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 ENOG4105YVS arsR family transcriptional regulator 0.010563
2 ENOG4105CYF SMP-30 gluconolaconase LRE domain protein 0.008537
3 ENOG4108D1Y Polypeptide-transport-associated domain protein, ShlB-type -0.008335
4 ENOG4105IB0 filamentous hemagglutinin family outer membrane protein -0.007808
5 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase -0.007619
6 ENOG4105CE7 Amidase, hydantoinase carbamoylase family 0.007595
7 ENOG4105NS2 LysR family transcriptional regulator 0.007581
8 ENOG4107YG7 methyl-accepting chemotaxis -0.007310
9 ENOG4107YHI Methyl-accepting chemotaxis -0.007281
10 ENOG4105DKT Transcriptional regulator 0.007270
11 ENOG4107RXV Inherit from COG: Hydrolase 0.007224
12 ENOG4105Q3R AsnC family transcriptional regulator 0.007067
13 ENOG4108W5V epimerase dehydratase 0.006937
14 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) 0.006915
15 ENOG4105VGJ Virulence-associated protein 0.006816
16 ENOG4105ECH ABC transporter substrate-binding protein 0.006727
17 ENOG4108K8R Glutathione S-transferase 0.006669
18 ENOG4105X1V Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity (By similarity) 0.006650
19 ENOG4105UK9 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity (By similarity) 0.006631
20 ENOG4107R4J Chloride channel 0.006622
21 ENOG4105FAW cDP-glucose 4,6-dehydratase -0.006544
22 ENOG4108YBQ cytochrome (b561) 0.006520
23 ENOG4108EV4 Bile acid sodium symporter 0.006494
24 ENOG4108RUT NADP oxidoreductase, coenzyme f420-dependent 0.006483
25 ENOG4105NF4 modulator of drug activity -0.006422
26 ENOG4107NQ8 LysR family Transcriptional regulator 0.006341
27 ENOG4108ZVH Protein of unknown function (DUF3225) 0.006315
28 ENOG4105JR5 N-formylglutamate amidohydrolase 0.006165
29 ENOG4105CIV prophage primase 0.006108
30 ENOG4105RKW reductase (By 0.006070
31 ENOG4108V5F Lysine exporter protein (Lyse ygga) -0.006052
32 ENOG4105G3W transcriptional regulator MERR family 0.006040
33 ENOG4105EHA HipA domain protein 0.006034
34 ENOG41060H1 pathway protein C -0.006033
35 ENOG4105XBG NA -0.006029
36 ENOG4105CNA YD repeat protein 0.005993
37 ENOG41062XA Antibiotic biosynthesis monooxygenase 0.005985
38 ENOG4105P6A (type IV) pilus -0.005984
39 ENOG4105VJR addiction module toxin, RelE StbE family -0.005981
40 ENOG4105GNX MltA-interacting MipA family protein 0.005974
41 ENOG4105WDY DNA (cytosine-5-)-methyltransferase -0.005955
42 ENOG4105GVR general secretion pathway protein D -0.005935
43 ENOG4107TE2 basic membrane 0.005935
44 ENOG4105C9B Cysteine desulfurase 0.005919
45 ENOG4105VDS fimbrial protein (Pilin) -0.005908
46 ENOG4107SN8 glycosyl transferase family 0.005898
47 ENOG4105KYA Uncharacterized ACR, COG1993 0.005890
48 ENOG4105PHQ Protein of unknown function (DUF1311) 0.005863
49 ENOG41068T5 Catalyzes the hydrolysis of methenyl-H(4)MPT( ) to 5- formyl-H(4)MPT (By similarity) -0.005791
50 ENOG41067V3 Antibiotic biosynthesis monooxygenase 0.005777
51 ENOG4105KRK doxx family 0.005773
52 ENOG4105EQ0 Major Facilitator superfamily 0.005753
53 ENOG4108UQ8 endoribonuclease L-psp -0.005748
54 ENOG4105J5T Amp-dependent synthetase and ligase -0.005729
55 ENOG4108EKF Catalyzes the synthesis of activated sulfate (By similarity) -0.005721
56 ENOG4105VK9 acetyltransferase -0.005716
57 ENOG4105H2U Biopolymer transport 0.005711
58 ENOG4105C5B carbamate kinase 0.005686
59 ENOG4108EZK carboxylase -0.005677
60 ENOG41071KM NA -0.005675
61 ENOG4108HGT Histidine kinase -0.005664
62 ENOG4105EV9 Alpha Beta Hydrolase 0.005640
63 ENOG4105Z9R Transporter 0.005612
64 ENOG4105Q9Q Sporulation domain-containing protein -0.005607
65 ENOG4105KVH Transcriptional regulator 0.005603
66 ENOG4106SDZ outer membrane autotransporter barrel 0.005593
67 ENOG4108RXX maleylacetoacetate isomerase -0.005582
68 ENOG4105MAY lambda NinG 0.005563
69 ENOG4108Q8Z Biotin carboxylase -0.005544
70 ENOG4108WUH Transcriptional regulator, TetR family 0.005523
71 ENOG4108TNN Histidine kinase 0.005496
72 ENOG4105KAC Antibiotic biosynthesis monooxygenase -0.005486
73 ENOG4108WT1 Transcriptional regulator 0.005483
74 ENOG4108ZG8 Gcn5-related n-acetyltransferase 0.005458
75 ENOG4105U2T secretion pathway protein J -0.005445
76 ENOG4105HEI LysR family (Transcriptional regulator -0.005442
77 ENOG4105CP5 Pfam:DUF88 0.005441
78 ENOG4108K0C Putative modulator of DNA gyrase 0.005418
79 ENOG4108HHA Transketolase 0.005393
80 ENOG4105W8H transhydrogenase (subunit alpha -0.002690
80 ENOG4108EPT The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity) -0.002690
81 ENOG4108ND8 Dehydratase 0.005371
82 ENOG4107QKW extracellular solute-binding protein family 1 0.005357
83 ENOG4106A18 integral membrane protein-like protein 0.005347
84 ENOG4105EQA Outer membrane autotransporter 0.005330
85 ENOG4105FJP NA 0.005318
86 ENOG41067M3 Membrane -0.005307
87 ENOG4106HK8 GPR1 FUN34 yaaH family protein 0.005305
88 ENOG4108ZRP NA -0.005301
89 ENOG4107ZT8 Transposition protein 0.005299
90 ENOG4107A1U NA -0.005292
91 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase -0.005288
92 ENOG4105IGV F pilus assembly Type-IV secretion system for plasmid transfer 0.005282
93 ENOG4105EWB Pfam:DUF1527 0.002641
93 ENOG4105I0F Secreted protein 0.002641
94 ENOG4105EXG Transcriptional regulator -0.005261
95 ENOG4105CPC Aldo Keto reductase 0.005257
96 ENOG4105NG1 exported protein -0.005227
97 ENOG4105KG3 cytidine deaminase 0.005224
98 ENOG41075ZE Protein of unknown function (DUF1049) 0.005212
99 ENOG4105SMQ Inherit from NOG: NADH flavin oxidoreductase, NADH oxidase -0.005199
100 ENOG4107T3I fad-binding protein -0.005197
101 ENOG41079KC membrAne -0.002598
101 ENOG4108KW7 amp-dependent synthetase and ligase -0.002598
102 ENOG4105T1S Transposase 0.005188
103 ENOG4105E6Z Enoyl-CoA hydratase -0.005188
104 ENOG4105WND isoprenylcysteine carboxyl methyltransferase -0.005183
105 ENOG4108JQ0 Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) 0.005179
106 ENOG4108N7C Aminotransferase 0.005174
107 ENOG4108EMM Sss sodium solute transporter superfamily -0.005168
108 ENOG4107ZG1 ABC-2 type transporter -0.005150
109 ENOG4108H15 Major Facilitator Superfamily 0.005137
110 ENOG4108BXC NA -0.005122
111 ENOG4105ETS cytosine purines uracil thiamine allantoin 0.005114
112 ENOG4105K6V RNA polymerase 0.005108
113 ENOG4108RPI (ABC) transporter -0.005080
114 ENOG4105CSJ Enoyl- acyl-carrier-protein reductase NADH -0.005079
115 ENOG4107R26 Methyl-accepting chemotaxis sensory transducer 0.005068
116 ENOG4105DCZ taurine catabolism dioxygenase TauD, TfdA 0.005058
117 ENOG4105WEF catalase -0.005058
118 ENOG4105CG3 alpha amylase, catalytic region -0.005031
119 ENOG410660K Sulfotransferase -0.005026
120 ENOG4105PCI Transcriptional regulator (XRE family -0.005019
121 ENOG4108V07 glutathione-dependent formaldehyde-activating Gfa -0.005011
122 ENOG4108ZGC gaf domain protein 0.004999
123 ENOG4105VV1 Protein of unknown function (DUF3423) 0.004993
124 ENOG4105EPY ABC transporter -0.004986
125 ENOG4105MS1 LysR family transcriptional Regulator 0.004970
126 ENOG41090BJ protein tyrosine serine phosphatase -0.004968
127 ENOG4107UR6 Protein of unknown function DUF72 -0.004967
128 ENOG4105ES4 Nitrilase 0.004965
129 ENOG4105FCI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate (By similarity) 0.004952
130 ENOG4105DTH ABC transporter substrate-binding protein -0.004923
131 ENOG4107GIZ Ornithine Cyclodeaminase -0.004921
132 ENOG4105V7Y membrAne -0.004913
133 ENOG4108Q56 NA 0.004905
134 ENOG4105D70 Integrase catalytic subunit 0.004903
135 ENOG41087Y0 Glycosyl transferase, family 2 0.004901
136 ENOG4105CM9 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG (By similarity) 0.001225
136 ENOG4105KPN Aminoglycoside phosphotransferase 0.001225
136 ENOG4107XQX choline ethanolamine kinase 0.001225
136 ENOG4108F09 Urease subunit gamma beta 0.001225
137 ENOG4105CPI Metal Dependent Phosphohydrolase -0.004884
138 ENOG4108AZT Acyl-transferase -0.004872
139 ENOG4108N50 Peptidase M11, gametolysin 0.004867
140 ENOG41080S2 dna polymerase III (Chi subunit) -0.004855
141 ENOG410655W relaxase 0.004846
142 ENOG4105ZWK Inherit from COG: Low-potential electron donor to a number of redox enzymes (By similarity) 0.004846
143 ENOG4106FJX Entericidin -0.004836
144 ENOG4108KT4 Ectoine hydroxyectoine ABC transporter solute-binding protein -0.004835
145 ENOG4107FKF Uncharacterized protein conserved in bacteria (DUF2138) -0.000966
145 ENOG4107S52 alpha-2-macroglobulin domain protein -0.000966
145 ENOG41081SK signal peptide protein -0.000966
145 ENOG4108MCY signal peptide protein -0.000966
145 ENOG4108QJJ Protein of unknown function (DUF1175) -0.000966
146 ENOG4107U3N Response regulator receiver modulated diguanylate phosphodiesterase 0.004825
147 ENOG4108S08 Protein of unknown function (DUF3487) 0.004825
148 ENOG4105JIM Phosphatidylserine synthase 0.004823
149 ENOG4108T86 baseplate J family protein 0.004814
150 ENOG41067WK Transcriptional regulator 0.004788
151 ENOG4106FHG NA -0.004786
152 ENOG4105CQF Transcriptional regulator -0.004783
153 ENOG4105DTR rard protein 0.004782
154 ENOG4105EUZ Beta-lactamase domain protein -0.004774
155 ENOG4105CKX Catalyzes the conversion of 3'-phosphate to a 2',3'- cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps (A) adenylation of the enzyme by ATP -0.004769
156 ENOG4105E9V Periplasmic binding protein LacI transcriptional regulator 0.004755
157 ENOG4106739 C-terminal region of Pasteurella multocida toxin residues 569-1285 0.004753
158 ENOG4108594 Permease of the drug metabolite transporter -0.004749
159 ENOG4107RIB phospholipase d -0.002374
159 ENOG4108V58 Endonuclease Exonuclease phosphatase -0.002374
160 ENOG4106G56 Alpha Beta Hydrolase 0.004747
161 ENOG4105C4D tonB-dependent Receptor -0.004734
162 ENOG4108X1T PAAR repeat-containing protein -0.004734
163 ENOG4105VME Acyl carrier protein -0.004734
164 ENOG4105D1M ATP-dependent endonuclease of the OLD 0.004717
165 ENOG410625M Putative trans-membrane protein -0.004715
166 ENOG4105E2K Glycosyl transferase (Group 1 -0.004715
167 ENOG4108R1J Diguanylate cyclase with PAS PAC sensor 0.004715
168 ENOG4105C02 permease -0.004711
169 ENOG4107V6X exodeoxyribonuclease III -0.004709
170 ENOG4105CQT polysaccharide deacetylase 0.004705
171 ENOG4108JQB penicillin-binding protein 1C 0.004704
172 ENOG4107YGK Uncharacterised ACR, COG2135 -0.004701
173 ENOG4108S67 amidohydrolase 2 -0.004690
174 ENOG4105WPQ NA 0.004689
175 ENOG4105D13 transposase 0.004687
176 ENOG41084EK SH3, type 3 domain protein -0.004685
177 ENOG4105K56 Transcriptional regulator 0.004680
178 ENOG4105MCR cAMP-binding protein-catabolite gene activator and regulatory subunit of cAMP-dependent protein kinase -0.004674
179 ENOG4106571 Short-chain dehydrogenase reductase Sdr -0.004673
180 ENOG4105XH4 Protein of unknown function (DUF2945) 0.004665
181 ENOG4105C1G acyl-Coa dehydrogenase -0.001555
181 ENOG4105CNZ decarboxylase family -0.001555
181 ENOG4105D16 lipopolysaccharide heptosyltransferase i -0.001555
182 ENOG4105J5W NA -0.004663
183 ENOG4108W40 LysR family (Transcriptional regulator 0.004662
184 ENOG4105D5W LysR family transcriptional regulator -0.004659
185 ENOG4105SY8 Alpha beta hydrolase -0.004659
186 ENOG4105WZK nitrite reductase NADPH small subunit 0.004646
187 ENOG4107UPT permease for cytosine purines, uracil, thiamine, allantoin 0.004634
188 ENOG4108MX3 Polysaccharide Biosynthesis Protein 0.004630
189 ENOG41061ZR Transcriptional regulator 0.004629
190 ENOG4107U5X Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity (By similarity) -0.004626
191 ENOG41074JJ Transcriptional regulator 0.004625
192 ENOG4105EDK PfkB domain protein 0.004623
193 ENOG4105XDZ Tripartite ATP-independent periplasmic transporter -0.004622
194 ENOG4105KPV Transcriptional regulator 0.004614
195 ENOG4107C6B Heterokaryon incompatibility protein Het-C 0.004609
196 ENOG4106H6R UPF0380 protein 0.004606
197 ENOG4105WQG acetyltransferase 0.004605
198 ENOG4106AJG NA 0.004591
199 ENOG4108EUE molybdopterin oxidoreductase 0.004582
200 ENOG4108EU9 Aminotransferase 0.004581
201 ENOG4108EAP nitrate reductase beta -0.004577
202 ENOG4108T1P restriction endonuclease -0.004571
203 ENOG4108URA DSBA oxidoreductase -0.004570
204 ENOG4107QWP ABC-2 type transporter -0.004560
205 ENOG4108ZJD Protein of unknown function (DUF1109) 0.004555
206 ENOG41078DE pathway protein -0.004543
207 ENOG4107W7X Aldolase -0.004537
208 ENOG4108UDW Transcriptional regulator, luxr family 0.004533
209 ENOG4108TUK Anti-feci sigma factor, fecr 0.004532
210 ENOG4108PZW LysR family Transcriptional regulator -0.004531
211 ENOG4107WD2 ec 2.7.10.2 0.004530
212 ENOG4108Z6S mosc domain -0.004524
213 ENOG4105TIV Cryptic phage CTXphi transcriptional repressor RstR -0.004518
214 ENOG4105M0J Toxic component of a toxin-antitoxin (TA) module. A 0.004509
215 ENOG4105I8X Membrane -0.004503
216 ENOG4108QBQ Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione (By similarity) 0.004502
217 ENOG4108DRD Transcriptional regulator -0.004497
218 ENOG41090A7 (LipO)protein 0.004491
219 ENOG4105GQR Chaperone 0.004489
220 ENOG4105WQB Cytochrome b(561) -0.004473
221 ENOG4107QIW Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism (By similarity) -0.004471
222 ENOG4107ZW7 Uncharacterised ACR, YkgG family COG1556 -0.004470
223 ENOG4105CHG glycolate oxidase (iron-sulfur subunit) -0.004467
224 ENOG4105PF5 Glyoxalase Bleomycin resistance protein (Dioxygenase 0.004466
225 ENOG4105IE8 Alpha-ketoglutarate permease 0.004457
226 ENOG4106JF3 nnrs family -0.004451
227 ENOG41084YH XRE family Transcriptional regulator 0.004449
228 ENOG41064UG Terminase, large subunit 0.004448
229 ENOG4105FQ6 thiopurine methyltransferase 0.004448
230 ENOG41067VG Peptidase A24A, prepilin type IV 0.004445
231 ENOG4108RFJ Protein-disulfide isomerase -0.004442
232 ENOG4105F73 Catalyzes the deformylation of 4-deoxy-4-formamido-L- arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose- phosphoundecaprenol. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides (By similarity) -0.004439
233 ENOG4108VXI Alpha Beta Hydrolase Fold protein 0.004438
234 ENOG4105GY0 Zeta toxin 0.004436
235 ENOG4108DKR ABC transporter, permease -0.004431
236 ENOG41067UG Cyd operon protein YbgT 0.004427
237 ENOG4107R6X pyruvate phosphate dikinase -0.004421