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 ENOG4108KAZ Involved in phosphonate degradation (By similarity) 0.059642
2 ENOG4107STF Involved in phosphonate degradation (By similarity) 0.057634
3 ENOG4107RCV ABC transporter, permease 0.021143
4 ENOG4105CV8 reductase 0.020789
5 ENOG4105C4Y ABC transporter 0.014235
6 ENOG4105D5G Transposase -0.014041
7 ENOG4105D44 asparaginase 0.013505
8 ENOG4107UDS transcriptional regulator, lysR family 0.013378
9 ENOG4107V9R abc transporter permease protein 0.013273
10 ENOG4108MX5 Converts alpha-N-acetylneuranimic acid (Neu5Ac) to the beta-anomer, accelerating the equilibrium between the alpha- and beta-anomers. Probably facilitates sialidase-negative bacteria to compete sucessfully for limited amounts of extracellular Neu5Ac, which is likely taken up in the beta-anomer. In addition, the rapid removal of sialic acid from solution might be advantageous to the bacterium to damp down host responses (By similarity) 0.013067
11 ENOG4105HS6 binding-protein-dependent transport systems inner membrane Component -0.011815
12 ENOG4105CPC Aldo Keto reductase 0.011547
13 ENOG4105C2C drug resistance transporter, Bcr CflA 0.011513
14 ENOG4107UUW glycyl-radical enzyme activating protein family 0.011400
15 ENOG4105CP5 Pfam:DUF88 -0.011259
16 ENOG4108U9H NA 0.011247
17 ENOG4106S9K Transcriptional regulator 0.011233
18 ENOG4107RMT Osmosensitive K channel His kinase sensor 0.011198
19 ENOG41061TZ Short-chain dehydrogenase reductase Sdr 0.011186
20 ENOG4107RNN dihydropyrimidinase (EC 3.5.2.2) 0.011089
21 ENOG4106FTQ Taurine ABC transporter, periplasmic 0.010960
22 ENOG4105WXW Antirepressor 0.010751
23 ENOG4108IY8 ABC, transporter 0.010652
24 ENOG4105F5I fad dependent oxidoreductase 0.010623
25 ENOG4105DRW binding-protein-dependent transport systems inner membrane Component -0.010506
26 ENOG4105C3Y UTP-glucose-1-phosphate uridylyltransferase 0.010411
27 ENOG4105K5C Phosphonate degradation operons associated HDIG domain protein 0.010241
28 ENOG4105CH2 amidohydrolase 0.010226
29 ENOG4108P8R NA -0.010216
30 ENOG4105FAV ABC, transporter -0.010182
31 ENOG4108IJ8 ABC transporter 0.010173
32 ENOG4105KAF membrAne 0.010126
33 ENOG4105EFZ amidohydrolase 0.010076
34 ENOG4108VGG Transmembrane Pair 0.010057
35 ENOG4105F8D glycoside hydrolase family 4 0.009967
36 ENOG4106GU5 conserved membrane protein 0.009943
37 ENOG4105C08 Histidine kinase 0.009594
38 ENOG4105CMT Dihydroxyacetone kinase 0.009584
39 ENOG4105C71 hydrolase family 65, central catalytic -0.009559
40 ENOG4105CF7 AraC family transcriptional regulator 0.009507
41 ENOG4105HQC NA 0.009475
42 ENOG41090BB DNA mismatch endonuclease (vsr) 0.009465
43 ENOG4107QJZ Glycosyl transferase, family 2 0.009420
44 ENOG4105KM0 Protein of unknown function (DUF1810) -0.009389
45 ENOG4105E2A Dehydrogenase 0.009383
46 ENOG4108IMY Transcriptional regulator 0.009323
47 ENOG4105FEY ROK family -0.009270
48 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.009197
49 ENOG4108UUM single-stranded DNA-binding protein 0.009188
50 ENOG4105DDM phosphonoacetate hydrolase 0.009178
51 ENOG4105VRA Glyoxalase Bleomycin resistance protein (Dioxygenase -0.009170
52 ENOG4105EEX Two component transcriptional regulator (Winged helix family 0.009147
53 ENOG4105C8X One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions (By similarity) 0.009134
54 ENOG4105DNH Major Facilitator 0.009008
55 ENOG4105DYB Isoaspartyl dipeptidase -0.009008
56 ENOG4105FFC UPF0187 protein 0.008994
57 ENOG4105HYG antirestriction protein -0.008948
58 ENOG410826V -acetyltransferase -0.008893
59 ENOG4105F3R pts system mannose fructose sorbose family iid 0.008881
60 ENOG4105D07 Signal peptide peptidase, SppA 0.008844
61 ENOG4105EY8 ABC transporter 0.008826
62 ENOG4106UX5 NA -0.008816
63 ENOG4105JGF anti-sigma regulatory factor serine threonine protein kinase 0.008758
64 ENOG4106F9V transposase IS116 IS110 IS902 family protein -0.008754
65 ENOG4105F2W methyltransferase 0.008711
66 ENOG4108V2W Carbonate dehydratase 0.008641
67 ENOG41060W2 glyoxylate carboligase 0.008619
68 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) 0.008608
69 ENOG4107QW3 Sucrose phosphorylase -0.008476
70 ENOG4105NG8 acetyltransferase 0.008463
71 ENOG4107QNT pyruvate dehydrogenase e1 component suBunit beta 0.008459
72 ENOG4108ZQX ybak prolyl-trna synthetase 0.008458
73 ENOG41090N0 alpha beta hydrolase fold-3 domain protein 0.008455
74 ENOG4105D9K One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions (By similarity) 0.008432
75 ENOG4105CID antiterminator 0.008357
76 ENOG4108RYC glycosyltransferase 0.008307
77 ENOG4105S5X Replication protein 0.008306
78 ENOG4105E2V Glycosyltransferase 36 -0.008266
79 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) 0.008249
80 ENOG4107TSP ABC, transporter 0.008248
81 ENOG410685M Sel1 domain protein repeat-containing protein 0.008246
82 ENOG4105EUS Binding-protein-dependent transport systems, inner membrane component 0.008183
83 ENOG4105CVK Glutamate decarboxylase 0.008149
84 ENOG4105WDP acetyltransferase 0.008139
85 ENOG4105DAZ ABC transporter 0.008139
86 ENOG4105CVR type I restriction-modification system 0.008070
87 ENOG4105EW8 cytosine purines, uracil, thiamine, allantoin permease 0.008052
88 ENOG41080C9 IA, variant 1 0.008033
89 ENOG4105DBM Siderophore biosynthesis protein -0.008003
90 ENOG4105DG4 malate L-lactate dehydrogenase 0.007999
91 ENOG4105KUS lysozyme 0.007968
92 ENOG4108R80 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. The C subunit may be involved in assembly of the KDP complex (By similarity) 0.007950
93 ENOG4105PSV Polysaccharide Biosynthesis Protein 0.007943
94 ENOG4105DIV Catalyzes the conversion of acetaldehyde to acetyl-CoA, using NAD( ) and coenzyme A. Is the final enzyme in the meta- cleavage pathway for the degradation of aromatic compounds (By similarity) 0.007938
95 ENOG4105CXW Synthesizes alpha-1,4-glucan chains using ADP-glucose (By similarity) -0.007930
96 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.007917
97 ENOG4107E9N Protein of unknown function DUF262 0.007902
98 ENOG4105BZG amino acid carrier protein -0.007878
99 ENOG4105C0D helicase 0.007869
100 ENOG4105K5P Membrane 0.007865
101 ENOG4105DF3 Catalyzes the retro-aldol cleavage of 4-hydroxy-2- oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds (By similarity) 0.007851
102 ENOG4107SS6 2-dehydro-3-deoxygluconokinase -0.007848
103 ENOG410908R Methenyltetrahydrofolate cyclohydrolase -0.007831
104 ENOG4105G6Z alkaline phosphatase 0.007826
105 ENOG4105C7F AcnD-accessory protein PrpF -0.007810
106 ENOG41090CX arginase 0.007809
107 ENOG4108YRF PTS System 0.007801
108 ENOG4108QJS PBS lyase HEAT domain protein repeat-containing protein 0.007800
109 ENOG4105FEE aaa atpase central domain protein 0.007741
110 ENOG4108EMD oxidoreductase Domain protein 0.007728
111 ENOG4105BZC d-serine deaminase 0.007697
112 ENOG4107QRG dna polymerase iii 0.007692
113 ENOG4107R26 Methyl-accepting chemotaxis sensory transducer 0.007692
114 ENOG4105EE9 pfkb domain protein 0.007676
115 ENOG4105P4J Allophanate hydrolase, subunit 1 0.007676
116 ENOG4105CHZ Catalyzes the dehydration of D-mannonate (By similarity) -0.007665
117 ENOG4105EHA HipA domain protein -0.007663
118 ENOG4105DZC cytosine deaminase 0.007650
119 ENOG4105C32 Amino acid ABC transporter (Permease) 0.007642
120 ENOG4105XDF Protein of unknown function (DUF1272) -0.007606
121 ENOG4105K42 metal-binding protein 0.007605
122 ENOG4105CR6 AtP-binding protein -0.007598
123 ENOG4108QQX Diguanylate cyclase 0.007589
124 ENOG4105CGU Enoyl-CoA hydratase 0.007572
125 ENOG4105EZ1 type I restriction enzyme -0.007562
126 ENOG4107R0V Pyruvate dehydrogenase 0.007546
127 ENOG4105CG6 trap dicarboxylate transporter dctm subunit 0.007522
128 ENOG4108I55 Aminotransferase class I and II 0.007517
129 ENOG4108F2A regulatory protein 0.007516
130 ENOG4105MT7 Arsenical resistance operon tranS-acting repressor -0.007515
131 ENOG4107WCV Phenazine biosynthesis protein 0.007508
132 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit -0.007503
133 ENOG4108R3F Nudix family 0.007494
134 ENOG4107YND lmbE family -0.007466
135 ENOG4105CVU peptidase s58 dmpa 0.007460
136 ENOG4107QTZ amino acid 0.007459
137 ENOG41090ME Restriction modification system DNA specificity -0.007401
138 ENOG4105F96 Transposase -0.007357
139 ENOG4105GXR PRTRC system ThiF family protein 0.003678
139 ENOG4108M9S PRTRC system protein B 0.003678
140 ENOG41067V7 50S ribosomal protein L36 -0.007356
141 ENOG4105C5P abc transporter permease protein -0.007340
142 ENOG41067R7 Sulfatase 0.007336
143 ENOG4107XPG G-D-S-l family -0.007314
144 ENOG4105D1U peptidase U62 modulator of DNA gyrase -0.007311
145 ENOG4105CAC Catalyzes the conversion of L-arabinose to L-ribulose (By similarity) -0.007309
146 ENOG4105EUJ GTP cyclohydrolase i 0.007300
147 ENOG4107RGH Aldehyde dehydrogenase 0.007292
148 ENOG4108F2G Chain length determinant protein 0.007283
149 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for 0.007282
150 ENOG4106HWX Inherit from COG: transposase 0.007265
151 ENOG4105DQ4 alcohol dehydrogenase 0.007252
152 ENOG4108UHE carbonic anhydrase -0.007241
153 ENOG4105E05 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.007231
154 ENOG4105KUW Hnh endonuclease 0.007229
155 ENOG41068PG O-Antigen polymerase 0.007227
156 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) 0.007221
157 ENOG4105D0U Arsenite-activated ATPase (ArsA) -0.007219
158 ENOG4105E2S oxidase) subunit II -0.007216
159 ENOG4105DC7 peptidase M24 -0.007212
160 ENOG4105CVJ phosphoglycerate mutase 0.007207
161 ENOG4105GFX Transcriptional regulator -0.007201
162 ENOG41076HS cation diffusion facilitator family transporter 0.007147
163 ENOG4105CF8 branched-chain amino acid ABC transporter, permease 0.007141
164 ENOG4105CJV Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase 0.007125
165 ENOG41081XD Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein (By similarity) 0.007112
166 ENOG4105E1C Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a) (By similarity) -0.007111
167 ENOG4108YZG isomerase 0.007111
168 ENOG4105CDW Resistance protein -0.007107
169 ENOG4105E09 nadh pyrophosphatase -0.007092
170 ENOG4108J4B Beta-lactamase 0.007084
171 ENOG4105CXG d-lactate dehydrogenase -0.007075
172 ENOG4105JEU Glycosyl transferase, family 2 0.007069
173 ENOG4105C2J ABC transporter -0.007056
174 ENOG4105NQN cytochrome C 0.007056
175 ENOG4108H0N domain protein 0.007054
176 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 0.007049
177 ENOG4108S3Z Histidine kinase 0.007045
178 ENOG4105NW6 solute symporter protein -0.007038
179 ENOG4107S0H decarboxylase 0.007035
180 ENOG4107QYD Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.007021
181 ENOG4106HNT NA -0.007016
182 ENOG4105I1K ABC transporter -0.007013
183 ENOG4108UHS Viral (Superfamily 1) RNA helicase -0.007013
184 ENOG4108MP3 ABC transporter, permease 0.007013
185 ENOG410624X efflux transporter, rnd family, mfp subunit 0.007011
186 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase 0.007009
187 ENOG4105CYW agmatinase 0.006992
188 ENOG41060PI NA 0.006989
189 ENOG4108RX9 RNA Polymerase -0.006981
190 ENOG410695M Pilus assembly protein 0.006959
191 ENOG4108JJA ABC, transporter 0.006958
192 ENOG4105F5R ABC transporter 0.006949
193 ENOG4105VGV redox-active disulfide protein 2 0.006938
194 ENOG4105ZS6 Protein of unknown function (DUF987) -0.006931
195 ENOG4108YY9 U mismatch-specific DNA glycosylase 0.006917
196 ENOG4105CUK Alpha-N-arabinofuranosidase (EC 3.2.1.55) -0.006916
197 ENOG41061GT Aldolase 0.006913
198 ENOG4105I7Z Short-chain dehydrogenase reductase Sdr -0.006912
199 ENOG4105CY2 Citrate transporter 0.006909
200 ENOG4105GWS NA -0.006907
201 ENOG4108WUH Transcriptional regulator, TetR family -0.006887
202 ENOG4107VWA Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation (By similarity) 0.006882
203 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) 0.006871
204 ENOG4105E4F Isochorismate synthase 0.006869
205 ENOG4108WXU NA -0.006849
206 ENOG4105DC1 bifunctional purine biosynthesis protein purh 0.006844
207 ENOG4105MSK Tetr family transcriptional regulator 0.006836
208 ENOG4105BZW Glycerate kinase 0.006824
209 ENOG41090G6 cupin superfamily protein -0.006818
210 ENOG4108UQ8 endoribonuclease L-psp -0.006810
211 ENOG4107SGM protein serine threonine phosphatase 0.006804
212 ENOG4105DV0 amidase (EC 3.5.1.4 -0.006802
213 ENOG4105DD7 kinase (PfkB family -0.006798
214 ENOG4107YT9 Methyltransferase 0.006786
215 ENOG4105EN6 Membrane 0.006780
216 ENOG410606Q NA -0.006779
217 ENOG4107R7Y intracellular protease Pfpi family 0.006779
218 ENOG4105C4C beta-galactosidase -0.006772
219 ENOG4107RB5 abc transporter permease protein -0.006755
220 ENOG4107XBN GntR Family Transcriptional Regulator -0.006755
221 ENOG4105CK1 PTS System 0.006748
222 ENOG4108RV2 acetyltransferase 0.006747
223 ENOG4105CI1 PTS System 0.006742
224 ENOG4108Z7F N-acetyltransferase 0.006728
225 ENOG4107QS2 Symporter -0.006728
226 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) 0.006721
227 ENOG4108NZ2 LysR family Transcriptional regulator 0.006716
228 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase 0.006714
229 ENOG4105M2Z protein tyrosine serine phosphatase 0.006712
230 ENOG4108IUY abc transporter atp-binding protein -0.006700
231 ENOG410736V Aminoglycoside phosphotransferase -0.006699
232 ENOG4105E2B Taurine dioxygenase 0.006696
233 ENOG4106MD1 NA 0.006694
234 ENOG4108MZV extracellular ligand-binding receptor 0.006693
235 ENOG4108XII Transporter DctQ -0.006690
236 ENOG4105C7S Dehydrogenase 0.006688
237 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) 0.006676
238 ENOG4105IDF Transposase -0.006651
239 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) 0.006648
240 ENOG4105DDW LysR family Transcriptional regulator -0.006648
241 ENOG4108UMN azlc family 0.006645
242 ENOG41080HJ 6-phospho 3-hexuloisomerase 0.006621
243 ENOG4108UJE IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of IGP and AICAR (By similarity) 0.006620
244 ENOG4105C90 Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction proline is first activated by ATP to form Pro- AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS (By similarity) 0.006608
245 ENOG4105EA4 abc transporter atp-binding protein -0.006608
246 ENOG4107RMI Periplasmic binding protein LacI transcriptional regulator 0.006604
247 ENOG4108R02 integrase family 0.006603
248 ENOG4107RRD Dehydrogenase -0.006600
249 ENOG4108N53 binding-protein-dependent transport systems inner membrane Component 0.006590