretion system protein e 0.013481
106 COG1655 Protein conserved in bacteria -0.013435
107 COG0459 protein refolding 0.013386
108 COG1509 lysine 2,3-aminomutase activity -0.013368
109 COG2006 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.013366
110 COG1145 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.013316
111 COG3449 Inhibits the supercoiling activity of DNA gyrase. Acts by inhibiting DNA gyrase at an early step, prior to (or at the step of) binding of DNA by the gyrase. It protects cells against toxins that target DNA gyrase, by inhibiting activity of these toxins and reducing the formation of lethal double-strand breaks in the cell -0.013216
112 COG0508 dehydrogenase complex catalyzes the overall conversion of 0.013033
113 COG1350 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine -0.012973
114 COG0410 ABC transporter -0.012963
115 345M7 C4-type zinc ribbon domain -0.012951
116 COG2346 COG2346, Truncated hemoglobins 0.012922
117 COG1151 hydroxylamine reductase activity -0.012918
118 COG1550 Protein conserved in bacteria -0.012861
119 COG0684 Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions 0.012662
120 COG4177 L-phenylalanine transmembrane transporter activity -0.012644
121 COG0674 pyruvate-flavodoxin oxidoreductase activity -0.012637
122 COG0420 3'-5' exonuclease activity 0.012606
123 COG2210 Belongs to the sulfur carrier protein TusA family -0.012517
124 COG3877 Protein conserved in bacteria -0.012483
125 COG0234 Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter 0.012439
126 COG3702 type iv secretory pathway 0.012381
127 COG2048 Heterodisulfide reductase, subunit B -0.012356
128 COG3664 PFAM glycoside hydrolase family 39 -0.012313
129 COG1278 Cold shock 0.012287
130 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin -0.012264
131 COG2842 Transposition protein -0.012205
132 COG1304 FMN binding 0.012172
133 COG0559 Belongs to the binding-protein-dependent transport system permease family -0.012105
134 COG1525 nuclease 0.012057
135 COG3182 Iron-regulated membrane protein 0.011941
136 COG0523 cobalamin synthesis protein 0.011940
137 COG3504 Conjugal transfer protein 0.011851
138 COG1342 Belongs to the UPF0251 family -0.011781
139 COG1668 transmembrane transport -0.011684
140 COG3033 Beta-eliminating lyase -0.011682
141 COG2030 dehydratase 0.011646
142 COG1647 Serine aminopeptidase, S33 0.011625
143 COG1328 CTP reductase activity -0.011568
144 COG2605 GHMP kinase -0.011558
145 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 -0.011548
146 COG2221 Nitrite and sulphite reductase 4Fe-4S -0.011542
147 COG1324 tolerance protein 0.011498
148 COG4656 Part of a membrane complex involved in electron transport -0.011465
149 COG3736 Type IV secretory pathway, component VirB8 0.011413
150 COG0604 alcohol dehydrogenase 0.011355
151 COG3620 sequence-specific DNA binding 0.011199
152 COG0279 D-glycero-D-manno-heptose 7-phosphate biosynthetic process -0.011195
153 COG2050 protein possibly involved in aromatic compounds catabolism 0.011192
154 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.011153
155 COG3505 Type IV secretory pathway VirD4 0.011124
156 COG0316 Belongs to the HesB IscA family 0.011042
157 COG4559 Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system -0.011029
158 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates -0.011015
159 COG1752 Esterase of the alpha-beta hydrolase superfamily -0.011008
160 COG0432 Pfam Uncharacterised protein family UPF0047 -0.010880
161 COG1030 water channel activity -0.010857
162 COG1908 Methyl-viologen-reducing hydrogenase, delta subunit -0.010836
163 COG1245 4Fe-4S binding domain -0.010834
164 COG2303 Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine at the same rate 0.010833
165 COG1003 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor -0.010821
166 COG4733 cellulase activity -0.010781
167 COG1013 pyruvate-flavodoxin oxidoreductase activity -0.010734
168 COG4623 carbon-oxygen lyase activity, acting on polysaccharides 0.010646
169 COG0026 Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR) 0.010644
170 COG3704 protein secretion by the type IV secretion system 0.010610
171 COG0632 four-way junction helicase activity 0.010537
172 COG2348 transferase activity, transferring amino-acyl groups -0.010406
173 COG1089 Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose -0.010377
174 COG1313 radical SAM domain protein -0.010363
175 COG1023 phosphogluconate dehydrogenase (decarboxylating) activity -0.010347
176 COG2089 acid synthase -0.010337
177 COG5006 permease, DMT superfamily 0.010291
178 COG5504 Zn-dependent protease 0.010262
179 COG1083 cytidylyl-transferase -0.010178
180 COG1139 Iron-sulfur cluster binding protein -0.010169
181 COG0757 Catalyzes a trans-dehydration via an enolate intermediate -0.010127
182 COG1876 peptidase activity 0.010098
183 COG5512 Zn-ribbon-containing possibly RNA-binding protein and truncated derivatives -0.010093
184 COG4119 NUDIX hydrolase -0.010026
185 COG3144 bacterial-type flagellum assembly -0.009970
186 COG0683 leucine binding -0.009970
187 COG4108 Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP 0.009953
188 COG1449 Belongs to the glycosyl hydrolase 57 family -0.009938
189 COG3262 NADH dehydrogenase (ubiquinone), 30 kDa subunit -0.009922
190 COG1695 Transcriptional regulator 0.009905
191 345AV Cyclic nucleotide-monophosphate binding domain -0.009897
192 COG3576 pyridoxamine 5-phosphate -0.009879
193 COG2844 Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen -0.009870
194 COG1294 oxidase, subunit 0.009855
195 COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase 0.009834
196 COG1666 GTP binding 0.009818
197 COG0276 Catalyzes the ferrous insertion into protoporphyrin IX 0.009775
198 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 -0.009772
199 COG4843 Uncharacterized protein conserved in bacteria (DUF2179) -0.009767
200 COG4097 nitric oxide dioxygenase activity 0.009750
201 COG1492 cobalamin metabolic process -0.009747
202 COG3426 butyrate kinase activity -0.009729
203 COG0509 glycine decarboxylation via glycine cleavage system -0.009677
204 COG2948 multi-organism process 0.009659
205 COG1764 response to oxidative stress 0.009650
206 COG3393 -acetyltransferase 0.009634
207 COG1905 PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit -0.009606
208 COG3635 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity -0.009603
209 COG1686 Belongs to the peptidase S11 family 0.009587
210 COG3655 Transcriptional regulator 0.009578
211 COG3221 ABC-type phosphate phosphonate transport system periplasmic component -0.009572
212 COG1514 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester -0.009498
213 COG0803 Belongs to the bacterial solute-binding protein 9 family -0.009485
214 COG3961 Belongs to the TPP enzyme family 0.009463
215 COG2309 aminopeptidase activity -0.009460
216 COG3853 Toxic anion resistance protein (TelA) 0.009454
217 COG1002 Type II restriction enzyme, methylase subunits -0.009441
218 COG1516 flagellar protein fliS -0.009433
219 COG3324 translation initiation factor activity 0.009396
220 COG3284 Transcriptional regulator 0.009387
221 COG0109 protoheme IX farnesyltransferase activity 0.009362
222 COG0827 DNA restriction-modification system 0.009338
223 COG0040 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of hisG enzymatic activity -0.009336
224 COG3384 dioxygenase 0.009328
225 COG2072 flavoprotein involved in K transport 0.009266
226 COG3024 Inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. Acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase 0.009260
227 COG2185 Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly -0.009258
228 COG0650 Formate hydrogenlyase subunit 4 -0.009248
229 33YJY -0.009234
230 COG2609 component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) 0.009227
231 COG3973 AAA domain 0.009217
232 COG4798 methyltransferase -0.009213
233 COG3303 Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process -0.009207
234 COG1150 heterodisulfide reductase subunit C -0.009206
235 COG2828 Protein conserved in bacteria 0.009204
236 COG0680 Initiates the rapid degradation of small, acid-soluble proteins during spore germination -0.009193
237 COG1226 (belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family) 0.009182
238 COG0583 DNA-binding transcription factor activity 0.009166
239 COG0342 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA -0.009152
240 COG4584 PFAM Integrase catalytic -0.009131
241 COG1566 PFAM secretion protein HlyD family protein -0.009105
242 COG0106 1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase -0.009098
243 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 0.009082
244 COG0753 catalase activity 0.009082
245 COG1237 beta-lactamase domain protein -0.009077
246 3482A -0.009073
247 COG1703 isobutyryl-CoA mutase activity -0.009057
248 COG3540 Alkaline phosphatase 0.009043
249 COG1454 alcohol dehydrogenase -0.009024
250 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 0.009015