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 ENOG4107QHE Choloylglycine hydrolase 0.034726
2 ENOG4108XXH specificity -0.019077
3 ENOG41084C3 integral membrane protein 0.016241
4 ENOG4105EAM Na Pi-cotransporter 0.015814
5 ENOG4105X0A Cell wall anchor domain protein 0.015296
6 ENOG4108HCJ Hydrolase -0.014628
7 ENOG4105D85 methylase 0.013389
8 ENOG4106UHR Inherit from COG: type I restriction-modification system -0.013322
9 ENOG4105XST NA 0.013305
10 ENOG4105F6A helicase 0.013063
11 ENOG4107RE8 Integrase -0.012825
12 ENOG4105ECI YeeC-like protein 0.012814
13 ENOG4105EUZ Beta-lactamase domain protein 0.012789
14 ENOG4105VTR Integrase 0.012272
15 ENOG4107T00 transcriptional regulator, lysR family 0.012248
16 ENOG4105DRA alpha beta 0.012191
17 ENOG4107RWR Sodium hydrogen exchanger -0.012174
18 ENOG41070S6 NA 0.012058
19 ENOG4105CHH sulfate transporter 0.011950
20 ENOG4107QZU type I restriction-modification system -0.011926
21 ENOG4105C6D Phage portal protein -0.005905
21 ENOG41065C6 NA -0.005905
22 ENOG4107TI4 Protein of unknown function (DUF554) 0.011714
23 ENOG4105D4Y metalloprotease 0.011651
24 ENOG4105DU0 nucleoside hydrolase 0.011625
25 ENOG4107RYX Type I site-specific deoxyribonuclease -0.011577
26 ENOG4108YZV phage major capsid protein, HK97 family -0.011547
27 ENOG41061F3 Diguanylate cyclase 0.011500
28 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) 0.011341
29 ENOG4108ZQ5 Polysaccharide biosynthesis protein 0.011333
30 ENOG4105T6C Cell surface-associated protein implicated in virulence by promoting bacterial attachment to both alpha- and beta-chains of human fibrinogen and inducing the formation of bacterial clumps -0.011287
31 ENOG4105X1N Glycosyl transferase family 8 -0.011281
32 ENOG4108U3E major tail protein, phi13 family -0.011241
33 ENOG4107SHI hydrolase, CocE NonD family protein 0.011226
34 ENOG4105HJE transcriptional regulator 0.011131
35 ENOG4107RSM transcriptional regulator 0.011097
36 ENOG4108VWU Histidine kinase -0.010987
37 ENOG4105F9F transposase 0.010948
38 ENOG4105CHU acetyl-coa acetyltransferase -0.010930
39 ENOG4105W0R Phage-Associated Protein 0.010866
40 ENOG4105QMN prophage pi2 protein 38 -0.010841
41 ENOG4108BKE Membrane 0.010821
42 ENOG41063ZK Transcriptional Regulator AraC Family 0.010788
43 ENOG4105P1Q Prophage pi2 protein 37 -0.010767
44 ENOG4106IUN Antibiotic biosynthesis monooxygenase 0.002688
44 ENOG410782R NA 0.002688
44 ENOG4107HBJ phospholipase C 0.002688
44 ENOG41081CJ Xylose isomerase-like TIM barrel 0.002688
45 ENOG4108IMX DNA-binding helix-turn-helix protein -0.010746
46 ENOG410737Z NA 0.010666
47 ENOG4107QQI Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity) 0.010609
48 ENOG4108IUH Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (By similarity) 0.010602
49 ENOG4105VR3 HNH endonuclease -0.010546
50 ENOG4105EWC Purine nucleoside phosphorylase 0.010481
51 ENOG4108NQ3 Phosphatidylinositol-specific phospholipase C 0.010470
52 ENOG4105ETU transcriptional activator (TenA -0.010455
53 ENOG4107S04 cyclase, family -0.010430
54 ENOG4105WZQ Membrane -0.010424
55 ENOG41060CM Protein of unknown function (DUF2712) 0.005206
55 ENOG4106NWU NA 0.005206
56 ENOG4108TZY GntR Family Transcriptional Regulator 0.010369
57 ENOG4108ZMX Domain of unknown function (DU1801) 0.010336
58 ENOG4108ZUI integrase family -0.010334
59 ENOG410830X 'Cold-shock' DNA-binding domain protein 0.010258
60 ENOG41089NQ Transcriptional regulator PadR-like family -0.010255
61 ENOG4105P6J NA -0.010200
62 ENOG4108K2R Glutathione-regulated potassium-efflux system ancillary protein -0.010192
63 ENOG4108ZXD NA 0.010147
64 ENOG4105GF1 NA -0.010130
65 ENOG4105WT3 Transcriptional regulator 0.010114
66 ENOG4105GI3 Cell wall anchor domain protein 0.010055
67 ENOG4106FJ5 NA -0.010020
68 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) 0.009968
69 ENOG4105CE1 Ferrous iron transport protein b 0.009966
70 ENOG4107ZFM Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) (By similarity) -0.009917
71 ENOG4105C19 ABC transporter 0.009863
72 ENOG4105D18 nicotinate-nucleotide pyrophosphorylase 0.009842
73 ENOG4106DW9 tail component -0.009801
74 ENOG4107QHX Phosphotransferase system, EIIC 0.009792
75 ENOG4105DY9 regulatoR -0.009791
76 ENOG4108PTT Chloride channel 0.009769
77 ENOG4107R1W mannose-6-phosphate isomerase 0.009755
78 ENOG4106H3J Lpxtg-motif cell wall anchor domain protein -0.009742
79 ENOG4106EFW NA -0.009721
80 ENOG4107S4H Major Facilitator -0.009718
81 ENOG4105FF0 ErfK YbiS YcfS YnhG 0.009711
82 ENOG41064M9 RNA Polymerase -0.009640
83 ENOG4105KBM acetyltransferase, (GNAT) family 0.009620
84 ENOG4105EFU Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin (By similarity) 0.009594
85 ENOG4107TBP PTS System 0.009573
86 ENOG410649U NA -0.009495
87 ENOG4108TP4 integral membrane protein -0.009451
88 ENOG4108IYU L-aspartate oxidase 0.009417
89 ENOG4106DR7 MORN repeat protein 0.009396
90 ENOG4108RJ0 (sortase) family 0.009385
91 ENOG4105KXT phage protein 0.009346
92 ENOG4108I66 PTS System -0.009333
93 ENOG4107T9Z Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.009320
94 ENOG4105VPE NA -0.003103
94 ENOG4107JK9 NlpC/P60 family -0.003103
94 ENOG4108URS primosomal replication protein n'' -0.003103
95 ENOG4106DUW Sporulation related domain -0.009310
96 ENOG4105C1W two component, sigma54 specific, transcriptional regulator, Fis family 0.009307
97 ENOG4105VPB 50S ribosomal protein L30 0.009273
98 ENOG4105CM3 Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate (By similarity) 0.009216
99 ENOG4105CIZ coA-substrate-specific enzyme activase 0.009205
100 ENOG4107WAT HTH_LACI -0.009203
101 ENOG4105C4P Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template (By similarity) 0.009180
102 ENOG4105WWN NA 0.009169
103 ENOG4105QUP low temperature requirement protein -0.009096
104 ENOG4105CI1 PTS System 0.009094
105 ENOG41078BE NA 0.003022
105 ENOG4108QXB NA 0.003022
105 ENOG4108VQT Alpha beta hydrolase fold protein 0.003022
106 ENOG4105DSE periplasmic solute binding protein -0.009056
107 ENOG410882V VanZ like family 0.009041
108 ENOG4108NF7 phage-type endonuclease -0.009017
109 ENOG4105VEQ Cold shock protein -0.009000
110 ENOG4105D0I Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity) 0.008992
111 ENOG4105KVH Transcriptional regulator -0.008981
112 ENOG41089SH Inherit from COG: Beta-lactamase -0.008977
113 ENOG4107RZ4 Methionine synthase 0.008892
114 ENOG4108U05 Transcriptional regulator 0.008887
115 ENOG4105KJ4 Antibiotic biosynthesis monooxygenase 0.008833
116 ENOG4108N1N Glycosyl hydrolase family 1 -0.008819
117 ENOG4105VDH Dihydroxyacetone kinase 0.008810
118 ENOG4105EY9 peptidase S8 and S53, subtilisin, kexin, sedolisin -0.008727
119 ENOG4106FFK NA 0.008710
120 ENOG41083QC transcriptional regulators 0.008704
121 ENOG4107QYD Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) -0.008698
122 ENOG4108W0I acetyltransferase 0.008682
123 ENOG41067YF Family Transcriptional Regulator 0.008564
124 ENOG4107X1J NA 0.008555
125 ENOG4105D7T ABC transporter 0.008525
126 ENOG41066JZ Integrase -0.008524
127 ENOG4105EKD Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism (By similarity) 0.008518
128 ENOG4105C4E Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (By similarity) 0.008499
129 ENOG4107WZB Membrane 0.008471
130 ENOG4108C33 Resolvase -0.008453
131 ENOG4105G9Q Protein of unknown function (DUF2089) 0.008421
132 ENOG410690S NA -0.008419
133 ENOG4105DAB fumarate reductase succinate dehydrogenase flavoprotein domain protein 0.008408
134 ENOG4107S7S glycoside hydrolase, family 3 domain protein -0.008403
135 ENOG41063TQ NA 0.008397
136 ENOG4108RF9 lipolytic protein, gdsl family 0.008396
137 ENOG41076YM VRR-NUC domain protein -0.008386
138 ENOG4106CUC NA 0.008378
139 ENOG4105DUK Catalyzes the conversion of 4-hydroxy- tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (By similarity) 0.008376
140 ENOG4108R6K riboflavin synthase, subunit alpha 0.008356
141 ENOG4105XJC Two component transcriptional regulator (Winged helix family 0.008322
142 ENOG4105MYW Pentapeptide repeat protein 0.008288
143 ENOG4108AHM Cadmium efflux system accessory protein -0.008285
144 ENOG4108E8A ABC transporter (Permease -0.008248
145 ENOG4108PXA Replication Protein -0.008246
146 ENOG41069HQ D-Ala-teichoic acid biosynthesis protein -0.008229
147 ENOG4105K6X Protein of unknown function (DUF3014) 0.008226
148 ENOG4108319 Transcriptional regulator (XRE family 0.008210
149 ENOG4105ESI atpase involved in dna repair -0.008198
150 ENOG4106GRJ chromatin binding -0.008195
151 ENOG4108940 Ribose/Galactose Isomerase -0.008166
152 ENOG4108JJA ABC, transporter -0.008147
153 ENOG4106KNT transcriptional regulator 0.008146
154 ENOG4105F1T DNA repair protein 0.008137
155 ENOG4105C7J ABC transporter, permease 0.004066
155 ENOG4105DB0 abc transporter atp-binding protein 0.004066
156 ENOG41082SA 50s ribosomal protein l29 -0.008115
157 ENOG41064BZ L-xylulose 5-phosphate 3-epimerase -0.008100
158 ENOG4105HBC Transcriptional regulator -0.008097
159 ENOG4105IKE Inherit from COG: peptidase' -0.008088
160 ENOG4107J0C type IIi -0.008085
161 ENOG4105E5P Sulfhydryl-activated toxin that causes cytolysis by forming pores in cholesterol containing host membranes. After binding to target membranes, the protein undergoes a major conformation change, leading to its insertion in the host membrane and formation of an oligomeric pore complex. Cholesterol may be required for binding to host membranes, membrane insertion and pore formation. Can be reversibly inactivated by oxidation 0.008084
162 ENOG410622W Family transcriptional regulator 0.008081
163 ENOG410814C multidrug resistance protein 0.008070
164 ENOG4108SDH ABC, transporter -0.008062
165 ENOG4107MNN Inherit from COG: Signal peptidase i -0.008044
166 ENOG41068Z8 NA 0.008029
167 ENOG4106UBQ NA 0.008019
168 ENOG4107ZN3 Ser Thr phosphatase family protein -0.008011
169 ENOG4107ZGP Competence protein 0.008010
170 ENOG41062FE ion transport 2 domain protein 0.008007
171 ENOG4105EQK -acetyltransferase -0.008005
172 ENOG4105FW8 Phage replisome organizer 0.007997
173 ENOG4108R6W Transcriptional regulator, ARAC family -0.007979
174 ENOG410692P Branched-chain amino acid transport -0.007962
175 ENOG4108ME1 Peptidase M55 D-aminopeptidase -0.007957
176 ENOG41083AA HTH_XRE 0.007949
177 ENOG4105XCN CopG family transcriptional regulator -0.007943
178 ENOG4106659 NA -0.007929
179 ENOG4106Z1N NA 0.002642
179 ENOG4107WJ3 integral membrane protein 0.002642
179 ENOG4108T9B Transcriptional regulator (LacI family 0.002642
180 ENOG4107N7Q CHAP domain 0.007927
181 ENOG4108IE0 Dehydrogenase 0.007920
182 ENOG4106T3F PTS system, IIB component -0.007896
183 ENOG4105GGR isoprenylcysteine carboxyl methyltransferase 0.007893
184 ENOG4108GMG NA 0.007880
185 ENOG4107Y1C Carboxypeptidase -0.007861
186 ENOG4105C3F Signal peptidase i 0.007852
187 ENOG4105DJ2 Major Facilitator Superfamily -0.007850
188 ENOG4105EYG tyrosine recombinase. Not involved in the cutting and rejoining of the recombining DNA molecules on dif(SL) site (By similarity) 0.007837
189 ENOG4105DV8 filamentation induced by cAMP protein Fic 0.007835
190 ENOG41067QW Transcriptional regulator 0.007819
191 ENOG4105M0U Resistance protein 0.007819
192 ENOG410908W Diguanylate cyclase -0.007804
193 ENOG4105F2H Diguanylate cyclase phosphodiesterase 0.007784
194 ENOG4105NN3 Response regulator of the LytR AlgR family 0.007783
195 ENOG4105EGD dinuclear metal center protein, YbgI family -0.007769
196 ENOG4107414 GntR family transcriptional regulator -0.007760
197 ENOG4105DAS pts system 0.007740
198 ENOG4106AUB Phage head-tail adaptor -0.007738
199 ENOG4105CTR Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity) 0.007730
200 ENOG4108TCI Transcriptional regulator 0.007730
201 ENOG4106DIW mucin-associated surface protein 0.007718
202 ENOG4108XXQ NA 0.007717
203 ENOG4108RI2 Phage recombination protein Bet -0.007705
204 ENOG4105VNP Methionine--tRNA ligase 0.007686
205 ENOG410834J oxidoreductase, short- chain dehydrogenase reductase 0.007686
206 ENOG4105J4Z extracellular solute-binding protein family 1 0.007679
207 ENOG4108NCP coat protein 0.007675
208 ENOG41082F8 epimerase dehydratase 0.007675
209 ENOG4108V25 recT protein 0.007664
210 ENOG4105UE6 PTS system cellobiose transporter subunit IIB 0.007649
211 ENOG4105ZV0 Sigma-70, region 4 -0.007642
212 ENOG4108NX2 acetyltransferase, (GNAT) family 0.007619
213 ENOG4105Z6D NA 0.007618
214 ENOG41084KY 50S ribosomal protein L30 -0.007612
215 ENOG4105KNA -acetyltransferase 0.007610
216 ENOG41090YN Protein of unknown function (DUF2785) 0.007594
217 ENOG4107W9S (ABC) transporter 0.007563
218 ENOG4105C5B carbamate kinase 0.007556
219 ENOG4108N10 NA 0.007554
220 ENOG41083RF phosphoribosyl-ATP pyrophosphatase -0.007551
221 ENOG4108USK AraC family transcriptional regulator 0.007544
222 ENOG4106E6N NA 0.007535
223 ENOG4105H2V Virulence-associated protein e 0.007529
224 ENOG4105CYW agmatinase -0.007528
225 ENOG4107RKR Mate efflux family protein 0.007519
226 ENOG4108RRA NA 0.007496
227 ENOG41090A1 ferritin -0.007479
228 ENOG4105KG3 cytidine deaminase -0.007475
229 ENOG4105US7 Histidine kinase -0.007473
230 ENOG4107YV7 response regulator -0.007467
231 ENOG4105MKB Helix-turn-helix 0.007429
232 ENOG4108HSQ NA 0.007410
233 ENOG4105JGP host cell surface-exposed lipoprotein 0.007408
234 ENOG4106EF3 NA 0.007390
235 ENOG4105DBQ SIS domain protein 0.007381
236 ENOG4105VJ8 Bacterial group 2 Ig-like protein 0.007367
237 ENOG41076KT IDEAL 0.003683
237 ENOG410845D Calcineurin-like phosphoesterase 0.003683