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 ENOG4105CJG carbon-monoxide dehydrogenase catalytic subunit 0.056236
2 ENOG41080XS Cobyrinic acid ac-diamide synthase 0.038421
3 ENOG4105E8X CO dehydrogenase acetyl-CoA synthase complex beta subunit 0.018436
4 ENOG41081SR 4fe-4s ferredoxin, iron-sulfur binding 0.017412
5 ENOG4105EYX Acetyl-CoA decarbonylase synthase complex subunit gamma 0.016563
6 ENOG4107FEI Cobyrinic acid ac-diamide synthase 0.016352
7 ENOG4106HYN CO dehydrogenase acetyl-CoA synthase delta subunit 0.016273
8 ENOG4108TK9 formylmethanofuran dehydrogenase, subunit E 0.015041
9 ENOG4105DSM The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components the iron protein and the molybdenum-iron protein (By similarity) 0.014692
10 ENOG4107QJZ Glycosyl transferase, family 2 -0.014496
11 ENOG4107ZBE zinc-finger protein 0.014254
12 ENOG4108RCY Nadph-dependent fmn reductase 0.014019
13 ENOG4108Z7N NA 0.013718
14 ENOG4105IP5 transcriptional regulator, crp fnr family 0.013286
15 ENOG4105C8J )-transporter -0.012921
16 ENOG4105D5U fad dependent oxidoreductase -0.012869
17 ENOG4105CCT upf0313 protein 0.012728
18 ENOG4105KVH Transcriptional regulator 0.012336
19 ENOG4105D0B Nitrogenase protein alpha chain 0.012255
20 ENOG4108NHZ Transposase 0.012164
21 ENOG4105MXR 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.011938
22 ENOG4105DXZ ribonuclease BN 0.011748
23 ENOG41080T5 domain protein 0.011706
24 ENOG4108UK0 indolepyruvate ferredoxin oxidoreductase 0.011648
25 ENOG4105DUM transcriptional regulator, lysR family 0.011612
26 ENOG4108JQ6 ABC transporter 0.011585
27 ENOG41073UA Dihydropteroate synthase, DHPS 0.011400
28 ENOG4105EAY pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.011352
29 ENOG4105KGY integral membrane protein -0.011315
30 ENOG4108UZW Haloacid dehalogenase domain protein hydrolase -0.011243
31 ENOG4105HQ9 methyltransferase 0.011011
32 ENOG4105CQZ Histidine kinase 0.010817
33 ENOG4105CY9 nitrogenase molybdenum-iron protein beta chain 0.010711
34 ENOG4105VMP Transcriptional regulator 0.010672
35 ENOG4105MQ4 Nitrogen regulatory protein pii 0.010671
36 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.010652
37 ENOG4108ITB Binding-protein-dependent transport systems, inner membrane component 0.010649
38 ENOG4108SD8 NA 0.010614
39 ENOG410855K transcriptional regulator), MarR family -0.010585
40 ENOG4105CFK Adenylylsulfate reductase subunit alpha 0.010583
41 ENOG4105CKK Glycosyl transferase, family 2 0.010565
42 ENOG4105CK0 Membrane bOund o-acyl transferase mboat family protein -0.010546
43 ENOG4105E9I Appr-1-p processing domain protein -0.010488
44 ENOG41060G5 NA 0.010455
45 ENOG4108RC0 Electron transport protein 0.010433
46 ENOG4107UPV Methylenetetrahydrofolate reductase 0.010391
47 ENOG4105M2E Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell (By similarity) -0.010387
48 ENOG4105XSR Transcriptional regulator, MarR family 0.010342
49 ENOG4105EEI dihydropteroate synthase 0.010221
50 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase -0.010173
51 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.010132
52 ENOG4108AW4 Transposase domain (DUF772) -0.010075
53 ENOG4105E5H Transposase 0.009984
54 ENOG4105CPC Aldo Keto reductase -0.009983
55 ENOG4105CN9 Peptidase m42 family protein 0.009981
56 ENOG4106MP8 UPF0754 membrane protein 0.009973
57 ENOG4108NJZ Sensory box GGDEF EAL domain protein -0.009915
58 ENOG4108UDG ABC transporter 0.009910
59 ENOG4105TFI NA -0.009868
60 ENOG4106C82 Dinitrogenase iron-molybdenum cofactor biosynthesis protein 0.009845
61 ENOG4107TVU Fumarate reductase succinate dehydrogenase flavoprotein domain-containing protein -0.009815
62 ENOG4105N56 NA 0.009801
63 ENOG4107ZGJ periplasmic 0.009719
64 ENOG4108IJ0 Aspartate ammonia-lyase 0.009709
65 ENOG41068YK Transposase, IS605 OrfB family 0.009674
66 ENOG4107XD6 NA 0.009663
67 ENOG4105E78 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity) 0.009621
68 ENOG4108FU3 Toxin-antitoxin system, toxin component 0.009614
69 ENOG4105KPB redox protein, regulator of disulfide bond 0.009610
70 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase -0.009575
71 ENOG4105MAX Superoxide reductase -0.009570
72 ENOG4105EY8 ABC transporter -0.009548
73 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) -0.009547
74 ENOG4105CGC Nitrogenase cofactor biosynthesis protein NifB 0.009533
75 ENOG4107SV4 abc transporter atp-binding protein 0.009499
76 ENOG4107RW8 Mate efflux family protein 0.009485
77 ENOG4105CRQ synthase (Component I) 0.009465
78 ENOG4107S7J Transporter, auxin efflux carrier (AEC) family protein -0.009458
79 ENOG4105FC6 Extracellular solute-binding protein, family 5 0.009423
80 ENOG4105GZ5 Transcriptional regulator, BadM Rrf2 family 0.009416
81 ENOG410619W NA 0.009386
82 ENOG4105GZW 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.009386
83 ENOG4108JHG HDOD domain 0.009379
84 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase 0.009368
85 ENOG4105EP0 Glycosyl transferase (Group 1 0.009365
86 ENOG4108KI7 Diguanylate cyclase 0.009354
87 ENOG4105F72 Domain of unknown function (DUF362) 0.009326
88 ENOG4108HNW Pyridine nucleotide-disulphide oxidoreductase 0.009306
89 ENOG4107RBB ABC transporter, permease -0.009299
90 ENOG4105DKK Benzoate 0.009292
91 ENOG4107XIH methyltransferase, type 11 0.009285
92 ENOG4108V1Y VTC domain protein 0.009280
93 ENOG4107XNR SufB sufD domain protein -0.009264
94 ENOG4107QWA transporter 0.009204
95 ENOG4105WPP transcriptional regulator, MarR family -0.009185
96 ENOG4105C5B carbamate kinase -0.009181
97 ENOG4105DVM PP-loop domain protein 0.009137
98 ENOG4108168 Methyltransferase 0.009125
99 ENOG4105CV9 cyclopropane-fatty-acyl-phospholipid synthase 0.009078
100 ENOG4107T22 epimerase 0.009070
101 ENOG4106AIG Preprotein translocase subunit SecB 0.008993
102 ENOG4105CFI type iii restriction protein res subunit 0.008957
103 ENOG4105C0D helicase -0.008924
104 ENOG4108IQE Amp-dependent synthetase and ligase 0.008921
105 ENOG4107GFK fumarate 0.008916
106 ENOG4108YZT Adenosylcobinamide kinase 0.008913
107 ENOG4108WD6 response regulator 0.008911
108 ENOG4105TNP oxidoreductase Domain protein -0.008906
109 ENOG41063MX thiamine biosynthesis protein ThiS 0.008897
110 ENOG41080JG Inherit from COG: 4Fe-4S Ferredoxin iron-sulfur binding domain protein 0.008890
111 ENOG4108VMK NA 0.008877
112 ENOG4108S4N thiJ PfpI domain-containing protein 0.008874
113 ENOG4105FDF Could be involved in DNA repair (By similarity) -0.008865
114 ENOG4107U32 Beta-lactamase domain protein 0.008857
115 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase 0.008828
116 ENOG41069TZ NA 0.008741
117 ENOG4107QN2 dihydrolipoyl dehydrogenase -0.008731
118 ENOG4105DGU Histone deacetylase 0.008714
119 ENOG4107TY6 Acylneuraminate cytidylyltransferase 0.008710
120 ENOG4108RE9 Phosphodiesterase 0.008708
121 ENOG4108SMP Nad-dependent epimerase dehydratase 0.008707
122 ENOG410901E Membrane -0.008705
123 ENOG4105D6W Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps (By similarity) 0.008670
124 ENOG4107RWR Sodium hydrogen exchanger -0.008667
125 ENOG4105N1R Nitrogen regulatory protein P-II 0.008660
126 ENOG4105EUJ GTP cyclohydrolase i 0.008617
127 ENOG4107S0C lytic transglycosylase -0.008602
128 ENOG4105BZN citrate synthase 0.008592
129 ENOG4105CQV NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient (By similarity) 0.008590
130 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase -0.008579
131 ENOG4105C9B Cysteine desulfurase -0.008577
132 ENOG4105CZR Oxidoreductase domain protein -0.008562
133 ENOG4107RX7 Glycogen debranching enzyme -0.008484
134 ENOG4105E0C molybdate abc transporter 0.008481
135 ENOG4105KAB Transcriptional regulator CarD family -0.008446
136 ENOG4107VJZ DNA modification (methyltransferase 0.008429
137 ENOG4105CCN Peptidase M56 0.008428
138 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) 0.008424
139 ENOG41061F3 Diguanylate cyclase 0.008412
140 ENOG4105F3H Histidine kinase 0.008412
141 ENOG4107QY8 reductase 0.008397
142 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) 0.008385
143 ENOG4105C7E Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA) (By similarity) 0.008371
144 ENOG4105RR1 C_GCAxxG_C_C family -0.008367
145 ENOG4105C93 Xylose Isomerase -0.008367
146 ENOG4105EGI Transcriptional regulator 0.008332
147 ENOG4105K8U 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.008331
148 ENOG4108DT4 serine threonine protein kinase -0.008319
149 ENOG4105DWF phosphomethylpyrimidine kinase -0.008316
150 ENOG4107RNY amino acid 0.008311
151 ENOG4107QW6 Glycoside hydrolase family 2 TIM barrel -0.008305
152 ENOG4105DRP amino acid AbC transporter 0.008297
153 ENOG4105EM8 binding-protein-dependent transport systems inner membrane Component 0.008296
154 ENOG4105BZS acriflavin resistance protein 0.008263
155 ENOG4105MME Sugar o-acyltransferase, sialic acid o-acetyltransferase neud family 0.008255
156 ENOG4108I51 response regulator receiver protein 0.008249
157 ENOG4105DDQ anthranilate synthase 0.008243
158 ENOG4105NA0 Transcriptional regulator 0.008223
159 ENOG4108KU3 Integrase -0.008211
160 ENOG4108099 Thioesterase -0.008209
161 ENOG4105IY4 methyltransferase 0.008206
162 ENOG4108EFR Formate dehydrogenase Alpha subunit 0.008201
163 ENOG4105J4Q Transcriptional regulator 0.008200
164 ENOG4105UIY Plasmid maintenance system antidote protein 0.008182
165 ENOG4105C1G acyl-Coa dehydrogenase -0.008177
166 ENOG4105QGR Transcriptional regulator 0.008155
167 ENOG410624A NA 0.008125
168 ENOG4105EEM helicase 0.008124
169 ENOG4105DTT CRISPR-associated helicase, cas3 0.008113
170 ENOG410782P NA 0.008088
171 ENOG41090K1 Metal dependent hydrolase -0.008078
172 ENOG4108UT2 hemolysin iii 0.008076
173 ENOG4105CDJ oxidoreductase FAD NAD(P)-binding domain protein -0.008072
174 ENOG4105Z8T Protein of unknown function DUF86 -0.008055
175 ENOG4105P4J Allophanate hydrolase, subunit 1 0.008039
176 ENOG4107BJW polysaccharide deacetylase -0.008031
177 ENOG4105D7V transposase 0.008027
178 ENOG4105K4S protein with conserved CXXC pairs -0.008020
179 ENOG4105D9V Binding-protein-dependent transport systems, inner membrane component -0.008020
180 ENOG4108WGH Protein of unknown function (DUF401) 0.008015
181 ENOG4107TE8 peptidase m48, ste24p 0.008003
182 ENOG4105N5D Protein of unknown function (DUF2089) -0.007996
183 ENOG4105F7J membrane-bound serine protease 0.007993
184 ENOG4107QK1 ImpB MucB SamB family protein -0.007989
185 ENOG4108WBJ Methyl-accepting chemotaxis 0.007986
186 ENOG41081HJ Transcriptional regulator, MarR family -0.007981
187 ENOG4105CEM UPF0597 protein 0.007979
188 ENOG410830X 'Cold-shock' DNA-binding domain protein 0.007970
189 ENOG410901W DNA repair protein (RadC -0.007969
190 ENOG4108HR6 Dehydrogenase -0.007963
191 ENOG4105D9Q decarboxylase (Beta subunit) 0.007951
192 ENOG4107QTY polymerase 0.007930
193 ENOG4107SYI Dehydrogenase -0.007926
194 ENOG410907F phage protein -0.007913
195 ENOG4108RG7 formate hydrogenlyase complex iron-sulfur subunit 0.007894
196 ENOG4108UMB Flavodoxin -0.007893
197 ENOG4105CG6 trap dicarboxylate transporter dctm subunit 0.007857
198 ENOG4105KCF 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). Functions as a ssRNA-specific endoribonuclease (By similarity) -0.007846
199 ENOG4105FSS solute-binding protein 0.007833
200 ENOG4105DH3 ABC transporter 0.007807
201 ENOG4108VSY crispr-associated protein Cas4 -0.007803
202 ENOG4105DF6 Fe-S oxidoreductase -0.007794
203 ENOG4108RHT Hydrolase 0.007794
204 ENOG4105N6W Protein of unknown function (DUF1113) 0.007793
205 ENOG4105HTX biosynthesis protein 0.007758
206 ENOG4105DJZ UPF0182 protein -0.007748
207 ENOG4108ZI0 d,d-heptose 1,7-bisphosphate phosphatase 0.007738
208 ENOG4108KMK Diguanylate cyclase 0.007729
209 ENOG4105E5D amino acid 0.007727
210 ENOG4107WB6 AhpC Tsa family -0.007724
211 ENOG4105CWC Acetylornithine deacetylase 0.007708
212 ENOG4108ZPR (CBS) domain 0.007707
213 ENOG4107RKQ Methyl-accepting chemotaxis sensory transducer -0.007699
214 ENOG41073UY NA 0.007695
215 ENOG4107QT9 Ferredoxin 0.007695
216 ENOG4105XRQ Xanthine dehydrogenase accessory factor -0.007690
217 ENOG4108409 von Willebrand factor, type A 0.007670
218 ENOG4105EAD ABC transporter 0.007660
219 ENOG4107SPF Quinolinate phosphoribosyl transferase 0.007649
220 ENOG4105WEF catalase 0.007638
221 ENOG4105CYX Short-chain dehydrogenase reductase Sdr -0.007615
222 ENOG4107VT3 K03386 peroxiredoxin (alkyl hydroperoxide reductase subunit C) EC 1.11.1.15 -0.007607
223 ENOG4105RFX Plasmid stabilization system 0.007595
224 ENOG4105DPX Hydrogenase, large subunit 0.007595
225 ENOG4107QW4 alcohol dehydrogenase -0.007566
226 ENOG4105CMU LysR family (Transcriptional regulator 0.007564
227 ENOG4108Z73 Siroheme synthase 0.007548
228 ENOG4105D7T ABC transporter 0.007545
229 ENOG4107QT3 pfkb domain protein 0.007537
230 ENOG4105D52 delta-aminolevulinic acid dehydratase 0.007532
231 ENOG4107QNT pyruvate dehydrogenase e1 component suBunit beta 0.007530
232 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase 0.007529
233 ENOG4105EJQ L-serine dehydratase 0.007528
234 ENOG4108J7D Nitroreductase 0.007522
235 ENOG41086WW Heavy-metal-associated domain 0.007501
236 ENOG4107XR9 resolvase -0.007494
237 ENOG4105EEA Binding-protein-dependent transport systems, inner membrane component -0.007483
238 ENOG4105C11 sulfate adenylyltransferase), subunit 2 0.007467
239 ENOG41060R1 head morphogenesis protein, SPP1 gp7 0.007462
240 ENOG4105E0S extracellular solute-binding protein family 1 -0.007454
241 ENOG4108V6E Cell division protein mraZ -0.007448
242 ENOG4105RW2 NA 0.007444
243 ENOG4105CFT Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import (By similarity) 0.007440
244 ENOG4106089 NA 0.007434
245 ENOG4108V1D Histidine kinase 0.007422
246 ENOG4105C45 hydrogenase expression formation protein (HypE) 0.007399
247 ENOG4108QZM esterase -0.007393
248 ENOG4107RIS Acyl-transferase 0.007390
249 ENOG4108RAV Conserved protein -0.007389
250 ENOG4105CPN adenine deaminase -0.007383