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 ENOG4105DJN thiJ pfpI 0.010895
2 ENOG4107R7A Allophanate hydrolase subunit 2 0.007576
3 ENOG4105CHF Glutathione S-transferase 0.007287
4 ENOG4105DR4 Methyltransferase -0.007215
5 ENOG4108ZFA transmembrane signal peptide protein -0.006997
6 ENOG41090DY Small-conductance mechano-sensitive channel -0.006767
7 ENOG4105CYW agmatinase 0.006709
8 ENOG4105E7W lamb ycsf family protein 0.006570
9 ENOG4105ECD TIGR00266 family -0.006440
10 ENOG4105C8J )-transporter 0.006251
11 ENOG4108KZM Rhomboid family 0.006235
12 ENOG4105DFP Integrase 0.006219
13 ENOG41068SR Protein of unknown function (DUF2970) 0.006076
14 ENOG4108JJA ABC, transporter 0.006043
15 ENOG4108Z1F Conserved Protein -0.006025
16 ENOG4105XA0 heptosyltransferase ii -0.005949
17 ENOG4105CR8 Transcriptional regulator 0.005843
18 ENOG4105NXH GreA GreB family elongation factor -0.005772
19 ENOG4108M36 Histidine kinase -0.005731
20 ENOG4105CAQ asparagine synthetase 0.005706
21 ENOG4106BHJ Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin (half-life of 2.1 minutes) that inhibits the endonuclease activity of cognate toxin RnlA but not that of non- cognate toxin LsoA 0.005702
22 ENOG4105EBA Specifically methylates the adenine in position 1618 of 23S rRNA (By similarity) 0.005670
23 ENOG41068W6 Capsular polysaccharide biosynthesis protein 0.005636
24 ENOG4108UWE Acyltransferase 0.005598
25 ENOG4107RCH Diaminopropionate ammonia-lyase 0.005556
26 ENOG4105K6H D-cysteine desulfhydrase 0.005542
27 ENOG4105CWG 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 (By similarity) 0.005536
28 ENOG4105ED2 Beta-lactamase 0.005535
29 ENOG41064QE NA 0.005525
30 ENOG4106DDA NA 0.005492
31 ENOG4106JF3 nnrs family 0.005491
32 ENOG41061N2 exported protein 0.005482
33 ENOG4108HWX NADH flavin oxidoreductase, NADH oxidase 0.005481
34 ENOG4108EQH DNA internalization-related competence protein ComEC Rec2 0.005419
35 ENOG4105NPD Membrane-bound metal-dependent hydrolase 0.005407
36 ENOG4105CXX synthase III 0.005396
37 ENOG4105CYQ Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate) (By similarity) -0.005383
38 ENOG4105JKW Valine--pyruvate aminotransferase 0.005360
39 ENOG4105NQA NA 0.005320
40 ENOG41081XQ Conserved Protein -0.005251
41 ENOG4107R09 zinc metalloprotease 0.005233
42 ENOG4105E4M (twin-arginine translocation) pathway signal -0.005217
43 ENOG4108UKG had-superfamily hydrolase, subfamily ia, variant 0.005151
44 ENOG4105KPV Transcriptional regulator 0.005151
45 ENOG4108BY2 phosphohistidine phosphatase 0.005143
46 ENOG4108EF9 Catalyzes two reactions the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR -0.005140
47 ENOG4105GW5 Histidine kinase 0.005113
48 ENOG4105DAZ ABC transporter 0.005104
49 ENOG4105E5H Transposase 0.005060
50 ENOG4105F1Y L-lysine 6-monooxygenase (NADPH) -0.005046
51 ENOG4105MEJ Gcn5-related n-acetyltransferase -0.005022
52 ENOG4105T0Z Conserved Protein -0.005019
53 ENOG4105KRQ Addiction module toxin, Txe YoeB family 0.005012
54 ENOG4105DUU IucA IucC family protein -0.004983
55 ENOG4105K5B UPF0225 protein 0.004982
56 ENOG4105QK0 Membrane 0.004909
57 ENOG4105NAQ phosphoglycerate mutase 0.004881
58 ENOG410848J type IV pilus biogenesis protein 0.004872
59 ENOG4108UR1 Protein of unknown function (DUF938) 0.004859
60 ENOG4105NBF ammecr1 domain protein 0.004855
61 ENOG4108ZI0 d,d-heptose 1,7-bisphosphate phosphatase -0.004841
62 ENOG4106023 Putative phosphatase (DUF442) 0.004821
63 ENOG4108JAW Trans_reg_C -0.004814
64 ENOG4105CXW Synthesizes alpha-1,4-glucan chains using ADP-glucose (By similarity) -0.004799
65 ENOG4107T6V glycerophosphoryl diester phosphodiesterase 0.004789
66 ENOG4107R69 radical SAM domain protein 0.004783
67 ENOG4108RS1 cytochrome C 0.004783
68 ENOG4105CRY pfkb domain protein 0.004773
69 ENOG4106PF6 Protein of unknown function (DUF1538) 0.004748
70 ENOG41074MP UPF0103 Mediator of ErbB2-driven cell motility-containing protein 0.004742
71 ENOG4105S1X fha domain-containing protein 0.004721
72 ENOG41075YS Protein of unknown function (DUF3624) -0.004719
73 ENOG4105P4J Allophanate hydrolase, subunit 1 0.004696
74 ENOG4107RAN Peptidase, M16 -0.004667
75 ENOG4108VYT Uncharacterized protein conserved in bacteria (DUF2063) 0.004659
76 ENOG4107V6F Dicarboxylate transport 0.004658
77 ENOG4105UQX Mate efflux family protein -0.004645
78 ENOG4107QIW Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism (By similarity) 0.004636
79 ENOG4105CCI Myosin-Cross-Reactive Antigen 0.004633
80 ENOG4108YWN peptidase 0.004624
81 ENOG4105N7M Isochorismatase, hydrolase 0.004618
82 ENOG4108EKH alcohol dehydrogenase 0.004609
83 ENOG4105C3N Participates in control of cell volume in low-osmolarity conditions (By similarity) -0.004592
84 ENOG4107R7Y intracellular protease Pfpi family -0.004592
85 ENOG4108DWY NAD(P) transhydrogenase (Alpha subunit -0.004587
86 ENOG4105EUD Transcriptional regulator -0.004585
87 ENOG4108TUQ NA 0.004585
88 ENOG4105CA3 membrane-bound lytic murein transglycosylase -0.004565
89 ENOG4105CH5 extracellular solute-binding protein, family 7 -0.004552
90 ENOG4107UKF beta-lactamase 0.004551
91 ENOG4105SYT Methylenetetrahydrofolate reductase -0.004548
92 ENOG4105HZ2 Diguanylate cyclase -0.004546
93 ENOG4105C72 UPF0176 protein 0.004535
94 ENOG4106CJB Phospholipase Carboxylesterase 0.004533
95 ENOG4105C8P )-transporter 0.004527
96 ENOG4105D9P serine threonine protein kinase 0.004517
97 ENOG4107URI Membrane-flanked domain-containing protein 0.004517
98 ENOG4108QVP Outer membrane efflux protein 0.004512
99 ENOG4105TBQ dsrE protein 0.004483
100 ENOG4105EE6 Alcohol dehydrogenase zinc-binding domain protein -0.004475
101 ENOG4105DJ2 Major Facilitator Superfamily 0.004473
102 ENOG4105FEX (ABC) transporter -0.004448
103 ENOG4105WDA Protein of unknown function (DUF1653) 0.004446
104 ENOG4107ZW7 Uncharacterised ACR, YkgG family COG1556 0.004437
105 ENOG4108Z4X TRANSCRIPTIONal -0.004436
106 ENOG4105C3A Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs) (By similarity) -0.004427
107 ENOG4108UMN azlc family 0.004423
108 ENOG410850B Membrane-flanked domain-containing protein 0.004417
109 ENOG4108UA8 signal transduction protein -0.004415
110 ENOG4107R1I NAD-dependent malic enzyme 0.004410
111 ENOG4107T9U Methyl-accepting chemotaxis -0.004394
112 ENOG4108XDN Transcriptional regulator -0.004393
113 ENOG4105KUA histidine triad (HIT) protein 0.004393
114 ENOG4108PXI ErfK YbiS YcfS YnhG -0.004389
115 ENOG4105KT5 UmuD protein -0.004388
116 ENOG4105EVN Prephenate dehydrogenase -0.004385
117 ENOG4105FVT Transposition protein 0.002191
117 ENOG4108VT7 tnsa endonuclease 0.002191
118 ENOG4105Y6A peptidase s9 prolyl oligopeptidase active site domain protein 0.004364
119 ENOG4105CM2 brancheD-chain amino acid aminotransferase 0.004361
120 ENOG4107MZ5 Short-chain dehydrogenase reductase Sdr 0.004340
121 ENOG41067V4 LysR family Transcriptional regulator -0.004340
122 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) -0.004326
123 ENOG4108HND NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. The first step is catalyzed by NqrF, which accepts electrons from NADH and reduces ubiquinone-1 to ubisemiquinone by a one-electron transfer pathway (By similarity) 0.004319
124 ENOG4105YB8 TM2 domain containing protein 0.004311
125 ENOG4105FR1 rard protein 0.004310
126 ENOG4105C11 sulfate adenylyltransferase), subunit 2 -0.004295
127 ENOG4105DN9 Na H antiporter 0.004291
128 ENOG4105CDV Ompa motb domain protein 0.004290
129 ENOG4105CBI The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.004290
130 ENOG4108U3U Membrane -0.004288
131 ENOG41090XQ Cytochrome b561 0.004288
132 ENOG4107QNW Aldolase 0.004286
133 ENOG4106DDM Ompa motb domain protein 0.004282
134 ENOG4105GFX Transcriptional regulator -0.004280
135 ENOG4106N3A copper homeostasis protein cutc -0.004272
136 ENOG4108VEJ NA 0.004270
137 ENOG4105DJ9 glucan biosynthesis protein -0.004265
138 ENOG41090N8 NA 0.004260
139 ENOG41080TB sigma 54 modulation protein ribosomal protein S30EA 0.004254
140 ENOG4105DX1 Conversion of NADPH, generated by peripheral catabolic pathways, to NADH, which can enter the respiratory chain for energy generation (By similarity) 0.004253
141 ENOG4108K0H serine threonine protein phosphatase 0.004238
142 ENOG4105CIF Ornithine Cyclodeaminase 0.004230
143 ENOG4105EJQ L-serine dehydratase 0.004227
144 ENOG4108V1J Has antioxidant activity. Could remove peroxides or H(2)O(2) (By similarity) -0.004225
145 ENOG4105Y6N NA 0.004221
146 ENOG4108K4P Dialkylrecorsinol condensing enzyme 0.004221
147 ENOG4106HRF NA 0.004212
148 ENOG4107SN8 glycosyl transferase family -0.004204
149 ENOG41068K6 glutaredoxin 2 0.004190
150 ENOG4105IPS esterase 0.004189
151 ENOG4108Q79 6-phosphogluconolactonase (EC 3.1.1.31) -0.004187
152 ENOG4105BZ3 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) (By similarity) -0.004173
153 ENOG4105YRZ Late competence development protein ComFB 0.004165
154 ENOG4105KVT NA 0.004149
155 ENOG4105KPY Small multidrug resistance protein -0.004145
156 ENOG410878N Protein of unknown function (DUF1499) 0.004136
157 ENOG4107SE0 Amino acid permease -0.004133
158 ENOG4106X31 NA 0.004129
159 ENOG4105YJI Anti-feci sigma factor, fecr 0.004122
160 ENOG4105D7T ABC transporter -0.004120
161 ENOG4108VKG metal-dependent hydrolase 0.004093
162 ENOG4107QQU Major facilitator superfamily MFS_1 0.004083
163 ENOG4106E0F Domain of unknown function (DUF1704) -0.004077
164 ENOG4106B1X NA 0.004076
165 ENOG4105EWE membrAne 0.004068
166 ENOG4108ZTW Nitrogen regulatory protein P-II 0.004068
167 ENOG4105NKC type III effector 0.004063
168 ENOG4108T6S 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) 0.004062
169 ENOG4107QUV Domain protein 0.004054
170 ENOG4105CK2 sodium dicarboxylate symporter 0.004048
171 ENOG41067JP NA 0.004038
172 ENOG4107TT5 NLP P60 protein -0.004034
173 ENOG4106A5Y Protein of unknown function (DUF2628) 0.004031
174 ENOG4105UD9 type ii secretion system 0.004028
175 ENOG4108PT8 Protein of unknown function (DUF3626) -0.004027
176 ENOG4108F1R TDP-4-oxo-6-deoxy-D-glucose transaminase 0.004019
177 ENOG4105CU8 Endonuclease Exonuclease phosphatase 0.004016
178 ENOG4107RUZ Sss sodium solute transporter superfamily 0.004015
179 ENOG4108IEH NADH dehydrogenase subunit g -0.004008
180 ENOG41068PV NA 0.003999
181 ENOG41075BF Protein of unknown function (DUF2986) -0.003997
182 ENOG4105D4Y metalloprotease -0.003996
183 ENOG4105DB0 abc transporter atp-binding protein 0.003975
184 ENOG4105WMR Protein CrcB homolog 0.003973
185 ENOG4105NIH orphan protein 0.003970
186 ENOG4108DR6 ABC transporter--like protein 0.003968
187 ENOG4108Q9C Periplasmic Protein -0.003968
188 ENOG4105KWG Pfam:DUF1696 0.003967
189 ENOG4105QX0 NA 0.003965
190 ENOG4105IRS NA 0.003961
191 ENOG4105DCH radical SAM domain protein -0.003956
192 ENOG4108TTY Protein of unknown function (DUF2927) -0.003953
193 ENOG4108V61 Thiopurine S-methyltransferase 0.003952
194 ENOG410691E abc transporter 0.003946
195 ENOG4105C1G acyl-Coa dehydrogenase 0.003935
196 ENOG4105CVR type I restriction-modification system -0.003932
197 ENOG4108VB5 Sel1 domain protein repeat-containing protein 0.003919
198 ENOG4108IDP Peptidase family M23 -0.003912
199 ENOG4105EW9 transcriptional regulator AsnC family 0.003906
200 ENOG4105CT4 transporter -0.003906
201 ENOG4107QZU type I restriction-modification system -0.003887
202 ENOG4108RMU ferritin dps family protein -0.003886
203 ENOG4105DUJ cytochrome C oxidase 0.003884
204 ENOG41060MZ NA 0.003884
205 ENOG4108NBI NA 0.003877
206 ENOG4108T0W nitrous oxide maturation protein NosY 0.003875
207 ENOG4107QMZ Dehydrogenase 0.003870
208 ENOG4107WCE Major Facilitator Superfamily -0.003867
209 ENOG4108F19 Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine (By similarity) 0.003864
210 ENOG4105E6Y alanine racemase domain protein 0.003862
211 ENOG4105UV7 Peptidase M14, carboxypeptidase A 0.003858
212 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.003854
213 ENOG4107U3U Sodium hydrogen exchanger 0.003851
214 ENOG4107M3I cytochrome 0.003847
215 ENOG4108M1T Cytochrome c-type biogenesis protein 0.003846
216 ENOG4105KRB Glutaredoxin 0.003845
217 ENOG4108ICA Prokaryotic N-terminal methylation motif 0.003841
218 ENOG4108MPI Phosphoesterase, PA-phosphatase related 0.003838
219 ENOG4108VKV Monofunctional biosynthetic peptidoglycan transglycosylase -0.003838
220 ENOG4105CZD Thiol oxidoreductase 0.003837
221 ENOG4105C7J ABC transporter, permease 0.003835
222 ENOG4108ZUB Lysine exporter protein (Lyse ygga) 0.003835
223 ENOG4105CNA YD repeat protein -0.003835
224 ENOG4106NQW sterol desaturase -0.003830
225 ENOG41087I2 Regulator of sigma E 0.003825
226 ENOG4105IJZ Pfam:DUF833 0.003821
227 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.003821
228 ENOG4105G2E Endonuclease Exonuclease phosphatase 0.003819
229 ENOG4105EQ1 Transcriptional regulator -0.003806
230 ENOG4108TSB LysR family Transcriptional regulator 0.003806
231 ENOG4105ZBC NA 0.003803
232 ENOG4105VR0 copper resistance 0.003798
233 ENOG4107RTD sua5 ycio yrdc ywlc family protein 0.003793
234 ENOG4105JKH Nudix Hydrolase -0.003792
235 ENOG4105MWK D-amino acid dehydrogenase, small subunit -0.003789
236 ENOG4105RKW reductase (By 0.003782
237 ENOG4108KC9 Glycosyl transferase family protein -0.003777
238 ENOG4107QWH The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity) 0.003771
239 ENOG4106I6Y NA -0.003768
240 ENOG4107RAD Sodium hydrogen exchanger 0.003756
241 ENOG4105MT4 Protein of unknown function (DUF3187) -0.003748
242 ENOG4105H24 Cell wall-active antibiotics response protein (DUF2154) 0.003746
243 ENOG4105YAT NA 0.003744
244 ENOG4108J1G ribonuclease 0.003744
245 ENOG4107RX3 Mg2 transporter protein cora family protein -0.003741
246 ENOG4105CDZ Carboxymethylenebutenolidase (EC 3.1.1.45) -0.003739
247 ENOG4105CUG Oligopeptidase b 0.003739
248 ENOG41061J1 NA 0.003734
249 ENOG4107TKD NA 0.003734