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 ENOG4105ER6 polysaccharide biosynthesis protein -0.013805
2 ENOG4105IXE Abortive infection protein 0.013458
3 ENOG4105DPE Conserved Protein 0.013076
4 ENOG4105VPX protein, conserved in bacteria 0.012822
5 ENOG4108VGH Abortive infection bacteriophage resistance protein 0.012542
6 ENOG4105EWC Purine nucleoside phosphorylase -0.012471
7 ENOG4108ZC8 IA, variant 3 0.012380
8 ENOG4105CE7 Amidase, hydantoinase carbamoylase family 0.012104
9 ENOG4105GZI Transcriptional regulator 0.012021
10 ENOG4105PAX Conserved Protein 0.011945
11 ENOG4107G74 ATP cone domain -0.011869
12 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.011837
13 ENOG4105D6U Sodium Glutamate Symporter 0.011815
14 ENOG4105VXN addiction module toxin, RelE StbE family 0.011779
15 ENOG4108V4B ThiJ pfpI 0.011735
16 ENOG4105C5Q Transcriptional regulator 0.011585
17 ENOG4107VJ1 Replication initiator protein A -0.011564
18 ENOG4105H1G trap transporter solute receptor taxi family 0.011285
19 ENOG4105CJT Mannose-1-phosphate guanylyltransferase 0.011153
20 ENOG4105HMI Membrane -0.011152
21 ENOG4106XIN polysaccharide biosynthesis protein 0.011145
22 ENOG4105MAX Superoxide reductase -0.011084
23 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) 0.010993
24 ENOG4105HAT NA -0.010967
25 ENOG4107QQE GntR family transcriptional regulator -0.010890
26 ENOG41080ZK Transcriptional regulator, arsR family -0.010852
27 ENOG4105KEM Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation (By similarity) -0.010699
28 ENOG4107R2R Chloride channel -0.010670
29 ENOG4105CYW agmatinase 0.010655
30 ENOG4108N80 biosynthesis protein -0.010571
31 ENOG4108N34 Vanz family 0.010493
32 ENOG4105VJG Transcriptional regulator -0.010457
33 ENOG4105EEM helicase 0.010448
34 ENOG4108RTI radical SAM domain protein 0.010424
35 ENOG4105X1N Glycosyl transferase family 8 -0.010394
36 ENOG4107QSK Phage infection protein 0.010388
37 ENOG4107QQP Pasta domain containing protein 0.010377
38 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) 0.010347
39 ENOG4105D59 Tetracycline resistance protein 0.010342
40 ENOG4105EMD TRANSCRIPTIONal -0.010284
41 ENOG4108Z9I -acetyltransferase -0.010232
42 ENOG4105DBN NA -0.010216
43 ENOG4108HMR Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) -0.010174
44 ENOG4105DH3 ABC transporter -0.010120
45 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) 0.010085
46 ENOG4105WF1 Addiction module antitoxin, RelB DinJ family 0.010075
47 ENOG4108WSK Inherit from COG: Alpha beta hydrolase 0.009998
48 ENOG4108JJ9 ABC, transporter 0.009965
49 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) -0.009950
50 ENOG4105CPQ Dehydrogenase 0.009868
51 ENOG4105CEV competence damage-inducible protein -0.009862
52 ENOG4105BZJ Electron transfer flavoprotein -0.009854
53 ENOG4105H3Q Primosomal protein, DnaI -0.009824
54 ENOG4108JQ1 Dehydrogenase 0.009808
55 ENOG4107U23 Amino acid permease 0.009793
56 ENOG4108S8M degv family -0.009763
57 ENOG4105EQ8 radical SAM domain protein -0.009746
58 ENOG4107QJP DTDP-glucose 4-6-dehydratase 0.009732
59 ENOG4105DFW ABC transporter 0.009730
60 ENOG41067V7 50S ribosomal protein L36 0.009652
61 ENOG4105D56 permease protein -0.009650
62 ENOG4105Y1R AtP-binding protein 0.009607
63 ENOG4107H8F NA -0.009580
64 ENOG4105D4H Membrane -0.009571
65 ENOG4105KME endoribonuclease L-psp 0.009570
66 ENOG4105VFB Binds the 23S rRNA (By similarity) 0.009569
67 ENOG4105DJR solute-binding protein 0.009556
68 ENOG4105CUC YeeE YedE family protein 0.009555
69 ENOG4107UEM Glycosyl transferase, family 2 0.009531
70 ENOG4107GZ4 SanA protein 0.009424
71 ENOG4105C6T cysteine synthase -0.009423
72 ENOG4105D7A ATP-binding protein -0.009322
73 ENOG4105CYC Transferase -0.009303
74 ENOG4108M96 Capsular polysaccharide synthesis protein -0.009301
75 ENOG4105EJ9 Membrane -0.009291
76 ENOG4105D7W serine acetyltransferase -0.009283
77 ENOG41090BB DNA mismatch endonuclease (vsr) 0.009263
78 ENOG4107U7W abc transporter permease protein -0.009243
79 ENOG4107AYK membrAne -0.009198
80 ENOG410810U membrane 0.009167
81 ENOG4105VMP Transcriptional regulator -0.009159
82 ENOG4107QPG succinate dehydrogenase, flavoprotein subunit 0.009154
83 ENOG4108Z58 rRNA Methylase -0.009137
84 ENOG4107SX2 Transcriptional Regulator AraC Family 0.009121
85 ENOG4107YV9 domain protein -0.009118
86 ENOG41082RJ Hydrogenase nickel insertion protein HypA -0.009101
87 ENOG4105DQ6 Transposase -0.009094
88 ENOG4107YH3 SUF system FeS assembly protein, NifU family -0.009077
89 ENOG4108IQK o-acetylhomoserine -0.009056
90 ENOG4107ZU8 PTS System 0.009052
91 ENOG4105CCX Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) 0.009048
92 ENOG4105EG2 ABC transporter, permease -0.009033
93 ENOG4105DUM transcriptional regulator, lysR family 0.009027
94 ENOG4105DMS mur ligase 0.009026
95 ENOG4108UHX Involved in the hydrolysis of glutamine to glutamate and ammonia. Channels an ammonia molecule to PdxS (By similarity) 0.008999
96 ENOG4105DYB Isoaspartyl dipeptidase 0.008999
97 ENOG4105D4T Citrate transporter -0.008995
98 ENOG41067US Addiction module antitoxin, RelB DinJ family -0.008967
99 ENOG4108FT7 Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) 0.008955
100 ENOG4105KPE licD family 0.008909
101 ENOG4107R37 Glutamate dehydrogenase 0.008893
102 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase -0.008889
103 ENOG4105C6B Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl- acyl-carrier-protein (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA (By similarity) -0.008888
104 ENOG4105CQB FAD linked oxidase domain protein -0.008886
105 ENOG4105FM6 NA 0.008860
106 ENOG4107EF8 Glycosyl transferase (Group 1 0.008855
107 ENOG4105EPR degv family -0.008831
108 ENOG4105F4P )-transporter -0.008802
109 ENOG4108UZ3 Transporter 0.008800
110 ENOG4105E09 nadh pyrophosphatase 0.008790
111 ENOG4105D43 The glycine cleavage system catalyzes the degradation of glycine (By similarity) -0.008764
112 ENOG4105VGV redox-active disulfide protein 2 -0.008758
113 ENOG4107SNF Na H antiporter -0.008741
114 ENOG4108IYT Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity) 0.008725
115 ENOG4105DSX permease -0.008723
116 ENOG4108VHV Membrane -0.008695
117 ENOG4106GGJ NA -0.008688
118 ENOG4108IY2 MazG family 0.008656
119 ENOG4105PSV Polysaccharide Biosynthesis Protein 0.008638
120 ENOG4105C48 Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (By similarity) 0.008619
121 ENOG4105QXD 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.008601
122 ENOG4107V2D Transporter Permease Protein -0.008590
123 ENOG4105KGS Membrane 0.008573
124 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.008569
125 ENOG4108IJ0 Aspartate ammonia-lyase 0.008538
126 ENOG4108TJ7 NA 0.008524
127 ENOG4105CAH Chromate 0.008488
128 ENOG410830J Heavy metal-associated domain protein 0.008443
129 ENOG4105E5D amino acid -0.008439
130 ENOG4105DEN Luciferase family -0.008342
131 ENOG4105Q8V NA 0.008328
132 ENOG4105KVH Transcriptional regulator 0.008325
133 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) -0.008305
134 ENOG4105S0E allantoin catabolism protein 0.008297
135 ENOG4107TCJ Inherit from COG: virion core protein (Lumpy skin disease 0.008269
136 ENOG4105DRM Cell surface protein 0.008254
137 ENOG4108E18 Redoxin 0.008237
138 ENOG4106DSS Tartrate dehydratase subunit alpha 0.008227
139 ENOG4105GM9 Membrane 0.008210
140 ENOG4108UQS dipeptidase 0.008201
141 ENOG4107R4I Periplasmic binding protein -0.008199
142 ENOG4105I22 NA 0.008184
143 ENOG4105FC6 Extracellular solute-binding protein, family 5 -0.008183
144 ENOG4105D1M ATP-dependent endonuclease of the OLD -0.008171
145 ENOG4105FF2 Type I DHQase -0.008112
146 ENOG41082QE Copper-sensing transcriptional repressor CsoR -0.008081
147 ENOG410602S Transferase -0.008076
148 ENOG4108YYV Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity) -0.008071
149 ENOG4107SFI Major Facilitator superfamily -0.008029
150 ENOG41067TB Fimbrial assembly family protein 0.008028
151 ENOG4106R3C NA -0.008018
152 ENOG4105D4X repressor -0.008016
153 ENOG4108UKM mov34 mpn pad-1 family protein 0.008008
154 ENOG41068AP DNA polymerase beta domain protein region -0.008004
155 ENOG4106I92 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. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol (By similarity) 0.008000
156 ENOG41066GC membrane 0.007995
157 ENOG4105CHW UPF0052 protein -0.007988
158 ENOG4105F8B mobA MobL family protein 0.007980
159 ENOG4105DND Transcriptional regulator 0.007966
160 ENOG4105CEH Catalyzes the synthesis of dihydrouridine a modified base found in the D-loop of most tRNAs (By similarity) -0.007950
161 ENOG4108K05 Pyridoxal kinase -0.007929
162 ENOG4108K3A Glutathione S-transferase -0.007925
163 ENOG4108URH decarboxylase -0.007921
164 ENOG4107IDS Ami_2 0.007897
165 ENOG4107UIE peptidase 0.007894
166 ENOG4105EIZ Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) -0.007890
167 ENOG4105EPD Oligopeptide transporter, Opt family 0.007880
168 ENOG4105DZW Dipeptidase -0.007879
169 ENOG4105E2R ROK family 0.007878
170 ENOG4105TQN Tetr family transcriptional regulator -0.007876
171 ENOG410604Q amidohydrolase -0.007869
172 ENOG4108C8Z NA 0.007869
173 ENOG41073MC NA 0.007850
174 ENOG41062PH NA 0.007835
175 ENOG4105K9J Membrane 0.007835
176 ENOG4105FB1 Polysaccharide Biosynthesis Protein 0.007822
177 ENOG4105CTQ phosphohexokinase -0.007812
178 ENOG4105EZC Histidine kinase 0.007810
179 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) -0.007809
180 ENOG4107KGK dmso reductase anchor subunit 0.007807
181 ENOG4105C7H Helicase, RecD TraA family -0.007806
182 ENOG4105CID antiterminator 0.007802
183 ENOG4106F9V transposase IS116 IS110 IS902 family protein 0.007791
184 ENOG4107UNS conserved inner membrane protein 0.007789
185 ENOG4108KMK Diguanylate cyclase 0.007785
186 ENOG4108ZWC acetyltransferase, (GNAT) family 0.007783
187 ENOG4105K4P CoA-binding domain protein -0.007777
188 ENOG4105DUF Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively (By similarity) 0.007776
189 ENOG4108WDU NA 0.007768
190 ENOG4105EEQ Na H antiporter 0.007765
191 ENOG4105CSH Transporter 0.007755
192 ENOG4105W2W Cytotoxic translational repressor of toxin-antitoxin stability system -0.007754
193 ENOG4108Z3G 3H domain protein -0.007747
194 ENOG4105D57 beta-galactosidase -0.007735
195 ENOG4105BZ4 penicillin-binding protein -0.007719
196 ENOG4105SRN Protein of unknown function (DUF1706) 0.007718
197 ENOG41084SB Carrier of the growing fatty acid chain in fatty acid biosynthesis (By similarity) -0.007718
198 ENOG4105E0C molybdate abc transporter -0.007713
199 ENOG4105DJ1 Phosphoenolpyruvate Carboxylase 0.007711
200 ENOG4108MY4 Endonuclease Exonuclease phosphatase 0.007711
201 ENOG4107ZEW GH3 auxin-responsive promoter 0.007697
202 ENOG4107U2I Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.007694
203 ENOG4105EN6 Membrane 0.007693
204 ENOG4107WP6 response regulator -0.007672
205 ENOG4108KZB NA -0.007642
206 ENOG4108IWU Membrane -0.007633
207 ENOG4105FB2 class II Aldolase 0.007628
208 ENOG4105NI1 DNA-binding protein with PD1-like DNA-binding motif -0.007627
209 ENOG4105E10 peptidase S8 and S53, subtilisin, kexin, sedolisin 0.007624
210 ENOG4105F1K Glutamine amidotransferase 0.007615
211 ENOG4105DWQ 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. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol (By similarity) 0.007592
212 ENOG4108WEG NA -0.007591
213 ENOG41063CS Replication Protein 0.007588
214 ENOG4108SQE Helix-turn-helix 0.007585
215 ENOG4105EVT domain protein 0.007584
216 ENOG4108HWW ABC transporter 0.007572
217 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit -0.007565
218 ENOG4107RZA Na+/H+ antiporter family 0.007562
219 ENOG410908R Methenyltetrahydrofolate cyclohydrolase -0.007544
220 ENOG4105E9U metal-dependent hydrolases of the beta-lactamase superfamily III 0.007539
221 ENOG4105DRR Transcriptional regulator, GntR family -0.007538
222 ENOG4108JIJ Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second (By similarity) -0.007537
223 ENOG4105FVU Cyclic nucleotide-binding domain protein 0.007527
224 ENOG4105H2V Virulence-associated protein e -0.007478
225 ENOG4108YXW Together with MoaA, is involved in the conversion of 5'- GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) -0.007477
226 ENOG4105EPM Diguanylate phosphodiesterase 0.007472
227 ENOG4105CK2 sodium dicarboxylate symporter -0.007468
228 ENOG4107QYE Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.007467
229 ENOG4107R7P Potassium proton antiporter -0.007465
230 ENOG4105VM8 Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity) -0.007465
231 ENOG4108UDG ABC transporter -0.007460
232 ENOG4105CD3 dihydroorotase -0.007437
233 ENOG4105KT7 mgtC SapB transporter 0.007437
234 ENOG4106AQV domain protein -0.007434
235 ENOG4108P9Q abc transporter atp-binding protein 0.007433
236 ENOG4108VUA TRANSCRIPTIONal 0.007405
237 ENOG4105NI6 heptaprenyl diphosphate synthase component I -0.007401
238 ENOG4107XU7 Lactoylglutathione lyase -0.007386
239 ENOG4105E2M Manganese-dependent inorganic pyrophosphatase -0.007374
240 ENOG4107XR9 resolvase -0.007372
241 ENOG4107WQ4 domain protein 0.007359
242 ENOG4106JRM HPT -0.007342
243 ENOG410847Q High-affinity nickel-transport protein -0.007320
244 ENOG4107ZFZ Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation (By similarity) 0.007318
245 ENOG4108IUB 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. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol (By similarity) 0.007305
246 ENOG410750B NA -0.007302
247 ENOG4105VZ8 Transcriptional regulator 0.007283
248 ENOG4105GF1 NA 0.007280
249 ENOG4108V2W Carbonate dehydratase -0.007280
250 ENOG4108JJ8 (ABC) transporter 0.007267