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 ENOG4105E39 Enoyl-CoA hydratase 0.021629
2 ENOG4105C1G acyl-Coa dehydrogenase 0.021311
3 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase 0.020764
4 ENOG4105CYC Transferase 0.015328
5 ENOG4105CHU acetyl-coa acetyltransferase 0.014129
6 ENOG4105EMZ Hydrogenase large subunit domain protein 0.013553
7 ENOG4105C10 Electron transfer flavoprotein 0.012450
8 ENOG4107SVV electron transport complex, RnfABCDGE type, B subunit 0.012446
9 ENOG4105BZJ Electron transfer flavoprotein 0.012122
10 ENOG4105CXN decarboxylase 0.011726
11 ENOG4105P1U NA 0.011509
12 ENOG4105DZB Electron transport complex 0.011138
13 ENOG4105FGV Chromate 0.010709
14 ENOG4107YHQ hydrolase 0.010286
15 ENOG4105NI6 heptaprenyl diphosphate synthase component I 0.010286
16 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) 0.010254
17 ENOG4105DGN Electron transport complex 0.010136
18 ENOG4108UGX Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity) -0.010133
19 ENOG4105D6A Electron transport complex 0.010120
20 ENOG4107RC7 uridine kinase 0.010050
21 ENOG4105D6N CoA-transferase, subunit a 0.009360
22 ENOG4107QZ5 glutamate synthase 0.009156
23 ENOG4107RQ4 Aldolase 0.009102
24 ENOG4105C33 Mate efflux family protein 0.009094
25 ENOG4105EXC Acyl-transferase -0.009087
26 ENOG4108I0Z Aconitate hydratase 0.008734
27 ENOG4105CM2 brancheD-chain amino acid aminotransferase -0.008685
28 ENOG4108Z1K This enzyme is involved in nucleotide metabolism it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA (By similarity) 0.008647
29 ENOG4105KPE licD family -0.008496
30 ENOG4105CJ2 (LipO)protein 0.008478
31 ENOG4107R47 Mate efflux family protein 0.008455
32 ENOG4107TM8 reductase 0.008442
33 ENOG4108IIH CoA-transferase subunit B 0.008388
34 ENOG4107R7P Potassium proton antiporter 0.008363
35 ENOG4105EFA 4-hydroxyphenylacetate 0.008287
36 ENOG4105E9Q Acyl-transferase 0.008276
37 ENOG41067MG lrgb family 0.008110
38 ENOG4105CZF Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism (By similarity) 0.008040
39 ENOG4105CNW domain protein 0.007984
40 ENOG4106KUD Membrane 0.007883
41 ENOG4105EQ8 radical SAM domain protein 0.007835
42 ENOG4105CWM branched-chain amino acid transport system II carrier protein -0.007775
43 ENOG4107XU7 Lactoylglutathione lyase 0.007685
44 ENOG4106KBT YibE F family protein 0.007664
45 ENOG4105P1P protein, conserved in bacteria 0.007660
46 ENOG4105CH8 Succinyl-CoA ligase ADP-forming subunit alpha -0.003825
46 ENOG4105CMV Succinyl-CoA synthetase subunit beta -0.003825
47 ENOG4105EAM Na Pi-cotransporter 0.007642
48 ENOG4105CH7 arginosuccinase -0.007610
49 ENOG4107QTR Required for nitrogen fixation. May be part of a membrane complex functioning as an intermediate in the electron transport to nitrogenase (By similarity) 0.007572
50 ENOG4107S8T NAD-dependent 4-hydroxybutyrate dehydrogenase 0.007543
51 ENOG4108Z3B V-type sodium ATPase, K subunit 0.007538
52 ENOG4105MBT YolD-like protein 0.007522
53 ENOG4105R6S NADP oxidoreductase, coenzyme f420-dependent 0.007511
54 ENOG4107U24 Radical SAM -0.007510
55 ENOG4107QN2 dihydrolipoyl dehydrogenase -0.007507
56 ENOG4105MAX Superoxide reductase 0.007440
57 ENOG4105CUX Signal transduction histidine kinase -0.007435
58 ENOG4107SW5 Peptidase M16 domain protein 0.007340
59 ENOG4108VH7 hemerythrin hhe cation binding domain protein 0.007318
60 ENOG4105CJW magnesium transporter 0.007315
61 ENOG4105CVM Molybdenum cofactor synthesis domain protein -0.007311
62 ENOG4108PUM FMN-binding domain protein 0.007298
63 ENOG4108ZWH TraX protein 0.007258
64 ENOG4105K4S protein with conserved CXXC pairs 0.007234
65 ENOG4108Z29 Flavodoxin 0.007219
66 ENOG4106KFQ NA -0.007213
67 ENOG4105CA8 Catalyzes the rearrangement of 1-deoxy-D-xylulose 5- phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S (By similarity) 0.007160
68 ENOG4108UYI beta-alanyl-CoA ammonia lyase 0.007144
69 ENOG4105K4W Could be involved in septation (By similarity) 0.007141
70 ENOG4107T4M dehydratase 0.007136
71 ENOG4105D41 biosynthesis protein thiH 0.007111
72 ENOG4105D2F Ig domain protein, group 2 domain protein 0.007111
73 ENOG410908R Methenyltetrahydrofolate cyclohydrolase 0.007074
74 ENOG4105D5U fad dependent oxidoreductase 0.007040
75 ENOG4105CMH dehydratase 0.007020
76 ENOG4108VHV Membrane 0.006993
77 ENOG4105C6X Major Facilitator -0.006976
78 ENOG4108UW5 maltose o-acetyltransferase -0.006970
79 ENOG4105C3S Mate efflux family protein 0.006960
80 ENOG4105CIZ coA-substrate-specific enzyme activase 0.006960
81 ENOG410775E NA -0.006960
82 ENOG4105DK0 Indole-3-glycerol phosphate synthase -0.006951
83 ENOG4105F1A Pyruvate formate-lyase -0.006882
84 ENOG4105C7W Xanthine dehydrogenase 0.006872
85 ENOG4105E33 succinate dehydrogenase -0.006867
86 ENOG4105K8R UPF0145 protein -0.006854
87 ENOG4105VF1 iron-only hydrogenase system regulator 0.006812
88 ENOG4105F6H The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3- phosphate (By similarity) -0.006807
89 ENOG4105DIW FeS assembly protein SUFB -0.006806
90 ENOG4107QNT pyruvate dehydrogenase e1 component suBunit beta -0.006802
91 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) -0.006769
92 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.006755
93 ENOG4107QIG Dehydrogenase 0.006743
94 ENOG4107SHE acetyltransferase, (GNAT) family 0.006721
95 ENOG4107CHF 5,6-aminomutase beta subunit 0.003350
95 ENOG4108S6F NA 0.003350
96 ENOG4108Q6H Signal transduction protein containing sensor and EAL domains 0.006698
97 ENOG4107BU2 esterase -0.006697
98 ENOG4108S37 Membrane 0.006675
99 ENOG41090A1 ferritin 0.006669
100 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase 0.006633
101 ENOG4108115 UPF0145 protein 0.006601
102 ENOG41090I5 UPF0735 ACT domain-containing protein 0.006573
103 ENOG4108UIN ybak prolyl-trna synthetase associated region 0.006572
104 ENOG4105CZM Major Facilitator -0.006568
105 ENOG4108XGR NA 0.006567
106 ENOG4107WIA FMN-dependent alpha-hydroxy acid dehydrogenase 0.006566
107 ENOG4105EQ5 D-Lysine 5,6-aminomutase alpha subunit 0.006562
108 ENOG4107RA1 nh(3)-dependent nad( ) synthetase -0.006561
109 ENOG4107QJX Aldo keto reductase 0.006550
110 ENOG4105PV1 biotin lipoyl attachment domaiN-containing protein 0.006547
111 ENOG4108FS3 Radical SAM superfamily 0.006542
112 ENOG4107WP6 response regulator 0.006500
113 ENOG4108JUB Transcriptional regulator 0.006498
114 ENOG4105CAH Chromate 0.006485
115 ENOG41086ZJ Inherit from NOG: Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S- specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX (By similarity) -0.006473
116 ENOG4107QJ1 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily 0.006457
117 ENOG4106VXV Conserved Protein 0.006428
118 ENOG4107UA6 flavin reductase domain protein 0.006421
119 ENOG4108I66 PTS System 0.006352
120 ENOG4105DKW ABC transporter -0.006351
121 ENOG4105H0B Domain-Containing protein -0.006333
122 ENOG4105D4H Membrane 0.006311
123 ENOG4108HQW ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins (By similarity) -0.006309
124 ENOG4105CER acetyl-CoA carboxylase biotin carboxylase -0.006295
125 ENOG4105EEI dihydropteroate synthase -0.006295
126 ENOG4105FRY Dehydrogenase 0.006291
127 ENOG4105MXR 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.006290
128 ENOG4107XR9 resolvase -0.006247
129 ENOG4107YV0 Membrane 0.006243
130 ENOG4105DCT glycerol dehydrogenase 0.006229
131 ENOG4108JQ6 ABC transporter -0.006222
132 ENOG4105CX7 Alpha-L-fucosidase -0.006217
133 ENOG4105TMB Formate nitrite transporter -0.006203
134 ENOG4105KRF dihydroneopterin aldolase -0.006195
135 ENOG4105CV8 reductase -0.006191
136 ENOG4105EUJ GTP cyclohydrolase i -0.006189
137 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.006184
138 ENOG4105MT7 Arsenical resistance operon tranS-acting repressor 0.006166
139 ENOG4107RY0 Catalyzes the conversion of dihydroorotate to orotate (By similarity) 0.006163
140 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.006156
141 ENOG4105EGG ABC transporter 0.006154
142 ENOG4105CK3 Lysine 2,3-aminomutase YodO family protein 0.006136
143 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) 0.006094
144 ENOG4105NN3 Response regulator of the LytR AlgR family -0.006083
145 ENOG4105KME endoribonuclease L-psp 0.006076
146 ENOG4105CQC Prephenate dehydratase -0.006066
147 ENOG4105C7S Dehydrogenase -0.006057
148 ENOG41088BK DNA mismatch repair protein muts 0.006055
149 ENOG4105JGR thioesterase Superfamily protein 0.006043
150 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase -0.006042
151 ENOG4105MQS Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate (By similarity) -0.006036
152 ENOG4108NRW Phospholipase, patatin family -0.006034
153 ENOG4105C6N Formate acetyltransferase -0.006032
154 ENOG4108UMN azlc family 0.006012
155 ENOG4105F42 AAA-ATPase 0.006006
156 ENOG41069SU NA 0.006001
157 ENOG4105E1G Band 7 protein -0.005989
158 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.005980
159 ENOG41090K1 Metal dependent hydrolase 0.005978
160 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) 0.005972
161 ENOG4105D1W Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate (By similarity) 0.005970
162 ENOG4105ZW9 acetyltransferase, (GNAT) family 0.005969
163 ENOG4105KGY integral membrane protein 0.005948
164 ENOG41082FQ alpha/beta hydrolase fold -0.005947
165 ENOG4107RE7 phosphate butyryltransferase 0.005942
166 ENOG4105DBW Multi-copper polyphenol oxidoreductase laccase -0.005929
167 ENOG4107SW2 integral membrane protein -0.005921
168 ENOG4105CPE K01197 hyaluronoglucosaminidase EC 3.2.1.35 -0.005921
169 ENOG4107SHJ sulfite reductase subunit b 0.005918
170 ENOG4107V9M epimerase dehydratase -0.005900
171 ENOG4105XC8 protein, conserved in bacteria 0.005897
172 ENOG410860H Protein of unknown function (DUF1312) 0.005873
173 ENOG4108UVJ appr-1-p processing domain protein 0.005868
174 ENOG4107QPR SAICAR synthetase -0.005856
175 ENOG4105CJ3 phosphate transporter -0.005853
176 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 0.005849
177 ENOG41068B1 Cob-I-yrinic acid a,c-diamide adenosyltransferase -0.005846
178 ENOG4105KA6 Transcriptional regulator, TetR family 0.005841
179 ENOG4105DB7 PHP domain protein 0.005840
180 ENOG41085E0 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity) 0.005797
181 ENOG4108QBV Monogalactosyldiacylglycerol synthase -0.005796
182 ENOG4108TGC Acyltransferase -0.005784
183 ENOG4105CIN aminoacyl-histidine dipeptidase 0.005769
184 ENOG4106G1Q PTS HPr component phosphorylation site -0.005763
185 ENOG4105D5B Sulfite reductase, subunit A 0.005761
186 ENOG4105XEP YhcH YjgK YiaL family protein -0.005749
187 ENOG4105W79 Lipoprotein LpqB, GerMN domain protein -0.005722
188 ENOG4105DE9 3-keto-5-aminohexanoate cleavage enzyme 0.005717
189 ENOG4105DY6 DNA replication protein DnaD 0.005711
190 ENOG4105XN2 DNA-binding helix-turn-helix protein 0.005665
191 ENOG4105DVE abc transporter atp-binding protein 0.005659
192 ENOG4108YZ4 nudix hydrolase 0.005652
193 ENOG4105HMI Membrane 0.005634
194 ENOG4105C0F tryptophanase EC 4.1.99.1 0.005629
195 ENOG4105CN1 protease 0.005624
196 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 -0.005615
197 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase -0.005615
198 ENOG4108IYU L-aspartate oxidase 0.005612
199 ENOG4107QRR aspartate 0.005600
200 ENOG4108UTT Catalyzes the formation of 6,7-dimethyl-8- ribityllumazine by condensation of 5-amino-6-(D- ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin (By similarity) 0.005598
201 ENOG410811P TRANSCRIPTIONAl REGULATOR GntR family 0.005587
202 ENOG4107VW5 LD-carboxypeptidase 0.005571
203 ENOG4107SGX Methyltransferase 0.005556
204 ENOG41080KV transcriptional regulator, lysR family -0.005552
205 ENOG4107EEK Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide (By similarity) -0.005546
206 ENOG4107TSJ Inherit from COG: deoxyguanosinetriphosphate triphosphohydrolase-like protein -0.005544
207 ENOG4105WMM Probably plays a role in a hydrogenase nickel cofactor insertion step (By similarity) -0.005531
208 ENOG4107TGU Thiamine biosynthesis protein ThiF 0.005495
209 ENOG41084SB Carrier of the growing fatty acid chain in fatty acid biosynthesis (By similarity) 0.005495
210 ENOG4105FAZ Membrane 0.005493
211 ENOG4105DRM Cell surface protein -0.005491
212 ENOG4105E05 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.005491
213 ENOG4105D43 The glycine cleavage system catalyzes the degradation of glycine (By similarity) -0.005484
214 ENOG4107R0V Pyruvate dehydrogenase -0.005481
215 ENOG4108RVA ribokinase -0.005476
216 ENOG4108IAB Phoh family 0.005468
217 ENOG4107SV9 thymidine kinase 0.005458
218 ENOG4107USE Diacylglycerol kinase 0.005452
219 ENOG4107T1A d-lactate dehydrogenase 0.005451
220 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) -0.005450
221 ENOG4107RE8 Integrase -0.005447
222 ENOG4105D95 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity) 0.005446
223 ENOG4105NQQ topology modulation protein 0.005440
224 ENOG4105CCS Glutamate formiminotransferase 0.005439
225 ENOG4106EP1 NA -0.005434
226 ENOG4105DBV ornithine carbamoyltransferase -0.005431
227 ENOG4105IJJ transcriptional regulator, crp fnr family -0.005422
228 ENOG4108Z66 YbaK ebsC protein -0.005416
229 ENOG4105ZMH deoxynucleoside kinase -0.005416
230 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.005408
231 ENOG41086WP Thiamine biosynthesis protein thiS 0.005402
232 ENOG4105CG0 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine (By similarity) -0.005400
233 ENOG4108UMS Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP- ribose 1''-2''-cyclic phosphate (APPR P). May function as an ADP- ribosylase (By similarity) 0.005379
234 ENOG4107QU9 hydrolase family 2, sugar binding -0.005378
235 ENOG4105CFY cytochrome d ubiquinol oxidase, subunit ii -0.005373
236 ENOG4105NRA 50s ribosomal protein l31 type b -0.005358
237 ENOG4108V3E phosphoribosylglycinamide formyltransferase 0.005353
238 ENOG4106GGA transcriptional regulator -0.005330
239 ENOG4105EBX v-type atpase 0.005323
240 ENOG4107QK8 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor -0.005310
241 ENOG4108KGH TRANSCRIPTIONal -0.005308
242 ENOG4105FJQ ParB-like nuclease domain 0.005308
243 ENOG4105CCZ Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched- chain and or straight-chain of fatty acids (By similarity) 0.005298
244 ENOG4105C2C drug resistance transporter, Bcr CflA -0.005289
245 ENOG4108MV5 ATPase associated with various cellular activities aaa_5 -0.005256
246 ENOG4105FVH SNARE-like domain protein 0.005248
247 ENOG4107TGA Ser Thr phosphatase family protein 0.005236
248 ENOG4105JTA DNA-binding helix-turn-helix protein 0.005230