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 ENOG4105DAA L-lactate 0.031931
2 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.018128
3 ENOG4105VEQ Cold shock protein -0.016624
4 ENOG4105ER6 polysaccharide biosynthesis protein 0.016250
5 ENOG4108YXW Together with MoaA, is involved in the conversion of 5'- GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.015688
6 ENOG41067TZ transcriptional regulator, MarR family 0.015386
7 ENOG4105CM1 Catalyzes, together with MoaC, the conversion of 5'-GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.015268
8 ENOG4105EZR dyp-type peroxidase family protein 0.014546
9 ENOG4105D9G High-affinity 0.014487
10 ENOG4106TCU acyl-CoA thioesterase 0.014278
11 ENOG4105E2A Dehydrogenase 0.014272
12 ENOG4105C3S Mate efflux family protein -0.014168
13 ENOG4105DIK (ABC) transporter -0.014062
14 ENOG41082FM Phosphatase 0.014056
15 ENOG4105DVT helicase -0.013840
16 ENOG4105DS2 Anaerobic c4-dicarboxylate transporter 0.013719
17 ENOG4105C5V Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate (By similarity) -0.013674
18 ENOG4106BUK Protein of unknown function (DUF1311) -0.013614
19 ENOG4105DPZ Two component transcriptional regulator (Winged helix family 0.013560
20 ENOG4105W05 Transcriptional regulator -0.013444
21 ENOG4105E0M Sulfatase -0.013443
22 ENOG4105E4P ATPase (AAA 0.013333
23 ENOG4107QK1 ImpB MucB SamB family protein 0.013278
24 ENOG4106954 NA 0.013278
25 ENOG4105D18 nicotinate-nucleotide pyrophosphorylase -0.013246
26 ENOG4105F9F transposase 0.013230
27 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) 0.013215
28 ENOG4105DCX Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Together with TatB, TatC is part of a receptor directly interacting with Tat signal peptides (By similarity) 0.013207
29 ENOG4107Z04 HAD-superfamily hydrolase subfamily IA 0.013095
30 ENOG4105EAM Na Pi-cotransporter -0.012865
31 ENOG4107UTK ABC transporter -0.012825
32 ENOG4108I5U Uridine phosphorylase -0.012798
33 ENOG4106SI0 NA -0.012791
34 ENOG4105WZQ Membrane 0.012729
35 ENOG4105E2Z phosphate ABC transporter (Permease 0.012658
36 ENOG4105CMR udp-glucose 4-epimerase -0.012640
37 ENOG410830X 'Cold-shock' DNA-binding domain protein 0.012593
38 ENOG4108J59 Extracellular solute-binding protein, family 5 0.012484
39 ENOG4105CSR polyphosphate kinase 2 -0.012385
40 ENOG4108IY1 (ABC) transporter 0.012385
41 ENOG4107THF Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine (By similarity) -0.012317
42 ENOG4108IHU transport system permease protein 0.012274
43 ENOG4105CXK mandelate racemase muconate lactonizing -0.012257
44 ENOG4108RVF Transcriptional regulator 0.012173
45 ENOG4105EFA 4-hydroxyphenylacetate -0.012091
46 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) 0.012073
47 ENOG4105DUM transcriptional regulator, lysR family -0.012071
48 ENOG4108RM5 Nad-dependent epimerase dehydratase 0.012066
49 ENOG4107VQM serine threonine protein phosphatase 0.011956
50 ENOG4107RVH Mandelate racemase muconate lactonizing protein 0.011939
51 ENOG4105EYF MMPL domain protein 0.011935
52 ENOG4106XRG NA -0.011906
53 ENOG4107VGB phage plasmid primase, p4 family 0.011903
54 ENOG4105EAG UDP-N-acetylglucosamine 2-epimerase -0.011854
55 ENOG4105EE8 May catalyze the methylation of C-1 in cobalt-precorrin- 5 and the subsequent extrusion of acetic acid from the resulting intermediate to form cobalt-precorrin-6A (By similarity) 0.011850
56 ENOG4105CJ2 (LipO)protein -0.011827
57 ENOG4107ZU8 PTS System 0.011738
58 ENOG41067V1 NA 0.011721
59 ENOG4106FTB Protein of unknwon function (DUF3310) 0.011719
60 ENOG4105X15 PTS System -0.011698
61 ENOG41062A4 Transcriptional regulator 0.011658
62 ENOG4108N80 biosynthesis protein 0.011644
63 ENOG4107PPM cobalt chelatase 0.011607
64 ENOG4105VUC UPF0237 protein -0.011597
65 ENOG4105G5W regulator Fur family 0.011547
66 ENOG4105VTR Integrase -0.011505
67 ENOG4107QWA transporter 0.011493
68 ENOG4107YSK Glycerol-3-phosphate cytidylyltransferase 0.011450
69 ENOG41076YT nitrate reductase, gamma subunit 0.011365
70 ENOG41067MG lrgb family -0.011300
71 ENOG4105CAG UPF0210 protein -0.011275
72 ENOG4105KHA Glyoxalase Bleomycin resistance protein (Dioxygenase -0.011212
73 ENOG4107RHJ d-lactate dehydrogenase 0.011207
74 ENOG4105CG1 Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (By similarity) 0.011137
75 ENOG4108NZA Cobalt transport protein 0.011119
76 ENOG4108Z58 rRNA Methylase 0.011113
77 ENOG4105N7C PTS IIA-like nitrogen-regulatory protein PtsN -0.011104
78 ENOG4108VEM Acyl-ACP thioesterase -0.011064
79 ENOG41083W5 Lyzozyme M1 (1,4-beta-N-acetylmuramidase) 0.011063
80 ENOG4108I66 PTS System 0.011043
81 ENOG4107R0B ComEC rec2-like protein -0.010961
82 ENOG4108UMN azlc family 0.010924
83 ENOG4108IQ3 PTS system 0.010906
84 ENOG4105WY8 addiction module toxin, RelE StbE family 0.010899
85 ENOG4105KX5 Zeta toxin -0.010859
86 ENOG4105C6N Formate acetyltransferase -0.010855
87 ENOG4107R7I amino acid 0.010837
88 ENOG4105KTU Transcriptional regulator, arsr family 0.010807
89 ENOG4108UJE IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of IGP and AICAR (By similarity) -0.010792
90 ENOG41076HS cation diffusion facilitator family transporter -0.010785
91 ENOG4108C1E Inherit from COG: transposase -0.010773
92 ENOG410609N protein encoded in hypervariable junctions of pilus gene clusters 0.010766
93 ENOG4108MUG Signal transduction histidine kinase, lyts -0.010760
94 ENOG4106884 ATP synthase 0.010723
95 ENOG4105EAU Plays a role in nitrite reduction (By similarity) 0.010716
96 ENOG4107RF0 pyruvate dehydrogenase -0.010714
97 ENOG4105CWI transcriptional regulator 0.010707
98 ENOG4107RZ4 Methionine synthase 0.010705
99 ENOG4105KZ5 Nudix family -0.010695
100 ENOG4105D07 Signal peptide peptidase, SppA -0.010694
101 ENOG4105DT3 PTS system, galactitol-specific IIc component -0.010662
102 ENOG41077QW NA 0.010642
103 ENOG4105KGY integral membrane protein 0.010623
104 ENOG4105CH6 catalase 0.010620
105 ENOG4108MRH transcriptional regulatory protein -0.010614
106 ENOG4105CQ9 aldose 1-epimerase 0.010588
107 ENOG4105C0W non-ribosomal peptide synthetase -0.010588
108 ENOG4108KHX Diguanylate cyclase 0.010577
109 ENOG4108SFX uridylyltransferase 0.010573
110 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component -0.010558
111 ENOG4105KPE licD family 0.010524
112 ENOG4105CIA precorrin-4 C(11)-methyltransferase 0.010522
113 ENOG4105CMH dehydratase -0.010506
114 ENOG4107GF8 Sugar (and other) transporter 0.010505
115 ENOG4108Z66 YbaK ebsC protein 0.010504
116 ENOG4105C4Y ABC transporter -0.010499
117 ENOG4105CK2 sodium dicarboxylate symporter 0.010464
118 ENOG4105E0X reductase 0.010444
119 ENOG41064BZ L-xylulose 5-phosphate 3-epimerase -0.010441
120 ENOG4105ENI DNA helicase 0.010430
121 ENOG4106KNT transcriptional regulator 0.010419
122 ENOG4105CRU nitrate reductase, alpha subunit 0.010411
123 ENOG4105CC5 ABC transporter -0.010410
124 ENOG4107RGN Homocysteine 0.010388
125 ENOG4107QS5 ATP-dependent DNA helicase RecQ 0.010381
126 ENOG4105CK1 PTS System 0.010352
127 ENOG4107UE4 Reverse transcriptase 0.010277
128 ENOG4105C09 Bile acid 0.010263
129 ENOG4107QMH DNA methylase 0.010254
130 ENOG4107TIF Phenazine biosynthesis protein, PhzF family -0.010241
131 ENOG4105EV1 Ribose uptake protein RbsU 0.010229
132 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic -0.010204
133 ENOG4105WXW Antirepressor -0.010184
134 ENOG4107RD9 carbohydrate kinase FGGY -0.010163
135 ENOG4105C2C drug resistance transporter, Bcr CflA 0.010151
136 ENOG4105E2R ROK family -0.010143
137 ENOG4107QX6 helicase -0.010103
138 ENOG4108UTW Plays a role in the regulation of phosphate uptake 0.010102
139 ENOG4105CBG Sulfatase 0.010087
140 ENOG4105C53 Part of the ABC transporter complex PotABCD involved in spermidine putrescine import. Responsible for energy coupling to the transport system (By similarity) -0.010079
141 ENOG4108JQ1 Dehydrogenase -0.010075
142 ENOG4105S10 periplasmic binding protein -0.010070
143 ENOG41080ZK Transcriptional regulator, arsR family 0.010068
144 ENOG4107QR9 Iron-sulfur cluster binding protein 0.010051
145 ENOG4106B6K Membrane 0.010039
146 ENOG4105CEU Arginine dihydrolase 0.009994
147 ENOG4105EEM helicase -0.009984
148 ENOG4105C5I Dehydrogenase 0.009974
149 ENOG4108C33 Resolvase 0.009957
150 ENOG41067S4 Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system (By similarity) 0.009933
151 ENOG4107RDV Dehydrogenase 0.009922
152 ENOG41085K5 NA 0.009915
153 ENOG4105CJV Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase -0.009908
154 ENOG4105CHG glycolate oxidase (iron-sulfur subunit) 0.009895
155 ENOG4107SIB radical SAM domain protein 0.009892
156 ENOG4107SJ0 degv family -0.009866
157 ENOG4105EUD Transcriptional regulator -0.009834
158 ENOG4108V3G Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity (By similarity) -0.009802
159 ENOG4105VAS Could be involved in insertion of integral membrane proteins into the membrane (By similarity) -0.009789
160 ENOG41065KT SIR2 family 0.009787
161 ENOG4107SE8 Nucleoside-diphosphate-sugar epimerase 0.009762
162 ENOG4105K85 Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) in DNA. Repairs alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated (By similarity) 0.009755
163 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.009749
164 ENOG4105C6G (ABC) transporter 0.009749
165 ENOG4108UIN ybak prolyl-trna synthetase associated region -0.009703
166 ENOG41090A1 ferritin -0.009676
167 ENOG4105E21 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity) -0.009664
168 ENOG4105D3Y Na H antiporter 0.009657
169 ENOG4108R1T membrAne -0.009627
170 ENOG4105EFC phage portal protein HK97 family 0.009603
171 ENOG4105X0R protein from nitrogen regulatory protein P-II 0.009593
172 ENOG4108S8M degv family 0.009587
173 ENOG4105W71 Phosphopantetheine attachment site. (EC 6.1.1.13) -0.009568
174 ENOG41068IA nitrate reductase molybdenum cofactor assembly chaperone 0.009562
175 ENOG4105D37 Low-affinity potassium transport system. Interacts with Trk system potassium uptake protein TrkA (By similarity) -0.009546
176 ENOG4105E4M (twin-arginine translocation) pathway signal 0.009540
177 ENOG4107SJB teichoic acid biosynthesis 0.009533
178 ENOG4107YZM F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity) 0.009486
179 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.009482
180 ENOG4105IKQ hydratase 0.009476
181 ENOG4105DFE Dna adenine methylase -0.009457
182 ENOG4107S0N DJ-1 family -0.009442
183 ENOG4108H0N domain protein 0.009434
184 ENOG4108UNM NA 0.009431
185 ENOG4107RGE Inherit from COG: ATPase (AAA -0.009427
186 ENOG4108HKT sucrose-6-phosphate hydrolase 0.009423
187 ENOG4108JQ7 (ABC) transporter 0.009422
188 ENOG4105X0A Cell wall anchor domain protein -0.009418
189 ENOG41067QW Transcriptional regulator 0.009415
190 ENOG4105CEC DNA methylase N-4 N-6 -0.009411
191 ENOG4105EN3 adenine specific DNA methyltransferase 0.009408
192 ENOG4105CQX Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.009391
193 ENOG4108SU3 transcriptional regulator 0.009389
194 ENOG4107URP Hydrolase 0.009378
195 ENOG4107REI 2',3'-cyclic-nucleotide 2'-phosphodiesterase EC 3.1.4.16 0.009375
196 ENOG4107T5V SNARE associated Golgi 0.009345
197 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.009337
198 ENOG4105BZ8 glutamate synthase 0.009330
199 ENOG4105K8F Phosphoribosyl-amp cyclohydrolase -0.009293
200 ENOG4105CJI Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate (By similarity) 0.009271
201 ENOG4105C5E polysaccharide biosynthesis protein 0.009266
202 ENOG4107RU5 Cysteine desulfurase -0.009257
203 ENOG4105EQ8 radical SAM domain protein -0.009254
204 ENOG4105CSP Major Facilitator Superfamily 0.009253
205 ENOG4105J4Q Transcriptional regulator -0.009253
206 ENOG41086MK sigma-e processing peptidase spoiiga 0.009186
207 ENOG4108JKK conserved domain protein -0.009183
208 ENOG4105DBM Siderophore biosynthesis protein 0.009179
209 ENOG4107QW4 alcohol dehydrogenase -0.009179
210 ENOG4108JSW Hydrolyase, Fe-S type, tartrate fumarate subfamily, alpha subunit 0.009174
211 ENOG4105WMR Protein CrcB homolog -0.009164
212 ENOG4105CBX hi0933 family -0.009145
213 ENOG4105WC9 nucleotidyltransferase substrate binding protein, HI0074 family 0.009130
214 ENOG4106ZX3 phosphonate ABC transporter, periplasmic phosphonate-binding protein 0.009116
215 ENOG4107T8W Transcriptional regulator 0.009113
216 ENOG4105EF7 Transcriptional regulator 0.009088
217 ENOG4107EF8 Glycosyl transferase (Group 1 -0.009082
218 ENOG4105VAW lrga family -0.009080
219 ENOG410787A Pts system, glucitol sorbitol-specific 0.009079
220 ENOG4107QQE GntR family transcriptional regulator 0.009052
221 ENOG4105EQD regulatoR -0.009036
222 ENOG4108KUQ ABC, transporter -0.009036
223 ENOG41069H0 dihydroorotase EC 3.5.2.3 -0.009032
224 ENOG4108R98 surface protein 0.009015
225 ENOG4105WH1 Two component transcriptional regulator luxr family 0.009012
226 ENOG4108HHM Glycosyl transferase, family 2 0.008989
227 ENOG4105ECI YeeC-like protein -0.008982
228 ENOG4105CG3 alpha amylase, catalytic region 0.008972
229 ENOG4105DKS phage plasmid primase, p4 family 0.008971
230 ENOG4108ZWG Glycosyl hydrolase, family 25 -0.008968
231 ENOG4105CN9 Peptidase m42 family protein -0.008962
232 ENOG4105CEK Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine (By similarity) -0.008961
233 ENOG4106YPC NA 0.008952
234 ENOG4106SVQ Phi ETA orf 55-like protein 0.008940
235 ENOG4105VWF Ferrous iron transport protein A -0.008936
236 ENOG4108Q23 replication initiation and membrane attachment protein 0.008923
237 ENOG4107EEM One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex (By similarity) -0.008921
238 ENOG4105C9B Cysteine desulfurase -0.008917
239 ENOG41080KV transcriptional regulator, lysR family 0.008913
240 ENOG4105D42 Cleaves the N-terminal amino acid of tripeptides (By similarity) 0.008906
241 ENOG4105HTX biosynthesis protein 0.008897
242 ENOG4105JVH oligopeptide transport system, permease 0.008886
243 ENOG410691X NA 0.008885
244 ENOG4108HVZ ABC transporter 0.008876
245 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.008875
246 ENOG4105EYG tyrosine recombinase. Not involved in the cutting and rejoining of the recombining DNA molecules on dif(SL) site (By similarity) -0.008875
247 ENOG4108WA6 metallo-beta-lactamase superfamily protein -0.008872
248 ENOG4105KA0 thioesterase Superfamily protein 0.008871
249 ENOG4107F50 Cbs domain protein 0.008863
250 ENOG4106YWY NA -0.008851