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 ENOG4105EMS pseudouridine synthase 0.140295
2 ENOG4105D0T Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs (By similarity) 0.135020
3 ENOG4108KG4 Pseudouridine synthase 0.134736
4 ENOG4105FE9 pseudouridine synthase 0.133897
5 ENOG4105I08 Pseudouridine synthase 0.133862
6 ENOG4105DI7 Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs (By similarity) 0.133510
7 ENOG4105C34 Pseudouridine synthase 0.131109
8 ENOG4105M33 TRANSCRIPTIONal -0.090433
9 ENOG41069F6 NA -0.089107
10 ENOG4106CZ6 NA -0.089107
11 ENOG41088CX ErfK YbiS YcfS YnhG -0.089107
12 ENOG4106U13 NA -0.089107
13 ENOG4107TSB Polypeptide-transport-associated domain protein ShlB-type -0.089093
14 ENOG4108PPP Transcriptional regulator, ARAC family -0.088812
15 ENOG4108VKT Abortive infection protein -0.088529
16 ENOG4107VQQ Glycosyl transferase, family 2 -0.088367
17 ENOG4107RDT Channel that permits osmotically driven movement of water in both directions. It is involved in the osmoregulation and in the maintenance of cell turgor during volume expansion in rapidly growing cells. It mediates rapid entry or exit of water in response to abrupt changes in osmolarity (By similarity) -0.087469
18 ENOG4105C9K Endothelin-converting enzyme 1 -0.086746
19 ENOG4105KUR CAAX amino terminal protease family protein -0.081694
20 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) -0.034048
21 ENOG4105F28 tonB-dependent Receptor -0.032396
22 ENOG4108JA0 Oxidoreductase, FAD NAD(P)-binding domain protein -0.030982
23 ENOG4108K3A Glutathione S-transferase -0.030924
24 ENOG4107SEV 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase -0.030877
25 ENOG4108JU7 Transcriptional regulator -0.030869
26 ENOG4108UMJ dihydrodipicolinate synthetase -0.030758
27 ENOG4107T8U membrane -0.030523
28 ENOG4108MKH alkane-1 monooxygenase -0.030420
29 ENOG4106AW1 Aromatic-ring-hydroxylating dioxygenase subunit beta -0.030420
30 ENOG4108SBK dioxygenase, subunit beta -0.030420
31 ENOG4106WR9 Aromatic-ring-hydroxylating dioxygenase subunit beta -0.030420
32 ENOG4105H37 Glyoxalase Bleomycin resistance protein (Dioxygenase -0.030406
33 ENOG4106DX9 Aromatic-ring-hydroxylating dioxygenase beta subunit -0.030387
34 ENOG4108UKV benzoate 1,2-dioxygenase -0.030378
35 ENOG4108Q89 anthranilate 1,2-dioxygenase large subunit -0.030378
36 ENOG4108QQN 4-oxalocrotonate decarboxylase EC 4.1.1.77 -0.030251
37 ENOG4105IS1 Rieske 2Fe-2S -0.030237
38 ENOG4105SYF dioxygenase -0.030167
39 ENOG4107NPM Ferredoxin -0.029931
40 ENOG4105VQD rieske 2fe-2S domain-containing protein -0.029920
41 ENOG4107R8Z faD-dependent pyridine nucleotide-disulfide oxidoreductase -0.029516
42 ENOG41085U4 4-oxalocrotonate tautomerase -0.029308
43 ENOG41082MH Domain of unknown function (DUF336) -0.029231
44 ENOG4108URA DSBA oxidoreductase -0.029131
45 ENOG4108QJ2 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase -0.028972
46 ENOG4107RIM Dehydrogenase -0.028878
47 ENOG410814W hydrolase -0.028557
48 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) -0.027867
49 ENOG4105FUY alpha subunit -0.027623
50 ENOG4105VF7 tolerance protein -0.027516
51 ENOG4105C26 Dehydrogenase -0.027184
52 ENOG4105F53 2,3-dioxygenase -0.027076
53 ENOG4105EJX conjugal transfer ATPase -0.026723
54 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase -0.026624
55 ENOG4106ZGV Orthopoxvirus protein of unknown function (DUF830) -0.026606
56 ENOG4107QJD pyruvate phosphate dikinase -0.026531
57 ENOG4105E4C Lytic transglycosylase catalytic -0.026516
58 ENOG4105W4Y transposase, IS3 IS911 family protein -0.026370
59 ENOG4108X7V cobyrinic Acid a,c-diamide synthase -0.026179
60 ENOG4105CJ9 Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions (By similarity) -0.026161
61 ENOG4105JJH Protein of unknown function (DUF1173) -0.026155
62 ENOG4105CMA conjugation trbi family protein -0.025951
63 ENOG4105EGP transfer protein -0.025705
64 ENOG4107U6T NA -0.025181
65 ENOG4105EPC oxidoreductase -0.025159
66 ENOG4105DIV Catalyzes the conversion of acetaldehyde to acetyl-CoA, using NAD( ) and coenzyme A. Is the final enzyme in the meta- cleavage pathway for the degradation of aromatic compounds (By similarity) -0.024881
67 ENOG41088UI Sodium hydrogen exchanger -0.024830
68 ENOG4105K5Y Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter (By similarity) -0.024701
69 ENOG41061KY NA -0.024611
70 ENOG41060YD NA -0.024581
71 ENOG4105DF3 Catalyzes the retro-aldol cleavage of 4-hydroxy-2- oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds (By similarity) -0.024556
72 ENOG4108XA2 Transposase -0.024469
73 ENOG4105F9F transposase -0.024415
74 ENOG4105XT9 zeta toxin -0.024349
75 ENOG4105KK6 nuclease -0.024300
76 ENOG4105PDG Type IV secretion system protein VirB8 -0.024297
77 ENOG4106N1G Conjugative transfer protein -0.024220
78 ENOG4107T2H Integrase, catalytic region -0.024195
79 ENOG4108EHY type IV secretion system -0.024182
80 ENOG4105TZD TrbL VirB6 plasmid conjugal transfer protein -0.024168
81 ENOG4105MFG Antirestriction protein -0.024164
82 ENOG410738M NA -0.024151
83 ENOG4108M0H Extracellular lipase -0.024151
84 ENOG4107NVD NA -0.024151
85 ENOG4106TPE NA -0.024151
86 ENOG4105QNU bleomycin resistance protein -0.024151
87 ENOG4105GNS type IV secretion system -0.024151
88 ENOG4108G7Y NA -0.024151
89 ENOG4106H70 NA -0.024151
90 ENOG4106HNH Acyl-transferase -0.024075
91 ENOG41068IM transcriptional regulator, copG family -0.024071
92 ENOG41086B1 Bacterial protein of unknown function (DUF896) -0.024035
93 ENOG4107YH7 Beta-lactamase (EC 3.5.2.6) -0.023872
94 ENOG410705U Transglutaminase-like superfamily -0.023309
95 ENOG4105IKQ hydratase -0.023161
96 ENOG4108R0M Aminoglycoside -0.022902
97 ENOG4105F8B mobA MobL family protein -0.021810
98 ENOG4108C33 Resolvase -0.018013
99 ENOG4105DMS mur ligase 0.013601
100 ENOG4107UT5 site-determining protein 0.013418
101 ENOG4105CHR reductase -0.013148
102 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F 0.012788
103 ENOG4105C2X Arabinose 5-phosphate isomerase -0.012758
104 ENOG4105F1K Glutamine amidotransferase 0.012335
105 ENOG4107QN8 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA (By similarity) -0.012090
106 ENOG4105C6I Resolvase 0.012031
107 ENOG4107R21 site-determining protein -0.011612
108 ENOG4106PT6 cdpdiacylglycerol-serine O-phosphatidyltransferase -0.011598
109 ENOG4107FPT Cell surface receptor IPT TIG domain protein 0.011428
110 ENOG4105CET Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria (By similarity) -0.011419
111 ENOG4105K4H Nlp p60 protein 0.011357
112 ENOG410855K transcriptional regulator), MarR family 0.011229
113 ENOG4105D5S Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity) 0.011216
114 ENOG4105C3S Mate efflux family protein -0.011151
115 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) 0.011019
116 ENOG4105DG4 malate L-lactate dehydrogenase -0.010972
117 ENOG4107XX8 ABC transporter substrate-binding protein 0.010909
118 ENOG4105CY3 ABC transporter, permease -0.010795
119 ENOG4105CQ4 Transcriptional regulator -0.010762
120 ENOG4105JZI cytochrome P450 0.010752
121 ENOG4108IIJ DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity) 0.010727
122 ENOG4108Z4R 3-deoxy-d-manno-octulosonate 8-phosphate phosphatase -0.010712
123 ENOG4105C6Y Udp-glucose 6-dehydrogenase -0.010619
124 ENOG4105C53 Part of the ABC transporter complex PotABCD involved in spermidine putrescine import. Responsible for energy coupling to the transport system (By similarity) -0.010558
125 ENOG4105DFF Rod shape-determining protein mreb -0.010539
126 ENOG4105C56 H( )-stimulated, divalent metal cation uptake system (By similarity) 0.010508
127 ENOG4105CX6 glutaminyL-tRNA synthetase -0.010502
128 ENOG4107QIH DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity) -0.010482
129 ENOG4107R0D fad dependent oxidoreductase -0.010430
130 ENOG4105CHD Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1- P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity) -0.010382
131 ENOG4108IUZ ABC transporter -0.010369
132 ENOG4105D6C Part of the ABC transporter complex MacAB involved in macrolide export. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation (By similarity) 0.010335
133 ENOG4107RPP radical SAM domain protein 0.010329
134 ENOG4105CXR Phospho-2-dehydro-3-deoxyoctonate aldolase -0.010310
135 ENOG4108JNY Cbs domain containing membrane protein -0.010115
136 ENOG4106862 septum formation initiator -0.010098
137 ENOG4105K7K Transcriptional regulator 0.010036
138 ENOG4105JKQ Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC (By similarity) -0.010014
139 ENOG4105D6J arsenicaL-resistance protein -0.009987
140 ENOG4108USZ hydrogenase -0.009956
141 ENOG4108WTY tRNA (Guanine-N(1)-)-methyltransferase -0.009872
142 ENOG4105C6P ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner (By similarity) -0.009802
143 ENOG4108I0X binding-protein-dependent transport systems inner membrane Component -0.009771
144 ENOG4107RFQ Polyprenyl synthetase 0.009756
145 ENOG4108VW9 Membrane 0.009708
146 ENOG41061NH Transcriptional regulator 0.009696
147 ENOG4105CKI cobalamin synthesis protein 0.009570
148 ENOG4107R8N Glycosyl transferase, family 2 -0.009489
149 ENOG4105VAT metal-binding protein 0.009310
150 ENOG4107QK4 glycoside hydrolase, family 3 domain protein 0.009245
151 ENOG4108UYF response regulator 0.009206
152 ENOG4105C2J ABC transporter -0.009153
153 ENOG4105FDS Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine (By similarity) -0.009132
154 ENOG4108UT2 hemolysin iii 0.009045
155 ENOG4105E1Z Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.009030
156 ENOG4108ZI0 d,d-heptose 1,7-bisphosphate phosphatase -0.009010
157 ENOG4105C5E polysaccharide biosynthesis protein -0.008983
158 ENOG4105CEV competence damage-inducible protein 0.008981
159 ENOG4105BZS acriflavin resistance protein -0.008979
160 ENOG4105D7M Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (By similarity) -0.008950
161 ENOG4105CE8 Transfers the fatty acyl group on membrane lipoproteins (By similarity) -0.008949
162 ENOG41082SA 50s ribosomal protein l29 0.008938
163 ENOG4108Z02 Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity) -0.008897
164 ENOG4107QID Threonine synthase 0.008884
165 ENOG4105CGH 5'-nucleotidase -0.008881
166 ENOG4105DAF Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (By similarity) -0.008812
167 ENOG4105C4C beta-galactosidase 0.008809
168 ENOG410902V Modulates RecA activity (By similarity) 0.008806
169 ENOG4107RUW arginyl-trna synthetase -0.008802
170 ENOG4107QQ8 peptidase 0.008788
171 ENOG4105C6Z Gluconate 0.008750
172 ENOG4105ETE Transcriptional regulator (LacI family 0.008745
173 ENOG41071I4 Phosphatidylserine decarboxylase proenzyme -0.008741
174 ENOG4105BZE flagellar hook protein, FlgE -0.008739
175 ENOG4105C2F Histidine kinase -0.008705
176 ENOG4105C1H Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34 (By similarity) -0.008702
177 ENOG41061H0 Monooxygenase 0.008669
178 ENOG4105CJZ response regulator 0.008655
179 ENOG4108IV0 ABC, transporter -0.008654
180 ENOG4108JPW Aminotransferase 0.008646
181 ENOG4105D7Q type ii secretion system -0.008623
182 ENOG4105CQ3 Poorly processive error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. Exhibits no 3-5 exonuclease (proofreading) activity. May be involved in translesional synthesis in conjunction with the beta clamp from polIII (By similarity) 0.008623
183 ENOG4105C19 ABC transporter 0.008607
184 ENOG4105CIW Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine (By similarity) -0.008559
185 ENOG410618C (LipO)protein -0.008535
186 ENOG4105CV2 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates (By similarity) -0.008524
187 ENOG4107S10 cell wall hydrolase, SleB 0.008502
188 ENOG4105E3W Two component transcriptional regulator (Winged helix family -0.008502
189 ENOG4105CMS peptidase U62, modulator of DNA gyrase -0.008434
190 ENOG4105CDG Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit (By similarity) -0.008420
191 ENOG4105VJH integral membrane protein CcmA involved in cell shape determination -0.008395
192 ENOG4105D3R alkyl hydroperoxide reductase -0.008389
193 ENOG4107XTC May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins -0.008383
194 ENOG4107SS7 Glycogen operon protein GlgX -0.008355
195 ENOG4107QZI cell division protein FtsK 0.008328
196 ENOG4107QW9 peptidase, M24 0.008323
197 ENOG4105PWN phosphate abc transporter -0.008302
198 ENOG4105CJ1 ABC, transporter 0.008294
199 ENOG4105C9A Phoh family 0.008269
200 ENOG4105ERH Fumarylacetoacetate hydrolase -0.008259
201 ENOG4106ARX NA 0.008257
202 ENOG4108Z0R Transferase -0.008252
203 ENOG4107SP8 Filamentation induced by cAMP protein fic -0.008212
204 ENOG4105BZG amino acid carrier protein 0.008196
205 ENOG4107RFG polymerase involved in DNA repair 0.008186
206 ENOG4108UTT Catalyzes the formation of 6,7-dimethyl-8- ribityllumazine by condensation of 5-amino-6-(D- ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin (By similarity) -0.008174
207 ENOG4105HQ9 methyltransferase -0.008144
208 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) -0.008137
209 ENOG4108MUX N-hydroxyarylamine O-acetyltransferase 0.008134
210 ENOG4105DXK abc transporter permease protein 0.008132
211 ENOG41061KA protein serine threonine phosphatase 0.008060
212 ENOG4105MD7 metal-dependent hydrolase 0.008056
213 ENOG4107FKK extracellular solute-binding protein family 1 -0.008049
214 ENOG4105DWK Membrane 0.008047
215 ENOG4108UMN azlc family -0.008038
216 ENOG4105CTJ Metal Dependent Phosphohydrolase -0.008033
217 ENOG4105CJR Integral membrane protein (MviN -0.008015
218 ENOG4105CCX Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) -0.008005
219 ENOG4105C66 Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate (By similarity) -0.007996
220 ENOG4105D8A 3-Deoxy-D-manno-octulosonic-acid transferase -0.007980
221 ENOG4105NHU Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group (By similarity) -0.007950
222 ENOG410620C Protein of unknown function (DUF1694) -0.007944
223 ENOG4105H3Q Primosomal protein, DnaI 0.007941
224 ENOG4105C7C involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (By similarity) -0.007939
225 ENOG41062BK proline dehydrogenase 0.007936
226 ENOG4107RE5 NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34 (By similarity) -0.007899
227 ENOG4105D0V Condensation of UDP-2,3-diacylglucosamine and 2,3- diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (By similarity) -0.007897
228 ENOG4107EEK Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide (By similarity) -0.007889
229 ENOG4108SAX Membrane 0.007867
230 ENOG4105WDI Membrane 0.007867
231 ENOG4105DZC cytosine deaminase 0.007853
232 ENOG4105D8X mechanosensitive ion channel 0.007839
233 ENOG4105C25 Primosomal protein n' -0.007814
234 ENOG4105CT1 (ABC) transporter 0.007798
235 ENOG4108SNF NA 0.007775
236 ENOG4107QWG 2-Nitropropane dioxygenase -0.007772
237 ENOG4105DG1 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) -0.007771
238 ENOG4105WDJ 50S ribosomal protein L33 0.007738
239 ENOG4108NEF RNA binding s1 domain protein -0.007728
240 ENOG4105CS9 pantothenic acid kinase 0.007727
241 ENOG4105UX5 NA 0.007726
242 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) -0.007721
243 ENOG4105DPX Hydrogenase, large subunit -0.007718
244 ENOG4108I6I Transcriptional regulator, TetR family -0.007711
245 ENOG4107RUP AcrB AcrD AcrF family protein -0.007701
246 ENOG4107QND Nitrite extrusion protein 0.007687
247 ENOG4105D78 K07001 NTE family protein -0.007658
248 ENOG4108DT4 serine threonine protein kinase 0.007654
249 ENOG4105C1W two component, sigma54 specific, transcriptional regulator, Fis family -0.007645
250 ENOG4108Q4G Pfam:TraG -0.007640