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 ENOG4105FUY alpha subunit 0.017669
2 ENOG4108QJ2 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase 0.013319
3 ENOG4105DPT Diguanylate cyclase phosphodiesterase 0.012752
4 ENOG4105ENE Histidine kinase 0.012372
5 ENOG4108VPQ HhH-GPD domain protein 0.011912
6 ENOG4108K2X pilus assembly 0.011877
7 ENOG4105DSQ Nitric oxide reductase 0.011646
8 ENOG4108ZA9 Transcriptional regulator, TetR family 0.011314
9 ENOG4107581 Glycosyl transferase (Group 1 0.011229
10 ENOG4105GVH Cyclase dehydrase 0.011028
11 ENOG4105FAE von Willebrand factor, type A 0.011016
12 ENOG4105C9T amidohydrolase 2 0.010687
13 ENOG4105H0C serine acetyltransferase 0.010655
14 ENOG4108UMJ dihydrodipicolinate synthetase 0.010602
15 ENOG4105NI8 Cytosine-specific methyltransferase 0.010550
16 ENOG4105E0A ABC, transporter -0.010450
17 ENOG4105GFX Transcriptional regulator -0.010354
18 ENOG4105CEQ signal transduction histidine kinase regulating citrate malate metabolism 0.010281
19 ENOG4108M16 Nad-dependent epimerase dehydratase 0.010056
20 ENOG4105DZT Gentisate 1,2-dioxygenase 0.010007
21 ENOG4105CGW short-chain dehydrogenase reductase 0.009972
22 ENOG4105BZK Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity) 0.009940
23 ENOG4105VQD rieske 2fe-2S domain-containing protein 0.009897
24 ENOG4105DNA ATP GTP Binding Protein 0.009835
25 ENOG4107UKK Pyruvate, water dikinase 0.009775
26 ENOG4105CJP fad dependent oxidoreductase -0.009758
27 ENOG4105CMM transposase 0.009740
28 ENOG4108Z67 carbohydrate kinase, thermoresistant glucokinase family 0.009713
29 ENOG4108J1M NA 0.009704
30 ENOG4105SKQ Membrane 0.009615
31 ENOG41061ZR Transcriptional regulator -0.009567
32 ENOG4105CQM Urea amidohydrolase subunit alpha 0.004776
32 ENOG4105KI2 Urea amidohydrolase subunit beta 0.004776
33 ENOG4108MFE oxidoreductase 0.009545
34 ENOG410624J NA 0.009491
35 ENOG4105D89 Nucleotidyl transferase of unknown function (DUF1814) 0.009368
36 ENOG4108Z9K Osmotically inducible protein 0.009332
37 ENOG4106FZ5 NA 0.009331
38 ENOG4108RGV mercury transport protein MerC -0.009306
39 ENOG4105MUA Resistance protein 0.009274
40 ENOG4105IYT NA 0.004619
40 ENOG4105K5N Transcriptional regulator 0.004619
41 ENOG4107PRG Protein of unknown function (DUF2933) 0.009050
42 ENOG4108VBY Glutathione S-transferase 0.009048
43 ENOG4105EPD Oligopeptide transporter, Opt family -0.009031
44 ENOG4105GMT ATPase associated with various cellular activities aaa_5 0.008992
45 ENOG4105N94 The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase (By similarity) 0.008926
46 ENOG4105ES2 NA 0.008854
47 ENOG4105F96 Transposase 0.008845
48 ENOG4108VUA TRANSCRIPTIONal 0.008833
49 ENOG4105KAG DsrE/DsrF-like family 0.002174
49 ENOG4105TJ8 Protein of unknown function (DUF3696) 0.002174
49 ENOG4106IAA NA 0.002174
49 ENOG41077R5 Membrane 0.002174
50 ENOG4105NGA NA 0.004324
50 ENOG4106D0I NA 0.004324
51 ENOG4108K6R strictosidine synthase 0.008586
52 ENOG4108MQ5 NA 0.008582
53 ENOG4105VWP Inherit from COG: 4Fe-4S ferredoxin, iron-sulfur binding 0.008564
54 ENOG4108TIB DUF35 OB-fold domain 0.008555
55 ENOG4105YG7 'Cold-shock' DNA-binding domain protein 0.008539
56 ENOG4108Z7R Chaperone CsaA 0.008532
57 ENOG4108H1Y NA 0.008439
58 ENOG4105F9F transposase -0.008277
59 ENOG4107EMZ glycosyl transferase family -0.008258
60 ENOG4105FH6 had-superfamily hydrolase, subfamily ia, variant 0.002747
60 ENOG4105HZW Transcriptional regulator 0.002747
60 ENOG4106BGH NA 0.002747
61 ENOG4108PD9 Integrase 0.008221
62 ENOG4105DKS phage plasmid primase, p4 family -0.008134
63 ENOG4105EIH LPPG Fo 2-phospho-L-lactate transferase 0.008129
64 ENOG4107QHU One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex (By similarity) -0.008128
65 ENOG4105IS1 Rieske 2Fe-2S 0.008092
66 ENOG4107AU0 Conserved hypothetical protein 95 -0.008089
67 ENOG4106H78 methyltransferase 0.008089
68 ENOG4107872 NA 0.008079
69 ENOG4108K45 Phage plasmid-related protein TIGR03299 0.008012
70 ENOG4105D66 Pfam:DUF2081 0.008006
71 ENOG4107UGN N-6 DNA Methylase 0.008003
72 ENOG4106CZX Domain of unknown function (DUF1707) 0.007986
73 ENOG4105UUD Membrane -0.007980
74 ENOG4105CNX Protein of unknown function (DUF3577) 0.007928
75 ENOG4105F63 Transcriptional regulator 0.007919
76 ENOG4105WZY NA 0.007876
77 ENOG4107T4N CheB methylesterase 0.007848
78 ENOG4105HXY Thiolase 0.007847
79 ENOG4105QEY Lipoprotein 0.007806
80 ENOG4105KMP Tetr family transcriptional regulator -0.007782
81 ENOG4105CAU Arsenical resistance protein, ArsH 0.007753
82 ENOG4108UV2 Transcriptional regulator 0.003876
82 ENOG410907V NA 0.003876
83 ENOG4105EHA HipA domain protein 0.007719
84 ENOG4105CUX Signal transduction histidine kinase 0.007716
85 ENOG41081I1 polysaccharide biosynthesis protein 0.007667
86 ENOG4105TNM Beta subunit 0.002554
86 ENOG41067EA NA 0.002554
86 ENOG4108UUZ Polyketide cyclase / dehydrase and lipid transport 0.002554
87 ENOG4105DJN thiJ pfpI 0.007659
88 ENOG41090VE Diguanylate cyclase 0.007645
89 ENOG4108XAN ABC transporter -0.007642
90 ENOG41090BB DNA mismatch endonuclease (vsr) 0.007626
91 ENOG41070KT NA 0.007611
92 ENOG4105EKJ Nitrile hydratase subunit alpha 0.007611
93 ENOG4105FN9 activator of Hsp90 ATPase 1 family protein -0.007603
94 ENOG4105VDQ RES domain-containing protein 0.007596
95 ENOG41075EB NA 0.007594
96 ENOG4105MP9 class II Aldolase -0.007566
97 ENOG4107R7T glycosyl transferase group 1 0.007559
98 ENOG4105D44 asparaginase -0.007539
99 ENOG4106EWM NA 0.001884
99 ENOG4106KKS NA 0.001884
99 ENOG4107GGN NA 0.001884
99 ENOG4107NSR Bacterial regulatory proteins, tetR family 0.001884
100 ENOG4106HNQ Excalibur 0.007526
101 ENOG4108QBY acyl-Coa dehydrogenase 0.007492
102 ENOG4105XEA Tetr family transcriptional regulator 0.007491
103 ENOG4105D4K integrase catalytic -0.007470
104 ENOG4107JEE Short-chain dehydrogenase reductase Sdr 0.007465
105 ENOG4105UHE 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) 0.002487
105 ENOG4108Q71 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) (By similarity) 0.002487
105 ENOG4108UAD H -transporting two-sector ATPase gamma subunit 0.002487
106 ENOG4108Z41 -acetyltransferase 0.007395
107 ENOG4107F61 NA 0.007370
108 ENOG4105EXU Membrane 0.007355
109 ENOG4105F8N transfer protein 0.007348
110 ENOG4108AXW Transposase 0.007336
111 ENOG4105CBC glutamate synthase 0.007328
112 ENOG4108US7 NA -0.007309
113 ENOG4108IJ0 Aspartate ammonia-lyase -0.007308
114 ENOG4105VEC DNA binding domain protein, excisionase family 0.007294
115 ENOG4106NZI LysR family Transcriptional regulator 0.007292
116 ENOG41072T1 NA 0.007273
117 ENOG4105CMA conjugation trbi family protein 0.007261
118 ENOG4106BEH NA 0.007258
119 ENOG4106MYW cytochrome P450 0.007255
120 ENOG4105MVV NAD binding domain of 6-phosphogluconate dehydrogenase 0.001803
120 ENOG4107UM7 2-Nitropropane dioxygenase 0.001803
120 ENOG41081WT Domain of unknown function (DUF309) 0.001803
120 ENOG4108M3W fumarate reductase succinate dehydrogenase flavoprotein domain protein 0.001803
121 ENOG4107VAA lipid a biosynthesis lauroyl acyltransferase 0.003593
121 ENOG41085XP transcriptional regulator), MarR family 0.003593
122 ENOG4105SZT Methyltransferase, type 11 0.007185
123 ENOG4106DX9 Aromatic-ring-hydroxylating dioxygenase beta subunit 0.007176
124 ENOG41063MH muconolactone delta-isomerase -0.007162
125 ENOG4107QMH DNA methylase 0.007161
126 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.007158
127 ENOG4106MEM Type III 0.007153
128 ENOG4105D45 K07001 NTE family protein -0.007126
129 ENOG410645I ompa motb domain protein 0.007124
130 ENOG4105HF1 Tetr family transcriptional regulator 0.003562
130 ENOG41061KA protein serine threonine phosphatase 0.003562
131 ENOG4105W2W Cytotoxic translational repressor of toxin-antitoxin stability system 0.007120
132 ENOG4106NKJ MmcI protein -0.007099
133 ENOG4105C6I Resolvase -0.007057
134 ENOG4105CE3 Membrane 0.001764
134 ENOG4105EWB Pfam:DUF1527 0.001764
134 ENOG4105IGV F pilus assembly Type-IV secretion system for plasmid transfer 0.001764
134 ENOG4105V16 exported protein 0.001764
135 ENOG4108Z6W dioxygenase, subunit beta 0.007041
136 ENOG4108S25 Inherit from NOG: Carboxymuconolactone decarboxylase family 0.007000
137 ENOG4108PZD NA 0.006988
138 ENOG4105M43 isoprenylcysteine carboxyl methyltransferase 0.006979
139 ENOG4105HQY Inherit from NOG: molybdopterin-guanine dinucleotide biosynthesis protein a-like protein 0.001394
139 ENOG4105MZF histidine triad (HIT) protein 0.001394
139 ENOG410630E NA 0.001394
139 ENOG4108QP1 Cdp-alcohol phosphatidyltransferase 0.001394
139 ENOG4108TI1 NA 0.001394
140 ENOG4105PW2 ggdef family 0.001741
140 ENOG41067MZ tonB-dependent Receptor 0.001741
140 ENOG4108P23 NA 0.001741
140 ENOG4108Q7G transcriptional regulator), MarR family 0.001741
141 ENOG4105RE0 Asp Glu hydantoin racemase -0.006959
142 ENOG4105G0T bifunctional deaminase-reductase domain protein 0.003479
142 ENOG4108AGM Major Facilitator superfamily 0.003479
143 ENOG4108SC8 transcriptional regulatory protein 0.006938
144 ENOG4105HA9 of methanol dehydrogenase type 0.006936
145 ENOG4107NHP NA -0.006920
146 ENOG4108RS1 cytochrome C 0.006911
147 ENOG4108YRB methyltransferase -0.006898
148 ENOG4105KBH arsR family transcriptional regulator 0.006896
149 ENOG4105E1X IstB domain-containing protein ATP-binding protein 0.006889
150 ENOG4108RDT NADH dehydrogenase NAD(P)H nitroreductase) -0.006880
151 ENOG4105ECE NA 0.006871
152 ENOG4107QQN Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties (By similarity) 0.006869
153 ENOG4105HSS phospholipase C -0.006867
154 ENOG4105YTY O-Antigen ligase 0.006865
155 ENOG4108SJV rieske 2fe-2S domain-containing protein 0.006855
156 ENOG4105CYY Plasma membrane H -transporting two-sector ATPase 0.006850
157 ENOG4105EHI Phosphonate ABC transporter, periplasmic -0.006848
158 ENOG4105H6R Polyketide cyclase / dehydrase and lipid transport 0.002282
158 ENOG41064UR NA 0.002282
158 ENOG4107STH Beta-lactamase domain-containing protein 0.002282
159 ENOG4108KGH TRANSCRIPTIONal -0.006819
160 ENOG4106TD9 Diguanylate cyclase 0.006809
161 ENOG4107RX3 Mg2 transporter protein cora family protein 0.006798
162 ENOG4107UWT Esterase, phb depolymerase family -0.006796
163 ENOG410906A Beta-Ig-H3 fasciclin 0.006792
164 ENOG4105C84 Histidine ammonia-lyase -0.002263
164 ENOG4105CGP Urocanate hydratase -0.002263
164 ENOG4105CI2 imidazolone-5-propionate hydrolase -0.002263
165 ENOG4105FEQ ParB domain protein nuclease 0.006782
166 ENOG4107G54 Aldolase_II 0.006767
167 ENOG4107RBR Receptor 0.006752
168 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) 0.006748
169 ENOG4105CFI type iii restriction protein res subunit 0.003369
169 ENOG4108104 S-isoprenylcysteine methyltransferase-like protein 0.003369
170 ENOG4108JZ8 Cation efflux protein -0.006734
171 ENOG4107S75 HAD-superfamily hydrolase subfamily IA variant 3 0.006725
172 ENOG4105CKY Catalyzes the cleavage of L-kynurenine (L-Kyn) and L-3- hydroxykynurenine (L-3OHKyn) into anthranilic acid (AA) and 3- hydroxyanthranilic acid (3-OHAA), respectively (By similarity) -0.006693
173 ENOG4108ZP6 Domain of unknown function (DU1801) 0.006690
174 ENOG4107U5G NA 0.006686
175 ENOG4105WT5 NA -0.006678
176 ENOG4105D8C 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) -0.003337
176 ENOG4108RKD Lipase esterase -0.003337
177 ENOG410672U NA 0.006673
178 ENOG4108QHR Inherit from NOG: sulfotransferase 0.006666
179 ENOG4106GZS NA 0.000949
179 ENOG4106UP2 GreA GreB family elongation factor 0.000949
179 ENOG4107R6K D-amino-acid dehydrogenase 0.000949
179 ENOG4107RZQ Nad-dependent epimerase dehydratase 0.000949
179 ENOG4108DT2 Carboxymuconolactone decarboxylase family 0.000949
179 ENOG4108I98 Major Facilitator superfamily 0.000949
179 ENOG4108K8K Transcriptional regulator 0.000949
180 ENOG4105GR3 Histidine kinase -0.006642
181 ENOG4105CK4 Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) -0.006642
182 ENOG4106G05 NA -0.006633
183 ENOG4105DFP Integrase 0.006631
184 ENOG4105CJH Alcohol dehydrogenase zinc-binding domain protein 0.006624
185 ENOG4107Y2X deaminase -0.006603
186 ENOG4107BSQ NA -0.006602
187 ENOG4106RUC dihydrodipicolinate 0.006594
188 ENOG4105KWT Pfam:DUF419 -0.006591
189 ENOG4108SNI TRANSCRIPTIONal 0.006586
190 ENOG4107ZWT protein with cbs domains 0.006576
191 ENOG41062PH NA 0.006576
192 ENOG4106BET Sodium calcium exchanger 0.006562
193 ENOG4108N61 Serine Threonine protein kinase 0.006551
194 ENOG41074JJ Transcriptional regulator -0.006524
195 ENOG4105WG4 Protein of unknown function (DUF3072) 0.006498
196 ENOG4105D4Z Chromate resistance -0.006497
197 ENOG41086D9 heavy metal transport detoxification protein -0.006496
198 ENOG4105FFF abc transporter permease protein -0.006495
199 ENOG4107DBN Cellulose-binding protein 0.006489
200 ENOG4108PBR AMP-binding enzyme 0.006484
201 ENOG41080KD TonB family -0.006471
202 ENOG4106AWJ NA 0.002154
202 ENOG4107V5K Protein of unknown function DUF58 0.002154
202 ENOG4107ZXH von Willebrand factor, type A 0.002154
203 ENOG4107Z47 Signal transduction histidine kinase 0.006460
204 ENOG4105GC8 NA 0.000585