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 ENOG41089S2 PQQ-dependent dehydrogenase, methanol ethanol family 0.004287
1 ENOG4108DY6 Extracellular solute-binding protein family 3 0.004287
2 ENOG4108QSG Methane monooxygenase ammonia monooxygenase, subunit C 0.007077
3 ENOG4106007 Formate dehydrogenase, delta subunit 0.007074
4 ENOG4105E7Z methane monooxygenase ammonia monooxygenase subunit A 0.002259
4 ENOG41064HC NA 0.002259
4 ENOG4108P7H monooxygenase, subunit B 0.002259
5 ENOG4105DHX tonB-dependent Receptor 0.006682
6 ENOG4105N1T NA 0.006606
7 ENOG4105EXI Selenium-binding protein 0.006414
8 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.006358
9 ENOG4105GUN MxaA protein 0.000676
9 ENOG4105P0N Methanol dehydrogenase beta subunit 0.000676
9 ENOG410616Y von Willebrand factor, type A 0.000676
9 ENOG4107ZMX NA 0.000676
9 ENOG4108M6X Dehydrogenase 0.000676
9 ENOG4108P4C Formaldehyde-activating enzyme 0.000676
9 ENOG4108Q1J Extracellular solute-binding protein, family 3 0.000676
9 ENOG4108QSI von Willebrand factor, type A 0.000676
9 ENOG4108VFM cytochrome C, class I 0.000676
10 ENOG41068T5 Catalyzes the hydrolysis of methenyl-H(4)MPT( ) to 5- formyl-H(4)MPT (By similarity) 0.006081
11 ENOG4105TC9 MxaK protein 0.006081
12 ENOG4108WF5 Protein of unknown function (DUF447) 0.005895
13 ENOG4105EPZ beta-ribofuranosylaminobenzene 5'-phosphate synthase family 0.002848
13 ENOG4108XVP Triphosphoribosyl-dephospho-CoA protein 0.002848
14 ENOG41084M5 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid (By similarity) 0.005688
15 ENOG41082IB Dihydropteroate synthase, DHPS 0.005687
16 ENOG4105DI8 ABC transporter 0.005629
17 ENOG4105EE6 Alcohol dehydrogenase zinc-binding domain protein 0.005614
18 ENOG4105CI7 Hopanoid biosynthesis associated RND transporter like protein HpnN 0.005521
19 ENOG4105C3V 40-residue yvtn family beta-propeller repeat protein 0.005513
20 ENOG4108HRF thiamine pyrophosphate 0.005489
21 ENOG4107SR7 Nitroreductase family 0.005375
22 ENOG4107QZF nitrite reductase NADPH large subunit 0.005298
23 ENOG41066EJ cytochrome C, class I 0.005256
24 ENOG4105EWU Squalene--hopene cyclase 0.005205
25 ENOG4105NAA Cytochrome C oxidase, subunit II 0.005184
26 ENOG4105SU0 efflux transporter, rnd family, mfp subunit 0.005048
27 ENOG4107RQ2 Cytochrome c oxidase, subunit I 0.004998
28 ENOG4105FIE Catalyzes the transfer of a formyl group from 5-formyl tetrahydromethanopterin (5-formyl-H(4)MPT) to methanofuran (MFR) so as to produce formylmethanofuran (formyl-MFR) and tetrahydromethanopterin (H(4)MPT) (By similarity) 0.000991
28 ENOG4105YFI Formylmethanofuran dehydrogenase, subunit B 0.000991
28 ENOG4108Q7C formylmethanofuran dehydrogenase subunit C 0.000991
28 ENOG4108TTP H4MPT-linked C1 transfer pathway protein 0.000991
28 ENOG4108UTS histidine biosynthesis protein 0.000991
29 ENOG4105ZJM Archease protein family (MTH1598/TM1083) 0.004954
30 ENOG410605C May protect the nitrogenase Fe-Mo protein from oxidative damage (By similarity) 0.002470
30 ENOG4108WFK NA 0.002470
31 ENOG4108SNY Protein of unknown function (DUF3455) 0.004927
32 ENOG4105C0A alcohol dehydrogenase -0.004919
33 ENOG410633V NA 0.004901
34 ENOG4105DCC Formylmethanofuran dehydrogenase subunit A 0.004803
35 ENOG4105K2K Domain of unknown function (DUF336) 0.004754
36 ENOG4107RBX acriflavin resistance protein 0.004749
37 ENOG4108Z3M integral membrane protein 0.004745
38 ENOG4105I4G carbonic anhydrase 0.004728
39 ENOG4108IEG Formate dehydrogenase Alpha subunit 0.004714
40 ENOG4105DWX Amino acid amide ABC transporter substrate-binding protein, HAAT family 0.001570
40 ENOG4107RIH serine-glyoxylate aminotransferase 0.001570
40 ENOG41090IV MxaD protein 0.001570
41 ENOG4105JIE May be involved in the transport of PQQ or its precursor to the periplasm (By similarity) 0.002349
41 ENOG41086XE Ring cyclization and eight-electron oxidation of 3a-(2- amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline- 7,9-dicarboxylic-acid to PQQ (By similarity) 0.002349
42 ENOG4105DSQ Nitric oxide reductase 0.004687
43 ENOG4105MK4 NA 0.004676
44 ENOG4105XV5 nifz family 0.001556
44 ENOG4106QR2 NA 0.001556
44 ENOG4108VQE nitrogen fixation protein 0.001556
45 ENOG4105DK8 Nitrogenase molybdenum-iron cofactor biosynthesis protein NifN 0.004669
46 ENOG4105PS4 nifq family 0.004669
47 ENOG4105UHE Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits (By similarity) 0.004659
48 ENOG4107QWZ Heavy metal efflux pump, CzcA 0.004551
49 ENOG4105C7S Dehydrogenase 0.004550
50 ENOG4105C6R Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo- MPT) cofactor (Moco or molybdenum cofactor) to form Mo- molybdopterin guanine dinucleotide (Mo-MGD) cofactor (By similarity) 0.004471
51 ENOG4108MFW O-Antigen polymerase 0.004461
52 ENOG4105NB0 Iron-sulfur cluster assembly accessory protein 0.004433
53 ENOG4106K52 DNA repair protein (RadC 0.004428
54 ENOG4107S73 homocitrate synthase 0.004420
55 ENOG4105CJE phosphoribulokinase (EC 2.7.1.19) 0.004418
56 ENOG4108Q71 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) (By similarity) 0.004414
57 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) 0.004402
58 ENOG4108VFZ ribulose bisphosphate carboxylase, small 0.004392
59 ENOG4105WH1 Two component transcriptional regulator luxr family 0.004389
60 ENOG4105CDA abc transporter atp-binding protein -0.004386
61 ENOG4105KY9 aspartate glutamate uridylate kinase 0.004374
62 ENOG4106B1D glycosyl transferase group 1 0.004373
63 ENOG4105GCW ATP synthase subunit gamma 0.001444
63 ENOG4105Q11 ATP synthase, epsilon 0.001444
63 ENOG4105XVH atp synthase 0.001444
64 ENOG4106KV1 phospholipase C 0.004322
65 ENOG4105NH0 PepSY-associated TM helix 0.004304
66 ENOG4105W8H transhydrogenase (subunit alpha 0.004294
67 ENOG4105FDJ formate dehydrogenase 0.004278
68 ENOG4105I5W Transporter 0.004277
69 ENOG410634J metallophosphoesterase 0.004258
70 ENOG4108VM9 ABC, transporter 0.004257
71 ENOG4107SP0 drug resistance transporter, EmrB QacA subfamily 0.004242
72 ENOG41069NW Lipid A 3-O-deacylase (PagL) 0.004237
73 ENOG4108ZCD Transcriptional coactivator pterin dehydratase 0.004234
74 ENOG4105DAN ATP-dependent protease 0.004233
75 ENOG4108QWQ LRV FeS4 cluster domain protein 0.004210
76 ENOG4106DSF NA 0.004210
77 ENOG4105VG1 fes assembly suf system protein 0.004209
78 ENOG4105ET3 Reduction of activated sulfate into sulfite (By similarity) 0.004188
79 ENOG410682V general secretion pathway protein h 0.004177
80 ENOG4107STD carbohydrate kinase, PfkB family 0.004168
81 ENOG4105ZPS nitrogen fixation protein 0.004162
82 ENOG4107QKF NADH Ubiquinone plastoquinone (Complex I) 0.004155
83 ENOG4105CGC Nitrogenase cofactor biosynthesis protein NifB 0.004144
84 ENOG410690C hydroxylamine oxidase 0.004137
85 ENOG4105WI7 Cupin 2, conserved barrel domain protein 0.004122
86 ENOG4105C15 The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity) 0.004120
87 ENOG4105C7B Threonine dehydratase -0.004103
88 ENOG41063G4 NA 0.004097
89 ENOG41082N3 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.004065
90 ENOG41080G9 Cdp-alcohol phosphatidyltransferase 0.004059
91 ENOG4108IGW Cytochrome c 0.004053
92 ENOG4107YQ7 ubiE/COQ5 methyltransferase family 0.004041
93 ENOG4107T7M Nitrogenase protein alpha chain 0.002020
93 ENOG4108UR2 Nitrogen fixation protein NifX 0.002020
94 ENOG4105XHW Sel1 domain protein repeat-containing protein 0.004034
95 ENOG41076NN NA 0.004032
96 ENOG4105E0C molybdate abc transporter 0.004028
97 ENOG4105EMH Formaldehyde-activating enzyme 0.004016
98 ENOG4105E3S small subunit 0.003991
99 ENOG4105C2J ABC transporter -0.003991
100 ENOG4105PW4 Sugar fermentation stimulation protein homolog -0.003984
101 ENOG4105JRK feS assembly protein SufD 0.003946
102 ENOG4105RKK Domain of unknown function (DUF202) 0.003931
103 ENOG4108QR0 ABC-2 type transporter 0.003930
104 ENOG4105FBD synthase 0.003921
105 ENOG4107QZ5 glutamate synthase 0.003912
106 ENOG4107SUI pyridine nucleotide-disulfide oxidoreductase 0.003904
107 ENOG4108V1U phospholipid-binding protein 0.003901
108 ENOG4105F9Q Hopanoid biosynthesis associated radical SAM protein HpnH 0.003888
109 ENOG4105F2W methyltransferase 0.003885
110 ENOG4105DT1 RuBisCO catalyzes two reactions the carboxylation of D- ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate 0.003880
111 ENOG4108TCM sulfur oxidation protein SoxZ 0.003872
112 ENOG4108ZU0 ErfK YbiS YcfS YnhG family protein -0.003867
113 ENOG41065UE NA 0.001288
113 ENOG4107VJC peptidase, M24 0.001288
113 ENOG4108770 NA 0.001288
114 ENOG4108ME3 Alpha amylase 0.003860
115 ENOG4105Z4T Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B) (By similarity) 0.003860
116 ENOG4108IQE Amp-dependent synthetase and ligase -0.003843
117 ENOG4105VQD rieske 2fe-2S domain-containing protein 0.003838
118 ENOG410842U beta-lactamase domain protein 0.003838
119 ENOG4105WQ5 TonB family 0.003824
120 ENOG4105C8V SAICAR synthetase 0.003823
121 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) 0.003821
122 ENOG4105DG4 malate L-lactate dehydrogenase -0.003819
123 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for 0.003807
124 ENOG4105C3U ABC transporter -0.003802
125 ENOG4105G1T Uncharacterised ACR, YagE family COG1723 0.003801
126 ENOG4105VQ7 Rod shape-determining protein MreD 0.003800
127 ENOG410855H Phosphoesterase, PA-phosphatase related 0.003788
128 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) 0.003785
129 ENOG4107TZ2 Cell division protein that is required for growth during stress conditions. May be involved in protecting or stabilizing the divisomal assembly under conditions of stress (By similarity) 0.003781
130 ENOG4107S4X peptidase U62, modulator of DNA gyrase 0.003781
131 ENOG4108V7B Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide (By similarity) 0.003780
132 ENOG4108IXY short-chain dehydrogenase reductase 0.003768
133 ENOG4107QK4 glycoside hydrolase, family 3 domain protein 0.003763
134 ENOG4105F7K copper resistance 0.003760
135 ENOG4108XU2 ATP-grasp domain 0.003750
136 ENOG4105E8U -transport system 0.003749
137 ENOG4105WKW Pfam:DUF1458 0.003739
138 ENOG4105MN5 HAD-superfamily hydrolase subfamily IA variant 3 0.003738
139 ENOG4105FCN von Willebrand factor 0.003728
140 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit 0.003719
141 ENOG4105CNN ABC, transporter -0.003696
142 ENOG4108Z45 hydrogenase maturation protease 0.003681
143 ENOG4107UZ9 Oxidoreductase domain protein 0.003676
144 ENOG4108UMI ABC transporter, permease -0.003666
145 ENOG4105DAA L-lactate -0.003665
146 ENOG4107XID 2'-5' rna ligase 0.003661
147 ENOG4108RDH integral membrane protein 0.003650
148 ENOG4105ZIE Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides (By similarity) 0.003643
149 ENOG4109004 phosphohistidine phosphatase, SixA 0.003643
150 ENOG4108UNH dienelactone hydrolase 0.003643
151 ENOG4105J50 NA 0.003640
152 ENOG4105VAS Could be involved in insertion of integral membrane proteins into the membrane (By similarity) -0.003634
153 ENOG4106200 flavin reductase domain protein, FMN-binding 0.003634
154 ENOG4105EEX Two component transcriptional regulator (Winged helix family 0.003631
155 ENOG4108HHM Glycosyl transferase, family 2 0.003629
156 ENOG4105EU8 FAD linked oxidase domain protein 0.003627
157 ENOG4107TUM Amidinotransferase 0.003625
158 ENOG4107EER 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. The flavoprotein component catalyzes the electron flow from NADPH - FAD - FMN to the hemoprotein component (By similarity) 0.003612
159 ENOG4109003 Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis (By similarity) 0.003605
160 ENOG4105YGD Enzyme of the cupin superfamily 0.003600
161 ENOG4105E7Q Cob(II)yrinic acid a,c-diamide reductase 0.003594
162 ENOG4105DCF alanine dehydrogenase 0.003578
163 ENOG4105C2Y STE24 endopeptidase EC 3.4.24.84 0.003572
164 ENOG4105XD5 NADH ubiquinone oxidoreductase, 20 kda subunit 0.003571
165 ENOG4105C5X domain protein -0.003569
166 ENOG4105CQX Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.003564
167 ENOG4105NPQ Pfam:DUF403 0.003549
168 ENOG4105MDH 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) -0.003549
169 ENOG4105DHM ATPase which is responsible for recognizing, binding, unfolding and translocation of pupylated proteins into the bacterial 20S proteasome core particle. May be essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase may function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis (By similarity) 0.001183
169 ENOG4105DVV Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine (By similarity) 0.001183
169 ENOG4105E5F proteasome 0.001183
170 ENOG4105CTD carboxy-peptidase -0.003537
171 ENOG4105ETP RND efflux system, outer membrane lipoprotein 0.003537
172 ENOG4105CEP NADH dehydrogenase 0.003535
173 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) -0.003525
174 ENOG4108JQ7 (ABC) transporter -0.003520
175 ENOG4105CY9 nitrogenase molybdenum-iron protein beta chain 0.003519
176 ENOG4108JJB ABC transporter -0.003515
177 ENOG4105CYX Short-chain dehydrogenase reductase Sdr -0.003504
178 ENOG4105W5Q DNA repair protein (RadC -0.003502
179 ENOG4108YFE Inherit from COG: heavy metal transport detoxification protein 0.003488
180 ENOG410613G Abortive infection protein 0.003483
181 ENOG4105C4Q deoxyguanosinetriphosphate triphosphohydrolase-like protein -0.003473
182 ENOG4108R96 Methyltransferase, YaeB family -0.003466
183 ENOG4107VJ8 Binding-protein-dependent transport systems, inner membrane component 0.003454
184 ENOG4107VG3 hydrogen dehydrogenase EC 1.12.1.2 0.003450
185 ENOG4105C47 NADH ubiquinone oxidoreductase 20 kda subunit 0.003449
186 ENOG4108V1T peptidylprolyl cis-trans isomerase 0.003440
187 ENOG4105DKB L-sorbosone dehydrogenase 0.003434
188 ENOG4105D6T Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine (By similarity) -0.003431
189 ENOG4105D0B Nitrogenase protein alpha chain 0.003427
190 ENOG41065QA UspA domain protein 0.003422
191 ENOG4107XG2 cytosine deaminase 0.003417
192 ENOG4105CJM Binding-protein-dependent transport systems, inner membrane component -0.003405
193 ENOG41082BD domain protein 0.003403
194 ENOG4105DHC Aminoglycoside phosphotransferase 0.003403
195 ENOG4105EXC Acyl-transferase 0.003400
196 ENOG4107RMT Osmosensitive K channel His kinase sensor 0.003398
197 ENOG4108Q1M ABC transporter 0.001698
197 ENOG4108VVS MxaD protein 0.001698
198 ENOG4108WT7 Histidine kinase 0.003395
199 ENOG4105DXN mazG family 0.003385
200 ENOG4105KPK Component of the proteasome core, a large protease complex with broad specificity involved in protein degradation (By similarity) 0.003381
201 ENOG4108WKR MotA TolQ exbB proton channel 0.003379
202 ENOG4105E98 transcriptional regulator DeoR family -0.003376
203 ENOG4105C9B Cysteine desulfurase 0.003376
204 ENOG4108I4C Hydrogenase 4, membrane component 0.003371
205 ENOG4108HM5 NADH-ubiquinone oxidoreductase chain 49kDa 0.003362
206 ENOG41084DK macrophage migration inhibitory factor family protein 0.003354
207 ENOG4105C8H hydrogenase maturation protein Hypf 0.003351
208 ENOG4105W6C Protein of unknown function (DUF2892) 0.003349
209 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) 0.003346
210 ENOG4105UV2 general secretion pathway protein K 0.003343
211 ENOG4107EXU Short-chain dehydrogenase reductase Sdr -0.003342
212 ENOG4105C0V Provides the sole de novo source of dTMP for DNA biosynthesis (By similarity) 0.003333
213 ENOG4108AWY Nucleoside-diphosphate-sugar epimerase 0.003332
214 ENOG4105QSJ Rhodanese sulfurtransferase protein 0.001666
214 ENOG4106G61 NA 0.001666
215 ENOG4107RPK ROK family 0.003327
216 ENOG4105CH6 catalase -0.003322
217 ENOG4105EK8 von Willebrand factor, type A 0.003318
218 ENOG4105D6J arsenicaL-resistance protein 0.003317
219 ENOG4105NDF NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. May also have NAD-dependent lysine demalonylase and desuccinylase activity (By similarity) -0.003316