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 ENOG4107RY0 Catalyzes the conversion of dihydroorotate to orotate (By similarity) -0.015118
2 ENOG4108KI7 Diguanylate cyclase -0.014383
3 ENOG4107QWP ABC-2 type transporter -0.013545
4 ENOG4105EGC Sodium-dependent bicarbonate transporter 0.013528
5 ENOG4105DSX permease -0.013349
6 ENOG4107TT5 NLP P60 protein 0.012715
7 ENOG4105VGV redox-active disulfide protein 2 -0.012451
8 ENOG4105M08 Membrane 0.012400
9 ENOG4108IV0 ABC, transporter -0.012218
10 ENOG4105D5G Transposase -0.012114
11 ENOG4107RCY amino acid -0.011832
12 ENOG4108S4H thioesterase Superfamily protein 0.011612
13 ENOG4107R37 Glutamate dehydrogenase 0.011608
14 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit -0.011469
15 ENOG4105CJD (Anaerobic) ribonucleoside-triphosphate reductase -0.011414
16 ENOG4105DQU oxidoreductase, subunit beta -0.011266
17 ENOG4105KHC sulfurtransferase 0.010566
18 ENOG4105C7S Dehydrogenase 0.010493
19 ENOG4105DEE biogenesis protein, MshL -0.010409
20 ENOG4108RAC Rubrerythrin -0.010324
21 ENOG4107QHI -hydrogenase -0.010275
22 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) -0.010234
23 ENOG4108JEB The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine (By similarity) -0.010233
24 ENOG4105DI2 Pyruvate flavodoxin ferredoxin oxidoreductase domain protein -0.010189
25 ENOG4105C7P 2-oxoglutarate dehydrogenase, E1 0.010021
26 ENOG4108YXI Secondary thiamine-phosphate synthase enzyme -0.009965
27 ENOG4108KHX Diguanylate cyclase -0.009947
28 ENOG4105FDK ABC transporter -0.009822
29 ENOG4105C32 Amino acid ABC transporter (Permease) -0.009817
30 ENOG4105C0Z ABC transporter -0.009746
31 ENOG4105ERH Fumarylacetoacetate hydrolase -0.009729
32 ENOG4105C6Y Udp-glucose 6-dehydrogenase -0.009727
33 ENOG4105D0M Protease HtpX homolog -0.009686
34 ENOG4107QPR SAICAR synthetase -0.009529
35 ENOG4108HNZ carboxyl transferase -0.009508
36 ENOG4105CKI cobalamin synthesis protein 0.009423
37 ENOG4105D0S secretion protein (HlyD -0.009377
38 ENOG4105EZY Pyrroloquinoline quinone biosynthesis protein E -0.009366
39 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic -0.009336
40 ENOG4108KMK Diguanylate cyclase -0.009185
41 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase -0.009166
42 ENOG4108JU2 Major facilitator superfamily MFS_1 -0.009089
43 ENOG4105ECQ AraC Family Transcriptional Regulator 0.009052
44 ENOG4107S6X Glycosyl transferase, family 2 -0.009003
45 ENOG4107EXU Short-chain dehydrogenase reductase Sdr -0.008984
46 ENOG4105DQQ Major facilitator superfamily MFS_1 0.008945
47 ENOG4105WMR Protein CrcB homolog -0.008915
48 ENOG4107QTC Aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding 0.008901
49 ENOG4107T22 epimerase -0.008857
50 ENOG4105G5W regulator Fur family -0.008839
51 ENOG4105CBR Major Facilitator superfamily -0.008804
52 ENOG4105C7Z Conserved Protein -0.008780
53 ENOG4107R0V Pyruvate dehydrogenase 0.008769
54 ENOG4108ZHB oxidoreductase -0.008753
55 ENOG4105CFY cytochrome d ubiquinol oxidase, subunit ii 0.008749
56 ENOG4107RIQ Sulfate adenylate transferase -0.008742
57 ENOG4107R69 radical SAM domain protein -0.008662
58 ENOG4105CJG carbon-monoxide dehydrogenase catalytic subunit -0.008648
59 ENOG4105DEN Luciferase family 0.008475
60 ENOG4105CGN Glycosyl transferase (Group 1 -0.008450
61 ENOG4108ZVT methylmalonyl-coA epimerase -0.008419
62 ENOG4105CE1 Ferrous iron transport protein b -0.008404
63 ENOG4105ZHF 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) -0.008368
64 ENOG4105MD7 metal-dependent hydrolase -0.008291
65 ENOG4108V0P LemA family -0.008286
66 ENOG4105CGM Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis (By similarity) -0.008225
67 ENOG41080IJ Diacylglycerol kinase -0.008211
68 ENOG4105E2A Dehydrogenase 0.008210
69 ENOG4105VN1 Heat shock protein -0.008193
70 ENOG4107U84 Methyl-accepting chemotaxis -0.008169
71 ENOG4105CBM Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12 (By similarity) -0.008134
72 ENOG4107GFK fumarate 0.008106
73 ENOG4105C0V Provides the sole de novo source of dTMP for DNA biosynthesis (By similarity) 0.008088
74 ENOG4107SE4 UDP-N-acetylglucosamine 2-epimerase -0.008055
75 ENOG4108YYX Globally modulates RNA abundance by binding to RNase E (Rne) and regulating its endonucleolytic activity. Can modulate Rne action in a substrate-dependent manner by altering the composition of the degradosome. Modulates RNA-binding and helicase activities of the degradosome (By similarity) 0.008041
76 ENOG4105CMQ Chloride channel -0.008012
77 ENOG4107QSA Oxaloacetate decarboxylase -0.008009
78 ENOG4105DSQ Nitric oxide reductase 0.007976
79 ENOG41068PG O-Antigen polymerase -0.007951
80 ENOG4105F0R Cytidylyltransferase -0.007856
81 ENOG4105CJQ hydrolase, family 31 -0.007846
82 ENOG4108JJ8 (ABC) transporter 0.007809
83 ENOG4105CPK Glycosyl transferase (Group 1 -0.007790
84 ENOG4105N5D Protein of unknown function (DUF2089) -0.007745
85 ENOG41090U9 Protein of unknown function, DUF488 0.007717
86 ENOG4105C0F tryptophanase EC 4.1.99.1 -0.007708
87 ENOG4105XEX type IV pilus assembly pilz -0.007705
88 ENOG4105DHI Methyltransferase 0.007700
89 ENOG4105CK3 Lysine 2,3-aminomutase YodO family protein -0.007697
90 ENOG4105EKQ RNA-directed DNA polymerase -0.007676
91 ENOG4105CF8 branched-chain amino acid ABC transporter, permease -0.007672
92 ENOG4108XXY Transposase (IS4 family) protein 0.007619
93 ENOG4105CZX twitching motility protein -0.007574
94 ENOG4105CVP deoxyribo-dipyrimidine photolyase 0.007548
95 ENOG4105F4I Transcriptional regulator -0.007545
96 ENOG4105F1R Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group (By similarity) 0.007534
97 ENOG4105D41 biosynthesis protein thiH -0.007517
98 ENOG4105CZN Potassium uptake protein -0.007514
99 ENOG4105F5W AtP-binding protein -0.007500
100 ENOG4105C72 UPF0176 protein 0.007488
101 ENOG4108UK0 indolepyruvate ferredoxin oxidoreductase -0.007487
102 ENOG4105DIK (ABC) transporter 0.007484
103 ENOG4105CIZ coA-substrate-specific enzyme activase -0.007483
104 ENOG4105C33 Mate efflux family protein -0.007452
105 ENOG4108ZA0 Protein of unknown function (DUF779) 0.007434
106 ENOG4105D2T synthase -0.007409
107 ENOG4107QYT Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor (By similarity) 0.007403
108 ENOG4105F55 Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate (By similarity) -0.007402
109 ENOG4105DR5 peptidase -0.007377
110 ENOG4105BZ9 Cytochrome C oxidase, subunit I 0.007376
111 ENOG410692J cytochrome C, class I 0.007365
112 ENOG4105E5Q amino acid AbC transporter -0.007365
113 ENOG4105C7F AcnD-accessory protein PrpF 0.007349
114 ENOG4107RC7 uridine kinase -0.007334
115 ENOG4105KN9 radical SAM domain protein -0.007326
116 ENOG4105DKC membrane protein involved in aromatic hydrocarbon degradation -0.007314
117 ENOG4105C8J )-transporter -0.007287
118 ENOG4105DFP Integrase 0.007280
119 ENOG4108XC5 EAL -0.007273
120 ENOG4105E1Q flagellar hook-associated protein -0.007270
121 ENOG4105DB7 PHP domain protein -0.007242
122 ENOG4105EHJ Leucyl aminopeptidase -0.007232
123 ENOG4105ES3 NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) -0.007218
124 ENOG4105DH9 Beta-lactamase domain protein 0.007209
125 ENOG4108RPH peptidase -0.007197
126 ENOG4105CWM branched-chain amino acid transport system II carrier protein 0.007191
127 ENOG4108HMX isocitrate dehydrogenase (NADP) 0.007182
128 ENOG4105CQ7 ATP-dependent helicase 0.007175
129 ENOG4105CKB glycosidase -0.007170
130 ENOG4105N94 The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase (By similarity) 0.007162
131 ENOG4107SK0 cytochrome c biogenesis protein -0.007151
132 ENOG4105WAN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein -0.007148
133 ENOG4105CJV Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase -0.007140
134 ENOG4108YYV Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity) 0.007139
135 ENOG4105E4P ATPase (AAA -0.007132
136 ENOG4105N2T Domain of unknown function DUF302 -0.007128
137 ENOG4108BDP Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate (By similarity) 0.007126
138 ENOG4105EN2 IstB domain-containing protein ATP-binding protein -0.007087
139 ENOG4108JQ1 Dehydrogenase -0.007066
140 ENOG4105CZ5 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate (By similarity) 0.007063
141 ENOG4105MFV ABC-2 type transporter -0.007061
142 ENOG4107QWG 2-Nitropropane dioxygenase -0.007060
143 ENOG4105CPP Dehydrogenase, E1 component 0.007049
144 ENOG4108N5B 2-phosphosulfolactate phosphatase -0.007047
145 ENOG4108HM5 NADH-ubiquinone oxidoreductase chain 49kDa -0.007035
146 ENOG4105DR9 pseudouridine synthase 0.007022
147 ENOG4105CKD glutathione-regulated potassium-efflux system protein -0.007021
148 ENOG4105W7A Protein of unknown function (DUF503) -0.007017
149 ENOG4105ET1 Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate (By similarity) 0.007015
150 ENOG410683Z Preprotein translocase SecE subunit -0.007009
151 ENOG4107RGW The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor -0.007000
152 ENOG4107R4I Periplasmic binding protein 0.006995
153 ENOG4108AJS Glycosyl transferase (Group 1 0.006987
154 ENOG4105CD3 dihydroorotase -0.006983
155 ENOG4105DJY efflux transporter, rnd family, mfp subunit -0.006982
156 ENOG4106E82 Cytochrome -0.006970
157 ENOG4105GKD Transcriptional regulator, Crp Fnr family -0.006964
158 ENOG4105W1Y Transcriptional regulator -0.006950
159 ENOG4107RKD Uncharacterized protein family (UPF0051) 0.006938
160 ENOG4108CCG Methyl-accepting chemotaxis -0.006925
161 ENOG41061WM D-Alanyl-D-Alanine 0.006903
162 ENOG4105KE9 The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity) -0.006898
163 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.006897
164 ENOG4105DKW ABC transporter 0.006896
165 ENOG4105C3I Nad-dependent epimerase dehydratase -0.006888
166 ENOG4105EMU Dehydrogenase 0.006873
167 ENOG4108VPT UPF0234 protein 0.006871
168 ENOG4105CNG UPF0061 protein 0.006857
169 ENOG4105DN4 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) -0.006855
170 ENOG4105WJY cytochrome C oxidoreductase subunit B 0.006852
171 ENOG4107AYK membrAne 0.006849
172 ENOG4105DF0 Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrD type B subunit to the ultimate electron acceptor NAD( ) (By similarity) -0.006849
173 ENOG4105CGK Exodeoxyribonuclease III 0.006836
174 ENOG4105C9W Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity (By similarity) 0.006824
175 ENOG4105EI2 Pseudouridine synthase -0.006819
176 ENOG4107QW8 radical SAM domain protein -0.006814
177 ENOG4105ET3 Reduction of activated sulfate into sulfite (By similarity) 0.006812
178 ENOG4105ZAI NA -0.006800
179 ENOG4105ECB domain protein 0.006789
180 ENOG4105F4F gtp-binding protein -0.006773
181 ENOG41065C5 Chromosome segregation ATPase 0.006771
182 ENOG4105CMS peptidase U62, modulator of DNA gyrase 0.006763
183 ENOG4108YX9 iron--sulfur cluster insertion protein erpA 0.006758
184 ENOG4105DAQ Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity) 0.006738
185 ENOG4105EPH radical SAM domain protein -0.006728
186 ENOG4105WMM Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity) -0.006715
187 ENOG4107TNZ alpha beta 0.006712
188 ENOG4105D70 Integrase catalytic subunit -0.006705
189 ENOG4107RHZ type iii restriction protein res subunit 0.006699
190 ENOG4105CJR Integral membrane protein (MviN -0.006655
191 ENOG4107QUV Domain protein -0.006651
192 ENOG4108R5K PPIases accelerate the folding of proteins (By similarity) -0.006650
193 ENOG4105D7Q type ii secretion system -0.006643
194 ENOG4105DQ6 Transposase -0.006636
195 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) 0.006628
196 ENOG4108J59 Extracellular solute-binding protein, family 5 -0.006623
197 ENOG4105DSF transport protein -0.006616
198 ENOG4107REZ Sodium hydrogen exchanger -0.006614
199 ENOG4108UR8 BAX protein -0.006613
200 ENOG4105CC1 hydrolase, CocE NonD family protein 0.006610
201 ENOG4105FGU Nitroreductase -0.006595
202 ENOG4105CH6 catalase 0.006580
203 ENOG41067ZN Thiamine biosynthesis protein thiS 0.006580
204 ENOG4107UV2 CDP-glycerol Poly(glycerophosphate) glycerophosphotransferase 0.006577
205 ENOG4105CBE radical SAM domain protein -0.006576
206 ENOG4105CQB FAD linked oxidase domain protein -0.006576
207 ENOG4108XWQ Pfam:DUF820 -0.006565
208 ENOG4108VJ1 Transcriptional regulator (CarD family -0.006565
209 ENOG4106TS7 Methyltransferase Type -0.006563
210 ENOG41090A1 ferritin -0.006563
211 ENOG4105CKM Branched-chain carboxylic acid kinase -0.006561
212 ENOG4105ZTF Membrane Spanning Protein -0.006545
213 ENOG4105CY8 phosphoribosylaminoimidazole carboxylase atpase subunit 0.006534
214 ENOG4107SNZ Competence protein -0.006527
215 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) -0.006521
216 ENOG4105CNR NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) -0.006510
217 ENOG4105CV2 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates (By similarity) -0.006489
218 ENOG4105DDK oxidoreductase, beta subunit -0.006488
219 ENOG4107ZYR domain protein -0.006475
220 ENOG4105E05 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.006474
221 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) -0.006470
222 ENOG4105UG0 O-Antigen Polymerase 0.006466
223 ENOG4107QIZ NADH dehydrogenase -0.006463
224 ENOG4107V49 Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P) (By similarity) 0.006458
225 ENOG41076HS cation diffusion facilitator family transporter -0.006449
226 ENOG4107QTG Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA (By similarity) 0.006441
227 ENOG4108UQY Iron-storage protein 0.006437
228 ENOG4106HRJ d-alanyl-d-alanine carboxypeptidase 0.006435
229 ENOG4105C9X ppx gppa phosphatase 0.006434
230 ENOG4107TAK Inherit from COG: ATPase (AAA 0.006422
231 ENOG4105C2C drug resistance transporter, Bcr CflA 0.006410
232 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) -0.006397
233 ENOG4105CMY 5-enolpyruvylshikimate-3-phosphate synthase -0.006392
234 ENOG4108Z4U Ferredoxin 0.006389
235 ENOG4107RYU helicase -0.006388
236 ENOG4108ZR6 An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes (By similarity) 0.006378
237 ENOG4107QNT pyruvate dehydrogenase e1 component suBunit beta 0.006374
238 ENOG4105D78 K07001 NTE family protein -0.006362
239 ENOG4105VNB Carrier of the growing fatty acid chain in fatty acid biosynthesis (By similarity) -0.006353
240 ENOG4106CMX Anti-Sigma-28 factor, FlgM -0.006345
241 ENOG4107S96 Type IIS restriction -0.006341
242 ENOG4105CUI Catalyzes the interconversion between ADP-D-glycero- beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose (By similarity) -0.006332
243 ENOG4105VFB Binds the 23S rRNA (By similarity) -0.006332
244 ENOG4108KDV TniB family -0.006319
245 ENOG4105K8F Phosphoribosyl-amp cyclohydrolase -0.006319
246 ENOG4105DM4 PTS System 0.006312
247 ENOG4106A32 NA -0.006311
248 ENOG4105F3B Sulfite exporter TauE/SafE 0.006308
249 ENOG4105CYC Transferase 0.006301
250 ENOG4108ZG8 Gcn5-related n-acetyltransferase 0.006290