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 ENOG4105VF7 tolerance protein 0.011632
2 ENOG4108EKG Sodium hydrogen exchanger 0.010713
3 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.010654
4 ENOG4105C1A potassium transporter peripheral membrane 0.010626
5 ENOG4105VDU S-adenosyl-l-methionine hydroxide adenosyltransferase 0.010250
6 ENOG4105CG6 trap dicarboxylate transporter dctm subunit 0.010074
7 ENOG4108IJ0 Aspartate ammonia-lyase -0.009889
8 ENOG4105Q8M Hnh endonuclease 0.009797
9 ENOG4108UTW Plays a role in the regulation of phosphate uptake 0.009683
10 ENOG4105KTH gatB Yqey 0.009439
11 ENOG4108UT2 hemolysin iii 0.009302
12 ENOG4105Y7X Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair (By similarity) 0.009028
13 ENOG4108KND Two-component system sensor kinase 0.009017
14 ENOG4105GR3 Histidine kinase 0.008940
15 ENOG4105C4B ABC transporter, permease 0.008864
16 ENOG4105H1G trap transporter solute receptor taxi family 0.008784
17 ENOG4105D6M Phosphoglucomutase Phosphomannomutase 0.008735
18 ENOG4108PAA Membrane 0.008493
19 ENOG4105CUX Signal transduction histidine kinase 0.008469
20 ENOG410683I Vanz family 0.008452
21 ENOG4108I0Q anthranilate phosphoribosyltransferase 0.008450
22 ENOG4108HRN Catalyzes the phosphorylation of pyruvate to phosphoenolpyruvate (By similarity) 0.008408
23 ENOG4105FEU K -dependent Na -Ca exchanger 0.008400
24 ENOG4105C94 Transporter 0.008379
25 ENOG41090A4 Pterin carbinolamine dehydratase 0.008352
26 ENOG4105DGU Histone deacetylase 0.008295
27 ENOG4107RGW The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.008266
28 ENOG4105D8X mechanosensitive ion channel 0.008241
29 ENOG4105D37 Low-affinity potassium transport system. Interacts with Trk system potassium uptake protein TrkA (By similarity) 0.008130
30 ENOG4105DE7 Sulfate ABC transporter periplasmic sulfate-binding protein -0.008013
31 ENOG4107RMT Osmosensitive K channel His kinase sensor -0.007920
32 ENOG4107XTC May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins -0.007843
33 ENOG4108YYA Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity) 0.007786
34 ENOG4107QN5 Band 7 protein 0.007747
35 ENOG4105D68 Ion transport protein 0.007738
36 ENOG4105CY0 Metallo-Beta-Lactamase 0.007672
37 ENOG4105EQ0 Major Facilitator superfamily -0.007578
38 ENOG4105CMQ Chloride channel 0.007547
39 ENOG4105D7A ATP-binding protein -0.007543
40 ENOG4105D48 metallophosphoesterase 0.007503
41 ENOG4105DR1 Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration (By similarity) 0.007456
42 ENOG4105ECW sulfate abc transporter -0.007442
43 ENOG4105D9K One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions (By similarity) -0.007373
44 ENOG4108ZFX Mannosyl-3-phosphoglycerate phosphatase 0.007365
45 ENOG4108YZA Nitrogen regulatory protein pii 0.007350
46 ENOG410902V Modulates RecA activity (By similarity) 0.007331
47 ENOG4105DC4 trap transporter, 4tm 12tm fusion protein 0.007330
48 ENOG4108R80 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. The C subunit may be involved in assembly of the KDP complex (By similarity) -0.007302
49 ENOG4108UZV Pfam:DUF833 0.007269
50 ENOG4107QJT sodium dicarboxylate symporter -0.007268
51 ENOG4108C33 Resolvase 0.007235
52 ENOG4105NW6 solute symporter protein 0.003613
52 ENOG4107QS2 Symporter 0.003613
53 ENOG4105EK0 Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (By similarity) 0.007225
54 ENOG4105EWK phytoene 0.007221
55 ENOG4105CBX hi0933 family 0.007205
56 ENOG4105E3W Two component transcriptional regulator (Winged helix family 0.007191
57 ENOG4105FNP Molybdopterin-guanine dinucleotide biosynthesis protein b -0.007188
58 ENOG4105F7J membrane-bound serine protease 0.007177
59 ENOG4107QZT geranylgeranyl reductase 0.007173
60 ENOG4108IAJ Nad-dependent epimerase dehydratase -0.007154
61 ENOG4105D3Z quinone oxidoreductase, yhdh yhfp family 0.007108
62 ENOG4105D5Q Arginine ornithine antiporter -0.007093
63 ENOG4106BRA Membrane -0.007082
64 ENOG4108I5D sulfate abc transporter -0.007080
65 ENOG4108376 Membrane 0.007032
66 ENOG4105K8I Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves (By similarity) 0.007029
67 ENOG4107R0V Pyruvate dehydrogenase -0.007020
68 ENOG4105E0A ABC, transporter 0.006980
69 ENOG4106KZE Peptidase M50 0.006977
70 ENOG4105DB7 PHP domain protein 0.006938
71 ENOG4108KVX Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves (By similarity) 0.006900
72 ENOG4105BZ8 glutamate synthase 0.006879
73 ENOG4105C8X One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions (By similarity) -0.006847
74 ENOG4105CTB Polyprenyl synthetase -0.006841
75 ENOG4105CPN adenine deaminase 0.006834
76 ENOG4105FE1 phytoene synthase 0.006808
77 ENOG410878N Protein of unknown function (DUF1499) 0.006806
78 ENOG4105D8V Glucose sorbosone dehydrogenase 0.006790
79 ENOG4108UR1 Protein of unknown function (DUF938) 0.006759
80 ENOG4107S6X Glycosyl transferase, family 2 -0.006750
81 ENOG4107R37 Glutamate dehydrogenase -0.006749
82 ENOG4105CEY Amp-dependent synthetase and ligase 0.006744
83 ENOG4105XRQ Xanthine dehydrogenase accessory factor -0.006732
84 ENOG4105C8J )-transporter 0.006726
85 ENOG4105DTD Dehydrogenase 0.006710
86 ENOG4108ZMD Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) 0.006649
87 ENOG4105EXU Membrane 0.006647
88 ENOG4107S6Z Na H antiporter 0.006645
89 ENOG4108IJ7 Glycine betaine 0.006637
90 ENOG4105EBP faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.006623
91 ENOG4105CBC glutamate synthase 0.006617
92 ENOG4108Z5Y thioesterase Superfamily protein 0.006604
93 ENOG4105EXZ Involved in the regulation of ptsG expression by binding and inactivating Mlc (By similarity) 0.006589
94 ENOG41080QG Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo- MPT) cofactor (Moco or molybdenum cofactor) to form Mo- molybdopterin guanine dinucleotide (Mo-MGD) cofactor (By similarity) 0.006573
95 ENOG4107RR9 sulfate transporter 0.006572
96 ENOG4107QUS 2-isopropylmalate synthase homocitrate synthase family protein 0.006561
97 ENOG4105VZ8 Transcriptional regulator 0.006559
98 ENOG4105DRD mechanosensitive ion channel 0.006558
99 ENOG4105VGV redox-active disulfide protein 2 0.006537
100 ENOG4105DR5 peptidase 0.006531
101 ENOG4105QDX NA 0.006529
102 ENOG4105KAV tspo and mbr like protein 0.006511
103 ENOG4106KBT YibE F family protein 0.006505
104 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.006448
105 ENOG4105CTX dehydratase -0.006433
106 ENOG4105CBH Hydroxymethylglutaryl-CoA lyase 0.006420
107 ENOG4107QNW Aldolase 0.006368
108 ENOG4105M6F mutator MutT protein 0.006352
109 ENOG4107QNT pyruvate dehydrogenase e1 component suBunit beta -0.006320
110 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) 0.006319
111 ENOG4108JIU phosphoribosylformylglycinamidine synthase ii 0.006305
112 ENOG4107QX3 carboxylase 0.006304
113 ENOG4105F03 Provides the (R)-glutamate required for cell wall biosynthesis (By similarity) -0.006301
114 ENOG4105QF0 Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit (By similarity) 0.006288
115 ENOG4105JEU Glycosyl transferase, family 2 0.006273
116 ENOG4105MN5 HAD-superfamily hydrolase subfamily IA variant 3 0.006249
117 ENOG4108UHN Glutamine amidotransferase 0.006218
118 ENOG4107QM6 fructose-bisphosphate aldolase 0.006209
119 ENOG4105EPR degv family 0.006195
120 ENOG4107AFY proteinase inhibitor I4 serpin 0.006184
121 ENOG4105DXN mazG family 0.006168
122 ENOG4108K0A Anthranilate phosphoribosyltransferase (EC 2.4.2.18) 0.006164
123 ENOG4108YYD acetyltransferase 0.006160
124 ENOG4105D0U Arsenite-activated ATPase (ArsA) 0.006158
125 ENOG4105CQ0 ABC transporter -0.006154
126 ENOG4105NDA Rhomboid family 0.006135
127 ENOG41090BB DNA mismatch endonuclease (vsr) 0.006129
128 ENOG4107T2Q AcrB AcrD AcrF family protein 0.006124
129 ENOG4105EIS 1,4-dihydroxy-2-naphthoate octaprenyltransferase 0.006096
130 ENOG41068AQ Anti-Sigma-28 factor, FlgM -0.006083
131 ENOG4105E2Z phosphate ABC transporter (Permease 0.006082
132 ENOG4105DE4 1-phosphofructokinase -0.006057
133 ENOG4105E6K 4-Hydroxyphenylpyruvate dioxygenase 0.006051
134 ENOG4105EM6 transcriptional Regulator LysR family 0.006039
135 ENOG4105VFB Binds the 23S rRNA (By similarity) 0.006027
136 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase 0.006000
137 ENOG4108UK0 indolepyruvate ferredoxin oxidoreductase 0.005957
138 ENOG4105CK2 sodium dicarboxylate symporter 0.005953
139 ENOG4105CZX twitching motility protein 0.005945
140 ENOG4105W2A integral membrane protein -0.005943
141 ENOG4107QPI nitrilase cyanide hydratase and apolipoprotein n-acyltransferase 0.005923
142 ENOG4105CNE Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane (By similarity) 0.005916
143 ENOG4105W5Q DNA repair protein (RadC 0.005913
144 ENOG4105MQ4 Nitrogen regulatory protein pii 0.002956
144 ENOG4105N1R Nitrogen regulatory protein P-II 0.002956
145 ENOG41060A6 UspA domain-containing protein 0.005900
146 ENOG4108Z4U Ferredoxin 0.005892
147 ENOG41063CS Replication Protein 0.005882
148 ENOG4105M3E Glyoxalase Bleomycin resistance protein (Dioxygenase 0.005861
149 ENOG4105DNF glutamate--cysteine ligase 0.005856
150 ENOG4105MBR gumn family 0.005856
151 ENOG4105DFD Na H antiporter 0.005831
152 ENOG4105CFP Peptidase U32 -0.005815
153 ENOG4105BZG amino acid carrier protein 0.005795
154 ENOG4105VAS Could be involved in insertion of integral membrane proteins into the membrane (By similarity) 0.005793
155 ENOG4105EHG Permease protein 0.005791
156 ENOG4108RMU ferritin dps family protein 0.005784
157 ENOG4105CHF Glutathione S-transferase 0.005771
158 ENOG4107N3Y integral membrane protein 0.005769
159 ENOG4105CM2 brancheD-chain amino acid aminotransferase 0.005752
160 ENOG4105KNI merR family transcriptional Regulator 0.005750
161 ENOG4105CUP Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6- dimethylbenzimidazole (DMB) (By similarity) 0.005729
162 ENOG4107EES Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide the precursor of murein (By similarity) -0.005721
163 ENOG4107QVX glycosyl transferase group 1 0.005714
164 ENOG4107RVX amidohydrolase 0.005713
165 ENOG4105D3R alkyl hydroperoxide reductase -0.005712
166 ENOG4105KEM Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation (By similarity) 0.005708
167 ENOG4105VRR gCN5-related N-acetyltransferase 0.005704
168 ENOG4107R69 radical SAM domain protein 0.005671
169 ENOG4107RKQ Methyl-accepting chemotaxis sensory transducer 0.005660
170 ENOG4106YN8 Prenyltransferase -0.005657
171 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) 0.005654
172 ENOG4105DHU Bile acid -0.005653
173 ENOG4105EK9 Dehydrogenase 0.005644
174 ENOG4108IV0 ABC, transporter 0.005639
175 ENOG4108XF7 MotA TolQ exbB proton channel 0.005629
176 ENOG4108H18 Polysaccharide biosynthesis protein 0.005613
177 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F 0.005608
178 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) -0.005607
179 ENOG4105RD8 TRAP dicarboxylate transporter 0.005601
180 ENOG4105EHH Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue (By similarity) 0.005598
181 ENOG4108S0G Protein of unknown function (DUF2959) 0.005596
182 ENOG4107ZI0 Inherit from NOG: 4fe-4S ferredoxin iroN-sulfur binding 0.005595
183 ENOG4107RZK Glycine betaine 0.005585
184 ENOG4105D21 Phosphoribosylformylglycinamidine synthase I 0.005585
185 ENOG4108JPX Catalyzes the transfer of the alpha-amino group from S- adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor (By similarity) -0.005575
186 ENOG4108YZN class I peptide chain release factor 0.005575
187 ENOG4105DM4 PTS System -0.005573
188 ENOG4108HKC peptidase 0.005571
189 ENOG41067V3 Antibiotic biosynthesis monooxygenase -0.005568
190 ENOG4105C8P )-transporter 0.005549
191 ENOG4105DP4 dak2 domain fusion protein ylov 0.005549
192 ENOG4108S6J ABC transporter, periplasmic molybdate-binding protein -0.005549
193 ENOG41081MC TRANSCRIPTIONAl REGULATOR GntR family -0.005540
194 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.005533
195 ENOG4105C88 aminopeptidase 0.005528
196 ENOG4107QSU Phosphoglucomutase phosphomannomutase alpha beta alpha domain -0.005526
197 ENOG4108YXI Secondary thiamine-phosphate synthase enzyme 0.005524
198 ENOG4105EHM Aminoglycoside phosphotransferase 0.005514
199 ENOG4105C5B carbamate kinase -0.005513
200 ENOG4108V4Y Phosphoribosyltransferase 0.005512
201 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.005511
202 ENOG4105KZE Death-On-Curing Family 0.005488
203 ENOG4105BZ3 General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) (By similarity) -0.005486
204 ENOG41067WU Molybdopterin converting factor (Subunit 1) -0.005485
205 ENOG4108KAC Two component transcriptional regulator, luxr family 0.005482
206 ENOG4107ZWR Sulfite exporter TauE/SafE 0.005481
207 ENOG41090IJ ACT domain protein 0.005480
208 ENOG4105FW7 aig2 family 0.005477
209 ENOG4105WDA Protein of unknown function (DUF1653) 0.005472
210 ENOG4107WEC Periplasmic Protein 0.005471
211 ENOG4107QTD permease 0.005470
212 ENOG4107QXT efflux transporter, rnd family, mfp subunit 0.005459
213 ENOG4105CH5 extracellular solute-binding protein, family 7 0.002729
213 ENOG4107SA5 Trap dicarboxylate transporter, dctm subunit 0.002729
214 ENOG4105DJ2 Major Facilitator Superfamily 0.005457
215 ENOG4105CI8 Negative regulator of class I heat shock genes (grpE- dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons (By similarity) 0.005452
216 ENOG4105KD5 RNA polymerase sigma-24 subunit, ECF subfamily 0.002721
216 ENOG4108WKU Beta-lactamase domain protein 0.002721
217 ENOG4108K1J Transporter DctQ 0.002719
217 ENOG4108KJ1 Trap dicarboxylate transporter, dctp subunit 0.002719
218 ENOG4107XSB type i phosphodiesterase nucleotide pyrophosphatase -0.005437
219 ENOG4105CG2 Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1 (By similarity) 0.005420
220 ENOG4108R8F zinc metallopeptidase 0.005418
221 ENOG4108J2C peptidase, M48 0.005416
222 ENOG4105DP0 ferredoxin-NADP reductase 0.005416
223 ENOG4108MHN TonB system biopolymer transport component 0.005403
224 ENOG4105C85 amino acid -0.005401
225 ENOG4105EI2 Pseudouridine synthase -0.005397
226 ENOG4107QM5 aconitate hydratase 0.005396
227 ENOG4107TXC Transcriptional regulator 0.005381
228 ENOG4105Y5F NA 0.005378
229 ENOG4105C0P Mg chelatase subunit ChlI 0.005377
230 ENOG4107XZC Restriction modification system DNA (Specificity 0.005374
231 ENOG410667J hydrolase 0.005367
232 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) -0.005367
233 ENOG4107RCI amp-dependent synthetase and ligase -0.005359
234 ENOG4108KMK Diguanylate cyclase 0.005347
235 ENOG4105WMR Protein CrcB homolog 0.005343
236 ENOG4105NNN FxsA cytoplasmic membrane protein 0.005340
237 ENOG4108JPW Aminotransferase -0.005336
238 ENOG4105Z93 Transcriptional regulator 0.005336
239 ENOG4105D4H Membrane 0.005334
240 ENOG4105MKJ Smr protein MutS2 0.005333
241 ENOG4105ZWU Transcriptional regulator 0.005327
242 ENOG4105CV8 reductase -0.005314
243 ENOG4105CJH Alcohol dehydrogenase zinc-binding domain protein 0.005309
244 ENOG4107S3D nitrogenase 0.005306
245 ENOG4107XD4 Reductive dehalogenase 0.005306