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 ENOG4105EAC phosphoserine phosphatase 0.019701
2 ENOG4108K8I sigma-70, region 4 0.019638
3 ENOG4105EP8 Glycosyl Hydrolase Family 88 0.019201
4 ENOG4105C1I TRANSCRIPTIONAl REGULATOR GntR family 0.019083
5 ENOG4105F2S Abortive infection protein AbiGII -0.018724
6 ENOG4105C85 amino acid 0.018712
7 ENOG4105EW4 (LipO)protein 0.018411
8 ENOG4105KRY conjugative transposon protein 0.018242
9 ENOG4105D5D udp-galactopyranose mutase -0.018125
10 ENOG4106DR7 MORN repeat protein 0.017006
11 ENOG4107YX4 Amino acid ABC transporter substrate-binding protein 0.016338
12 ENOG4105F1A Pyruvate formate-lyase 0.015872
13 ENOG4105MBQ Excisionase 0.015816
14 ENOG4105CNA YD repeat protein -0.015483
15 ENOG4108RTX Nitroreductase -0.015462
16 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) 0.015454
17 ENOG4105D59 Tetracycline resistance protein 0.015447
18 ENOG4108HVN site-specific recombinase, phage integrase family 0.015364
19 ENOG4108YBA Histidine kinase 0.015352
20 ENOG41074UY bacteriocin-associated integral membrane 0.015089
21 ENOG4106AA1 Histidine kinase -0.014883
22 ENOG4106M9Z response regulator 0.014798
23 ENOG41085UN Transcriptional regulator (XRE family 0.014790
24 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) -0.014715
25 ENOG4108WM5 site-specific recombinase, phage integrase family 0.014707
26 ENOG4105GI3 Cell wall anchor domain protein 0.014430
27 ENOG4105M0U Resistance protein -0.014346
28 ENOG4107S6X Glycosyl transferase, family 2 0.014298
29 ENOG4105ENQ Alpha-L-fucosidase -0.014263
30 ENOG4105DT3 PTS system, galactitol-specific IIc component 0.014248
31 ENOG4107XD6 NA 0.014192
32 ENOG4105D5G Transposase -0.014153
33 ENOG4108KK3 hydrolase family 2, sugar binding 0.014125
34 ENOG4105MGU response regulator 0.014114
35 ENOG4108RYC glycosyltransferase 0.014022
36 ENOG4107BU2 esterase -0.014009
37 ENOG41083CY cytidine deoxycytidylate deaminase -0.013973
38 ENOG4105NDF NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. May also have NAD-dependent lysine demalonylase and desuccinylase activity (By similarity) -0.013935
39 ENOG4105CH2 amidohydrolase -0.013915
40 ENOG4105CZC PTS system ascorbate-specific transporter subunit IIC 0.013908
41 ENOG4105KGS Membrane 0.013756
42 ENOG4107QM2 Aldo Keto reductase 0.013705
43 ENOG4107R0P L-ribulose-5-phosphate 4-epimerase 0.013698
44 ENOG4107QT3 pfkb domain protein 0.013637
45 ENOG41068XQ NA 0.013482
46 ENOG4108ITR TRANSCRIPTIONal 0.013481
47 ENOG4105I08 Pseudouridine synthase 0.013465
48 ENOG4105WKA pts system 0.013456
49 ENOG4105HIK Protein of unknown function (DUF1697) 0.013450
50 ENOG4108ZME abc transporter atp-binding protein 0.013392
51 ENOG4106A3J Protein of unknown function (DUF3298) -0.013377
52 ENOG4107FYG PRD domain protein 0.013305
53 ENOG4105J6G PTS System 0.013292
54 ENOG4107R37 Glutamate dehydrogenase 0.013235
55 ENOG4105ITW cytosolic protein 0.013079
56 ENOG4105CGY Dna recombination protein 0.013071
57 ENOG4107T27 Major Facilitator -0.013060
58 ENOG4105E2D ec 3.2.1.52 -0.013015
59 ENOG4105ETW Luciferase-like 0.012997
60 ENOG4106U7E alpha beta 0.012990
61 ENOG4108UHC Glycosyl transferase, wecb taga cpsf family -0.012952
62 ENOG4105DUK Catalyzes the conversion of 4-hydroxy- tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (By similarity) 0.012950
63 ENOG410646G Proteins of 100 residues with WXG -0.012934
64 ENOG4107QM5 aconitate hydratase -0.012918
65 ENOG4105H6Q decarboxylase 0.012869
66 ENOG4105S7S phosphonate abc transporter -0.012836
67 ENOG410631I Domain of unknown function (DUF3173) -0.012781
68 ENOG4108HMX isocitrate dehydrogenase (NADP) -0.012746
69 ENOG4105DNG Major Facilitator superfamily 0.012723
70 ENOG4106GQV Protein of unknown function (DUF3021) 0.012713
71 ENOG4105NC8 NA 0.012543
72 ENOG4108S90 response regulator 0.012438
73 ENOG4105D07 Signal peptide peptidase, SppA -0.012385
74 ENOG4105UKW Inherit from COG: PAAR repeat-containing protein -0.012379
75 ENOG4107V9M epimerase dehydratase 0.012346
76 ENOG4105EJJ Dehydrogenase -0.012299
77 ENOG4105G40 Pfam:DUF567 0.012256
78 ENOG4105DA5 (ABC) transporter 0.012223
79 ENOG4108RDQ ABC transporter 0.012192
80 ENOG4105WUU PTS System 0.012185
81 ENOG4105CC5 ABC transporter 0.012160
82 ENOG4108N1N Glycosyl hydrolase family 1 0.012143
83 ENOG41061DJ NA -0.012142
84 ENOG4105MBT YolD-like protein -0.012090
85 ENOG4107USW pfkb domain protein -0.012076
86 ENOG4106F1P AAA ATPase, central domain protein -0.012074
87 ENOG4106WR4 Replication Protein 0.012041
88 ENOG4108W1B Beta-lactamase 0.012040
89 ENOG4106H34 NA -0.011998
90 ENOG4105CG3 alpha amylase, catalytic region 0.011997
91 ENOG4105C6N Formate acetyltransferase 0.011993
92 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase -0.011990
93 ENOG41063G6 hmm pf04634 -0.011962
94 ENOG4106AM8 polysaccharide lyase family 8 0.011956
95 ENOG4108JII Oxaloacetate decarboxylase 0.011867
96 ENOG41077EQ NA 0.011809
97 ENOG41066HJ ATP-dependent Clp protease, proteolytic subunit -0.011805
98 ENOG4106BHR ftsk SpoIIIE family protein 0.011796
99 ENOG4105CAM NA 0.011782
100 ENOG4108Z3G 3H domain protein 0.011781
101 ENOG41073XV NA -0.011772
102 ENOG4107R36 histidyl-tRNA synthetase -0.011757
103 ENOG4108ZHV (ABC) transporter 0.011756
104 ENOG41084YC -acetyltransferase -0.011745
105 ENOG4106FEC NA -0.011738
106 ENOG4105ETE Transcriptional regulator (LacI family 0.011718
107 ENOG4105F1N DNA alkylation repair 0.011716
108 ENOG4108N80 biosynthesis protein -0.011705
109 ENOG4105RW1 NA 0.011702
110 ENOG4105CZP Outer surface protein 0.011695
111 ENOG4105GHK Carboxymethylenebutenolidase-related protein -0.011668
112 ENOG4105CAC Catalyzes the conversion of L-arabinose to L-ribulose (By similarity) 0.011662
113 ENOG4108UKQ HTH_XRE 0.011654
114 ENOG410830X 'Cold-shock' DNA-binding domain protein -0.011630
115 ENOG4105NMU Transcriptional regulator -0.011620
116 ENOG4105FBU hydrolase family 16 0.011583
117 ENOG4108VZQ DNA-binding helix-turn-helix protein 0.011565
118 ENOG4105C2U cobyrinic Acid a,c-diamide synthase -0.011548
119 ENOG4105D3D Catalyzes the decarboxylation of carboxynorspermidine and carboxyspermidine (By similarity) 0.011520
120 ENOG41085UV Uncharacterised protein, DegV family COG1307 -0.011480
121 ENOG4105CCX Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) 0.011431
122 ENOG4107QJD pyruvate phosphate dikinase 0.011404
123 ENOG4108J59 Extracellular solute-binding protein, family 5 -0.011401
124 ENOG41067UN Domain of unknown function (DUF955) 0.011386
125 ENOG4107S7Q NAD dependent epimerase/dehydratase family -0.011383
126 ENOG4105CIU binding-protein-dependent transport systems inner membrane Component 0.011381
127 ENOG41090RU Pyridoxamine 5'-phosphate oxidase 0.011364
128 ENOG41065MV ATP GTP-binding protein 0.011310
129 ENOG4105KNA -acetyltransferase 0.011294
130 ENOG4105EE0 oxidoreductase 0.011293
131 ENOG4105CDW Resistance protein -0.011281
132 ENOG41085NV Membrane 0.011279
133 ENOG4107R91 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position (By similarity) 0.011263
134 ENOG4105HRZ Inherit from COG: permease -0.011229
135 ENOG4106H3A restriction -0.011184
136 ENOG4108RYK Nad-dependent epimerase dehydratase 0.011150
137 ENOG4108W59 nitroreductase 0.011147
138 ENOG4107SQZ Integrase core domain -0.011127
139 ENOG4105WPR Transcriptional regulator, ARAC family 0.011126
140 ENOG4105F6C peptidase, M20 -0.011123
141 ENOG4107R9Y phosphoglycerol transferase alkaline phosphatase superfamily protein 0.011120
142 ENOG4105CFW Choline kinase 0.011114
143 ENOG4108WZ2 response regulator 0.011091
144 ENOG4108FTC NlpC/P60 family 0.011087
145 ENOG41069KV Bacterial regulatory proteins, tetR family 0.011084
146 ENOG4108S53 NA 0.010977
147 ENOG4105D50 Catalyzes the isomerization of 5-dehydro-4-deoxy-D- glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate (By similarity) 0.010953
148 ENOG4105CPK Glycosyl transferase (Group 1 -0.010950
149 ENOG4107XR9 resolvase -0.010937
150 ENOG4105N55 NA 0.010910
151 ENOG4105DWR Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin (By similarity) 0.010889
152 ENOG4105M0C cytoplasmic protein 0.010884
153 ENOG41086WW Heavy-metal-associated domain -0.010878
154 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.010868
155 ENOG4105G8G Hydrolase -0.010867
156 ENOG4105DET Rhamnulokinase 0.010831
157 ENOG4106EEZ NA -0.010795
158 ENOG4109085 ABC transporter, permease 0.010790
159 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.010787
160 ENOG4105EEW auxin efflux carrier 0.010765
161 ENOG4107QHZ cell cycle protein -0.010756
162 ENOG4105DY9 regulatoR 0.010755
163 ENOG4105QBQ NA 0.010748
164 ENOG41072F6 NA -0.010730
165 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.010705
166 ENOG4106U6R NA 0.010703
167 ENOG4105GH9 galactofuranosyltransferase -0.010695
168 ENOG41088M9 Inherit from NOG: Nad-dependent epimerase dehydratase 0.010682
169 ENOG4105CKD glutathione-regulated potassium-efflux system protein -0.010671
170 ENOG4105DRM Cell surface protein 0.010659
171 ENOG4108QHG Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) -0.010646
172 ENOG4107ZYX Probably functions as a manganese efflux pump (By similarity) 0.010642
173 ENOG4108QY0 Membrane 0.010635
174 ENOG41068RU NA 0.010632
175 ENOG4105EFU Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin (By similarity) 0.010619
176 ENOG4106NDE Ammonium Transporter Family 0.010605
177 ENOG4105F9F transposase 0.010595
178 ENOG4105YRW Domain of unknown function (DUF1836) 0.010543
179 ENOG4105MEV Acyl-transferase -0.010541
180 ENOG4105EFC phage portal protein HK97 family -0.010533
181 ENOG4105PIQ isochorismatase hydrolase 0.010530
182 ENOG4105DKG l-rhamnose isomerase 0.010509
183 ENOG4105CID antiterminator 0.010507
184 ENOG4105E39 Enoyl-CoA hydratase -0.010477
185 ENOG4107YTV GtrA-like protein 0.010453
186 ENOG41078WQ NA 0.010446
187 ENOG4108RYM conjugative transposon protein 0.010429
188 ENOG4105CS2 ec 3.2.1.21 0.010400
189 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.010391
190 ENOG4105WCN acetyltransferase -0.010389
191 ENOG4107QZW Altronate oxidoreductase 0.010389
192 ENOG4105EP4 Histidine kinase 0.010386
193 ENOG4105EVW Acyl-transferase 0.010366
194 ENOG41090E9 conjugative transposon protein 0.010325
195 ENOG4106B6K Membrane 0.010312
196 ENOG4107QJZ Glycosyl transferase, family 2 -0.010311
197 ENOG4108X80 Transposase -0.010309
198 ENOG4105C0A alcohol dehydrogenase 0.010309
199 ENOG4108NQ8 ATPase histidine kinase DNA gyrase B HSP90 domain protein -0.010307
200 ENOG4107Y0I Protein of unknown function (DUF1697) -0.010307
201 ENOG4106TG4 CHAP domain protein 0.010292
202 ENOG4105DZC cytosine deaminase -0.010278
203 ENOG4105E80 TraG TraD family protein -0.010274
204 ENOG4106T3F PTS system, IIB component 0.010264
205 ENOG4105C1M carbamoyl-phosphate synthetase glutamine chain 0.010256
206 ENOG4105D7T ABC transporter 0.010255
207 ENOG410903F conjugative transposon membrane protein 0.010252
208 ENOG4108ZKP Bacteriocin ABC exporter, ATP binding permease protein -0.010246
209 ENOG4105C56 H( )-stimulated, divalent metal cation uptake system (By similarity) -0.010244
210 ENOG4108M4B domain protein -0.010229
211 ENOG4106NWV Membrane 0.010205
212 ENOG4105XE0 NA -0.010175
213 ENOG4105WS8 NA 0.010162
214 ENOG4106G3J NA 0.010157
215 ENOG4105C75 arginyL-tRNA synthetase 0.010148
216 ENOG4107EFR Flavocytochrome c -0.010144
217 ENOG41084A5 Transcriptional regulator 0.010136
218 ENOG41066JZ Integrase -0.010125
219 ENOG41090A3 NA 0.010121
220 ENOG4105F30 conjugative transposon membrane protein 0.010116
221 ENOG4105DC1 bifunctional purine biosynthesis protein purh 0.010094
222 ENOG410901E Membrane 0.010088
223 ENOG4108ZIV NA 0.010068
224 ENOG4105EBX v-type atpase -0.010067
225 ENOG4105D5T phosphonate abc transporter -0.010062
226 ENOG4106HV1 Cell surface protein 0.010061
227 ENOG4108RQU Transcriptional regulator 0.010039
228 ENOG4108Y5R Protein of unknown function (DUF1189) 0.010038
229 ENOG4105CTK cobaltochelatase, cobn subunit -0.010020
230 ENOG4105GZI Transcriptional regulator 0.009986
231 ENOG4108J5G 6-phosphogluconate dehydrogenase 0.009983
232 ENOG41080JW Membrane 0.009977
233 ENOG4105CD0 Phage Integrase Family -0.009976
234 ENOG4105ER6 polysaccharide biosynthesis protein -0.009970
235 ENOG410696E Membrane -0.009968
236 ENOG4105M5T NA -0.009946
237 ENOG4105EKT )-iron permease -0.009919
238 ENOG4107REI 2',3'-cyclic-nucleotide 2'-phosphodiesterase EC 3.1.4.16 -0.009899
239 ENOG4105C44 Serine transporter 0.009890
240 ENOG4105C5I Dehydrogenase 0.009863
241 ENOG41068W6 Capsular polysaccharide biosynthesis protein 0.009856
242 ENOG4106BJA NA -0.009842
243 ENOG4105MRB Catalyzes the interconversion of beta-pyran and beta- furan forms of D-ribose (By similarity) 0.009821
244 ENOG4107YVR Diacylglycerol kinase -0.009806
245 ENOG41082UY Transcriptional regulator, arsr family -0.009805
246 ENOG4105DZY Pts system, glucitol sorbitol-specific -0.009805
247 ENOG4108I63 ABC transporter 0.009804
248 ENOG4106571 Short-chain dehydrogenase reductase Sdr -0.009801
249 ENOG4106PHI plasmid recombination enzyme -0.009791
250 ENOG4105IGJ Zn-dependent Hydrolase of the beta-lactamase fold protein -0.009789