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 ENOG4107QS5 ATP-dependent DNA helicase RecQ -0.011632
2 ENOG4105CFT Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) 0.011446
3 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) 0.011268
4 ENOG4107R76 Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) 0.011265
5 ENOG4105E0Y RtcB Protein 0.010892
6 ENOG4105DZR Type I site-specific deoxyribonuclease 0.010847
7 ENOG4105KJJ Uncharacterized ACR, COG1993 0.010398
8 ENOG4107R69 radical SAM domain protein 0.010388
9 ENOG4107XZE radical SAM domain protein 0.009862
10 ENOG4105C7R Atpase associated with various cellular activities aaa_3 0.009762
11 ENOG4108UVJ appr-1-p processing domain protein 0.009418
12 ENOG4107TZP faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.009355
13 ENOG4105VDU S-adenosyl-l-methionine hydroxide adenosyltransferase 0.009128
14 ENOG4105C5H ABC transporter -0.009020
15 ENOG4108RN8 Uncharacterised protein family UPF0047 0.008957
16 ENOG4105DTT CRISPR-associated helicase, cas3 0.008930
17 ENOG4107TXC Transcriptional regulator -0.008724
18 ENOG4105VF7 tolerance protein 0.008679
19 ENOG4105C7Z Conserved Protein 0.008373
20 ENOG410681U heavy metal transport detoxification protein 0.008261
21 ENOG4105DKQ ROK family 0.008236
22 ENOG4105EF4 Pfam:DUF151 0.008235
23 ENOG4107XJQ DihydrolipoyLLysine-residue acetyltransferase 0.008219
24 ENOG4105KVH Transcriptional regulator -0.008211
25 ENOG4105U2P bfd domain protein (2fe-2s)-binding domain protein 0.008192
26 ENOG4105N7I GtrA-like protein 0.008177
27 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase 0.008104
28 ENOG4105NBF ammecr1 domain protein 0.008039
29 ENOG4105D4C amylO-alpha-16-glucosidase 0.008038
30 ENOG4105D08 cbs domain and cyclic nucleotide-regulated nucleotidyltransferase 0.008018
31 ENOG4108V4Y Phosphoribosyltransferase 0.008011
32 ENOG4108SK6 type III restriction system methylase 0.007998
33 ENOG4107Y9E nuclease 0.007956
34 ENOG410604X glycoside hydrolase, family 57 0.007927
35 ENOG4105C30 Nad-dependent epimerase dehydratase -0.007904
36 ENOG4105CYW agmatinase 0.007841
37 ENOG4105D8I Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity) 0.007785
38 ENOG4105EEX Two component transcriptional regulator (Winged helix family -0.007673
39 ENOG4105DGU Histone deacetylase 0.007659
40 ENOG4105D5S 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 (By similarity) -0.007647
41 ENOG4105F9F transposase 0.007535
42 ENOG4105C8A 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 (By similarity) -0.007519
43 ENOG4107SE7 Glycosyl transferase, family 2 0.007484
44 ENOG4107QWE )-transporter -0.007457
45 ENOG4106IPI cyclase, family 0.007413
46 ENOG4107B04 DUF218 domain 0.007392
47 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.007390
48 ENOG4105X3E Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine (By similarity) 0.007374
49 ENOG4107YE2 glutaredoxin-like protein, YruB-family 0.007372
50 ENOG4108Z73 Siroheme synthase 0.007367
51 ENOG4105CH2 amidohydrolase 0.007344
52 ENOG4106YN8 Prenyltransferase 0.007342
53 ENOG4105C53 Part of the ABC transporter complex PotABCD involved in spermidine putrescine import. Responsible for energy coupling to the transport system (By similarity) 0.007290
54 ENOG4108ZEK Roadblock lc7 family protein 0.007268
55 ENOG41061AI Protein of unknown function (DUF2905) 0.007254
56 ENOG4105C5I Dehydrogenase 0.007196
57 ENOG4105DCG PHP domain protein 0.007194
58 ENOG4105IQ5 FAD linked oxidase domain protein 0.007184
59 ENOG4108UYR glutaredoxin-like domain protein 0.007159
60 ENOG4105E3W Two component transcriptional regulator (Winged helix family -0.007131
61 ENOG41064PG 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 (By similarity) 0.007129
62 ENOG4108RG3 short-chain dehydrogenase reductase 0.007116
63 ENOG4108V1U phospholipid-binding protein 0.007107
64 ENOG4105P52 geranylgeranyl reductase 0.007097
65 ENOG4108MJI response regulator 0.007083
66 ENOG4108Z66 YbaK ebsC protein -0.007063
67 ENOG4105MME Sugar o-acyltransferase, sialic acid o-acetyltransferase neud family -0.007044
68 ENOG4105ERM Periplasmic serine protease 0.007041
69 ENOG4108EZH mechanosensitive ion channel 0.007028
70 ENOG4106MEM Type III 0.007007
71 ENOG4108EF1 Bacterial extracellular solute-binding protein 0.006965
72 ENOG4105CPC Aldo Keto reductase 0.006905
73 ENOG4105E26 Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and or degradation of damaged proteins (By similarity) 0.006893
74 ENOG4105D38 putrescine abc transporter 0.006843
75 ENOG4105C1J atp-dependent rna helicase -0.006835
76 ENOG4108JU2 Major facilitator superfamily MFS_1 0.006821
77 ENOG4105EFU 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 (By similarity) 0.006812
78 ENOG4105WI7 Cupin 2, conserved barrel domain protein -0.006788
79 ENOG4105CEP NADH dehydrogenase -0.006776
80 ENOG4106IVZ signal transduction Histidine kinase -0.006741
81 ENOG4108YYA Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity) 0.006694
82 ENOG4105DER m42 family -0.006676
83 ENOG41081FK Mediates zinc uptake. May also transport other divalent cations (By similarity) -0.006671
84 ENOG4105K4P CoA-binding domain protein 0.006667
85 ENOG41085CW NA 0.006664
86 ENOG4107W76 Pfam:DUF548 0.006662
87 ENOG4105KHC sulfurtransferase 0.006647
88 ENOG4105CCX Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) 0.006622
89 ENOG4107QYG anthranilate phosphoribosyltransferase 0.006588
90 ENOG41068Y2 NA 0.006563
91 ENOG4105F8F radical SAM domain protein -0.006529
92 ENOG4108V9Q carbonic anhydrase -0.006509
93 ENOG4105DFE Dna adenine methylase 0.006485
94 ENOG4108VDZ Binding-protein-dependent transport systems, inner membrane component 0.006472
95 ENOG4107JU3 glycosyl transferase group 1 0.006471
96 ENOG4108Z4T Peptidase M50 0.006467
97 ENOG4105F8C transglutaminase domain-containing protein 0.006446
98 ENOG4105C94 Transporter -0.006437
99 ENOG4105EZI multiple antibiotic resistance (MarC)-related protein 0.006433
100 ENOG4108VX5 3-methyladenine DNA glycosylase -0.006431
101 ENOG4106K5Q Modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. It cleaves transiently a single DNA strand and remains covalently bound to the 5' DNA end through a tyrosine residue. May be involved in rewinding the DNA strands in the regions of the chromosome that have opened up to allow transcription or replication (By similarity) 0.006392
102 ENOG4107R7Y intracellular protease Pfpi family 0.006381
103 ENOG4108V06 Glutathione peroxidase -0.006368
104 ENOG4105ECP epimerase -0.006311
105 ENOG4105D56 permease protein 0.006308
106 ENOG4105X1V 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 (By similarity) 0.006291
107 ENOG4107YDG Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization (By similarity) 0.006284
108 ENOG4105W4R Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) 0.006258
109 ENOG4107RIU May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins (By similarity) 0.006209
110 ENOG4106C3K NA 0.006201
111 ENOG4105CSX c4-dicarboxylate anaerobic carrier -0.006199
112 ENOG4105MKH Cupin 2 Conserved Barrel Domain Protein -0.006186
113 ENOG4107QN2 dihydrolipoyl dehydrogenase 0.006177
114 ENOG4108ZVT methylmalonyl-coA epimerase 0.006171
115 ENOG4107TR4 phosphate binding protein 0.006170
116 ENOG410908R Methenyltetrahydrofolate cyclohydrolase 0.006160
117 ENOG4107VT3 K03386 peroxiredoxin (alkyl hydroperoxide reductase subunit C) EC 1.11.1.15 0.006157
118 ENOG41082AZ Galactose-1-phosphate uridyl transferase, N-terminal domain 0.006141
119 ENOG4108VHV Membrane 0.006138
120 ENOG4105C1X Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity (By similarity) -0.006136
121 ENOG4105D5T phosphonate abc transporter -0.006126
122 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 -0.006124
123 ENOG4107MS2 NA 0.006117
124 ENOG4105CK0 Membrane bOund o-acyl transferase mboat family protein -0.006091
125 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase 0.006089
126 ENOG4107RR9 sulfate transporter -0.006087
127 ENOG4108UN4 phage SPO1 DNA polymerase-related protein 0.006084
128 ENOG4105DWF phosphomethylpyrimidine kinase -0.006081
129 ENOG4105CI3 gtp-binding protein typa -0.006078
130 ENOG4107R56 PP-loop domain protein 0.006072
131 ENOG4106FN3 tellurium resistance protein -0.006067
132 ENOG4108T47 CRISPR-associated RAMP protein, Csm4 family 0.006065
133 ENOG4105CHW UPF0052 protein 0.006038
134 ENOG4105D2M Aldolase -0.006036
135 ENOG4105ICD Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.005982
136 ENOG4107QRA Extracellular solute-binding protein, family 5 0.005980
137 ENOG4107QPR SAICAR synthetase 0.005967
138 ENOG4107YVA Cytidine and deoxycytidylate deaminase zinc-binding region 0.005952
139 ENOG4105KI2 Urea amidohydrolase subunit beta 0.005948
140 ENOG4105D9N nucleoside -0.005942
141 ENOG4108IJ7 Glycine betaine -0.005940
142 ENOG4105BZX nudix hydrolase 0.005910
143 ENOG4105DAP Nicotinate phosphoribosyltransferase 0.005879
144 ENOG4108DZW glycine betaine transport system -0.005879
145 ENOG4105US7 Histidine kinase 0.005877
146 ENOG41086ZZ preprotein translocase subunit SecE 0.005876
147 ENOG4108V0P LemA family -0.005872
148 ENOG4106985 NA 0.005865
149 ENOG4108M67 NA 0.005864
150 ENOG4105MA4 psp1 domain protein 0.005855
151 ENOG4108MAW Extracellular solute-binding protein family 3 -0.005847
152 ENOG4105D53 Catalyzes the hydrolysis of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil (By similarity) 0.005834
153 ENOG410664T MutT NUDIX family protein 0.005749
154 ENOG4107SJW iron permease, FTR1 0.005730
155 ENOG4108XWQ Pfam:DUF820 0.005717
156 ENOG4108V4M Cobalt abc transporter 0.005716
157 ENOG4107V9G glycyl-radical enzyme activating protein family -0.005706
158 ENOG4108UNR Metal Dependent Phosphohydrolase 0.005697
159 ENOG4105CQ9 aldose 1-epimerase -0.005695
160 ENOG4105EI6 lantibiotic dehydratase domain protein 0.005691
161 ENOG4105EHU Circadian clock protein KaiC 0.005690
162 ENOG4108ZVP Domain of unknown function (DUF1931) 0.005654
163 ENOG4105D3Y Na H antiporter -0.005654
164 ENOG4105TNC Membrane 0.005653
165 ENOG4105JZI cytochrome P450 -0.005641
166 ENOG4107QUS 2-isopropylmalate synthase homocitrate synthase family protein 0.005627
167 ENOG4106BPA glutaredoxin 2 0.005626
168 ENOG4108K3X Transposase, IS605 OrfB family 0.005621
169 ENOG41063MK Putative zinc ribbon domain 0.005615
170 ENOG4108J5B ABC transporter 0.005614
171 ENOG4105DQR SNARE associated Golgi -0.005579
172 ENOG4107QSG brancheD-chain amino acid aminotransferase 0.005575
173 ENOG4105CS2 ec 3.2.1.21 0.005573
174 ENOG4105DQU oxidoreductase, subunit beta 0.005560
175 ENOG4107QZI cell division protein FtsK -0.005560
176 ENOG4108PDN Crispr-associated ramp protein, Cmr4 family 0.005547
177 ENOG4108YH3 Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.005537
178 ENOG4105PW2 ggdef family 0.005533
179 ENOG4105CRD Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) (By similarity) 0.005529
180 ENOG4108M6S metallophosphoesterase 0.005529
181 ENOG4105J5G Transferase hexapeptide repeat containing protein 0.005519
182 ENOG4105C4H Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA (By similarity) -0.005514
183 ENOG41063VM cytochrome C, class I 0.005513
184 ENOG4108YSP acyltransferase 3 0.005513
185 ENOG4107UR0 Sodium hydrogen exchanger 0.005513
186 ENOG4105CZ5 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate (By similarity) 0.005512
187 ENOG4105DIH basic membrane 0.005498
188 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) 0.005496
189 ENOG41075KK NA 0.005484
190 ENOG4105WAN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.005480
191 ENOG41063A7 NA 0.005468
192 ENOG4108R5K PPIases accelerate the folding of proteins (By similarity) -0.005454
193 ENOG4107QYY faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.005446
194 ENOG41074MP UPF0103 Mediator of ErbB2-driven cell motility-containing protein 0.005446
195 ENOG4108YXI Secondary thiamine-phosphate synthase enzyme 0.005436
196 ENOG4108UGV hypoxanthine phosphoribosyltransferase 0.005429
197 ENOG4105D6C Part of the ABC transporter complex MacAB involved in macrolide export. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation (By similarity) -0.005422
198 ENOG4108K0A Anthranilate phosphoribosyltransferase (EC 2.4.2.18) -0.005418
199 ENOG4107WIP permease 0.005417
200 ENOG4105C56 H( )-stimulated, divalent metal cation uptake system (By similarity) 0.005414
201 ENOG4108IMY Transcriptional regulator -0.005405
202 ENOG4108JVH Protein of unknown function DUF43 0.005402
203 ENOG4106BC8 NA 0.002696
203 ENOG4108RMW NA 0.002696
204 ENOG4108Y1G NA 0.005392
205 ENOG4105QNR S1 RNA binding domain protein -0.005390
206 ENOG4108ZY4 thioesterase Superfamily protein 0.005381
207 ENOG4105DX0 Hemolysin A 0.005380
208 ENOG4108WJV had superfamily (subfamily IIIa) phosphatase 0.005375
209 ENOG4107RNE DNA polymerase -0.005362
210 ENOG4105DYN 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) 0.005355
211 ENOG4105V13 Pyruvate kinase 0.005348
212 ENOG4107SPW HsdM N-terminal domain 0.005338
213 ENOG4108UV5 Lanthionine synthetase C family protein 0.005338
214 ENOG41090IC Protein of unknown function DUF89 0.005332
215 ENOG4105FBS glycosyl transferase group 1 0.005328
216 ENOG4108RSN SNARE associated Golgi -0.005328
217 ENOG4105YNR glycerophosphoryl diester phosphodiesterase -0.005323
218 ENOG4105DSX permease 0.005309
219 ENOG4105CD5 CoA-binding domain protein 0.005307
220 ENOG4105RAI NA 0.005294
221 ENOG4105CJX Molecular chaperone. Has ATPase activity (By similarity) -0.005294
222 ENOG41082QR Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity) 0.005292
223 ENOG4107YAT Pfam:DUF477 -0.005292
224 ENOG4105FGM Fructosamine kinase 0.005291
225 ENOG4108QF3 pyruvate flavodoxin ferredoxin oxidoreductase 0.005286
226 ENOG4105CWF integral membrane protein -0.005285
227 ENOG4107RIQ Sulfate adenylate transferase 0.005281
228 ENOG4105HFY transporter, permease 0.005275
229 ENOG4105FNI atp gtp-binding protein 0.005275
230 ENOG41060M0 Crispr-associated protein, cse4 family 0.005272
231 ENOG4105KT5 UmuD protein -0.005270
232 ENOG4105C1Q protoporphyrinogen oxidase 0.005259
233 ENOG4106NDE Ammonium Transporter Family 0.005259
234 ENOG4106BBN aaa ATPase -0.005258
235 ENOG41083S7 flagellar protein FlaG 0.005258
236 ENOG4108UTW Plays a role in the regulation of phosphate uptake 0.005256
237 ENOG4107QHF type ii secretion system protein e 0.005255
238 ENOG4108UC2 radical SAM domain protein 0.005248
239 ENOG4107XFK Glycosyl transferase 0.005244
240 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.005243
241 ENOG4105EKQ RNA-directed DNA polymerase -0.005242
242 ENOG4105CK6 Two component transcriptional regulator (Winged helix family 0.005230
243 ENOG4105MCT stage V sporulation protein S 0.005227
244 ENOG4105TZK 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) 0.005226
245 ENOG4105IAM Domain of unknown function DUF87 0.002609
245 ENOG4108KI5 NA 0.002609
246 ENOG4105CQX Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.005216
247 ENOG41090A1 ferritin 0.005212
248 ENOG4105W5Q DNA repair protein (RadC 0.005208