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 ENOG4105DYN 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) -0.015047
2 ENOG4105ENN converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity) 0.014308
3 ENOG4107QPI nitrilase cyanide hydratase and apolipoprotein n-acyltransferase -0.014297
4 ENOG4105CMW The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity) 0.014058
5 ENOG4105DWK Membrane 0.013880
6 ENOG4105CUR 5'-nucleotidase, lipoprotein e(p4) family -0.013614
7 ENOG4107QWS glycogen debranching enzyme glgx 0.013476
8 ENOG4105D2T synthase -0.013231
9 ENOG4105D2N Aldolase 0.012961
10 ENOG4106KNT transcriptional regulator 0.012947
11 ENOG4105H1G trap transporter solute receptor taxi family -0.012873
12 ENOG4105EHG Permease protein -0.012802
13 ENOG4105MZU cell filamentation protein 0.012622
14 ENOG4108ZMD Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) -0.012534
15 ENOG4105D3A purine nucleoside phosphorylase DeoD-type 0.012405
16 ENOG4105CMG Carbohydrate kinase 0.012321
17 ENOG4105EAG UDP-N-acetylglucosamine 2-epimerase -0.012155
18 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) -0.012126
19 ENOG4108RVA ribokinase 0.012057
20 ENOG4105CBT Fructose-1,6-bisphosphatase -0.012049
21 ENOG4107XK1 Protein of unknown function (DUF421) -0.011992
22 ENOG4105FD2 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) -0.011844
23 ENOG4107SPW HsdM N-terminal domain -0.011765
24 ENOG4105CE4 GlcNAc 6-P deacetylase 0.011761
25 ENOG4108URH decarboxylase -0.011564
26 ENOG4105C4J Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits (By similarity) 0.011493
27 ENOG4105C0A alcohol dehydrogenase 0.011377
28 ENOG4105S10 periplasmic binding protein -0.011348
29 ENOG4105BZN citrate synthase 0.011342
30 ENOG4107TN3 Dicarboxylate carrier -0.011311
31 ENOG4105DC4 trap transporter, 4tm 12tm fusion protein -0.011186
32 ENOG4108R5D Transcriptional regulator, TetR family -0.011146
33 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.011120
34 ENOG4108K88 Membrane 0.011050
35 ENOG4107BU2 esterase 0.010944
36 ENOG4108RCY Nadph-dependent fmn reductase 0.010937
37 ENOG4105J80 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex (By similarity) 0.010920
38 ENOG4105VDH Dihydroxyacetone kinase 0.010904
39 ENOG4107QHF type ii secretion system protein e -0.010852
40 ENOG4107T8J thymidine kinase -0.010814
41 ENOG4107RBB ABC transporter, permease -0.010702
42 ENOG4105MEV Acyl-transferase -0.010669
43 ENOG4105E98 transcriptional regulator DeoR family 0.010599
44 ENOG4107STB Periplasmic binding protein -0.010524
45 ENOG4107SW2 integral membrane protein 0.010492
46 ENOG4105DME alpha-galactosidase 0.010491
47 ENOG4105EBX v-type atpase -0.010438
48 ENOG4105D7A ATP-binding protein -0.010401
49 ENOG4107VXF methyltransferase 0.010393
50 ENOG4105CKA Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion (By similarity) 0.010389
51 ENOG4108Z0Z intracellular protease Pfpi family 0.010317
52 ENOG4107QQI Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity) 0.010266
53 ENOG4108UHU Aldolase 0.010246
54 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 0.010246
55 ENOG4105JSC dimethylmenaquinone methyltransferase -0.010202
56 ENOG410908R Methenyltetrahydrofolate cyclohydrolase -0.010196
57 ENOG4107QJD pyruvate phosphate dikinase 0.010158
58 ENOG4108VPX Involved in 1,2-propanediol (1,2-PD) degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate (By similarity) 0.010139
59 ENOG4108TK9 formylmethanofuran dehydrogenase, subunit E -0.010044
60 ENOG4105C8J )-transporter -0.010031
61 ENOG4105C7F AcnD-accessory protein PrpF -0.010008
62 ENOG4105CDG Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit (By similarity) 0.009997
63 ENOG4105DDZ Methyltransferase required for the conversion of demethylmenaquinone (DMKH2) to menaquinone (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) (By similarity) -0.009984
64 ENOG41089BK Glutamine amido-transferase 0.009973
65 ENOG4105Z3A Cation antiporter -0.009904
66 ENOG4105C4B ABC transporter, permease -0.009868
67 ENOG4105C5Y PTS System 0.009840
68 ENOG4105WY8 addiction module toxin, RelE StbE family 0.009833
69 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) 0.009785
70 ENOG4105CZG Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity) 0.009749
71 ENOG4105KNY Microcompartments protein 0.009682
72 ENOG4105ECB domain protein -0.009655
73 ENOG4108VHV Membrane 0.009567
74 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.009488
75 ENOG4105ZW9 acetyltransferase, (GNAT) family 0.009451
76 ENOG4108QY0 Membrane 0.009447
77 ENOG4108Y76 addiction module toxin, RelE StbE family -0.009420
78 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) 0.009346
79 ENOG4107RAP type iii restriction -0.009328
80 ENOG4105EN2 IstB domain-containing protein ATP-binding protein 0.009311
81 ENOG4107QWP ABC-2 type transporter -0.009308
82 ENOG4105C94 Transporter -0.009287
83 ENOG4105DKQ ROK family 0.009252
84 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) 0.009249
85 ENOG4108VTX Hhh-gpd family -0.009240
86 ENOG410859T Inherit from COG: Thioredoxin 0.009228
87 ENOG4108IJ1 Dehydrogenase -0.009216
88 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) 0.009208
89 ENOG4105C6Z Gluconate 0.009203
90 ENOG4105MXV Polyketide cyclase / dehydrase and lipid transport -0.009203
91 ENOG4107EE0 NA -0.009127
92 ENOG4108YXY alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen -0.009107
93 ENOG4105D4P Coproporphyrinogen iii oxidase -0.009080
94 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) 0.009076
95 ENOG4108IA5 tonB-dependent Receptor -0.009046
96 ENOG4108Z3B V-type sodium ATPase, K subunit -0.008980
97 ENOG4108KE5 Membrane -0.008973
98 ENOG4105CX6 glutaminyL-tRNA synthetase 0.008973
99 ENOG4105VUF Transcriptional regulator 0.008966
100 ENOG4108ZN0 Chromate transport protein -0.008965
101 ENOG4105ITI NA 0.008937
102 ENOG4108I66 PTS System -0.008936
103 ENOG4106X7A NA -0.008924
104 ENOG4105GA3 phage protein 0.008916
105 ENOG4105ENJ RND efflux system, outer membrane lipoprotein -0.008908
106 ENOG4105FDP GntR family transcriptional regulator 0.008899
107 ENOG4105WQ5 TonB family -0.008866
108 ENOG4105CTK cobaltochelatase, cobn subunit -0.008859
109 ENOG4105D2H Uronic isomerase 0.008823
110 ENOG4105C8D Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen (By similarity) -0.008755
111 ENOG4107QRM domain protein 0.008754
112 ENOG4105CTQ phosphohexokinase 0.008740
113 ENOG4105KRQ Addiction module toxin, Txe YoeB family -0.008740
114 ENOG4105EJ9 Membrane -0.008739
115 ENOG4108E0S reductase -0.008718
116 ENOG4105EMD TRANSCRIPTIONal 0.008704
117 ENOG4106BEE NA -0.008701
118 ENOG4105D42 Cleaves the N-terminal amino acid of tripeptides (By similarity) 0.008687
119 ENOG4105E4N tonB-dependent Receptor -0.008673
120 ENOG4105D9M gamma-glutamylcysteine synthetase -0.008643
121 ENOG4108YYD acetyltransferase -0.008634
122 ENOG4107TJD ABC transporter, permease protein -0.008628
123 ENOG4107ZNW DNA protecting protein DprA -0.008621
124 ENOG4105D3U 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) -0.008616
125 ENOG4108YYQ gCN5-related N-acetyltransferase 0.008586
126 ENOG4105D7V transposase 0.008552
127 ENOG4107T27 Major Facilitator -0.008525
128 ENOG4105BZC d-serine deaminase 0.008520
129 ENOG4105VSH 4-oxalocrotonate tautomerase -0.008501
130 ENOG4107RA0 type I restriction modification -0.008472
131 ENOG4107U7Y Peptidase M48, Ste24p -0.008466
132 ENOG4105DG6 mannose-6-phosphate isomerase 0.008452
133 ENOG4105HI2 (NAD(P)H dehydrogenase) (Quinone) -0.008436
134 ENOG4108U05 Transcriptional regulator -0.008435
135 ENOG4107VAQ metallophosphoesterase -0.008421
136 ENOG4105DUA (citrate (pro-3S)-lyase ligase -0.008420
137 ENOG4105XSJ toxin secretion phage lysis holin 0.008417
138 ENOG4105C5E polysaccharide biosynthesis protein -0.008388
139 ENOG4105EET magnesium chelatase -0.008388
140 ENOG4108DBC nitroreductase 0.008380
141 ENOG4105GZI Transcriptional regulator 0.008363
142 ENOG4105CV8 reductase 0.008337
143 ENOG4106FUX Inherit from NOG: transposase 0.008333
144 ENOG410631K Membrane -0.008330
145 ENOG4105F1K Glutamine amidotransferase 0.008328
146 ENOG4106CVF DNA replication protein -0.008317
147 ENOG4105CPE K01197 hyaluronoglucosaminidase EC 3.2.1.35 0.008272
148 ENOG4105CSR polyphosphate kinase 2 -0.008269
149 ENOG4108HCJ Hydrolase 0.008244
150 ENOG4105EFS Binding-protein-dependent transport systems, inner membrane component -0.008239
151 ENOG4108QDY Endonuclease Exonuclease phosphatase -0.008233
152 ENOG41067QG Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides (By similarity) 0.008205
153 ENOG4107QMG Nad synthetase 0.008187
154 ENOG4105DPZ Two component transcriptional regulator (Winged helix family -0.008177
155 ENOG4105C6T cysteine synthase 0.008169
156 ENOG4105DCF alanine dehydrogenase 0.008168
157 ENOG4105D6T Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L- homocysteine, respectively. Is also able to deaminate adenosine (By similarity) -0.008165
158 ENOG4105C26 Dehydrogenase -0.008156
159 ENOG4105GH4 LemA family 0.008151
160 ENOG4105VNF NA 0.008142
161 ENOG4105CPN adenine deaminase -0.008120
162 ENOG4105ENE Histidine kinase 0.008118
163 ENOG4105VIE preprotein translocase, subunit YajC -0.008118
164 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) -0.008115
165 ENOG4105VXX VRR-NUC domain protein 0.008112
166 ENOG41063JJ Phage derived protein Gp49-like (DUF891) 0.008075
167 ENOG4107XR9 resolvase 0.008072
168 ENOG4105DVM PP-loop domain protein 0.008029
169 ENOG4105D0S secretion protein (HlyD -0.007984
170 ENOG4105CR5 Class II aldolase adducin family protein 0.007977
171 ENOG41067M3 Membrane -0.007952
172 ENOG410642B Protein of unknown function (DUF805) -0.007947
173 ENOG4108X4Q Hydrolase 0.007945
174 ENOG4105E70 isomerase 0.007942
175 ENOG4105CJJ Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress (By similarity) 0.007939
176 ENOG4105DET Rhamnulokinase 0.007897
177 ENOG4105CK4 Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) -0.007895
178 ENOG4107SC7 Inner membrane transporter yjeM -0.007893
179 ENOG4106UJV Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity) -0.007889
180 ENOG41088KT Iclr family transcriptional regulator 0.007870
181 ENOG4105DID DevR family -0.007826
182 ENOG4105C87 Aminotransferase class I and II 0.007803
183 ENOG4108W76 histidinol phosphate phosphatase hisj family 0.007803
184 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) -0.007789
185 ENOG4105QB7 gCN5-related N-acetyltransferase -0.007769
186 ENOG4105DSJ YicC domain protein -0.007768
187 ENOG4107GFK fumarate -0.007754
188 ENOG4108QA2 CRISPR-associated protein, Csm6 0.007739
189 ENOG4105D7W serine acetyltransferase 0.007733
190 ENOG4108225 domain protein -0.007730
191 ENOG4107R69 radical SAM domain protein -0.007726
192 ENOG4105DKJ Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate (By similarity) 0.007711
193 ENOG4108TKT Luciferase-like monooxygenase -0.007709
194 ENOG4105CFZ Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III (By similarity) -0.007707
195 ENOG4108UMS Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP- ribose 1''-2''-cyclic phosphate (APPR P). May function as an ADP- ribosylase (By similarity) 0.007685
196 ENOG4107XEC aspartate racemase -0.007684
197 ENOG41068F2 Conserved hypothetical, protein 0.007682
198 ENOG41075SE NA 0.007674
199 ENOG41090A3 NA 0.007649
200 ENOG4107KVK NA 0.007638
201 ENOG4109051 YadA domain protein -0.007638
202 ENOG41080GV L-lysine permease 0.007634
203 ENOG4105C60 DNA-binding protein 0.007633
204 ENOG4107US6 Glycosyl transferase -0.007631
205 ENOG4108FM6 Dehydrogenase 0.007615
206 ENOG4105T6S Protein of unknown function (DUF3737) 0.007602
207 ENOG4106X1X NA 0.007587
208 ENOG4107HQM Transposase, Mutator family 0.007583
209 ENOG4105R55 associated with various cellular activities 0.007566
210 ENOG4105DZR Type I site-specific deoxyribonuclease -0.007562
211 ENOG4105CZF Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism (By similarity) -0.007555
212 ENOG4105K7D Required for maturation of 30S ribosomal subunits (By similarity) -0.007551
213 ENOG4107QKV phosphomannomutase -0.007540
214 ENOG4108JJ8 (ABC) transporter 0.007525
215 ENOG4105CG5 Glycosyl transferase (Group 1 0.007520
216 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase 0.007507
217 ENOG4107RB9 PTS System 0.007492
218 ENOG4107RVN Periplasmic binding protein -0.007492
219 ENOG4105UGZ Periplasmic binding protein -0.007488
220 ENOG4107R13 MMPL domain protein 0.007485
221 ENOG410905Q NA -0.007464
222 ENOG4105FKQ transcriptional regulator 0.007464
223 ENOG4105NUU permease -0.007455
224 ENOG4106PMH Extracellular solute-binding protein family 3 0.007444
225 ENOG4105M56 Produces ATP from ADP in the presence of a proton gradient across the membrane (By similarity) -0.007443
226 ENOG4105C0V Provides the sole de novo source of dTMP for DNA biosynthesis (By similarity) 0.007442
227 ENOG4107R52 fad dependent oxidoreductase -0.007436
228 ENOG4105D3Q Sugar transferase -0.007436
229 ENOG4108UN4 phage SPO1 DNA polymerase-related protein -0.007428
230 ENOG4105DFP Integrase -0.007420
231 ENOG4107UCG Phospholipase, patatin family -0.007419
232 ENOG4107YRV Mechanosensitive ion channel -0.007414
233 ENOG4105D4F Synthesizes selenophosphate from selenide and ATP (By similarity) -0.007414
234 ENOG4108IMM HTH_XRE 0.007409
235 ENOG4108R6W Transcriptional regulator, ARAC family 0.007408
236 ENOG41080E8 Transcriptional regulator, Spx MgsR family 0.007407
237 ENOG4106XVW NA 0.007404
238 ENOG4107PQW transporter major facilitator family protein 0.007404
239 ENOG4106KJE Pfam:HIM 0.007404
240 ENOG41060U7 NA 0.007404
241 ENOG4105FJH Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions (By similarity) -0.007398
242 ENOG4108K6F triphosphoribosyl-dephospho-CoA synthase -0.007386
243 ENOG4105VRA Glyoxalase Bleomycin resistance protein (Dioxygenase 0.007371
244 ENOG41067MG lrgb family -0.007359
245 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F -0.007358
246 ENOG4105CTS PTS system mannitol-specific 0.007358
247 ENOG4108RRS Transcriptional regulator 0.007355
248 ENOG4105EPD Oligopeptide transporter, Opt family 0.007353
249 ENOG4105NRA 50s ribosomal protein l31 type b -0.007352
250 ENOG4107U2I Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.007345