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 ENOG4105DGK type VI secretion protein, EvpB VC_A0108 family 0.041711
2 ENOG4105FHN type VI secretion protein, VC_A0111 family 0.038094
3 ENOG4105CU3 Type VI secretion protein IcmF 0.037184
4 ENOG4105EG5 type VI secretion protein, VC_A0114 family 0.032784
5 ENOG4105DHY type VI secretion protein 0.032489
6 ENOG4105CS6 Rhs element vgr protein 0.029038
7 ENOG4105NIK Type IV VI secretion system protein, DotU family 0.026312
8 ENOG4108R52 Type VI secretion protein, VC_A0107 family 0.019070
9 ENOG4108VI5 type VI secretion protein 0.017589
10 ENOG4108KU0 Virulence Protein SciE Type 0.014686
11 ENOG4105IQ3 FHA domain 0.014602
12 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) 0.011644
13 ENOG4108WRD type VI secretion system, lysozyme-related protein 0.011280
14 ENOG4108MQR type VI secretion-associated protein, ImpA family 0.011208
15 ENOG4105XFU type VI secretion lipoprotein, VC_A0113 family 0.010996
16 ENOG4108QK1 type VI secretion system, lysozyme-related protein 0.010915
17 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) 0.010888
18 ENOG4105KXH PAAR repeat-containing protein 0.010674
19 ENOG4105C3T may be the GTPase, regulating ATP sulfurylase activity (By similarity) 0.010597
20 ENOG4108IJ0 Aspartate ammonia-lyase 0.010393
21 ENOG4108ZF3 Phosphatase 0.010386
22 ENOG4106RZ4 Peptidase U32 0.010256
23 ENOG4105DG4 malate L-lactate dehydrogenase -0.009928
24 ENOG4105MQD type VI secretion-associated protein, BMA_A0400 family 0.009867
25 ENOG4108N5P type VI secretion-associated protein, ImpA family 0.009807
26 ENOG4105PV3 Inner membrane protein yqiJ 0.009786
27 ENOG4108WC9 type VI secretion system effector, hcp1 family 0.009781
28 ENOG4107R7A Allophanate hydrolase subunit 2 0.009758
29 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.009742
30 ENOG4106JHG type VI secretion system effector, hcp1 family 0.009646
31 ENOG4107RB3 L-asparaginase 0.009643
32 ENOG4107S78 Band 7 protein 0.009567
33 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) 0.009466
34 ENOG4105CFP Peptidase U32 0.009335
35 ENOG4105D01 (LipO)protein 0.009190
36 ENOG4105DKP glycosyl transferase, family 9 0.009178
37 ENOG4108N39 Endonuclease 0.009158
38 ENOG4105XPQ lipid carrier protein 0.008947
39 ENOG4107A8D Type IV VI secretion system protein 0.008923
40 ENOG4105KT7 mgtC SapB transporter 0.008903
41 ENOG4105D05 Receptor 0.008839
42 ENOG4107RMT Osmosensitive K channel His kinase sensor 0.008791
43 ENOG4105CP2 von willebrand factor, type a 0.008706
44 ENOG4105UQX Mate efflux family protein 0.008693
45 ENOG4105DRC Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.008680
46 ENOG4105VIR ycii-related 0.008674
47 ENOG4108RYK Nad-dependent epimerase dehydratase 0.008506
48 ENOG4105SA9 Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides (By similarity) 0.008489
49 ENOG4109083 pas pac sensor-containing diguanylate cyclase 0.008449
50 ENOG4105MWK D-amino acid dehydrogenase, small subunit 0.008425
51 ENOG4107HP6 Transcriptional regulator 0.008417
52 ENOG4105C6H Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction (By similarity) 0.008360
53 ENOG4105KAV tspo and mbr like protein 0.008294
54 ENOG4105C11 sulfate adenylyltransferase), subunit 2 0.008294
55 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) 0.008281
56 ENOG4105Y68 type VI secretion system, lysozyme-related protein 0.008175
57 ENOG4105E2S oxidase) subunit II 0.008153
58 ENOG4106BVW Protein of unknown function (DUF877) 0.008133
59 ENOG4105P8F nudix hydrolase 0.008131
60 ENOG4105D08 cbs domain and cyclic nucleotide-regulated nucleotidyltransferase -0.008129
61 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) 0.008099
62 ENOG4105DS2 Anaerobic c4-dicarboxylate transporter 0.008041
63 ENOG4105Z2T NA 0.008016
64 ENOG4108W5W 3-Oxoacyl-(Acyl carrier protein) synthase 0.007950
65 ENOG4105CW7 secretion protein, HlyD family 0.007856
66 ENOG4105G7T Catalyzes the Claisen rearrangement of chorismate to prephenate (By similarity) 0.007830
67 ENOG4105WPN DNA integration recombination invertion protein -0.007827
68 ENOG4105EQ2 LysR family Transcriptional regulator 0.007764
69 ENOG4105DN4 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.007763
70 ENOG4108U18 CAAX amino terminal protease family protein 0.007761
71 ENOG4105DI9 type VI secretion-associated protein, VC_A0119 family 0.007700
72 ENOG4105CH2 amidohydrolase 0.007617
73 ENOG4107RF9 Periplasmic binding protein 0.007615
74 ENOG4105CR7 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA (By similarity) 0.007560
75 ENOG4105E9K Isocitrate dehydrogenase 0.007521
76 ENOG4105C54 Major Facilitator superfamily 0.007515
77 ENOG4105E97 Metal dependent phosphohydrolase 0.007493
78 ENOG4108Q6H Signal transduction protein containing sensor and EAL domains -0.007491
79 ENOG4105C09 Bile acid -0.007488
80 ENOG4105DFP Integrase -0.007426
81 ENOG4105CBF Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction (By similarity) 0.007404
82 ENOG4105E0Y RtcB Protein 0.007380
83 ENOG4105EAC phosphoserine phosphatase 0.007361
84 ENOG4105GIA Uncharacterized protein conserved in bacteria (DUF2169) 0.007336
85 ENOG4105EFC phage portal protein HK97 family -0.007323
86 ENOG4105DN3 alpha-2-macroglobulin domain protein 0.007321
87 ENOG4107RDB Major Facilitator 0.007288
88 ENOG41067UG Cyd operon protein YbgT 0.007283
89 ENOG4108XTP Transcriptional regulator 0.007249
90 ENOG4105DGM nitrilase cyanide hydratase and apolipoprotein n-acyltransferase 0.007248
91 ENOG4108F0V Aminotransferase 0.007210
92 ENOG4108RAV Conserved protein 0.007198
93 ENOG4108JMC lipopolysaccharide core biosynthesis protein 0.007198
94 ENOG4105C0R drug resistance transporter emrb qaca subfamily 0.007189
95 ENOG4105EEQ Na H antiporter 0.007173
96 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) 0.007165
97 ENOG4105DJ5 Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis (By similarity) -0.007145
98 ENOG4105CTU Proline racemase 0.007133
99 ENOG4105VW4 glutaredoxin 3 -0.007113
100 ENOG4108S2Y peptide Chain Release factor 0.007099
101 ENOG4107QHF type ii secretion system protein e 0.007097
102 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin 0.007069
103 ENOG4105QA4 4Fe-4S Ferredoxin, iron-sulfur binding domain protein -0.007050
104 ENOG4105J76 Periplasmic binding protein 0.007048
105 ENOG4106PZ8 LysR family transcriptional regulator 0.007040
106 ENOG4108ETY sodium dicarboxylate symporter 0.007018
107 ENOG4105E1Q flagellar hook-associated protein 0.006994
108 ENOG4105VS7 Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation (By similarity) -0.006964
109 ENOG4108IYU L-aspartate oxidase 0.006957
110 ENOG4105EHA HipA domain protein -0.006904
111 ENOG4105CR4 methylisocitrate lyase 0.006895
112 ENOG41084DX Pfam:DUF583 0.006878
113 ENOG4105MAG toluene tolerance family protein 0.006809
114 ENOG4107TG6 ABC transporter, periplasmic molybdate-binding protein 0.006789
115 ENOG4105X3E Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine (By similarity) 0.006751
116 ENOG4105KPV Transcriptional regulator 0.006742
117 ENOG4105P3U NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) 0.006736
118 ENOG4107QTZ amino acid 0.006682
119 ENOG4105C1B dTDP-glucose 4-6-dehydratase -0.006652
120 ENOG4108QRM SapC family -0.006641
121 ENOG4108R99 pseudouridine synthase -0.006620
122 ENOG4105VFU Rna-binding protein 0.006591
123 ENOG4108XC3 NADH ubiquinone oxidoreductase 0.006588
124 ENOG4108ZKG OsmC family 0.006578
125 ENOG4108N92 Thiol disulfide Interchange Protein 0.006574
126 ENOG4108ZMS Electron transfer subunit of the periplasmic nitrate reductase complex NapAB (By similarity) 0.006541
127 ENOG4105WI7 Cupin 2, conserved barrel domain protein -0.006538
128 ENOG41090JN Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl- L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway (By similarity) 0.006504
129 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) 0.006483
130 ENOG410626B catechol 1,2-dioxygenase 0.006469
131 ENOG4105KHU inner membrane protein YohD 0.006413
132 ENOG4105CCC Dihydrolipoamide dehydrogenase 0.006410
133 ENOG41068JT domain protein -0.006409
134 ENOG4107XTH Alpha Beta Hydrolase Fold protein 0.006401
135 ENOG41060QE Glycosyl transferase, family 2 0.006399
136 ENOG4106NZI LysR family Transcriptional regulator 0.006389
137 ENOG4108K5D type VI secretion-associated protein, VC_A0119 family 0.006379
138 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.006372
139 ENOG4105X7T Ni Fe-hydrogenase, b-type cytochrome subunit 0.006372
140 ENOG4106A6I hemolysin 0.006359
141 ENOG4105DP5 Catalyzes the biosynthesis of agmatine from arginine (By similarity) 0.006356
142 ENOG4108SSQ Type IV pilus assembly protein PilW 0.006340
143 ENOG4105F28 tonB-dependent Receptor -0.006339
144 ENOG4107Z47 Signal transduction histidine kinase -0.006329
145 ENOG4108ISG Major Facilitator 0.006327
146 ENOG4108YDI single-species biofilm formation on inanimate substrate 0.006305
147 ENOG4107QI2 Domain of unknown function DUF20 0.006301
148 ENOG4108UMI ABC transporter, permease 0.006300
149 ENOG4105FJH Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions (By similarity) 0.006299
150 ENOG4105CNA YD repeat protein 0.006293
151 ENOG41077RS Phosphatase 0.006291
152 ENOG4105N9F Low molecular weight phosphotyrosine protein phosphatase 0.006289
153 ENOG410606R oxidoreductase (molybdopterin binding 0.006276
154 ENOG4105W39 Membrane 0.006265
155 ENOG4105N6D Fimbrial assembly family protein 0.006237
156 ENOG4108VJ6 FHA domain-containing protein 0.006224
157 ENOG4105ETE Transcriptional regulator (LacI family 0.006219
158 ENOG4105CSX c4-dicarboxylate anaerobic carrier -0.006191
159 ENOG4105C6Z Gluconate 0.006187
160 ENOG4105DWT malate dehydrogenase (quinone) 0.006187
161 ENOG4108SNX Mammalian cell entry related domain protein 0.006171
162 ENOG4105M08 Membrane -0.006159
163 ENOG4105N7W NA 0.006156
164 ENOG4105UP8 type VI secretion-associated protein, VC_A0118 family 0.006150
165 ENOG4105K78 MarR family Transcriptional regulator 0.006142
166 ENOG4107SP9 transport system permease protein -0.006121
167 ENOG4108I5A Tetratricopeptide tpr_2 repeat protein 0.006114
168 ENOG4105MFX 4-diphosphocytidyl-2c-methyl-d-erythritol synthase 0.006109
169 ENOG4105VRT cytoplasmic protein 0.006106
170 ENOG4105CG5 Glycosyl transferase (Group 1 0.006102
171 ENOG4105MJ6 selenium-dependent hydroxylase accessory protein YqeC 0.006098
172 ENOG4105EFA 4-hydroxyphenylacetate 0.006096
173 ENOG4107R9J drug resistance transporter, EmrB QacA subfamily -0.006090
174 ENOG4105MQ6 Disulfide Bond Formation Protein 0.006082
175 ENOG4105C44 Serine transporter 0.006068
176 ENOG4105ERH Fumarylacetoacetate hydrolase 0.006063
177 ENOG4107QUY Guanine deaminase 0.006061
178 ENOG4105FQ6 thiopurine methyltransferase 0.006060
179 ENOG4108VIA integral membrane protein 0.006048
180 ENOG4105KEG ribosomal-protein-alanine acetyltransferase 0.006041
181 ENOG4105C0F tryptophanase EC 4.1.99.1 -0.006034
182 ENOG4107SM4 Transcriptional regulator, GntR family 0.006020
183 ENOG4105VTN Protein of unknown function (DUF1311) 0.006019
184 ENOG4108PSN Required for disulfide bond formation in some proteins. Part of a redox system composed of DsbI and DsbL that mediates formation of an essential disulfide bond in AssT (By similarity) 0.006003
185 ENOG4105S6R Iron-hydroxamate transporter permease subunit 0.005989
186 ENOG4105BZ9 Cytochrome C oxidase, subunit I 0.005969
187 ENOG4108R5F Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis (By similarity) -0.005962
188 ENOG4105R5S Transcriptional regulator (XRE family -0.005958
189 ENOG4105CHH sulfate transporter -0.005949
190 ENOG4106MFT Citrate-proton symporter 0.005923
191 ENOG4105KMD Thioesterase 0.005909
192 ENOG4105ZXK Dehydrogenase 0.005904
193 ENOG4105M3K binding-protein-dependent transport systems inner membrane Component 0.005892
194 ENOG4105EU7 Protocatechuate 3,4-dioxygenase, beta 0.005890
195 ENOG4105PX9 Transcriptional regulator, MarR family -0.005887
196 ENOG4105VMP Transcriptional regulator 0.005856
197 ENOG4108HHI Type III secretion system protein 0.005843
198 ENOG4105R3G BNR Asp-box repeat protein 0.005839
199 ENOG41088R0 Uncharacterized protein conserved in bacteria N-term (DUF3322) 0.005822
200 ENOG4105N94 The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase (By similarity) -0.005821
201 ENOG4105S10 periplasmic binding protein -0.005819
202 ENOG4105E7W lamb ycsf family protein 0.005814
203 ENOG4105CWI transcriptional regulator -0.005803
204 ENOG4105DS5 Uncharacterized protein conserved in bacteria (DUF2248) 0.005790
205 ENOG4108QK2 Membrane-bound metal-dependent hydrolase -0.005789
206 ENOG4105D78 K07001 NTE family protein -0.005787
207 ENOG4105EV5 Peptidase, M16 0.005787
208 ENOG4105HA6 Glycosyl transferase, family 2 0.005783
209 ENOG4105KQ5 peptidylprolyl cis-trans isomerase 0.005774
210 ENOG4108TUY outer membrane protein PgaA 0.005767
211 ENOG4105KHC sulfurtransferase 0.005751
212 ENOG4108KYP polysaccharide deacetylase 0.005746
213 ENOG4108UXE Protein tyrosine phosphatase -0.005731
214 ENOG4105CE5 Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) 0.005730
215 ENOG4108ZU0 ErfK YbiS YcfS YnhG family protein 0.005727
216 ENOG4105DHP deoxycytidine triphosphate deaminase 0.005724
217 ENOG4108B2D Squalene phytoene synthase 0.005718
218 ENOG4105NGH ompa motb domain protein 0.005715
219 ENOG4108HPI phosphatidate Cytidylyltransferase 0.005715
220 ENOG4105D9P serine threonine protein kinase 0.005686
221 ENOG4105DU2 Extracellular solute-binding protein family 3 0.001893
221 ENOG4105DUG amino acid AbC transporter 0.001893
221 ENOG41086HZ amino acid AbC transporter 0.001893
222 ENOG4105EJQ L-serine dehydratase 0.005675
223 ENOG41069AG Ankyrin repeat -0.005670
224 ENOG4105VYA Uncharacterized conserved protein (DUF2132) 0.005668
225 ENOG4105BZW Glycerate kinase 0.005655
226 ENOG4105TMB Formate nitrite transporter 0.005653
227 ENOG4105DHS permease protein 0.005648
228 ENOG4105CM4 permease protein 0.005642
229 ENOG4107RAW 3-carboxy-cis-cis-muconate cycloisomerase 0.005639
230 ENOG4105C1U Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein (By similarity) 0.005630
231 ENOG4105EGS Mechanosensitive ion channel -0.005615
232 ENOG4108UHF Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin) (By similarity) -0.005607
233 ENOG4107RU8 SPFH domain, Band 7 family protein -0.005596
234 ENOG4107P0T Selenium-dependent molybdenum hydroxylase system protein, YqeB family 0.005588
235 ENOG4108P54 dihydrodipicolinate 0.005581
236 ENOG4105XSC ribosomal subunit Interface protein 0.005578
237 ENOG4107XDA flavin reductase domain protein, FMN-binding -0.005576
238 ENOG4107W89 Serine Threonine protein kinase 0.005572
239 ENOG4105KEU Polysaccharide deacetylase 0.005569
240 ENOG4108HQN Adenylate guanylate Cyclase -0.005567
241 ENOG4105I9N NA 0.005528
242 ENOG4107T8Q Glycosyl transferase (Group 1 -0.005521
243 ENOG4108WEH Type VI secretion 0.005518
244 ENOG4105CNR NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) 0.005514
245 ENOG4107RMF Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes (By similarity) 0.005510
246 ENOG4105F2K FkbH Like Protein 0.005500
247 ENOG4105EFZ amidohydrolase -0.005483
248 ENOG4105E6E Nickel transport complex, NikM subunit, transmembrane -0.005478