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 ENOG4105WAN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.013401
2 ENOG4105CCG Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate (By similarity) 0.012712
3 ENOG4105DUM transcriptional regulator, lysR family 0.010908
4 ENOG4108M2T Binding Domain protein 0.009859
5 ENOG4105CKM Branched-chain carboxylic acid kinase 0.009858
6 ENOG4107SW2 integral membrane protein -0.009321
7 ENOG410665I Acyl-transferase 0.009236
8 ENOG4108UIN ybak prolyl-trna synthetase associated region 0.009027
9 ENOG4105C6G (ABC) transporter 0.008847
10 ENOG41060IW transcriptional regulator PadR family 0.008799
11 ENOG4107WTI Transcriptional regulator, ARAC family 0.008743
12 ENOG4108UZ3 Transporter -0.008736
13 ENOG4105NYF Cytidylyltransferase 0.008712
14 ENOG4105KE9 The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein (By similarity) 0.008688
15 ENOG4105DSJ YicC domain protein 0.008622
16 ENOG4108ZNJ -acetyltransferase 0.008576
17 ENOG4105FNI atp gtp-binding protein 0.008490
18 ENOG4108ZHB oxidoreductase 0.008371
19 ENOG41063ZK Transcriptional Regulator AraC Family 0.008333
20 ENOG4105KR2 Chorismate binding enzyme 0.004115
20 ENOG4107V3Y chorismate binding enzyme 0.004115
21 ENOG4105MKX n-acetylmuramoyl-l-alanine amidase 0.008102
22 ENOG4108SJI hydrolase, family 25 -0.008065
23 ENOG4105NK8 RNA Polymerase -0.008041
24 ENOG4105C2J ABC transporter -0.008020
25 ENOG4105C4B ABC transporter, permease -0.007951
26 ENOG4108UMN azlc family -0.007925
27 ENOG4108N38 Cobalt transport protein 0.007774
28 ENOG4106B9P NA 0.007765
29 ENOG4105BZW Glycerate kinase 0.007694
30 ENOG4105EE8 May catalyze the methylation of C-1 in cobalt-precorrin- 5 and the subsequent extrusion of acetic acid from the resulting intermediate to form cobalt-precorrin-6A (By similarity) 0.007667
31 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 0.007662
32 ENOG4107SHE acetyltransferase, (GNAT) family -0.007650
33 ENOG4105CD9 Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring (By similarity) 0.007640
34 ENOG410908R Methenyltetrahydrofolate cyclohydrolase 0.007568
35 ENOG4105KH7 Phage head-tail adaptor -0.007568
36 ENOG4105DZR Type I site-specific deoxyribonuclease 0.007547
37 ENOG4108K6U Transcriptional regulator, TetR family 0.007546
38 ENOG4105C4X radical SAM domain protein -0.007494
39 ENOG4105E4D integral membrane protein TIGR02185 0.007484
40 ENOG4107R0P L-ribulose-5-phosphate 4-epimerase -0.007459
41 ENOG4105VJV 50s ribosomal protein L35 0.007415
42 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) 0.007386
43 ENOG4105BZN citrate synthase 0.007383
44 ENOG4107RHE UDP-glucose 6-dehydrogenase 0.007381
45 ENOG4108ZWI Transcriptional regulator, TetR family 0.007358
46 ENOG4107RQ4 Aldolase 0.007352
47 ENOG4105EJ7 Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O (By similarity) 0.007293
48 ENOG4107RE7 phosphate butyryltransferase 0.007276
49 ENOG4108XI6 Spore germination -0.007267
50 ENOG41074B5 NA 0.007258
51 ENOG4105D7V transposase -0.007227
52 ENOG4105KEG ribosomal-protein-alanine acetyltransferase -0.007191
53 ENOG4105D43 The glycine cleavage system catalyzes the degradation of glycine (By similarity) 0.007176
54 ENOG4105KVH Transcriptional regulator 0.007121
55 ENOG4107WIA FMN-dependent alpha-hydroxy acid dehydrogenase 0.007120
56 ENOG4107XDH radical SAM domain protein 0.007103
57 ENOG4105I31 Domain of unknown function (DUF1887) -0.007099
58 ENOG4106H6E excisionase family 0.007097
59 ENOG41067V7 50S ribosomal protein L36 -0.007086
60 ENOG4108RDQ ABC transporter 0.007078
61 ENOG4105NTP transcriptional regulator 0.007073
62 ENOG4108VIJ Transposase -0.007051
63 ENOG4108K05 Pyridoxal kinase 0.007045
64 ENOG410801F ribosomal-protein-alanine acetyltransferase 0.007041
65 ENOG4105CHT Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity) -0.007012
66 ENOG4105C3S Mate efflux family protein 0.006977
67 ENOG4105WEG NA 0.006966
68 ENOG4105XUK Acyl-transferase 0.006946
69 ENOG4105MDI NA 0.006912
70 ENOG4105KIP Thioesterase -0.006850
71 ENOG4105IXE Abortive infection protein 0.006840
72 ENOG410821B Transcriptional regulator -0.006831
73 ENOG4108ZW7 flagellar rod assembly protein muramidase flgj 0.006825
74 ENOG41071B2 NA -0.006783
75 ENOG41068WV flagellar FlbD family protein -0.006730
76 ENOG4107U9B transcriptional regulator 0.006705
77 ENOG4108I55 Aminotransferase class I and II 0.006703
78 ENOG41080EZ Pfam:DUF156 -0.006667
79 ENOG4105CJD (Anaerobic) ribonucleoside-triphosphate reductase -0.006624
80 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase -0.006597
81 ENOG4105F61 Uvrd rep helicase 0.006577
82 ENOG4107QVE (Anaerobic) ribonucleoside-triphosphate reductase 0.006559
83 ENOG4105CBA glutamine phosphoribosylpyrophosphate amidotransferase -0.006532
84 ENOG4105VMI -acetyltransferase 0.006503
85 ENOG4108TK9 formylmethanofuran dehydrogenase, subunit E 0.006491
86 ENOG4107RWA tonB-dependent Receptor 0.006484
87 ENOG4105C3P Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity) -0.006449
88 ENOG4106KBT YibE F family protein -0.006444
89 ENOG4105CTJ Metal Dependent Phosphohydrolase 0.006437
90 ENOG4105XXU Phage terminase small subunit -0.006423
91 ENOG4108VCG Ser Thr phosphatase family protein -0.006410
92 ENOG4107S55 Peptidase m29 aminopeptidase ii 0.006384
93 ENOG4105JFD Transcriptional regulator, GntR family 0.006356
94 ENOG4105NA0 Transcriptional regulator -0.006355
95 ENOG4105D90 Nadph-dependent fmn reductase 0.003176
95 ENOG4107WFN Malate lactate 0.003176
96 ENOG4105C03 ribonuclease 0.006330
97 ENOG4107RZ4 Methionine synthase -0.006298
98 ENOG41068PG O-Antigen polymerase -0.006289
99 ENOG4107S79 RHS repeat-associated core domain protein -0.006282
100 ENOG41081U1 ABC transporter 0.006225
101 ENOG4107UWY Methyltransferase -0.006213
102 ENOG41065QQ NA -0.006213
103 ENOG4108VHV Membrane -0.006209
104 ENOG4107RCH Diaminopropionate ammonia-lyase 0.006199
105 ENOG4105ZTF Membrane Spanning Protein 0.006183
106 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) 0.006175
107 ENOG4105WPN DNA integration recombination invertion protein 0.006165
108 ENOG4108YZT Adenosylcobinamide kinase 0.006163
109 ENOG4108Z0R Transferase -0.006159
110 ENOG4107F0N abc transporter permease protein 0.006158
111 ENOG4107QMS site-determining protein 0.006158
112 ENOG4105MFB Transcriptional regulator AbrB family 0.006157
113 ENOG4107R1M Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction proline is first activated by ATP to form Pro- AMP and then transferred to the acceptor end of tRNA(Pro) (By similarity) 0.006143
114 ENOG4108HHA Transketolase 0.006141
115 ENOG4105PUV cyclic nucleotide-binding domain protein -0.006128
116 ENOG4108ZIW QueT transporter 0.006125
117 ENOG4108XZ0 DNA replication protein DnaD -0.006114
118 ENOG4108DEY Inherit from COG: acetyltransferase -0.006109
119 ENOG4105FF0 ErfK YbiS YcfS YnhG 0.006106
120 ENOG4107B38 PQ loop repeat 0.006102
121 ENOG4108W62 ykgG family 0.006100
122 ENOG4105E2X shikimate dehydrogenase -0.006094
123 ENOG4105C71 hydrolase family 65, central catalytic 0.006091
124 ENOG4107TIF Phenazine biosynthesis protein, PhzF family 0.006089
125 ENOG41065PP NA 0.006085
126 ENOG4108VJJ Nitroreductase -0.006081
127 ENOG4105CGQ conserved protein UCP033563 0.006078
128 ENOG4107RX7 Glycogen debranching enzyme 0.006071
129 ENOG4105DFF Rod shape-determining protein mreb 0.006031
130 ENOG410658B Spore coat protein 0.002010
130 ENOG4106931 NA 0.002010
130 ENOG4107V1N corrinoid protein 0.002010
131 ENOG4108YZV phage major capsid protein, HK97 family -0.006019
132 ENOG4105E33 succinate dehydrogenase -0.006008
133 ENOG4108Z9I -acetyltransferase -0.005995
134 ENOG4105C7J ABC transporter, permease -0.001998
134 ENOG4105DAZ ABC transporter -0.001998
134 ENOG4105DB0 abc transporter atp-binding protein -0.001998
135 ENOG4105C8H hydrogenase maturation protein Hypf 0.005983
136 ENOG410802S Integrase core domain protein 0.005978
137 ENOG4108WIN Transcriptional regulator -0.005976
138 ENOG4105MCG Phage protein, HK97 gp10 family -0.005966
139 ENOG4108UMI ABC transporter, permease -0.005939
140 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) -0.005939
141 ENOG4105E5I abc transporter atp-binding protein 0.005933
142 ENOG4107EXU Short-chain dehydrogenase reductase Sdr 0.005930
143 ENOG4107MD5 glycoside hydrolase, family -0.005916
144 ENOG4107V9H nitrite transporter 0.005898
145 ENOG4105E9V Periplasmic binding protein LacI transcriptional regulator -0.005894
146 ENOG4106KA5 tonB-dependent Receptor 0.005890
147 ENOG4107Y3V -acetyltransferase -0.005880
148 ENOG4107XPB Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ 0.005856
149 ENOG4108IAB Phoh family 0.005835
150 ENOG4106YRZ NA 0.005833
151 ENOG4105J79 toxin secretion phage lysis holin 0.005819
152 ENOG4108EKH alcohol dehydrogenase 0.005814
153 ENOG4107RHH site-specific recombinase, phage integrase family 0.005810
154 ENOG41068II XapX domain-containing protein -0.005791
155 ENOG41083DH Inherit from COG: Metal Dependent Phosphohydrolase -0.005789
156 ENOG4107FHI NA -0.005785
157 ENOG4107QR9 Iron-sulfur cluster binding protein 0.005782
158 ENOG4108HX1 Membrane 0.005779
159 ENOG4108WB7 Ferric uptake 0.005774
160 ENOG4108VP5 UreA transporter -0.005767
161 ENOG4105ITR Domain of unknown function (DUF1836) 0.005767
162 ENOG41084XC Protein of unknown function, DUF606 -0.005765
163 ENOG4105C3D Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA (By similarity) 0.005759
164 ENOG4105EF1 ribulokinase -0.005756
165 ENOG4107QW8 radical SAM domain protein 0.005755
166 ENOG4105KUM terminase (Small subunit) 0.005754
167 ENOG4105FCD Major Facilitator 0.005751
168 ENOG41080XV Thioredoxin 0.005750
169 ENOG4105E80 TraG TraD family protein -0.005739
170 ENOG4105F4F gtp-binding protein 0.005728
171 ENOG4105CAR Terminase, large subunit -0.005728
172 ENOG4105TEU NA -0.005718
173 ENOG410847T Crispr-associated ramp protein -0.005716
174 ENOG4107RY2 2 glycosyl transferase -0.005707
175 ENOG4108VQW C_GCAxxG_C_C family 0.005702
176 ENOG4107Y3X Transcriptional regulator, ARAC family 0.005700
177 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) 0.005690
178 ENOG4107QRM domain protein -0.005689
179 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) 0.005676
180 ENOG4105MD7 metal-dependent hydrolase -0.005675
181 ENOG4105DSX permease 0.005672
182 ENOG4105D01 (LipO)protein -0.005660
183 ENOG4108NRW Phospholipase, patatin family -0.005657
184 ENOG4105EQK -acetyltransferase 0.005649
185 ENOG4105T16 Transcriptional regulator (AraC family) -0.005637
186 ENOG4105ECY inositol monophosphatase -0.005634
187 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) -0.005634
188 ENOG4105JVQ RNA Polymerase -0.005633
189 ENOG4107YFU NA -0.005630
190 ENOG4106G6Y NA 0.005626
191 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) 0.005622
192 ENOG4107QWA transporter 0.005620
193 ENOG4108NHZ Transposase -0.005620
194 ENOG4108UNP Transcriptional regulator, TetR family -0.005613
195 ENOG4108ZGC gaf domain protein 0.005613
196 ENOG4105KT5 UmuD protein -0.005607
197 ENOG4107QSZ Mate efflux family protein -0.005597
198 ENOG4108XBC -acetyltransferase 0.005593
199 ENOG4105CV8 reductase -0.005584
200 ENOG4107X8B Domain of unknown function DUF20 0.005583
201 ENOG4105C80 Catalyzes the reversible oxidation of malate to oxaloacetate (By similarity) -0.005578
202 ENOG4107USQ tetratricopeptide 0.005574
203 ENOG4105GG2 protein (LPxTG motif) 0.005571
204 ENOG4106Q9X NA -0.005566
205 ENOG4105E0A ABC, transporter 0.005566
206 ENOG4105CUU Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) (By similarity) -0.005544
207 ENOG4107IS4 domain protein -0.005543
208 ENOG4108VPT UPF0234 protein -0.005537
209 ENOG4108ITR TRANSCRIPTIONal 0.005534
210 ENOG4107XHN domain protein -0.005533
211 ENOG4105W9U CRISPR-associated protein, Cmr5 family -0.005531
212 ENOG4105CM3 Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate (By similarity) 0.005527
213 ENOG4105IB9 phosphoesterase PA-phosphatase related protein -0.000502
213 ENOG4105UWF heterodisulfide reductase -0.000502
213 ENOG4105ZP4 NA -0.000502
213 ENOG4106BRN NA -0.000502
213 ENOG4106DX6 P-47 protein -0.000502
213 ENOG4106GAC NA -0.000502
213 ENOG4106N7U NA -0.000502
213 ENOG4107183 NA -0.000502
213 ENOG4107VWM Alpha beta hydrolase -0.000502
213 ENOG410837S sigma (54) modulation protein -0.000502
213 ENOG410880C NA -0.000502
214 ENOG4108ZI4 Glyoxalase Bleomycin resistance protein (Dioxygenase -0.005525
215 ENOG41063M2 Major facilitator superfamily MFS_1 -0.005525
216 ENOG4105DMC D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3 0.005511
217 ENOG4105VZ8 Transcriptional regulator 0.005504
218 ENOG4105CD5 CoA-binding domain protein 0.005495
219 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) -0.005489
220 ENOG41081QN Phage tail tape measure protein, TP901 family -0.005471
221 ENOG4105QTV Membrane -0.005469
222 ENOG4107U7W abc transporter permease protein 0.005467
223 ENOG4107XT4 ROK family -0.005466
224 ENOG4108XSA NA 0.005449
225 ENOG4105JF5 Protein of unknown function (DUF2400) 0.005445
226 ENOG4108ZBF iron (metal) dependent repressor, dtxr family -0.005444
227 ENOG4105CPN adenine deaminase 0.005442
228 ENOG4105DP4 dak2 domain fusion protein ylov -0.005424
229 ENOG4107RYX Type I site-specific deoxyribonuclease -0.005421
230 ENOG4105C93 Xylose Isomerase -0.005418
231 ENOG4105GJD protein, conserved in bacteria -0.005410
232 ENOG4105XJC Two component transcriptional regulator (Winged helix family -0.005404
233 ENOG4105CVG Homoserine O-transsuccinylase -0.005396
234 ENOG4106703 NA 0.005391