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 ENOG4108UIN ybak prolyl-trna synthetase associated region 0.013348
2 ENOG4105WAN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.012134
3 ENOG4105CI0 Citrate lyase -0.011572
4 ENOG4108M2T Binding Domain protein 0.011518
5 ENOG4105DFH Transport of potassium into the cell (By similarity) -0.011057
6 ENOG4106VXV Conserved Protein 0.010948
7 ENOG4105MT7 Arsenical resistance operon tranS-acting repressor 0.010551
8 ENOG4108NHK Site-specific recombinase, phage integrase family -0.010304
9 ENOG4108YZT Adenosylcobinamide kinase 0.010242
10 ENOG410801F ribosomal-protein-alanine acetyltransferase 0.010119
11 ENOG4105M5N Metal Dependent Phosphohydrolase -0.009921
12 ENOG410908R Methenyltetrahydrofolate cyclohydrolase 0.009831
13 ENOG4105C4B ABC transporter, permease -0.009687
14 ENOG4108UZ3 Transporter -0.009419
15 ENOG4108YYQ gCN5-related N-acetyltransferase 0.009407
16 ENOG4105NI8 Cytosine-specific methyltransferase -0.009393
17 ENOG4105CRD Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) (By similarity) -0.009314
18 ENOG4105GR3 Histidine kinase -0.009177
19 ENOG4105D59 Tetracycline resistance protein -0.008967
20 ENOG4108I55 Aminotransferase class I and II 0.008962
21 ENOG4108PI2 O-Methyltransferase 0.008898
22 ENOG4105C3P Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity) -0.008762
23 ENOG41090WY Protein of unknown function (DUF3298) 0.008718
24 ENOG4107F0N abc transporter permease protein 0.008716
25 ENOG4107WTI Transcriptional regulator, ARAC family 0.008629
26 ENOG410724J NA 0.008613
27 ENOG4105PZT NA -0.008606
28 ENOG41063ZK Transcriptional Regulator AraC Family 0.008494
29 ENOG4105FNI atp gtp-binding protein 0.008493
30 ENOG4105YGP holo-ACP synthase CitX -0.008480
31 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) -0.008459
32 ENOG4108PMS NA -0.008318
33 ENOG4107RQ4 Aldolase 0.008303
34 ENOG4106GJX NA -0.008296
35 ENOG4105EVT domain protein -0.008234
36 ENOG4105DZR Type I site-specific deoxyribonuclease 0.008225
37 ENOG410800A inner membrane protein YbaN 0.008218
38 ENOG4105C6G (ABC) transporter 0.008209
39 ENOG410769N NA 0.008202
40 ENOG4105MFB Transcriptional regulator AbrB family 0.008173
41 ENOG4105D0U Arsenite-activated ATPase (ArsA) 0.008161
42 ENOG4105FF2 Type I DHQase 0.008101
43 ENOG4108RYC glycosyltransferase 0.008069
44 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.008025
45 ENOG41080ME methyltransferase 0.007992
46 ENOG4107R1M 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) (By similarity) 0.007971
47 ENOG4105DZB Electron transport complex 0.007956
48 ENOG41062BI Domain of unknown function (DUF1851) -0.007893
49 ENOG4108UGX Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate (By similarity) -0.007867
50 ENOG4105VJV 50s ribosomal protein L35 0.007802
51 ENOG4105SF2 Protein of unknown function (DUF1510) 0.007795
52 ENOG4107V9H nitrite transporter 0.007785
53 ENOG4105QTV Membrane -0.007755
54 ENOG4108YY9 U mismatch-specific DNA glycosylase -0.007752
55 ENOG4108J4B Beta-lactamase -0.007728
56 ENOG4108ZXD NA -0.007718
57 ENOG4105KEG ribosomal-protein-alanine acetyltransferase -0.007716
58 ENOG41063CS Replication Protein -0.007707
59 ENOG4107V2F Group II intron, maturase-specific domain -0.007703
60 ENOG41082RA The GLUG motif protein family protein -0.007699
61 ENOG4107RWA tonB-dependent Receptor 0.007685
62 ENOG4107C8B NA 0.007664
63 ENOG4108D31 Hsp20/alpha crystallin family 0.007660
64 ENOG4105CAQ asparagine synthetase 0.007657
65 ENOG4108K6U Transcriptional regulator, TetR family 0.007651
66 ENOG4108K8S endonuclease I -0.007634
67 ENOG4105CHY citrate lyase, alpha -0.003817
67 ENOG4105XGS Covalent carrier of the coenzyme of citrate lyase (By similarity) -0.003817
68 ENOG4108RDQ ABC transporter 0.007631
69 ENOG4108PDC Glycosyl transferase 0.007609
70 ENOG4107QMG Nad synthetase 0.007606
71 ENOG4107QW9 peptidase, M24 0.007551
72 ENOG4105D90 Nadph-dependent fmn reductase 0.002515
72 ENOG4105NYF Cytidylyltransferase 0.002515
72 ENOG4107WFN Malate lactate 0.002515
73 ENOG4107SKU permease protein 0.007527
74 ENOG4107GTR NA 0.007527
75 ENOG4105FCD Major Facilitator 0.007403
76 ENOG4105DTB Protein of unknown function (DUF3584) 0.007398
77 ENOG4105GPV NA 0.007398
78 ENOG4105EAC phosphoserine phosphatase 0.007387
79 ENOG4105DGN Electron transport complex 0.007352
80 ENOG4107SW2 integral membrane protein -0.007346
81 ENOG4105EQ0 Major Facilitator superfamily -0.007346
82 ENOG4106JVC NA -0.007342
83 ENOG4107RCE radical SAM domain protein 0.007335
84 ENOG4108YXI Secondary thiamine-phosphate synthase enzyme -0.007332
85 ENOG4105C2J ABC transporter -0.007323
86 ENOG410636M NA 0.007257
87 ENOG4108469 NA -0.007242
88 ENOG4105ET8 NA 0.007214
89 ENOG4107SP8 Filamentation induced by cAMP protein fic -0.007175
90 ENOG4108HHA Transketolase 0.007173
91 ENOG4106RXW NA -0.007167
92 ENOG4108K0D peptidase, M48 0.007153
93 ENOG4105C3S Mate efflux family protein 0.007149
94 ENOG41060IW transcriptional regulator PadR family 0.007147
95 ENOG4105DUM transcriptional regulator, lysR family 0.007145
96 ENOG41067S9 phage shock protein C, PspC 0.007144
97 ENOG4107QK4 glycoside hydrolase, family 3 domain protein 0.007113
98 ENOG4105DYC esterase 0.007093
99 ENOG4107RY2 2 glycosyl transferase -0.007079
100 ENOG4105DME alpha-galactosidase -0.007074
101 ENOG4105ZNN NA 0.007042
102 ENOG4108RMZ D-isomer specific 2-hydroxyacid dehydrogenase 0.007038
103 ENOG4105DUA (citrate (pro-3S)-lyase ligase -0.007034
104 ENOG4105CGQ conserved protein UCP033563 0.007013
105 ENOG41081GH DNA-binding protein -0.007004
106 ENOG4105CEZ Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP) (By similarity) 0.006979
107 ENOG4108KG0 acyl-coenzyme A 6-aminopenicillanic acid acyl-transferase 0.006975
108 ENOG4106HMI NA -0.006970
109 ENOG4108IAB Phoh family 0.006925
110 ENOG4105J79 toxin secretion phage lysis holin 0.006923
111 ENOG4105X3U lytTr DNA-binding domain protein -0.006910
112 ENOG4108JI7 Exporters of the RND superfamily -0.006900
113 ENOG410803F peptidylprolyl cis-trans isomerase 0.006895
114 ENOG4105D6A Electron transport complex 0.006881
115 ENOG4105IXE Abortive infection protein 0.006865
116 ENOG4106EUY NA -0.006865
117 ENOG4108064 transposase, IS204 IS1001 IS1096 IS1165 family protein -0.006865
118 ENOG4105EDR glucose galactose transporter -0.006854
119 ENOG41082E5 radical SAM domain protein -0.006851
120 ENOG4105CEN a g-specific adenine glycosylase 0.006850
121 ENOG4107QTX glutamine synthetase -0.006812
122 ENOG4107E03 (LipO)protein 0.006758
123 ENOG4108G5V Capsule synthesis protein 0.006741
124 ENOG4105MA7 Tetratricopeptide repeat protein 0.006715
125 ENOG41083DH Inherit from COG: Metal Dependent Phosphohydrolase -0.006705
126 ENOG4108Z0R Transferase -0.006700
127 ENOG41068WM gliding motility-associated protein GldL 0.006684
128 ENOG4105W5A BNR Asp-box repeat protein -0.006673
129 ENOG4106EQW NA 0.006660
130 ENOG4105E9V Periplasmic binding protein LacI transcriptional regulator -0.006648
131 ENOG4105V96 NA 0.006626
132 ENOG4107ZET Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin) (By similarity) 0.006622
133 ENOG4108R8Y Beta-lactamase domain protein 0.006615
134 ENOG4107QJZ Glycosyl transferase, family 2 -0.006615
135 ENOG4108XSA NA 0.006613
136 ENOG4105JFD Transcriptional regulator, GntR family 0.006576
137 ENOG4105D07 Signal peptide peptidase, SppA -0.006562
138 ENOG4106M5T DNA binding domain, excisionase family -0.006551
139 ENOG4106AUG peptidase M23 0.006550
140 ENOG4105H2E NA 0.006550
141 ENOG4108WGT Hydrolase 0.006539
142 ENOG4105RWF major outer membrane protein OmpA 0.006534
143 ENOG4105XTP TatD-related deoxyribonuclease -0.006513
144 ENOG4105Y0E NA 0.006511
145 ENOG4105EH4 helicase -0.006505
146 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.006504
147 ENOG4108XI6 Spore germination -0.006494
148 ENOG4105TG9 domain protein -0.006487
149 ENOG4106BIA NA 0.006479
150 ENOG4108KWJ integral membrane protein 0.006478
151 ENOG4105DXT Histidine kinase 0.006474
152 ENOG4105MDI NA 0.006470
153 ENOG4105N5T Radical SAM Protein 0.006467
154 ENOG4106B9P NA 0.006449
155 ENOG4108SJI hydrolase, family 25 -0.006433
156 ENOG4105H6T DNA RNA NON-specific endonuclease 0.006431
157 ENOG4106HBE NA 0.006415
158 ENOG410665I Acyl-transferase 0.006414
159 ENOG4105KW1 Predicted metal-binding protein (DUF2284) 0.006412
160 ENOG4105NAQ phosphoglycerate mutase 0.006407
161 ENOG4108U2B NA 0.006404
162 ENOG4105FVH SNARE-like domain protein -0.006402
163 ENOG41066CE NA -0.006396
164 ENOG4105DFF Rod shape-determining protein mreb 0.006393
165 ENOG4105CHH sulfate transporter 0.006383
166 ENOG4105C4X radical SAM domain protein -0.006371
167 ENOG4105C1M carbamoyl-phosphate synthetase glutamine chain 0.006357
168 ENOG4106AX9 NA -0.006352
169 ENOG4106BHF NA -0.006352
170 ENOG4108VH7 hemerythrin hhe cation binding domain protein 0.006343
171 ENOG4105D7N magnesium and cobalt transport protein CorA -0.006330
172 ENOG4106BAM Tetratricopeptide repeat -0.006327
173 ENOG4105EUB pirin domain protein -0.006323
174 ENOG4105KVT NA 0.006316
175 ENOG4105EBX v-type atpase 0.006296
176 ENOG41061YX Domain of unknown function (DUF1910) -0.006281
177 ENOG4105CEA Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) (By similarity) 0.006279
178 ENOG4105CVG Homoserine O-transsuccinylase -0.006276
179 ENOG41081PU Cytosine-specific methyltransferase -0.006268
180 ENOG4108HX1 Membrane 0.006267
181 ENOG4108HD9 NA 0.006266
182 ENOG4107RE7 phosphate butyryltransferase 0.006262
183 ENOG4105E79 Binding Domain protein 0.006260
184 ENOG4105HFJ DNA binding domain, excisionase family -0.006256
185 ENOG4108DUP Bacterial extracellular solute-binding proteins, family 5 Middle -0.006227
186 ENOG4105W1Y Transcriptional regulator -0.006226
187 ENOG4108ZQD Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A (By similarity) -0.006220
188 ENOG4105CHT Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity) -0.006218
189 ENOG4107R19 alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.006216
190 ENOG4105D5N isocitrate dehydrogenase (NADP) -0.006213
191 ENOG41089UC methyltransferase, type 11 -0.006211
192 ENOG4108JYN Transketolase 0.006209
193 ENOG4108NEE chain length determinant protein 0.006208
194 ENOG4108HIT NA -0.006204
195 ENOG4106ANW SMI1_KNR4 -0.006188
196 ENOG4105RPD PTS System 0.006182
197 ENOG4107ZHN Glycosyl transferase family 2 0.006169
198 ENOG4105E4D integral membrane protein TIGR02185 0.006153
199 ENOG41067MG lrgb family -0.006146
200 ENOG4105VHV Acyl carrier protein 0.006136
201 ENOG4108RY1 ATP synthase, subunit E 0.006135
202 ENOG4107UWY Methyltransferase -0.006120
203 ENOG4105KR2 Chorismate binding enzyme 0.003057
203 ENOG4107V3Y chorismate binding enzyme 0.003057
204 ENOG4107JFT NA 0.006113
205 ENOG41061U9 NA -0.006105
206 ENOG4108NPN HpaII restriction endonuclease -0.006097
207 ENOG4105NNR Phage minor structural protein -0.003042
207 ENOG4106DW9 tail component -0.003042
208 ENOG41075D4 Aminoglycoside 6-adenylyltransferase -0.006077
209 ENOG4106YRZ NA 0.006058
210 ENOG4108SX0 NA 0.006058
211 ENOG41076C2 Ser Thr phosphatase family protein -0.006050
212 ENOG4106Z86 ATP-nad acox kinase 0.006048
213 ENOG41068YK Transposase, IS605 OrfB family -0.006034
214 ENOG4105D52 delta-aminolevulinic acid dehydratase 0.006031
215 ENOG4105E0C molybdate abc transporter -0.006024
216 ENOG4105HWB Predicted metal-binding protein (DUF2284) -0.006015
217 ENOG4108R7K Metal Dependent Phosphohydrolase 0.006013
218 ENOG4105KR4 ggdef family 0.006006
219 ENOG410757I NA -0.005999
220 ENOG4107T4M dehydratase 0.005996
221 ENOG4107Y3N Cell surface protein -0.005989
222 ENOG4108IQ4 Endonuclease Exonuclease phosphatase -0.005986
223 ENOG4106C35 abc transporter atp-binding protein 0.005982
224 ENOG4108J79 RNA polymerase 0.005977
225 ENOG41076U0 Type II restriction 0.005955
226 ENOG4107WH3 DNA Methylase -0.005950
227 ENOG4108N38 Cobalt transport protein 0.005950
228 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) -0.005948
229 ENOG4105XJF stress responsive alpha-beta barrel domain-containing protein 0.005936
230 ENOG4105C3I Nad-dependent epimerase dehydratase -0.005920
231 ENOG4108MES Periplasmic binding protein -0.005919
232 ENOG4108NE6 tetratricopeptide repeat domain protein -0.005899
233 ENOG4105NI6 heptaprenyl diphosphate synthase component I 0.005897
234 ENOG4105CTZ aminopeptidase c 0.005886
235 ENOG4105P25 HAD-superfamily hydrolase subfamily IA variant 3 -0.005879
236 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.005871
237 ENOG4107D72 Bacterial regulatory proteins, gntR family -0.005870
238 ENOG4108NHZ Transposase -0.005869
239 ENOG4108ZGC gaf domain protein 0.005865
240 ENOG4105Y30 NA -0.005864
241 ENOG4105CAA catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) 0.005862
242 ENOG4107U9B transcriptional regulator 0.005849
243 ENOG4106J09 NA -0.005848
244 ENOG4106CKA Bacteriocin transport accessory protein 0.005848
245 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase -0.005846