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 ENOG4107R37 Glutamate dehydrogenase 0.018144
2 ENOG4108IQD Involved in the biosynthesis of D-alanyl-lipoteichoic acid (LTA). Catalyzes an ATP-dependent two-step reaction where it forms a high energy D-alanyl AMP intermediate and transfers the alanyl residues from AMP to Dcp (By similarity) -0.017512
3 ENOG4107EMB crispr-associated protein -0.017439
4 ENOG4108RTX Nitroreductase -0.016674
5 ENOG41065KT SIR2 family -0.016626
6 ENOG4107ST9 nucleoside hydrolase -0.016214
7 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) -0.016116
8 ENOG4105D5G Transposase -0.016106
9 ENOG41073DP NA 0.015844
10 ENOG4108QH2 crispr-associated protein -0.015423
11 ENOG4105C4U 4-methyl-5-beta-hydroxyethylthiazole kinase 0.015180
12 ENOG4107TIF Phenazine biosynthesis protein, PhzF family 0.015167
13 ENOG4107SQ3 mannitol-1-phosphate 5-dehydrogenase -0.014881
14 ENOG4105C0R drug resistance transporter emrb qaca subfamily -0.014855
15 ENOG410817Y Primosomal protein DnaI -0.014761
16 ENOG4108K4B hydrolase -0.014669
17 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) 0.014663
18 ENOG4107WSP decarboxylase 0.014643
19 ENOG4105C0A alcohol dehydrogenase 0.014558
20 ENOG4105ESI atpase involved in dna repair 0.013994
21 ENOG4105HUF DNA protection during starvation protein -0.013961
22 ENOG4108HW8 Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine (By similarity) -0.013751
23 ENOG4105EYF MMPL domain protein -0.013668
24 ENOG4108VWQ crispr-associated protein -0.013587
25 ENOG41060M0 Crispr-associated protein, cse4 family -0.013531
26 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.013398
27 ENOG4108ZI8 NA 0.013382
28 ENOG4107RBP Transcriptional regulator -0.013250
29 ENOG4107T5V SNARE associated Golgi -0.013233
30 ENOG4107T27 Major Facilitator -0.013198
31 ENOG4105KPY Small multidrug resistance protein -0.013136
32 ENOG4105HA6 Glycosyl transferase, family 2 0.013001
33 ENOG4105MGU response regulator 0.012934
34 ENOG4105VZJ PTS System -0.012892
35 ENOG4105CFC Transporter -0.012795
36 ENOG4105C4Y ABC transporter 0.012699
37 ENOG4105C0X amino acid 0.012688
38 ENOG4105K9X Membrane 0.012688
39 ENOG4105C5Y PTS System -0.012618
40 ENOG4108MUX N-hydroxyarylamine O-acetyltransferase -0.012598
41 ENOG4105KGH Transcriptional regulator, MarR family 0.012469
42 ENOG4105CVK Glutamate decarboxylase 0.012467
43 ENOG4105Z4Y Transcriptional regulator 0.012465
44 ENOG4105TAQ integral membrane protein 0.012405
45 ENOG4108MKI Glycosyl transferase, family 2 -0.012384
46 ENOG4105NJQ (LipO)protein -0.012378
47 ENOG41081UC Inherit from COG: Competence protein -0.012365
48 ENOG4107T9Z Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.012360
49 ENOG4105D4U had-superfamily hydrolase, subfamily iia -0.012311
50 ENOG4105C1I TRANSCRIPTIONAl REGULATOR GntR family 0.012285
51 ENOG4107QJD pyruvate phosphate dikinase 0.012210
52 ENOG4105CEV competence damage-inducible protein 0.012193
53 ENOG4105F1N DNA alkylation repair 0.012178
54 ENOG4105BZ8 glutamate synthase -0.012172
55 ENOG4108SGB Transcriptional regulator -0.012154
56 ENOG4108KPS methyltransferase 0.012146
57 ENOG4105M02 This protein specifically catalyzes the removal of signal peptides from prolipoproteins (By similarity) -0.012110
58 ENOG4105CPN adenine deaminase 0.012046
59 ENOG4105CQ3 Poorly processive error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. Exhibits no 3-5 exonuclease (proofreading) activity. May be involved in translesional synthesis in conjunction with the beta clamp from polIII (By similarity) -0.012037
60 ENOG4108HRN Catalyzes the phosphorylation of pyruvate to phosphoenolpyruvate (By similarity) -0.012019
61 ENOG4105CTR Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity) 0.012001
62 ENOG4105FFF abc transporter permease protein -0.011994
63 ENOG4105D29 Helix-turn-helix type 11 domain protein -0.011923
64 ENOG4105EKQ RNA-directed DNA polymerase -0.011896
65 ENOG4107YSK Glycerol-3-phosphate cytidylyltransferase -0.011877
66 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase 0.011839
67 ENOG4105KMT branched-chain amino acid -0.011820
68 ENOG4105ZWK Inherit from COG: Low-potential electron donor to a number of redox enzymes (By similarity) -0.011793
69 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) -0.011750
70 ENOG4105FEX (ABC) transporter 0.011680
71 ENOG4107QXA Aminotransferase 0.011667
72 ENOG4105CK0 Membrane bOund o-acyl transferase mboat family protein -0.011658
73 ENOG4105T58 Dithiol-disulfide isomerase -0.011609
74 ENOG4107B8Q NA 0.011580
75 ENOG4105XBY Regulates arginine biosynthesis genes (By similarity) 0.011571
76 ENOG4105FCD Major Facilitator 0.011527
77 ENOG4105KRJ gCN5-related N-acetyltransferase -0.011517
78 ENOG4108QXE glycerophosphoryl diester phosphodiesterase -0.011466
79 ENOG4107QR6 type I restriction-modification system -0.011434
80 ENOG4106SI0 NA 0.011381
81 ENOG4105F8Q Arylsulfotransferase (ASST) -0.011369
82 ENOG4105NC8 NA 0.011325
83 ENOG4105CVJ phosphoglycerate mutase -0.011300
84 ENOG4108UHU Aldolase -0.011298
85 ENOG4105G5W regulator Fur family 0.011273
86 ENOG4105DV0 amidase (EC 3.5.1.4 -0.011213
87 ENOG41080NW Alkylphosphonate utilization operon protein PhnA -0.011188
88 ENOG4105N9C Transposase 0.011184
89 ENOG4105DHW Required for the insertion and or proper folding and or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins 0.011153
90 ENOG4105CF9 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation dephosphorylation (By similarity) -0.011105
91 ENOG4108UIN ybak prolyl-trna synthetase associated region -0.011096
92 ENOG4108UVJ appr-1-p processing domain protein -0.011085
93 ENOG4105C6H Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction (By similarity) -0.011069
94 ENOG4105WMR Protein CrcB homolog -0.011065
95 ENOG4105PWE CRISPR-associated protein cas2 -0.011061
96 ENOG4105EQK -acetyltransferase 0.011059
97 ENOG4107YZX Universal stress protein -0.011025
98 ENOG4106GUS NA 0.011019
99 ENOG4107YKN alpha beta hydrolase fold-3 domain protein 0.011016
100 ENOG4105CAF HipA N-terminal domain protein -0.010810
101 ENOG4108WBA 2'-3'-cyclic nucleotide -0.010793
102 ENOG4108YKX Filamentation induced by cAMP protein fic 0.010779
103 ENOG4105TZK 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) -0.010751
104 ENOG4105ENX hydrolase -0.010745
105 ENOG41070JI NA 0.010717
106 ENOG4106J8C Chaperone -0.010715
107 ENOG4107UIB metallophosphoesterase 0.010697
108 ENOG4106QP4 HTH_ARSR -0.010680
109 ENOG4105HJE transcriptional regulator -0.010667
110 ENOG41079Y6 NA 0.010649
111 ENOG4105N4B CRISPR system CASCADE complex protein CasB -0.010604
112 ENOG41064WA Binding-protein-dependent transport systems, inner membrane component -0.010601
113 ENOG4105MJ2 Competence protein 0.010592
114 ENOG4108JCJ Caulimovirus viroplasmin -0.010542
115 ENOG4108HKT sucrose-6-phosphate hydrolase -0.010532
116 ENOG4106GT1 NA -0.010524
117 ENOG4105F2I Transposase -0.010516
118 ENOG4105GHK Carboxymethylenebutenolidase-related protein -0.010503
119 ENOG4105WCN acetyltransferase -0.010464
120 ENOG4105CAC Catalyzes the conversion of L-arabinose to L-ribulose (By similarity) 0.010445
121 ENOG4107YMB cmp dcmp deaminase zinc-binding -0.010410
122 ENOG4105KE9 The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity) 0.010410
123 ENOG4105KQV Binds directly to 16S ribosomal RNA (By similarity) 0.010379
124 ENOG4107S08 filamentation induced by cAMP protein Fic -0.010373
125 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) 0.010342
126 ENOG4107QP7 CoA-transferase subunit A -0.010315
127 ENOG4107S04 cyclase, family -0.010282
128 ENOG4108SGY acetyltransferase -0.010278
129 ENOG4108PRV ABC transporter substrate-binding protein 0.010272
130 ENOG4107RRU Involved in both the arginine and lysine biosynthetic pathways (By similarity) 0.010268
131 ENOG4107QQ8 peptidase 0.010268
132 ENOG4107QY6 N-6 DNA Methylase -0.010246
133 ENOG41068W6 Capsular polysaccharide biosynthesis protein 0.010246
134 ENOG4106CTQ NA -0.010243
135 ENOG4105CIS alcohol dehydrogenase 0.010210
136 ENOG4108UV6 Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) (By similarity) 0.010201
137 ENOG4105CEY Amp-dependent synthetase and ligase 0.010199
138 ENOG4105ESV Glycosyl transferase, family 4 -0.010195
139 ENOG4108UM6 Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) (By similarity) 0.010194
140 ENOG4107RSD Multi-copper polyphenol oxidoreductase laccase -0.010191
141 ENOG4105CPC Aldo Keto reductase 0.010163
142 ENOG4105CWX Alpha-1,2-mannosidase 0.010162
143 ENOG4105D6J arsenicaL-resistance protein -0.010154
144 ENOG4105T6U NA -0.010141
145 ENOG4107R0P L-ribulose-5-phosphate 4-epimerase 0.010125
146 ENOG4105N3I Involved in formation and maintenance of cell shape (By similarity) 0.010071
147 ENOG4107RR9 sulfate transporter -0.010058
148 ENOG4108C3H Magnesium-importing ATPase -0.010055
149 ENOG41066F8 ROK family 0.010039
150 ENOG4105VJG Transcriptional regulator -0.010035
151 ENOG4108SUX PTS System -0.010020
152 ENOG4106M9Z response regulator 0.010003
153 ENOG4105KK6 nuclease -0.009991
154 ENOG4105C65 Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism (By similarity) 0.009989
155 ENOG4108UHC Glycosyl transferase, wecb taga cpsf family -0.009974
156 ENOG41088M9 Inherit from NOG: Nad-dependent epimerase dehydratase 0.009966
157 ENOG4108RS6 transposase 0.009961
158 ENOG41084W1 Type I site-specific deoxyribonuclease 0.009957
159 ENOG4105CPQ Dehydrogenase 0.009954
160 ENOG4105ZRH Transcriptional regulator -0.009939
161 ENOG4106FIB Lpxtg-motif cell wall anchor domain protein -0.009919
162 ENOG4105IJS Transcriptional regulator 0.009899
163 ENOG41085S6 NA -0.009880
164 ENOG4106TJR NA -0.009867
165 ENOG4108VKW Endonuclease Exonuclease phosphatase 0.009856
166 ENOG4105EVW Acyl-transferase 0.009820
167 ENOG410828D Pfam:TraG 0.009804
168 ENOG4107UTK ABC transporter 0.009785
169 ENOG4108SFF CAAX protease self-immunity -0.009784
170 ENOG4107SPW HsdM N-terminal domain 0.009783
171 ENOG4105CI2 imidazolone-5-propionate hydrolase -0.009756
172 ENOG4107QN2 dihydrolipoyl dehydrogenase 0.009753
173 ENOG4108ZWG Glycosyl hydrolase, family 25 0.009718
174 ENOG4105DJ2 Major Facilitator Superfamily 0.009693
175 ENOG4107XM4 PTS system sorbose subfamily IIB component -0.009684
176 ENOG4105DVT helicase 0.009672
177 ENOG4107S6X Glycosyl transferase, family 2 0.009664
178 ENOG4107R9Y phosphoglycerol transferase alkaline phosphatase superfamily protein 0.009627
179 ENOG4107YCR Transcriptional regulator, ARSR family 0.009592
180 ENOG4105W8V TRANSCRIPTIONAl REGULATOR GntR family 0.009579
181 ENOG4108YHM serine threonine protein phosphatase 0.009576
182 ENOG4108YSS Bacterial protein of unknown function (DUF925) 0.009571
183 ENOG4108VP3 Lysine exporter protein (LysE YggA) -0.009571
184 ENOG41066RB phage protein -0.009566
185 ENOG4108SB7 Esterase lipase -0.009563
186 ENOG4105DTZ bifunctional PTS system fructose-specific transporter subunit IIA HPr protein -0.009500
187 ENOG4105XKQ RelB antitoxin -0.009499
188 ENOG4105XBT phage protein -0.009493
189 ENOG4108Z31 TetR family Transcriptional regulator -0.009486
190 ENOG4106DR7 MORN repeat protein 0.009472
191 ENOG4105MAE phage protein -0.009465
192 ENOG4107R13 MMPL domain protein -0.009449
193 ENOG4107QSK Phage infection protein 0.009449
194 ENOG4105H3Q Primosomal protein, DnaI 0.009429
195 ENOG4105BZF Glycosyl transferase (Group 1 -0.009412
196 ENOG4105DBV ornithine carbamoyltransferase 0.009410
197 ENOG4105EQD regulatoR 0.009392
198 ENOG4105C72 UPF0176 protein -0.009371
199 ENOG4107WPY Inherit from COG: peptidase (S8 and S53, subtilisin, kexin, sedolisin -0.009366
200 ENOG4108STX response regulator 0.009347
201 ENOG4107X32 dedA family -0.009342
202 ENOG4105C84 Histidine ammonia-lyase -0.009325
203 ENOG4108DT4 serine threonine protein kinase -0.009310
204 ENOG4105CZG Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity) 0.009301
205 ENOG41084MY 50S ribosomal protein L33 -0.009277
206 ENOG4108EZH mechanosensitive ion channel -0.009253
207 ENOG4107YDN peptide deformylase -0.009252
208 ENOG410733X NA -0.009252
209 ENOG4108FN5 Enoyl-CoA hydratase/isomerase family 0.009247
210 ENOG4106UAB Chloride channel 0.009241
211 ENOG4107QIT glycosyl transferase -0.009226
212 ENOG4107QMH DNA methylase 0.009222
213 ENOG4106KBT YibE F family protein -0.009219
214 ENOG4105NJS thiw protein 0.009219
215 ENOG41064BZ L-xylulose 5-phosphate 3-epimerase 0.009211
216 ENOG410829Z GntR Family Transcriptional Regulator -0.009202
217 ENOG4107TTW Catalyzes the ferrous insertion into protoporphyrin IX (By similarity) -0.009168
218 ENOG4107ZU5 Polypeptide deformylase -0.009149
219 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin -0.009148
220 ENOG410624W Protein of unknown function (DUF1093) -0.009140
221 ENOG4105EN6 Membrane 0.009139
222 ENOG4105DA5 (ABC) transporter 0.009132
223 ENOG4105EA6 outer membrane usher protein -0.009124
224 ENOG4107SQ8 Glycine betaine 0.009104
225 ENOG4105XP4 Major Facilitator superfamily -0.009099
226 ENOG4105M59 Phosphodiesterase, mj0936 family 0.009089
227 ENOG4105Z9G Pfam:DUF1200 -0.009079
228 ENOG41067Y4 Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division (By similarity) 0.009078
229 ENOG4108JM9 Inherit from NOG: transposase -0.009065
230 ENOG4105C6M Alpha-keto-beta-hydroxylacyl reductoisomerase -0.009064
231 ENOG4105EY8 ABC transporter -0.009054
232 ENOG4105D7A ATP-binding protein -0.009050
233 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.009041
234 ENOG4108UMN azlc family -0.009040
235 ENOG4105M0A domain protein 0.009038
236 ENOG410733V NA -0.009029
237 ENOG4105EDE A stabilizing protein that is part of the accessory SecA2 SecY2 system specifically required to export serine-rich repeat cell wall proteins usually encoded upstream in the same operon. Stabilizes the glycosylation activity of Gtf1 (By similarity) 0.009024
238 ENOG4107SNZ Competence protein 0.009021
239 ENOG4105ETU transcriptional activator (TenA 0.009012
240 ENOG4105D8W glucose-6-phosphate 1-dehydrogenase -0.008993
241 ENOG4108ZFK Gcn5-related n-acetyltransferase -0.008989
242 ENOG410683M YopX protein 0.008981
243 ENOG4108S8M degv family -0.008954
244 ENOG4105C7K acetolactate synthase -0.008926
245 ENOG4105HB9 NA -0.008918
246 ENOG4105WQI isochorismatase 0.008906
247 ENOG41060ZY NA -0.008902
248 ENOG4107YUH hydrolase -0.008898
249 ENOG4105NI8 Cytosine-specific methyltransferase 0.008898
250 ENOG4107Z04 HAD-superfamily hydrolase subfamily IA 0.008892