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 ENOG4105DEG Vwa containing coxe family protein -0.010634
2 ENOG4105ECP epimerase -0.010168
3 ENOG4105F0R Cytidylyltransferase 0.010042
4 ENOG4108VGH Abortive infection bacteriophage resistance protein 0.009865
5 ENOG4105ESV Glycosyl transferase, family 4 -0.009359
6 ENOG4105C1V Peptidase, M16 0.009349
7 ENOG4105KKX ATPase associated with various cellular activities aaa_5 -0.009039
8 ENOG4105UQX Mate efflux family protein 0.008851
9 ENOG4107NHW Inherit from COG: Helicase 0.008850
10 ENOG4105RD5 NA -0.008769
11 ENOG4108IQF Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA (By similarity) 0.008769
12 ENOG4105CF4 DegT DnrJ EryC1 StrS aminotransferase 0.008630
13 ENOG4105JF5 Protein of unknown function (DUF2400) 0.008301
14 ENOG4105CNA YD repeat protein 0.008224
15 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase -0.008153
16 ENOG4106B26 peptidase M15 0.008151
17 ENOG4107TN3 Dicarboxylate carrier 0.008137
18 ENOG4108E0S reductase 0.008120
19 ENOG41082RA The GLUG motif protein family protein -0.008103
20 ENOG4105D6J arsenicaL-resistance protein -0.008059
21 ENOG4105D5G Transposase 0.007988
22 ENOG4108R96 Methyltransferase, YaeB family 0.007899
23 ENOG4108KMX efflux transporter, rnd family, mfp subunit -0.007704
24 ENOG4105QVV ADP-ribosylglycohydrolase 0.007683
25 ENOG4107B0G NA 0.007662
26 ENOG4105C36 SPFH domain, Band 7 family protein 0.007656
27 ENOG4108H0W NADP-dependent L-serine L-allo-threonine dehydrogenase YdfG 0.007632
28 ENOG410622M DNA alkylation repair enzyme -0.007586
29 ENOG4105CSH Transporter 0.007550
30 ENOG4105HMI Membrane 0.007549
31 ENOG4105R5B NA 0.007493
32 ENOG4105C26 Dehydrogenase 0.007397
33 ENOG4105H22 cyclic nucleotide-binding domain protein 0.007353
34 ENOG4105Z9G Pfam:DUF1200 0.007319
35 ENOG4105VXP Protein of unknown function DUF86 0.007302
36 ENOG4105N27 NA -0.007269
37 ENOG410757D NLPA lipoprotein -0.007232
38 ENOG4105WB2 Transcriptional regulator, arsR family -0.007210
39 ENOG4105NNJ SMI1_KNR4 -0.007194
40 ENOG4106Q48 NA -0.007181
41 ENOG4106PA7 NA 0.007178
42 ENOG4105D76 Glutaminase 0.007176
43 ENOG4107SW5 Peptidase M16 domain protein -0.007153
44 ENOG4105C3R Methionine synthase -0.007148
45 ENOG4108ZUP Transcriptional regulator, ARAC family -0.007027
46 ENOG4106DMR domain protein 0.007021
47 ENOG4105CD0 Phage Integrase Family 0.007014
48 ENOG41085BW type i restriction modification DNA specificity domain protein 0.007001
49 ENOG4105DCB Transcriptional regulator 0.006994
50 ENOG4108PSV Pantothenate kinase 0.006983
51 ENOG4105EAG UDP-N-acetylglucosamine 2-epimerase 0.006976
52 ENOG4105C5E polysaccharide biosynthesis protein 0.006939
53 ENOG4106VN7 NA 0.006930
54 ENOG41063GB abc transporter atp-binding protein 0.006854
55 ENOG4107QR9 Iron-sulfur cluster binding protein 0.006830
56 ENOG4105G6Z alkaline phosphatase -0.006830
57 ENOG4105FCI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate (By similarity) -0.006793
58 ENOG4106RHM NA 0.006771
59 ENOG4105C04 l-carnitine dehydratase bile acid-inducible protein F 0.006751
60 ENOG4108PKI Glycosyl hydrolase family 92 -0.006743
61 ENOG4108KWB SusD family 0.006737
62 ENOG4105D2T synthase 0.006699
63 ENOG41067VK repeat protein 0.006695
64 ENOG4108806 TonB-linked outer membrane protein, SusC RagA family 0.006665
65 ENOG4105CYC Transferase -0.006665
66 ENOG4107RAP type iii restriction 0.006653
67 ENOG4106NXM membrAne 0.006645
68 ENOG4105D26 NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. The first step is catalyzed by NqrF, which accepts electrons from NADH and reduces ubiquinone-1 to ubisemiquinone by a one-electron transfer pathway (By similarity) 0.006631
69 ENOG41089XS Glycosyl transferase family 2 0.006628
70 ENOG4105TRN Carbohydrate binding family 6 -0.006613
71 ENOG4105C1B dTDP-glucose 4-6-dehydratase -0.006604
72 ENOG4105DU5 N-acetylneuraminate lyase 0.006587
73 ENOG4105T6S Protein of unknown function (DUF3737) 0.006571
74 ENOG4107SCT Transcriptional regulator 0.006556
75 ENOG4108NE6 tetratricopeptide repeat domain protein -0.006549
76 ENOG4108IUM Glycogen debranching enzyme 0.006549
77 ENOG4107S9M Inherit from COG: type iii restriction protein res subunit -0.006539
78 ENOG4106MY0 NA -0.006530
79 ENOG4107M0B NA 0.006523
80 ENOG4107UIE peptidase 0.006495
81 ENOG4108TK7 group 1 glycosyl transferase 0.006480
82 ENOG4105DPE Conserved Protein -0.006480
83 ENOG41088T4 Helicase IV -0.006451
84 ENOG4108SHR vitamin B12 dependent methionine synthase activation -0.006436
85 ENOG4105KYB Mazg nucleotide pyrophosphohydrolase -0.006435
86 ENOG4108ZPG Dehydratase 0.006400
87 ENOG4108ZQX ybak prolyl-trna synthetase -0.006386
88 ENOG4106G18 Zinc finger, swim domain protein -0.006365
89 ENOG4108KGD glucose galactose transporter 0.006330
90 ENOG4108376 Membrane 0.006326
91 ENOG41072M3 transporter major facilitator family protein -0.006309
92 ENOG4108NF5 Ragb susd domain-containing protein 0.006308
93 ENOG4105F4J NA 0.006300
94 ENOG4105RHA ABC transporter, permease -0.006291
95 ENOG41067TB Fimbrial assembly family protein 0.006285
96 ENOG4105TAP Redoxin -0.006278
97 ENOG4106F9J NA -0.006269
98 ENOG4108ZGB N-(5'-phosphoribosyl)anthranilate isomerase 0.006260
99 ENOG4108TSH transposase 0.006252
100 ENOG4108VEM Acyl-ACP thioesterase -0.006245
101 ENOG4106T2M NA 0.006233
102 ENOG4108P3Z response regulator (Receiver 0.006231
103 ENOG4107QTS cobalamin synthesis protein, P47K 0.006208
104 ENOG4105ECE NA 0.006191
105 ENOG4105N0P glycosyl transferase group 1 0.006187
106 ENOG4108HVP ATPase histidine kinase DNA gyrase B HSP90 domain protein 0.006179
107 ENOG4105C30 Nad-dependent epimerase dehydratase 0.006157
108 ENOG4107DKY pseudaminic acid biosynthesis-associated protein PseG 0.006157
109 ENOG4105DDD glycerophosphoryl diester phosphodiesterase 0.006112
110 ENOG4105QHG type I restriction-modification system, S subunit 0.006105
111 ENOG41069R5 rhs family -0.006104
112 ENOG4107KYD )-transporter -0.006097
113 ENOG4108M2Y site-specific recombinase, phage integrase family -0.006083
114 ENOG4106UMM TonB-linked outer membrane protein, SusC RagA family -0.006050
115 ENOG41068R6 NA -0.006046
116 ENOG4108PAV RagB SusD domain protein -0.006044
117 ENOG41075GS Ragb susd domain-containing protein -0.006033
118 ENOG41090BB DNA mismatch endonuclease (vsr) -0.006030
119 ENOG41080GV L-lysine permease -0.006024
120 ENOG4108UZF 3-5 exonuclease 0.006015
121 ENOG41087AP Two component transcriptional regulator, lyttr family -0.006012
122 ENOG4107M53 biosynthesis protein 0.006012
123 ENOG410757I NA 0.006011
124 ENOG4107UDQ NA 0.006007
125 ENOG4106JFX NA 0.003003
125 ENOG4106U08 VirE N-terminal domain protein 0.003003
126 ENOG4105WH1 Two component transcriptional regulator luxr family -0.005995
127 ENOG4105K8S NA 0.005992
128 ENOG4108TTI Anti-feci sigma factor, fecr 0.005984
129 ENOG4105PV6 Rhodanese domain protein 0.005982
130 ENOG4106XPE Inherit from NOG: cyclin related protein -0.005960
131 ENOG4108IJ8 ABC transporter 0.005954
132 ENOG4107QJD pyruvate phosphate dikinase -0.005945
133 ENOG4105ECI YeeC-like protein -0.005945
134 ENOG4108NRW Phospholipase, patatin family 0.005943
135 ENOG4108KBJ Inner membrane protein YkgB 0.005927
136 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.005922
137 ENOG4105CK7 Sodium proline symporter -0.005921
138 ENOG41060KZ Hepn domain protein 0.005916
139 ENOG4105KUI Membrane 0.005883
140 ENOG4107RGE Inherit from COG: ATPase (AAA -0.005877
141 ENOG4107YM1 mraZ protein 0.005874
142 ENOG4106MU0 NA -0.005873
143 ENOG4107JKB Peptidase family M23 -0.005872
144 ENOG4108UB9 transcriptional regulator, AsnC family 0.005868
145 ENOG4105EKQ RNA-directed DNA polymerase -0.005855
146 ENOG4106GZC NA -0.005853
147 ENOG4105CQE ragb susd domaiN-containing protein 0.005849
148 ENOG4106FDP NA 0.005847
149 ENOG4106AB2 Activator of Hsp90 ATPase homolog 1-like protein 0.005847
150 ENOG4105G3P Lipoprotein lpqB 0.001462
150 ENOG4105RM6 Redox protein 0.001462
150 ENOG410727J NA 0.001462
150 ENOG4107PPT NA 0.001462
151 ENOG4107RN2 Peptidase family S49 0.005845
152 ENOG4105D7J NA -0.005826
153 ENOG4105E4F Isochorismate synthase 0.005824
154 ENOG4105FPS Phosphoesterase, PA-phosphatase related 0.005818
155 ENOG4105Q1Q NA 0.005818
156 ENOG4105VHJ Membrane protein implicated in regulation of membrane protease activity 0.005807
157 ENOG4105CV8 reductase -0.005795
158 ENOG4105CFZ Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III (By similarity) 0.005794
159 ENOG41088Q5 VirE N-terminal domain 0.005776
160 ENOG4105JB0 ompA family -0.005774
161 ENOG41075X2 NA 0.005772
162 ENOG4108P33 TonB family 0.005768
163 ENOG4105KX2 NA 0.005767
164 ENOG4108EGU NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. The first step is catalyzed by NqrF, which accepts electrons from NADH and reduces ubiquinone-1 to ubisemiquinone by a one-electron transfer pathway (By similarity) -0.005749
165 ENOG4107QWS glycogen debranching enzyme glgx -0.005739
166 ENOG41084DX Pfam:DUF583 0.005730
167 ENOG4105STB RNA polymerase sigma-70 factor 0.005717
168 ENOG41063R0 NA 0.005714
169 ENOG4108KKM NA 0.005714
170 ENOG4106A7Y prophage antirepressor 0.005699
171 ENOG4105BZG amino acid carrier protein 0.005697
172 ENOG41087FV NA 0.005691
173 ENOG4105NK8 RNA Polymerase -0.005691
174 ENOG4106RVR NA 0.005688
175 ENOG4105FDR Membrane -0.005686
176 ENOG41081FK Mediates zinc uptake. May also transport other divalent cations (By similarity) -0.005678
177 ENOG4107RV4 alkaline phosphatase 0.005677
178 ENOG4105F6A helicase -0.005674
179 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) -0.005671
180 ENOG4107J9Y NA 0.005669
181 ENOG41063U2 NA 0.005666
182 ENOG4105FBG NA 0.005648
183 ENOG4105GIN NA 0.005642
184 ENOG4106VQ2 NA -0.005640
185 ENOG4106WQ7 repeat protein -0.005637
186 ENOG4105IH7 synthase 0.005623
187 ENOG4105I82 acetyl xylan esterase -0.005622
188 ENOG41085SR NA 0.005619
189 ENOG4107EXU Short-chain dehydrogenase reductase Sdr 0.005608
190 ENOG4108VZK Histidine kinase 0.005608
191 ENOG4105CMG Carbohydrate kinase -0.005606
192 ENOG4108T77 Cmr1 family CRISPR-associated RAMP protein 0.005600
193 ENOG4108WUJ DNA RNA NON-specific endonuclease -0.005593
194 ENOG4105DEF Extracellular solute-binding protein, family 5 0.005577
195 ENOG4105FRY Dehydrogenase -0.005571
196 ENOG4107REH Major facilitator superfamily MFS_1 0.005562
197 ENOG4107SJQ Polysulfide reductase, NrfD 0.005559
198 ENOG4106REX NA 0.005559
199 ENOG410618Y Phosphopantetheine attachment site 0.005555
200 ENOG4106HR6 NA 0.005551
201 ENOG41061IC NA 0.005545
202 ENOG4105U3H NA -0.005539
203 ENOG4107SE4 UDP-N-acetylglucosamine 2-epimerase 0.005526
204 ENOG4108494 NA 0.005517
205 ENOG41068ZA NA 0.005514
206 ENOG4105K0J acyltransferase 3 0.005514
207 ENOG4106DWS NA 0.005510
208 ENOG4107SJR transporter 0.005505
209 ENOG41064EH NA 0.005492
210 ENOG4108QRJ conjugative transposon protein TraO -0.005488
211 ENOG41071PB NA -0.005484
212 ENOG41069ST general stress protein 0.005481
213 ENOG4108G8K HTH_XRE -0.005478
214 ENOG4105CMZ 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. This subunit may bind ubiquinone (By similarity) -0.005476
215 ENOG41076NT NA 0.005475
216 ENOG4106G7N NA 0.005469
217 ENOG4105R6S NADP oxidoreductase, coenzyme f420-dependent 0.005457
218 ENOG4108UE2 O-Antigen Polymerase -0.005454
219 ENOG4106JM6 NA 0.005449
220 ENOG41060NS NA 0.005447
221 ENOG4105M5W response regulator (Receiver -0.005438
222 ENOG4108SGH ABC transporter 0.005430
223 ENOG4107QMH DNA methylase 0.005428
224 ENOG41075FK NA 0.005419
225 ENOG4107AFY proteinase inhibitor I4 serpin 0.005416
226 ENOG4105NAE bifunctional deaminase-reductase domain protein -0.005411
227 ENOG4106JTU AhpC Tsa family 0.005406
228 ENOG4105CGY Dna recombination protein -0.005403
229 ENOG4106U8X sigma factor regulatory protein, FecR PupR family -0.005402
230 ENOG4105QXC NA 0.005401
231 ENOG4105C28 cystathionine -0.005400
232 ENOG4108354 transcriptional regulator), MarR family -0.005399
233 ENOG4105CMQ Chloride channel -0.005388
234 ENOG4105ECB domain protein 0.005384
235 ENOG4105TIJ NA -0.005384
236 ENOG4105D4P Coproporphyrinogen iii oxidase 0.005381
237 ENOG4107YCB isochorismatase 0.005379
238 ENOG4106ACM NA 0.005377
239 ENOG4105NV6 An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes (By similarity) 0.005368
240 ENOG4106KA5 tonB-dependent Receptor 0.005364
241 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase -0.005362
242 ENOG4107T82 DegT DnrJ EryC1 StrS aminotransferase 0.005358
243 ENOG4107ZN0 Ragb susd domain-containing protein -0.005356
244 ENOG4105Y5F NA 0.005352
245 ENOG4108RAV Conserved protein -0.005349
246 ENOG4107SU4 glycoside hydrolase, family 31 -0.005347