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 ENOG4105DJT lAO AO transport system ATPase 0.015274
2 ENOG4108YZT Adenosylcobinamide kinase 0.015171
3 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) 0.015154
4 ENOG4105CMN Methylmalonyl-coA mutase 0.014891
5 ENOG4108ZVT methylmalonyl-coA epimerase 0.014509
6 ENOG4105D5P Methylmalonyl-coA mutase 0.014014
7 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) 0.013927
8 ENOG4108KMX efflux transporter, rnd family, mfp subunit 0.012436
9 ENOG4105DH2 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group (By similarity) 0.012382
10 ENOG4107QU8 Transferase 0.012080
11 ENOG4105E4R Precorrin-3B C17-methyltransferase 0.011837
12 ENOG4106762 Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5- dihydroxy-2,3-pentadione (DPD) (By similarity) -0.011822
13 ENOG4108IJ0 Aspartate ammonia-lyase 0.011727
14 ENOG4107GFK fumarate -0.011527
15 ENOG4105C94 Transporter -0.011500
16 ENOG4105C8H hydrogenase maturation protein Hypf 0.011394
17 ENOG4108S37 Membrane -0.011297
18 ENOG4107QS5 ATP-dependent DNA helicase RecQ 0.011237
19 ENOG4108WBT adenosyltransferase 0.011199
20 ENOG4105CB8 Multifunctional enzyme that catalyzes the SAM-dependent methylation of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 and then position C-12 or C-18 to form trimethylpyrrocorphin 2. It also catalyzes the conversion of precorrin-2 into siroheme. This reaction consists of the NAD- dependent oxidation of precorrin-2 into sirohydrochlorin and its subsequent ferrochelation into siroheme (By similarity) 0.011157
21 ENOG4105CU9 asparagine synthetase A -0.011092
22 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.010969
23 ENOG4105CA8 Catalyzes the rearrangement of 1-deoxy-D-xylulose 5- phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S (By similarity) 0.010940
24 ENOG41068B1 Cob-I-yrinic acid a,c-diamide adenosyltransferase 0.010922
25 ENOG4108S4H thioesterase Superfamily protein -0.010872
26 ENOG4105M3W utilization protein 0.010867
27 ENOG4105C4Y ABC transporter 0.010840
28 ENOG4107QR9 Iron-sulfur cluster binding protein 0.010748
29 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) 0.010717
30 ENOG41081F0 Precorrin-8x methylmutase 0.010670
31 ENOG4105CG5 Glycosyl transferase (Group 1 0.010452
32 ENOG4107R28 alpha amylase, catalytic region -0.010451
33 ENOG4107RUP AcrB AcrD AcrF family protein 0.010231
34 ENOG4105C5I Dehydrogenase -0.010148
35 ENOG4105C0Y Responsible for the amidation of carboxylic groups at position A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) 0.009999
36 ENOG4108W62 ykgG family 0.009999
37 ENOG4105CBF Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction (By similarity) 0.009995
38 ENOG4105T6S Protein of unknown function (DUF3737) 0.009815
39 ENOG4108VMD Methyltransferase -0.009728
40 ENOG4107YCB isochorismatase -0.009646
41 ENOG4105MKX n-acetylmuramoyl-l-alanine amidase 0.009644
42 ENOG4105FGH MotA TolQ exbB proton channel 0.009584
43 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) -0.009563
44 ENOG4108QXE glycerophosphoryl diester phosphodiesterase 0.009538
45 ENOG4107SNF Na H antiporter 0.009473
46 ENOG4108ZGC gaf domain protein 0.009419
47 ENOG41090F1 C_GCAxxG_C_C family -0.009402
48 ENOG4108IAB Phoh family 0.009288
49 ENOG4105M6F mutator MutT protein -0.009224
50 ENOG4105KTW ethanolamine utilization protein 0.009215
51 ENOG4108RYC glycosyltransferase 0.009108
52 ENOG4105DPS NA 0.009058
53 ENOG4105FCD Major Facilitator -0.008975
54 ENOG41084JX Inherit from COG: Transcriptional regulator -0.008966
55 ENOG4108JTB NA 0.008931
56 ENOG410901E Membrane 0.008901
57 ENOG4105KAH Phosphoesterase 0.008879
58 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) 0.008837
59 ENOG4105E1G Band 7 protein 0.008837
60 ENOG4105DB9 Binding-protein-dependent transport systems inner membrane component -0.008804
61 ENOG4105CMT Dihydroxyacetone kinase 0.008768
62 ENOG41063CS Replication Protein -0.008755
63 ENOG4105M18 -acetyltransferase -0.008754
64 ENOG4108P0Z Tetratricopeptide repeat protein 0.008692
65 ENOG4105JF5 Protein of unknown function (DUF2400) 0.008671
66 ENOG4107RWA tonB-dependent Receptor 0.008662
67 ENOG4107R44 filamentation induced by cAMP protein fic 0.008598
68 ENOG4107TGU Thiamine biosynthesis protein ThiF 0.008580
69 ENOG4105FRY Dehydrogenase 0.008564
70 ENOG4107RJE )-transporter 0.008543
71 ENOG4105DCF alanine dehydrogenase 0.008516
72 ENOG4105CQS hydrogenase expression formation protein HypD 0.008472
73 ENOG4105DPX Hydrogenase, large subunit 0.008460
74 ENOG4108JQ6 ABC transporter 0.008453
75 ENOG4108UVJ appr-1-p processing domain protein 0.008423
76 ENOG4105X7Q transcriptional regulator 0.008409
77 ENOG4105D6J arsenicaL-resistance protein -0.008391
78 ENOG4105CM2 brancheD-chain amino acid aminotransferase -0.008376
79 ENOG4105C10 Electron transfer flavoprotein 0.008375
80 ENOG4105C3E May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine (By similarity) 0.008363
81 ENOG4107SVV electron transport complex, RnfABCDGE type, B subunit 0.008246
82 ENOG4105KR2 Chorismate binding enzyme 0.004120
82 ENOG4107V3Y chorismate binding enzyme 0.004120
83 ENOG4108JIJ Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second (By similarity) -0.008240
84 ENOG4105DWF phosphomethylpyrimidine kinase 0.008229
85 ENOG4105M2Z protein tyrosine serine phosphatase 0.008199
86 ENOG4105D5N isocitrate dehydrogenase (NADP) -0.008195
87 ENOG4107TB6 phosphoglycerate mutase 0.008099
88 ENOG4106DSS Tartrate dehydratase subunit alpha -0.008092
89 ENOG4107RPD radical SAM domain protein 0.008092
90 ENOG4105CQJ Aminoglycoside phosphotransferase 0.008083
91 ENOG4105D41 biosynthesis protein thiH 0.008054
92 ENOG4108IQF Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA (By similarity) -0.008048
93 ENOG41084R8 NA 0.008043
94 ENOG4108HNZ carboxyl transferase 0.008033
95 ENOG4108KMV Glycosyl transferase (Group 1 0.008021
96 ENOG4105BZ8 glutamate synthase 0.008021
97 ENOG4105CNA YD repeat protein -0.008001
98 ENOG4107QW8 radical SAM domain protein 0.007995
99 ENOG4105CIA precorrin-4 C(11)-methyltransferase 0.007962
100 ENOG4105XSJ toxin secretion phage lysis holin 0.007906
101 ENOG41085JV Type II DNA modification methyltransferase 0.007884
102 ENOG4105CH8 Succinyl-CoA ligase ADP-forming subunit alpha -0.007879
103 ENOG4105CHH sulfate transporter 0.007850
104 ENOG4108URH decarboxylase -0.007837
105 ENOG4105N5T Radical SAM Protein 0.007832
106 ENOG4105D5I Catalyzes the ATP-dependent phosphorylation of L- homoserine to L-homoserine phosphate (By similarity) -0.007823
107 ENOG4107R0S symporter -0.007820
108 ENOG4107RNE DNA polymerase -0.007817
109 ENOG4105W0X NA -0.007793
110 ENOG4105FF5 Membrane 0.007742
111 ENOG41083AA HTH_XRE 0.007738
112 ENOG4105ZG0 Transcriptional regulator 0.007734
113 ENOG4105C8Y Acetylornithine aminotransferase -0.007723
114 ENOG41062D9 Histidine kinase 0.007717
115 ENOG41086WP Thiamine biosynthesis protein thiS 0.007713
116 ENOG4105CMV Succinyl-CoA synthetase subunit beta -0.007650
117 ENOG4105XC8 protein, conserved in bacteria 0.007644
118 ENOG4105C45 hydrogenase expression formation protein (HypE) 0.007628
119 ENOG4108VGH Abortive infection bacteriophage resistance protein -0.007603
120 ENOG4105WA0 Thioesterase superfamily protein 0.007600
121 ENOG410686K NA 0.007589
122 ENOG4108VWQ crispr-associated protein -0.007560
123 ENOG4108VN1 NA 0.007556
124 ENOG4105C3R Methionine synthase 0.007539
125 ENOG4107RBB ABC transporter, permease -0.007527
126 ENOG4106855 Competence protein 0.007500
127 ENOG4105MCQ NA 0.007489
128 ENOG4107QWS glycogen debranching enzyme glgx 0.007489
129 ENOG4108JEB The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine (By similarity) -0.007484
130 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) 0.007473
131 ENOG4105PI3 Domain of unknown function DUF77 -0.007473
132 ENOG4108RY1 ATP synthase, subunit E 0.007466
133 ENOG4108ZC1 mosc domain containing protein 0.007455
134 ENOG4105CEM UPF0597 protein 0.007453
135 ENOG4108MXX Oxidoreductase short chain dehydrogenase reductase family 0.007449
136 ENOG4108Z0R Transferase 0.007442
137 ENOG4105ENI DNA helicase 0.007437
138 ENOG41061PC Inherit from NOG: (LipO)protein 0.007434
139 ENOG4107SE4 UDP-N-acetylglucosamine 2-epimerase -0.007427
140 ENOG4105C3J Cysteine desulfurase -0.007423
141 ENOG4107Y3V -acetyltransferase -0.007403
142 ENOG4108TSH transposase 0.007396
143 ENOG4105E5S Enoyl-CoA hydratase 0.007395
144 ENOG4105CEC DNA methylase N-4 N-6 0.007394
145 ENOG4105F4F gtp-binding protein 0.007393
146 ENOG4106P11 Radical SAM 0.007386
147 ENOG4105MH0 NA -0.007372
148 ENOG4106G2M NA 0.007369
149 ENOG4105E7X Protein of unknown function 0.007363
150 ENOG4105KM4 Acetyl-CoA carboxylase, biotin carboxyl carrier protein -0.007362
151 ENOG4105DWD nucleoside recognition domain protein -0.007349
152 ENOG4108IUM Glycogen debranching enzyme 0.007339
153 ENOG4105F4I Transcriptional regulator -0.007334
154 ENOG4105C5E polysaccharide biosynthesis protein 0.007329
155 ENOG4105D7N magnesium and cobalt transport protein CorA 0.007311
156 ENOG4107QID Threonine synthase -0.007295
157 ENOG4105KX5 Zeta toxin 0.007276
158 ENOG4105CHM Aminotransferase -0.007272
159 ENOG4105CYW agmatinase -0.007254
160 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) 0.007229
161 ENOG4107QSZ Mate efflux family protein -0.007226
162 ENOG4108QH2 crispr-associated protein -0.007218
163 ENOG4105VFF UPF0102 protein 0.007208
164 ENOG4107QJ7 formate dehydrogenase alpha subunit -0.007205
165 ENOG4106BRA Membrane 0.007205
166 ENOG4105IU9 (LipO)protein -0.007202
167 ENOG4108IUQ atp-dependent protease 0.007198
168 ENOG4105C1A potassium transporter peripheral membrane -0.007196
169 ENOG4105S8Z NA 0.007194
170 ENOG4106CA4 NA 0.007178
171 ENOG4105C3F Signal peptidase i -0.007172
172 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) 0.007164
173 ENOG4107QUV Domain protein 0.007164
174 ENOG4105C1G acyl-Coa dehydrogenase 0.007161
175 ENOG4105D6W Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps (By similarity) 0.007152
176 ENOG41090A1 ferritin 0.007140
177 ENOG4105FEN Deacylase 0.007113
178 ENOG4105E2M Manganese-dependent inorganic pyrophosphatase -0.007082
179 ENOG4105WBM Protein of unknown function (DUF1232) 0.007065
180 ENOG4105ECB domain protein -0.007057
181 ENOG4108ZK3 Conserved domain protein 0.007056
182 ENOG4105IUU Protein of unknown function (DUF3575) 0.007056
183 ENOG4105CYQ Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate) (By similarity) -0.007056
184 ENOG4105D7J NA -0.007052
185 ENOG4105E2R ROK family -0.007052
186 ENOG4108RAC Rubrerythrin 0.007031
187 ENOG4105CJ1 ABC, transporter -0.007022
188 ENOG4107NSS NA 0.007021
189 ENOG4106A8E Transcriptional regulator, luxr family -0.007007
190 ENOG4107KRG NA 0.007006
191 ENOG4108UQ1 hydrolase, family 25 -0.006996
192 ENOG4105K4T epimerase -0.006982
193 ENOG4105CRJ Dihydroorotate dehydrogenase 0.006979
194 ENOG4105CF3 3-Hydroxyisobutyrate dehydrogenase -0.006961
195 ENOG4105KVH Transcriptional regulator 0.006942
196 ENOG4105F42 AAA-ATPase 0.006938
197 ENOG4105SKN orotidine 5''-phosphate decarboxylase 0.006918
198 ENOG4108THW HD domain protein 0.006917
199 ENOG4108VJJ Nitroreductase -0.006909
200 ENOG41074NN NA -0.006903
201 ENOG4105DQ6 Transposase -0.006887
202 ENOG4107RY2 2 glycosyl transferase -0.006884
203 ENOG4106409 NA 0.006881
204 ENOG41076NG NA 0.006873
205 ENOG4105VUF Transcriptional regulator 0.006872
206 ENOG4106JM6 NA 0.003433
206 ENOG4106RHM NA 0.003433
207 ENOG4105E0A ABC, transporter 0.006837
208 ENOG4107SS9 Mate efflux family protein 0.006836
209 ENOG4108C33 Resolvase -0.006834
210 ENOG4105CBT Fructose-1,6-bisphosphatase 0.006834
211 ENOG4105CQ4 Transcriptional regulator -0.006833
212 ENOG4107UBK integral membrane protein -0.006828
213 ENOG4105CER acetyl-CoA carboxylase biotin carboxylase -0.006824
214 ENOG41090I9 Protein of unknown function (DUF3575) 0.006805
215 ENOG4107SHE acetyltransferase, (GNAT) family 0.006788
216 ENOG4105RIJ domain protein -0.006779
217 ENOG4105CSD Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) (By similarity) 0.006775
218 ENOG4108RE5 NA 0.006773
219 ENOG4105DFE Dna adenine methylase 0.006772
220 ENOG4107S10 cell wall hydrolase, SleB 0.006766
221 ENOG4105CEB Aspartate aminotransferase 0.006747
222 ENOG4107XQA Inherit from COG: Involved in DNA double-strand break repair (DSBR). The Rad50 Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity. Rad50 provides an ATP-dependent control of Mre11 by unwinding and or repositioning DNA ends into the Mre11 active site (By similarity) 0.006740
223 ENOG4105DAA L-lactate 0.006738
224 ENOG4107RC7 uridine kinase 0.006738
225 ENOG4108VP5 UreA transporter -0.006733
226 ENOG4105FFF abc transporter permease protein -0.006731
227 ENOG4105FJH Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions (By similarity) -0.006730
228 ENOG4105CRP Part of the ABC transporter FtsEX involved in -0.006726
229 ENOG4107TGY peptidase 0.006704
230 ENOG4105K7K Transcriptional regulator 0.006686
231 ENOG41068ZA NA 0.006679
232 ENOG4108RT7 Glycosyl transferase, family 2 -0.006675
233 ENOG41069AG Ankyrin repeat 0.006673
234 ENOG4107QK1 ImpB MucB SamB family protein -0.006668
235 ENOG4107SVJ Dehydrogenase -0.006663
236 ENOG4107BJW polysaccharide deacetylase 0.006660
237 ENOG41069BS Inherit from NOG: Leucine rich repeat protein, bspa family protein -0.006656
238 ENOG4105D7V transposase -0.006652
239 ENOG41085E0 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) 0.006641
240 ENOG4108K8S endonuclease I -0.006639
241 ENOG4108TMS Uncharacterized protein conserved in bacteria (DUF2263) 0.006633
242 ENOG4107V6T Extracellular solute-binding protein, family 5 0.006631
243 ENOG41082RA The GLUG motif protein family protein -0.006601
244 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) 0.006593
245 ENOG41082BM Transcriptional regulator, arsr family -0.006584
246 ENOG4105D8I Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity) -0.006550
247 ENOG4105C0F tryptophanase EC 4.1.99.1 0.006548
248 ENOG4108VYM NA -0.006546