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 ENOG4107RHE UDP-glucose 6-dehydrogenase -0.015454
2 ENOG4105CYW agmatinase -0.015285
3 ENOG41090A1 ferritin 0.013546
4 ENOG4108Z9K Osmotically inducible protein -0.013203
5 ENOG4105ETU transcriptional activator (TenA -0.011736
6 ENOG4105CU1 amidohydrolase -0.011533
7 ENOG410604Q amidohydrolase -0.011322
8 ENOG4105KTU Transcriptional regulator, arsr family 0.011189
9 ENOG4107RD8 Nad-dependent epimerase dehydratase -0.010764
10 ENOG4108WBT adenosyltransferase -0.010623
11 ENOG4105CJD (Anaerobic) ribonucleoside-triphosphate reductase 0.010572
12 ENOG4107ZA5 polysaccharide biosynthesis protein -0.010559
13 ENOG4106H7W NA -0.010528
14 ENOG4105FDF Could be involved in DNA repair (By similarity) -0.010455
15 ENOG4105G3U fad dependent oxidoreductase 0.010287
16 ENOG4105DQE DNA ligase -0.009914
17 ENOG4105C8J )-transporter -0.009860
18 ENOG4105FKZ Methyl-accepting chemotaxis -0.009773
19 ENOG41066Z3 extracellular ligand-binding receptor 0.009756
20 ENOG4106DIW mucin-associated surface protein -0.009636
21 ENOG4105C7S Dehydrogenase -0.009622
22 ENOG4106Z86 ATP-nad acox kinase -0.009583
23 ENOG4106BXB NA -0.009550
24 ENOG4105T4R ABC transporter, permease -0.009511
25 ENOG4105C19 ABC transporter -0.009505
26 ENOG4105RAK Histidine kinase -0.009498
27 ENOG4105C2X Arabinose 5-phosphate isomerase -0.009384
28 ENOG4106MEM Type III -0.009370
29 ENOG4105WWK YheO domain protein -0.009357
30 ENOG4105D8C Channel that permits osmotically driven movement of water in both directions. It is involved in the osmoregulation and in the maintenance of cell turgor during volume expansion in rapidly growing cells. It mediates rapid entry or exit of water in response to abrupt changes in osmolarity (By similarity) -0.009255
31 ENOG4108JEC DNA methylase n-4 n-6 domain protein -0.009168
32 ENOG4105CBA glutamine phosphoribosylpyrophosphate amidotransferase 0.009136
33 ENOG4105UPH NA 0.009123
34 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.009122
35 ENOG4105DCH radical SAM domain protein -0.009092
36 ENOG4105C0G Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives (By similarity) -0.009044
37 ENOG4105CF8 branched-chain amino acid ABC transporter, permease 0.008910
38 ENOG4107R73 Mate efflux family protein -0.008907
39 ENOG4108KEZ Dehydrogenase -0.008903
40 ENOG4105FD5 transport protein TctC -0.008869
41 ENOG4108V7B Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide (By similarity) 0.008843
42 ENOG410866H pfkb domain protein -0.008637
43 ENOG4108VM0 tpr domain protein -0.008625
44 ENOG4107VJ8 Binding-protein-dependent transport systems, inner membrane component -0.008501
45 ENOG4107QJZ Glycosyl transferase, family 2 -0.008467
46 ENOG4105CMT Dihydroxyacetone kinase -0.008452
47 ENOG410803D Zinc finger helix-turn-helix protein, YgiT family 0.008417
48 ENOG41068Q2 NA -0.008410
49 ENOG4105E5N succinylglutamate desuccinylase aspartoacylase -0.008389
50 ENOG4108AE0 extracellular solute-binding protein family 1 -0.008331
51 ENOG4108NJ6 sugar ABC transporter (Permease) -0.008325
52 ENOG4105J4Q Transcriptional regulator -0.008315
53 ENOG4108TR2 NA -0.008311
54 ENOG4105E4I Glycoside hydrolase family 28 -0.008306
55 ENOG4105DBA pectate lyase -0.008305
56 ENOG4107QMJ Recombinase 0.008284
57 ENOG4105EE5 Membrane protein terC -0.008275
58 ENOG4106CRE NA -0.008266
59 ENOG41066VC NA -0.008215
60 ENOG4107QRA Extracellular solute-binding protein, family 5 0.008195
61 ENOG4105E2U transposase, IS204 IS1001 IS1096 IS1165 family protein 0.008191
62 ENOG4105RTF NA 0.008191
63 ENOG4107WCI zn-dependent hydrolase of the beta-lactamase fold-like protein -0.008190
64 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase 0.008182
65 ENOG4105RDE Protein of unknown function (DUF3667) -0.008172
66 ENOG4105C30 Nad-dependent epimerase dehydratase -0.008152
67 ENOG4105DAZ ABC transporter 0.008136
68 ENOG4108TKQ ADP-specific Phosphofructokinase/Glucokinase conserved region -0.008135
69 ENOG410902R phosphoglycerate mutase -0.008102
70 ENOG4105U2P bfd domain protein (2fe-2s)-binding domain protein 0.008096
71 ENOG4107S6X Glycosyl transferase, family 2 0.008074
72 ENOG4107XEC aspartate racemase -0.008055
73 ENOG4105C32 Amino acid ABC transporter (Permease) 0.008043
74 ENOG4105DFE Dna adenine methylase 0.008036
75 ENOG4107W49 Methyl-accepting chemotaxis 0.008018
76 ENOG410761E Dna topoisomerase -0.008007
77 ENOG4107ZCT C-terminal domain of 1-Cys peroxiredoxin -0.008005
78 ENOG4107DUA NA -0.007989
79 ENOG4107ISQ Inherit from COG: transposase -0.007989
80 ENOG4105NGE extracellular solute-binding protein family 1 -0.007989
81 ENOG4105XJC Two component transcriptional regulator (Winged helix family -0.007983
82 ENOG4107QCS Inherit from COG: UDP-N-acetylglucosamine 2-epimerase -0.007982
83 ENOG4105DQX Zinc finger domain -0.007974
84 ENOG4108IJK 4Fe-4S ferredoxin, iron-sulfur binding domain protein -0.007973
85 ENOG41086T2 Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system (By similarity) -0.007960
86 ENOG4106I70 Peptidase family M50 -0.007957
87 ENOG4105GGG UvrD/REP helicase N-terminal domain -0.003968
87 ENOG4108PCT NA -0.003968
88 ENOG4108FHJ NA -0.007925
89 ENOG4106P21 NA -0.007914
90 ENOG4105CH6 catalase -0.007912
91 ENOG4108IJ7 Glycine betaine -0.007902
92 ENOG4108UQY Iron-storage protein -0.007898
93 ENOG4107S7S glycoside hydrolase, family 3 domain protein -0.007876
94 ENOG4105EZI multiple antibiotic resistance (MarC)-related protein -0.007869
95 ENOG4105CGT Catalyzes the transfer of a phosphate group to glutamate to form glutamate 5-phosphate which rapidly cyclizes to 5- oxoproline (By similarity) 0.007837
96 ENOG41070J0 NA -0.007833
97 ENOG4105CUQ mRNA 3'-end processing factor -0.007824
98 ENOG4105EXU Membrane -0.007810
99 ENOG4105F1J Homogentisate 1,2-dioxygenase -0.007801
100 ENOG410808U Methyltransferase -0.007788
101 ENOG4108UBR NA -0.007775
102 ENOG4108JPX Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor (By similarity) -0.007757
103 ENOG4108ATP flagellar FlbD family protein -0.007753
104 ENOG4106849 propeptide, pepSY amd peptidase M4 -0.007748
105 ENOG4106IDR NA -0.007733
106 ENOG4107794 NA -0.007721
107 ENOG4108J3A Aldo Keto reductase 0.007716
108 ENOG4108IXY short-chain dehydrogenase reductase -0.007701
109 ENOG4108ZES Glyoxalase Bleomycin resistance protein (Dioxygenase -0.007682
110 ENOG4105F2K FkbH Like Protein 0.007656
111 ENOG4105JSC dimethylmenaquinone methyltransferase -0.007649
112 ENOG4108PTD n-acetylmuramoyl-l-alanine amidase 0.007647
113 ENOG4105E78 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity) -0.007646
114 ENOG4105CGM Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis (By similarity) -0.007646
115 ENOG410650C NA -0.007645
116 ENOG4107QWS glycogen debranching enzyme glgx -0.007643
117 ENOG4105CAF HipA N-terminal domain protein 0.007641
118 ENOG4107FSS Endonuclease that specifically degrades the RNA of RNA- DNA hybrids (By similarity) -0.007638
119 ENOG4108RGW (NAD(P)H dehydrogenase) (Quinone) -0.007601
120 ENOG4105KCV RNA signal recognition particle 4.5S RNA -0.007601
121 ENOG4108E4T NA -0.007599
122 ENOG4105YQB acyl carrier protein 0.007592
123 ENOG4107DZK NA 0.007584
124 ENOG410838Z CoA-binding domain protein 0.007565
125 ENOG4105C3V 40-residue yvtn family beta-propeller repeat protein -0.007563
126 ENOG41086IP 50S ribosomal protein L33 0.007549
127 ENOG4105DFW ABC transporter -0.007517
128 ENOG4105MD1 YeeE YedE family protein -0.007513
129 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase -0.007511
130 ENOG4105GVH Cyclase dehydrase -0.007477
131 ENOG4105C0K Gdp-mannose 4,6-dehydratase -0.007469
132 ENOG4108T1X regulatory protein FlaEY -0.007461
133 ENOG41083E0 ribosomal-protein-alanine acetyltransferase -0.007460
134 ENOG4108QZX TPR repeat-containing protein -0.007448
135 ENOG4105DFS Conserved Protein -0.007440
136 ENOG4108V3U Membrane -0.007436
137 ENOG4108KSJ Site-specific recombinase 0.007426
138 ENOG4105WJ5 NA -0.007420
139 ENOG4105EI3 2-dehydro-3-deoxygalactonokinase EC 2.7.1.58 -0.007398
140 ENOG4108M16 Nad-dependent epimerase dehydratase -0.007392
141 ENOG4105MDS 4-oxalocrotonate tautomerase 0.007382
142 ENOG4108QQ0 integrase family 0.007371
143 ENOG4105GP5 transposase 0.007362
144 ENOG4107SET aldo keto reductase -0.007360
145 ENOG4108EKG Sodium hydrogen exchanger -0.007359
146 ENOG4107QR9 Iron-sulfur cluster binding protein 0.007358
147 ENOG4105X04 NA -0.007349
148 ENOG4105ED7 Catalyzes the specific phosphorylation of 1,6-anhydro-N- acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling (By similarity) -0.007333
149 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) 0.007320
150 ENOG4108HII Binding-protein-dependent transport systems, inner membrane component 0.007310
151 ENOG4108JDZ Glycosyl transferase (Group 1 -0.007294
152 ENOG4105SAU Coenzyme PQQ synthesis protein D (PqqD) -0.007291
153 ENOG4105VSK Copper amine oxidase domain protein -0.007283
154 ENOG4105D0X Efflux ABC transporter, permease protein -0.007276
155 ENOG4108ZC1 mosc domain containing protein 0.007274
156 ENOG4107W87 polysaccharide biosynthesis protein 0.007257
157 ENOG4105RD7 BadF BadG BcrA BcrD -0.007256
158 ENOG4108EQM faD-dependent pyridine nucleotide-disulfide oxidoreductase -0.007248
159 ENOG4105C6H Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction (By similarity) 0.007247
160 ENOG4107TY6 Acylneuraminate cytidylyltransferase -0.007242
161 ENOG4107RJ1 sodium solute 0.007242
162 ENOG4105CP5 Pfam:DUF88 -0.007241
163 ENOG4107QP7 CoA-transferase subunit A -0.007240
164 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) -0.007210
165 ENOG4108TIN Resolvase 0.007198
166 ENOG4108UMB Flavodoxin 0.007191
167 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) -0.007176
168 ENOG4107EUR Flagellar hook-length control protein 0.007169
169 ENOG4108IQF 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 (By similarity) -0.007162
170 ENOG41068WV flagellar FlbD family protein 0.007160
171 ENOG4108U05 Transcriptional regulator -0.007152
172 ENOG4107QW3 Sucrose phosphorylase -0.007145
173 ENOG4108ZY0 Glyoxalase Bleomycin resistance protein (Dioxygenase -0.007116
174 ENOG4105FFF abc transporter permease protein 0.007111
175 ENOG4107BYT NA 0.007109
176 ENOG4108W83 NA 0.007109
177 ENOG4108UY2 Chloramphenicol acetyltransferase 0.007105
178 ENOG4108Z28 Cupin 2, conserved barrel domain protein -0.007104
179 ENOG4108KQJ Type 11 methyltransferase -0.007096
180 ENOG4105C2C drug resistance transporter, Bcr CflA -0.007069
181 ENOG4105DEU major facilitator superfamily -0.007051
182 ENOG4105Q33 Has nucleotide phosphatase activity towards ATP, GTP, CTP, TTP and UTP. May hydrolyze nucleoside diphosphates with lower efficiency 0.007044
183 ENOG4107UR6 Protein of unknown function DUF72 -0.007023
184 ENOG4105EYW Ion transport protein -0.007016
185 ENOG4107PMM dextranase 0.007013
186 ENOG41080XS Cobyrinic acid ac-diamide synthase -0.007001
187 ENOG4107UTJ K01838 beta-phosphoglucomutase EC 5.4.2.6 -0.006995
188 ENOG4105NC1 PRS2 protein -0.006982
189 ENOG4107SCW Pfam:UPF0027 -0.006977
190 ENOG41080SS PepSY-associated TM helix 0.006963
191 ENOG4105GYY polyketide cyclase dehydrase -0.006949
192 ENOG4108R87 pep phosphonomutase -0.006947
193 ENOG4108QHA NA -0.006941
194 ENOG4105F8C transglutaminase domain-containing protein -0.006931
195 ENOG4105W6C Protein of unknown function (DUF2892) 0.006928
196 ENOG4108Z73 Siroheme synthase 0.006918
197 ENOG4105D29 Helix-turn-helix type 11 domain protein -0.006916
198 ENOG4105D4Y metalloprotease -0.006878
199 ENOG4105EG6 Saccharopine dehydrogenase -0.006878
200 ENOG4107RS9 Glycosyl transferase (Group 1 -0.006874
201 ENOG4105KIR Thiol-disulfide oxidoreductase dcc -0.006871
202 ENOG4105DZR Type I site-specific deoxyribonuclease 0.006871
203 ENOG41062RU (ABC) transporter 0.006861
204 ENOG4105VMP Transcriptional regulator -0.006845
205 ENOG4105VXP Protein of unknown function DUF86 -0.006838
206 ENOG4105GSD Glycosyl transferase, family 2 -0.006829
207 ENOG4105EEF Alkane 1-monooxygenase -0.006826
208 ENOG4105C0F tryptophanase EC 4.1.99.1 0.006815
209 ENOG4105C7R Atpase associated with various cellular activities aaa_3 -0.006800
210 ENOG4105DPZ Two component transcriptional regulator (Winged helix family 0.006784
211 ENOG4108JQ1 Dehydrogenase -0.006772
212 ENOG4108MJI response regulator 0.006759
213 ENOG4108JJB ABC transporter 0.006745
214 ENOG4105DIW FeS assembly protein SUFB 0.006717
215 ENOG4107SKJ peptidase s9 prolyl oligopeptidase active site domain protein -0.006711
216 ENOG4105KWG Pfam:DUF1696 0.006697
217 ENOG4108NF7 phage-type endonuclease 0.006675
218 ENOG4107R0V Pyruvate dehydrogenase -0.006671
219 ENOG4105KFG YeeE YedE family protein -0.006663
220 ENOG4105PV1 biotin lipoyl attachment domaiN-containing protein 0.006656
221 ENOG4105FBJ fumarylacetoacetate (faa) hydrolase -0.006646
222 ENOG4105K85 Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) in DNA. Repairs alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated (By similarity) -0.006638
223 ENOG4105CU8 Endonuclease Exonuclease phosphatase -0.006633
224 ENOG4105DG4 malate L-lactate dehydrogenase -0.006622
225 ENOG41090DD ISPg5 transposase Orf1 -0.006609
226 ENOG4105CGU Enoyl-CoA hydratase -0.006606
227 ENOG4105EUB pirin domain protein -0.006594
228 ENOG4108URH decarboxylase -0.006582
229 ENOG4106WC5 Cytochrome b561 -0.006579
230 ENOG4105VKA DNA Polymerase Beta Domain Protein Region 0.006565
231 ENOG4105NKR Glycosyl hydrolase family 76 0.006563
232 ENOG4105C72 UPF0176 protein -0.006555
233 ENOG4105DSQ Nitric oxide reductase 0.006551
234 ENOG4106XI0 Protein of unknown function (DUF3575) -0.006545
235 ENOG4107J5X Diguanylate cyclase with PAS PAC sensor -0.006544
236 ENOG4107RTZ reductase -0.006542
237 ENOG4105FCI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate (By similarity) 0.006533
238 ENOG4108JU3 Alkyl hydroperoxide reductase -0.006526
239 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase 0.006525
240 ENOG410806K diacylglycerol kinase, catalytic 0.006519
241 ENOG4105CMG Carbohydrate kinase -0.006514
242 ENOG4105CPP Dehydrogenase, E1 component -0.006514
243 ENOG4105VCH membrane -0.006514
244 ENOG4105ED2 Beta-lactamase -0.006504
245 ENOG4108KQE Capsular polysaccharide biosynthesis protein -0.006496
246 ENOG4105EN3 adenine specific DNA methyltransferase 0.006475
247 ENOG4105W6F restriction endonuclease 0.006471
248 ENOG4105FCN von Willebrand factor -0.006469
249 ENOG41088IW HlyD family secretion protein 0.006447