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 ENOG4105KNY Microcompartments protein 0.030511
2 ENOG4105NZS Microcompartments protein 0.029234
3 ENOG4107QIG Dehydrogenase 0.027076
4 ENOG4105WUQ NA 0.026502
5 ENOG4107RWI ethanolamine utilization protein eutJ 0.025385
6 ENOG4107UUW glycyl-radical enzyme activating protein family 0.025077
7 ENOG4107YCW transcriptional regulator, merr family 0.024830
8 ENOG4108VPX Involved in 1,2-propanediol (1,2-PD) degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate (By similarity) 0.023701
9 ENOG4107S9V Inherit from NOG: Membrane 0.022794
10 ENOG4109067 Microcompartments protein 0.022228
11 ENOG4105M3W utilization protein 0.021727
12 ENOG4108WV6 NA 0.019939
13 ENOG4105KTW ethanolamine utilization protein 0.018951
14 ENOG4105NDK ethanolamine utilization protein 0.017384
15 ENOG4105HNG Microcompartments protein 0.014665
16 ENOG4105J28 Tetr family transcriptional regulator 0.014079
17 ENOG4108YI6 Resistance protein 0.013860
18 ENOG4105KEG ribosomal-protein-alanine acetyltransferase -0.013655
19 ENOG4105S10 periplasmic binding protein 0.013208
20 ENOG4105WVM ethanolamine utilization protein EutN carboxysome structural protein Ccml 0.012947
21 ENOG4105Q27 ethanolamine utilization protein EutN carboxysome structural protein Ccml 0.006265
21 ENOG41061GI NA 0.006265
22 ENOG4105VCP PTS System -0.012452
23 ENOG4107SUC TPR repeat-containing protein 0.012360
24 ENOG4108EKI Dehydrogenase 0.012195
25 ENOG4105E5H Transposase -0.012159
26 ENOG4105E66 phosphoriboisomerase A -0.012064
27 ENOG4108TJJ NA 0.011971
28 ENOG4105C6N Formate acetyltransferase 0.011918
29 ENOG4105E2A Dehydrogenase -0.011883
30 ENOG4105XNF BMC domain 0.011805
31 ENOG4108PJD permease -0.011652
32 ENOG4108UMN azlc family -0.011313
33 ENOG4108ZE5 Microcompartments protein 0.011202
34 ENOG4107RCH Diaminopropionate ammonia-lyase 0.011123
35 ENOG410638C tail fiber protein -0.010686
36 ENOG4105CBC glutamate synthase -0.010589
37 ENOG4105DFD Na H antiporter 0.010482
38 ENOG4107RMT Osmosensitive K channel His kinase sensor -0.010442
39 ENOG41080J9 Membrane 0.010258
40 ENOG4105WX5 TRANSCRIPTIONal 0.010189
41 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) 0.010185
42 ENOG4107QUC restriction endonuclease 0.010083
43 ENOG4107QQE GntR family transcriptional regulator 0.010080
44 ENOG4108IJ8 ABC transporter -0.010017
45 ENOG4107SXU methyl-accepting chemotaxis 0.010013
46 ENOG4105HA6 Glycosyl transferase, family 2 0.009957
47 ENOG4105G2D NA 0.009820
48 ENOG4105DKS phage plasmid primase, p4 family -0.009688
49 ENOG4105NI8 Cytosine-specific methyltransferase 0.009484
50 ENOG4105C5B carbamate kinase 0.009473
51 ENOG4105HGD Antitermination protein -0.009422
52 ENOG4107RKQ Methyl-accepting chemotaxis sensory transducer 0.009416
53 ENOG4108V08 YfdX protein -0.009379
54 ENOG4105WBN Transcriptional regulator (LacI family 0.009378
55 ENOG4107XNE ABC transporter, periplasmic molybdate-binding protein 0.009358
56 ENOG4107WTH Galactitol-1-phosphate dehydrogenase -0.009355
57 ENOG4105MKH Cupin 2 Conserved Barrel Domain Protein 0.009295
58 ENOG4105DSE periplasmic solute binding protein 0.009056
59 ENOG41067V3 Antibiotic biosynthesis monooxygenase 0.009019
60 ENOG4105MFX 4-diphosphocytidyl-2c-methyl-d-erythritol synthase 0.008998
61 ENOG4106050 phage regulatory protein, rha family -0.008992
62 ENOG4105ZEE Protein of unknown function (DUF1019) 0.008985
63 ENOG4106YHM NA 0.004490
63 ENOG4107IX8 TPR 0.004490
64 ENOG4105CRZ Nucleotidyl transferase of unknown function (DUF1814) -0.008951
65 ENOG4108HIZ formate dehydrogenase alpha subunit 0.008943
66 ENOG4107YU3 Protein of unknown function DUF45 -0.008885
67 ENOG4108IYU L-aspartate oxidase -0.008823
68 ENOG4105CBT Fructose-1,6-bisphosphatase 0.008821
69 ENOG4108PWF lysozyme -0.008812
70 ENOG4105VXN addiction module toxin, RelE StbE family -0.008758
71 ENOG4105C94 Transporter 0.008752
72 ENOG4107USW pfkb domain protein 0.008751
73 ENOG4105D6N CoA-transferase, subunit a -0.008744
74 ENOG41061GT Aldolase -0.008738
75 ENOG4107R7Y intracellular protease Pfpi family -0.008719
76 ENOG4107QJP DTDP-glucose 4-6-dehydratase -0.008715
77 ENOG4108XPP DNA N-6-adenine-methyltransferase -0.008625
78 ENOG4105EN2 IstB domain-containing protein ATP-binding protein 0.008598
79 ENOG4107RNN dihydropyrimidinase (EC 3.5.2.2) 0.008538
80 ENOG41061PY Histidine kinase 0.008494
81 ENOG4107EI0 non-ribosomal peptide synthetase 0.008436
82 ENOG4107QJX Aldo keto reductase -0.008431
83 ENOG4108H1Y NA -0.008400
84 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.008382
85 ENOG4105D50 Catalyzes the isomerization of 5-dehydro-4-deoxy-D- glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate (By similarity) 0.008357
86 ENOG4105DMQ Methyltransferase 0.008350
87 ENOG4106VZK Membrane 0.008344
88 ENOG4107U2I Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.008301
89 ENOG4105D49 3-dehydroquinate synthase 0.008298
90 ENOG4107RIA ABC 3 transport family 0.004140
90 ENOG4107ZDB Pfam:SBP_bac_9 0.004140
91 ENOG410680U NA -0.008247
92 ENOG4105C1B dTDP-glucose 4-6-dehydratase 0.008214
93 ENOG4105UZW Tail fiber assembly protein -0.008213
94 ENOG4108ZDX Binds together with S18 to 16S ribosomal RNA (By similarity) -0.008210
95 ENOG4107S2N Type III effector Hrp-dependent 0.008208
96 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) -0.008197
97 ENOG4108UY0 (LipO)protein -0.008186
98 ENOG4105CA0 peroxidase -0.008171
99 ENOG4107WGV tail tape measure protein -0.008167
100 ENOG4105Q7J Fimbrial 0.008158
101 ENOG4107S33 PTS System -0.008156
102 ENOG410608V Tail Fiber Assembly protein -0.008144
103 ENOG41064SU resolvase -0.008142
104 ENOG4107U4H Methyl-accepting chemotaxis 0.008081
105 ENOG4107XR9 resolvase -0.008055
106 ENOG4105Y0F caax amino terminal protease family protein -0.008000
107 ENOG4105FB9 CRISPR-associated protein -0.007997
108 ENOG4105CS2 ec 3.2.1.21 -0.007984
109 ENOG4105C4Y ABC transporter 0.007956
110 ENOG41065NP Protein of unknown function (DUF1471) 0.007921
111 ENOG4107SVG Filamentation induced by cAMP protein fic -0.007918
112 ENOG4108JPM phospho-2-dehydro-3-deoxyheptonate aldolase 0.007909
113 ENOG4106RDH Protein of unknown function (DUF2544) -0.002635
113 ENOG4106ZB7 Protein of unknown function (DUF1391) -0.002635
113 ENOG4107I69 Allophanate hydrolase subunit 1 -0.002635
114 ENOG4107QZU type I restriction-modification system -0.007869
115 ENOG4105X15 PTS System -0.007809
116 ENOG410679B prophage CP4-57 regulatory protein alpA -0.007797
117 ENOG4107DMW NA 0.007776
118 ENOG4105DHY type VI secretion protein 0.007769
119 ENOG4106A3A glycosyltransferase 0.007751
120 ENOG4106AXJ AraC family transcriptional regulator -0.007731
121 ENOG4105NFZ NA -0.007711
122 ENOG4107EXU Short-chain dehydrogenase reductase Sdr -0.007695
123 ENOG4105D6U Sodium Glutamate Symporter -0.007694
124 ENOG4105DVW rieske (2Fe-2S) -0.007690
125 ENOG4107RT5 aminobenzoyl-glutamate utilization protein B -0.007672
126 ENOG4105DA0 Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity) -0.007659
127 ENOG4105MN3 Resolvase -0.007629
128 ENOG4106EI2 helix-turn-helix domain protein 0.007623
129 ENOG4105JKY NA -0.007605
130 ENOG41075DT PerC transcriptional activator -0.007572
131 ENOG4107R3N Filamentation induced by cAMP protein fic 0.007555
132 ENOG4105CEU Arginine dihydrolase 0.007547
133 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) -0.007536
134 ENOG4105KHV Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate (By similarity) 0.007500
135 ENOG4105C7H Helicase, RecD TraA family -0.007498
136 ENOG4105BZE flagellar hook protein, FlgE 0.007471
137 ENOG4108SX9 cell division membrane protein-like protein 0.007461
138 ENOG4105CM2 brancheD-chain amino acid aminotransferase -0.007448
139 ENOG4105I03 Flagellin 0.007447
140 ENOG4105EBY tonB-dependent Receptor 0.007440
141 ENOG41080JE two component transcriptional regulator, arac family -0.007382
142 ENOG4107X32 dedA family -0.007362
143 ENOG41083CF Conserved repeat 0.007321
144 ENOG4105CSX c4-dicarboxylate anaerobic carrier 0.007275
145 ENOG4106GGA transcriptional regulator -0.007241
146 ENOG4105KRQ Addiction module toxin, Txe YoeB family -0.007237
147 ENOG4108VSY crispr-associated protein Cas4 -0.007221
148 ENOG4108ESE uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center 0.007212
149 ENOG4108VBH Uncharacterized protein conserved in bacteria (DUF2251) -0.007198
150 ENOG4105D78 K07001 NTE family protein 0.007195
151 ENOG41069VB Protein of unknown function (DUF3343) 0.007190
152 ENOG4105DT3 PTS system, galactitol-specific IIc component -0.007183
153 ENOG4106NS3 Anaerobic dimethyl sulfoxide reductase chain a -0.007180
154 ENOG410688J Ferredoxin -0.007170
155 ENOG4105G63 Type III effector Hrp-dependent -0.007150
156 ENOG4108YZY peptidylprolyl cis-trans isomerase 0.007144
157 ENOG4107QX6 helicase -0.007142
158 ENOG4105M0Y NA -0.007141
159 ENOG4108V06 Glutathione peroxidase -0.007131
160 ENOG4107TGY peptidase 0.007131
161 ENOG4105EG2 ABC transporter, permease -0.007129
162 ENOG4107ZFB 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) 0.007118
163 ENOG410810A EamA-like transporter family -0.007117
164 ENOG410901E Membrane -0.007110
165 ENOG4105TGK Efflux transporter rnd family, mfp subunit -0.007081
166 ENOG4106YSC NA -0.007076
167 ENOG4105DD7 kinase (PfkB family 0.007068
168 ENOG4108Q5U germination protein, ger(x)c family 0.007013
169 ENOG4107Y71 ybbr family -0.007007
170 ENOG41060IM Heme exporter protein -0.007007
171 ENOG41079AI NA 0.007006
172 ENOG4105EHR propanediol utilization protein pduB -0.007004
173 ENOG4107QKW extracellular solute-binding protein family 1 0.007002
174 ENOG4105D1I oligoendopeptidase, m3 family -0.006999
175 ENOG4107SZF amino acid aminotransferase 0.006995
176 ENOG410657F sodium sulfate symporter 0.006983
177 ENOG4108437 Domain of unknown function (DUF1980) -0.006976
178 ENOG4105F5P DNA-damage-inducible protein d -0.006968
179 ENOG4107R0D fad dependent oxidoreductase 0.006958
180 ENOG4105D8I Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity) -0.006952
181 ENOG4106FTQ Taurine ABC transporter, periplasmic -0.006941
182 ENOG4105MQ3 flagellar protein FliS 0.006941
183 ENOG41062KR FRG domain-containing protein 0.006928
184 ENOG4106Q19 Bacterial protein of unknown function (DUF977) -0.006922
185 ENOG41080HJ 6-phospho 3-hexuloisomerase -0.006922
186 ENOG4108TTM chaperone -0.006919
187 ENOG4108JJA ABC, transporter 0.006880
188 ENOG4107QTH restriction modification system DNA specificity domain 0.006874
189 ENOG4107QIZ NADH dehydrogenase 0.006868
190 ENOG4105G0K glycine radical enzyme YjjI family 0.006860
191 ENOG4107YND lmbE family 0.006859
192 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) -0.006857
193 ENOG4107MB2 Extracellular solute-binding protein, family 5 -0.006857
194 ENOG4108M24 von Willebrand factor, type A -0.006854
195 ENOG4105PTU response to oxidative stress -0.006845
196 ENOG4108IUM Glycogen debranching enzyme -0.006840
197 ENOG4108UUM single-stranded DNA-binding protein -0.006828
198 ENOG4105D19 Role in flagellar biosynthesis (By similarity) 0.006825
199 ENOG4105J9R Ci repressor -0.006819
200 ENOG4105WBR NA 0.006813
201 ENOG4108JQ6 ABC transporter 0.006790
202 ENOG4107RMW DNA Methylase -0.006786
203 ENOG4106QID NA 0.006771
204 ENOG4107RG8 helicase -0.006769
205 ENOG4105XWI UPF0304 protein 0.006764
206 ENOG41090IX small terminase subunit -0.006758
207 ENOG4108M7J Carbamoyl phosphate synthase-like protein 0.006749
208 ENOG4108H31 Aldo/keto reductase family 0.006740
209 ENOG4108EF9 Catalyzes two reactions the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR 0.006737
210 ENOG4105VYA Uncharacterized conserved protein (DUF2132) 0.003366
210 ENOG4108IEF Nitrate reductase 0.003366
211 ENOG4105CN9 Peptidase m42 family protein -0.006730
212 ENOG4105CFW Choline kinase 0.006729
213 ENOG4105ED6 mmge prpd family protein 0.006725
214 ENOG4108IJ1 Dehydrogenase -0.006721
215 ENOG4105FX9 transmembrane pair domain-containing protein 0.006717
216 ENOG41076UI NA -0.006717
217 ENOG4108M1R NA 0.006716
218 ENOG410631I Domain of unknown function (DUF3173) -0.006710
219 ENOG41084EM Transcriptional regulator 0.006707
220 ENOG4107TKP dihydrodipicolinate reductase 0.006698
221 ENOG4106PAS Inherit from COG: Dehydrogenase 0.006691
222 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit 0.006661
223 ENOG4105Q44 Fimbrial protein 0.002220
223 ENOG4105SUJ cs1 type fimbrial major subunit 0.002220
223 ENOG4108WCN CblD family pilus biogenesis initiator protein 0.002220
224 ENOG4105DB7 PHP domain protein -0.006658
225 ENOG4105DCT glycerol dehydrogenase -0.006650
226 ENOG4105DXZ ribonuclease BN -0.006622
227 ENOG4108T07 Bacteriophage protein -0.006619
228 ENOG4107QVT Binding-protein-dependent transport systems, inner membrane component 0.006615
229 ENOG4108MP1 NA -0.006601
230 ENOG4107RG2 Amino acid amide ABC transporter substrate-binding protein, HAAT family 0.006600
231 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase -0.006593
232 ENOG4108Z8I decarboxylase -0.006580
233 ENOG4106MG4 NA 0.006579
234 ENOG4106UW1 Major Facilitator superfamily -0.006575
235 ENOG4107WWY Transcriptional regulator 0.006574
236 ENOG4108ZTW Nitrogen regulatory protein P-II 0.006567
237 ENOG4105KCF CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease (By similarity) -0.006564
238 ENOG4105EG5 type VI secretion protein, VC_A0114 family 0.006561
239 ENOG4105IW6 Carbamoyltransferase 0.006560
240 ENOG4108SMI Domain of unknown function (DUF364) 0.006553
241 ENOG4108KI7 Diguanylate cyclase 0.006551
242 ENOG4108H52 Oxidoreductase family, C-terminal alpha/beta domain 0.006550