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 ENOG4107T8Z oxidoreductase FAD NAD(P)-binding domain protein 0.009796
2 ENOG4107G5A Sulfite exporter TauE/SafE 0.009643
3 ENOG4107F7H Sulfite exporter TauE/SafE 0.009574
4 ENOG4108RS8 adenylylsulfate reductase beta subunit 0.009430
5 ENOG4105DYM Methyl-viologen-reducing hydrogenase, delta subunit 0.008967
6 ENOG4105CFK Adenylylsulfate reductase subunit alpha 0.008412
7 ENOG4108Z4H NA 0.007267
8 ENOG4108EK9 domain protein 0.007263
9 ENOG4105FTH cobyrinic Acid a,c-diamide synthase 0.007219
10 ENOG4105PXJ Haloacid dehalogenase domain protein hydrolase 0.007103
11 ENOG4107QY1 Aminotransferase 0.007101
12 ENOG4108WA5 NIL domain-containing protein 0.007085
13 ENOG4108VJ3 apbe family lipoprotein 0.007085
14 ENOG4105DH6 Domain of unknown function DUF39 0.007085
15 ENOG4105D0G cobyrinic Acid a,c-diamide synthase 0.007065
16 ENOG4105GZW 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.007043
17 ENOG4105Z5G 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.006867
18 ENOG4107UKH Sulfite exporter TauE/SafE 0.006768
19 ENOG4105C28 cystathionine -0.006745
20 ENOG4105MQ4 Nitrogen regulatory protein pii 0.003349
20 ENOG4105N1R Nitrogen regulatory protein P-II 0.003349
21 ENOG4108TNR Uncharacterised ArCR, COG2043 0.006649
22 ENOG4107XQ4 tetratricopeptide -0.006639
23 ENOG4107RV6 Sulfite exporter TauE/SafE 0.003239
23 ENOG4108ZR0 NA 0.003239
24 ENOG4105CD5 CoA-binding domain protein 0.006417
25 ENOG41080K0 TusE DsrC DsvC family sulfur relay protein (EC 1.8.99.3) 0.006366
26 ENOG4107RIQ Sulfate adenylate transferase 0.006364
27 ENOG410619J SirA family 0.006265
28 ENOG4107EAK nitrate reductase, gamma subunit 0.003095
28 ENOG4107SP1 IroN-sulfur binding 0.003095
29 ENOG4106IVZ signal transduction Histidine kinase 0.006152
30 ENOG4105D5B Sulfite reductase, subunit A 0.006026
31 ENOG4105XWZ Dinitrogenase iron-molybdenum cofactor biosynthesis protein 0.005987
32 ENOG4108ZGY Transcriptional regulator (AsnC family) 0.005922
33 ENOG4108Z1U Pfam:UPF0153 0.005774
34 ENOG4105DRW binding-protein-dependent transport systems inner membrane Component -0.005747
35 ENOG4107RN8 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity) 0.005711
36 ENOG4107VU0 4fe-4S ferredoxin iroN-sulfur binding 0.005655
37 ENOG4105ZRA NA 0.005653
38 ENOG4105DJZ UPF0182 protein 0.005640
39 ENOG4107SE5 nitrilase cyanide hydratase and apolipoprotein n-acyltransferase 0.005633
40 ENOG4105YTV Dinitrogenase iron-molybdenum cofactor biosynthesis protein 0.005586
41 ENOG4108VCZ phospholipase C 0.005571
42 ENOG4107TGY peptidase 0.005565
43 ENOG4105C1A potassium transporter peripheral membrane 0.005549
44 ENOG4107RVX amidohydrolase -0.005541
45 ENOG4108TNS 4Fe-4S ferredoxin iron-sulfur binding domain protein 0.005499
46 ENOG4108JUB Transcriptional regulator 0.005496
47 ENOG4105HKU nucleoside recognition domain-containing protein 0.005456
48 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) 0.005445
49 ENOG4105GSV Inherit from COG: galactose-1-phosphate uridylyltransferase 0.005444
50 ENOG4105P3C Molybdopterin 0.005421
51 ENOG4105VTS DnaJ-like, subfamily C 0.005408
52 ENOG4105F43 Membrane 0.005391
53 ENOG4107FH4 Spore coat associated protein JA (CotJA) 0.005390
54 ENOG4105CY1 sulfite reductase, dissimilatory-type alpha subunit 0.002656
54 ENOG4105PJW Sulfite reductase dissimilatory-type beta subunit 0.002656
55 ENOG410805V Pfam:UPF0153 0.005275
56 ENOG4105C8W ABC transporter 0.005268
57 ENOG41085C7 Domain of unknown function (DUF1858) -0.005267
58 ENOG4105KJP alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen -0.005265
59 ENOG410822G Putative transmembrane protein (Alph_Pro_TM) 0.005254
60 ENOG41090IC Protein of unknown function DUF89 0.005253
61 ENOG4108W7D UspA domain-containing protein 0.005230
62 ENOG4107UWM molybdopterin oxidoreductase -0.005166
63 ENOG4107Z3S ThiF family 0.005157
64 ENOG4107ZY1 (4Fe-4S) ferredoxin -0.005154
65 ENOG4108EQF Aldehyde oxidAse and xanthine dehydrogenase 0.005142
66 ENOG4105X36 (ribosomal) protein -0.005098
67 ENOG4105C8P )-transporter 0.005088
68 ENOG4108UMR transcriptional regulator AsnC family 0.005067
69 ENOG4108Z1Z gCN5-related N-acetyltransferase 0.005033
70 ENOG41088CB thiamine biosynthesis protein ThiS 0.005000
71 ENOG4107R7M peptidase 0.004998
72 ENOG4108ZDX Binds together with S18 to 16S ribosomal RNA (By similarity) 0.004989
73 ENOG4105EWC Purine nucleoside phosphorylase 0.004989
74 ENOG4105E14 MotA TolQ exbB proton channel 0.004980
75 ENOG4105ICY CGGC 0.004975
76 ENOG4105NDA Rhomboid family 0.004971
77 ENOG4105UIA NA 0.000993
77 ENOG41079UY NA 0.000993
77 ENOG4107CFT ATP synthase I chain 0.000993
77 ENOG4107QVU Dead deah box helicase domain protein 0.000993
77 ENOG41084WV DSHCT 0.000993
78 ENOG4105D0B Nitrogenase protein alpha chain 0.002475
78 ENOG4105DSM The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components the iron protein and the molybdenum-iron protein (By similarity) 0.002475
79 ENOG4105KTH gatB Yqey -0.004947
80 ENOG4107VC4 Methyl-accepting chemotaxis 0.004947
81 ENOG4107K54 NA 0.004944
82 ENOG4107ZW0 Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) 0.004941
83 ENOG4107EMA Anti-Sigma-28 factor, FlgM 0.004936
84 ENOG41083MR nifu domain-containing protein 0.004919
85 ENOG4107TP2 heterodisulfide reductase, subunit 0.004914
86 ENOG4107VRK Methyl-accepting chemotaxis 0.004910
87 ENOG4105CFZ Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III (By similarity) -0.004890
88 ENOG4105VR9 phosphoribosylformylglycinamidine synthase -0.004869
89 ENOG4107UBU 4fe-4S ferredoxin iron-sulfur binding domain protein 0.004864
90 ENOG4105VF1 iron-only hydrogenase system regulator 0.004837
91 ENOG4106V1Z NA 0.004805
92 ENOG4105CZ1 Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA (By similarity) -0.004773
93 ENOG4105C40 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs (By similarity) -0.004761
94 ENOG4105WC9 nucleotidyltransferase substrate binding protein, HI0074 family -0.004757
95 ENOG4105CVJ phosphoglycerate mutase 0.004746
96 ENOG4107EEV 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.004738
97 ENOG4108KIK Peptidase, M22 -0.004723
98 ENOG4105K4X Cupin 2, conserved barrel domain protein 0.004714
99 ENOG4105EZY Pyrroloquinoline quinone biosynthesis protein E 0.004709
100 ENOG4105BZQ cdp-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase 0.004689
101 ENOG4107RDK Nucleotidyl transferase 0.004678
102 ENOG4108IQK o-acetylhomoserine -0.004676
103 ENOG41066A7 Inherit from COG: transposase 0.004673
104 ENOG4105IMU UspA domain-containing protein 0.004655
105 ENOG41066FR extracellular solute-binding protein 0.004654
106 ENOG4108R7S Histidine triad (Hit) protein 0.004646
107 ENOG4105DKQ ROK family -0.004640
108 ENOG4105FD2 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) -0.004634
109 ENOG4108R51 NA 0.004617
110 ENOG4105VM8 Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity) 0.004614
111 ENOG4107A5B Binding-protein-dependent transport systems, inner membrane component 0.004608
112 ENOG4105Z0W Dissimilatory sulfite reductase D 0.004597
113 ENOG4105HA9 of methanol dehydrogenase type -0.004595
114 ENOG4108F1B Lactate utilization protein B C 0.004587
115 ENOG4108IZ0 ABC transporter 0.004583
116 ENOG4105STK Helix-turn-helix type 11 domain protein 0.004578
117 ENOG4105BZI indolepyruvate ferredoxin oxidoreductase 0.004573
118 ENOG4105XRQ Xanthine dehydrogenase accessory factor 0.004547
119 ENOG4105M6F mutator MutT protein 0.004541
120 ENOG4105DRC Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.004525
121 ENOG41060K3 Methyltransferase -0.004522
122 ENOG4105KKR C_GCAxxG_C_C family 0.004521
123 ENOG4107R5Y anaerobic glycerol-3-phosphate dehydrogenase, subunit A 0.004515
124 ENOG4105NME NA 0.004507
125 ENOG4106QM5 NA 0.004495
126 ENOG41086B8 CoB-CoM heterodisulfide reductase 0.004484
127 ENOG4105HDW SNARE associated Golgi 0.004480
128 ENOG4105WQX Branched-chain amino acid transport 0.004469
129 ENOG4107XFH GTP-binding signal recognition particle SRP54 G- domain-containing protein 0.004465
130 ENOG4105XU7 response regulator (Receiver 0.002226
130 ENOG4108JWK Fha domain containing protein 0.002226
131 ENOG4107V2P Drtgg domain protein 0.004446
132 ENOG41080V4 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) 0.004443
133 ENOG41073TP transcriptional regulator 0.004439
134 ENOG4107S7T Pyruvate, water dikinase 0.004435
135 ENOG4107FDG Regulatory protein, FmdB family 0.004433
136 ENOG41080QU phosphonate ABC transporter, periplasmic phosphonate-binding protein -0.004432
137 ENOG4105W6K NA 0.004432
138 ENOG4107TI1 Sulfite exporter TauE/SafE 0.004424
139 ENOG4107FJA NA 0.004422
140 ENOG410685X flagellar -0.004421
141 ENOG4105C8M UPF0272 protein 0.004418
142 ENOG4105KRI phosphocarrier protein (HPr -0.004403
143 ENOG4105DTC 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (air) carboxylase 0.004401
144 ENOG4106960 type IV pilus assembly pilz 0.004398
145 ENOG410864T NA 0.004397
146 ENOG4108S24 Fumarate reduCtase 0.004397
147 ENOG4105PW4 Sugar fermentation stimulation protein homolog 0.004393
148 ENOG410855K transcriptional regulator), MarR family 0.004384
149 ENOG4105CRP Part of the ABC transporter FtsEX involved in -0.004384
150 ENOG4107QUS 2-isopropylmalate synthase homocitrate synthase family protein 0.004380
151 ENOG4107S5X heterodisulfide reductase 0.004368
152 ENOG410830X 'Cold-shock' DNA-binding domain protein 0.004366
153 ENOG4105CCM phage protein 0.004363
154 ENOG4105D1C Catalyzes the ATP- as well as the pyrophosphate- dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P- Ser-HPr). The two antagonistic activities of HprK P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion (By similarity) -0.004354
155 ENOG4105BZJ Electron transfer flavoprotein -0.004345
156 ENOG4107RYM Hydantoinase oxoprolinase 0.004343
157 ENOG4107QHI -hydrogenase 0.004342
158 ENOG4106A50 NA 0.004341
159 ENOG4105D4P Coproporphyrinogen iii oxidase -0.004336
160 ENOG4107QQB Ribonuclease E 0.004335
161 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase 0.004333
162 ENOG4105HEE Binding Domain protein -0.004330
163 ENOG4108K9K Uncharacterised protein family (UPF0236) 0.004329
164 ENOG4107F2B Uncharacterized protein conserved in bacteria (DUF2062) 0.004322
165 ENOG4105WE2 aldehyde ferredoxin oxidoreductase 0.004316
166 ENOG4105CY7 stage II sporulation protein E 0.004305
167 ENOG4108VJ1 Transcriptional regulator (CarD family 0.004299
168 ENOG4108UIH futalosine nucleosidase 0.004299
169 ENOG4107QI8 radical SAM domain protein 0.004293
170 ENOG41066Z3 extracellular ligand-binding receptor 0.004290
171 ENOG4106EZU NA 0.004289
172 ENOG4105E21 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity) -0.004288
173 ENOG4105TC6 Nadph-dependent fmn reductase 0.004287
174 ENOG4105DVM PP-loop domain protein 0.004282
175 ENOG41086VZ NA 0.004282
176 ENOG4108EFR Formate dehydrogenase Alpha subunit 0.004279
177 ENOG4105Q0K NA 0.004277
178 ENOG4105E5H Transposase 0.004276
179 ENOG4107DEE NA 0.004274
180 ENOG4107UFN 4Fe-4S Ferredoxin, iron-sulfur binding domain protein -0.004264
181 ENOG4105CNK Required, probably indirectly, for the hydroxylation of 2-octaprenylphenol to 2-octaprenyl-6-hydroxy-phenol, the fourth step in ubiquinone biosynthesis (By similarity) -0.004261
182 ENOG410641Z NA 0.004246
183 ENOG41089BK Glutamine amido-transferase 0.004245
184 ENOG4105NDK ethanolamine utilization protein 0.004241
185 ENOG41075YZ radical SAM domain protein 0.004233
186 ENOG4107Y4S ABC-type sugar transport system, periplasmic 0.004227
187 ENOG4105K8I Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves (By similarity) -0.004226
188 ENOG41067V3 Antibiotic biosynthesis monooxygenase 0.004221
189 ENOG41085BR 4Fe-4S ferredoxin, iron-sulfur binding -0.004220
190 ENOG4107R0Z Flagellar hook-associated protein 3 0.004219
191 ENOG4105FI1 (CBS) domain 0.004204
192 ENOG4108VQW C_GCAxxG_C_C family 0.004202
193 ENOG4108T1X regulatory protein FlaEY 0.004194
194 ENOG4107VIF Cobalt abc transporter 0.004186
195 ENOG4105CB5 ATP-dependent DNA helicase recG -0.004185
196 ENOG41084BT 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.004181
197 ENOG41066IF cbs domain containing protein 0.004172
198 ENOG4106MIY NA 0.004172
199 ENOG4107WBW phosphoribosylaminoimidazolecarboxamideformyltra nsferase (EC 2.1.2.3) 0.004167
200 ENOG4105CJ5 hydrogenase 2 b cytochrome subunit 0.004166
201 ENOG4105I08 Pseudouridine synthase -0.004165
202 ENOG4105HS6 binding-protein-dependent transport systems inner membrane Component -0.004162
203 ENOG4107QXD PAS PAC sensor protein 0.004151
204 ENOG4105K4P CoA-binding domain protein 0.004150
205 ENOG4108Z6V CGGC 0.004148
206 ENOG4107QPI nitrilase cyanide hydratase and apolipoprotein n-acyltransferase 0.004145
207 ENOG4105EHE chorismate mutase- prephenate dehydrogenase 0.004144
208 ENOG4107UPF Outer membrane efflux protein 0.004140
209 ENOG4105WS6 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity) 0.004132
210 ENOG4105DQ9 4Fe-4S Ferredoxin, iron-sulfur binding domain protein 0.004127
211 ENOG4108KR5 Type iv secretory pathway vird4 0.004124
212 ENOG4105TMU NA 0.004117
213 ENOG4105E44 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.004115
214 ENOG4105DDZ Methyltransferase required for the conversion of demethylmenaquinone (DMKH2) to menaquinone (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) (By similarity) 0.004105
215 ENOG4108562 Rod shape-determining protein MreD 0.004103
216 ENOG4107RZH Nitrite and sulphite reductase 4Fe-4S region 0.004099
217 ENOG4108JPM phospho-2-dehydro-3-deoxyheptonate aldolase -0.004092
218 ENOG4105CR6 AtP-binding protein 0.004090
219 ENOG4105CQP nitrilase cyanide hydratase and apolipoprotein n-acyltransferase -0.004083
220 ENOG41089BY NADH_4Fe-4S 0.004080
221 ENOG4105P6G Protein of unknown function (DUF3189) -0.004077
222 ENOG4105DG4 malate L-lactate dehydrogenase -0.004073
223 ENOG4107PPM cobalt chelatase 0.004072
224 ENOG4105EDA )-transporter -0.004070
225 ENOG4105PWN phosphate abc transporter -0.004070
226 ENOG4107QZI cell division protein FtsK 0.004068
227 ENOG4105C1Q protoporphyrinogen oxidase -0.004063
228 ENOG4105XNI Cytochrome c class III 0.004060
229 ENOG4106AZN NA 0.004050
230 ENOG4108U3U Membrane -0.004049
231 ENOG41084K5 addiction module toxin, RelE StbE family 0.004045
232 ENOG4105DY7 DnaK-related protein 0.002022
232 ENOG4105PKC Domain of unknown function (DUF2760) 0.002022
233 ENOG4105FXS Diguanylate cyclase and serine threonine protein kinase with TPR repeats 0.004042
234 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) -0.004041
235 ENOG4108IQJ site-determining protein 0.004035
236 ENOG4108WVM Adenylate guanylate Cyclase 0.004027
237 ENOG4105FKQ transcriptional regulator -0.004017
238 ENOG4105KTW ethanolamine utilization protein 0.004016
239 ENOG4108PK2 permease that is required for glycolipid anchoring of LTA. May facilitate the transport of diglucosyl- diacylglycerol (Glc2-DAG) from the inner to the outer leaflet of the cytoplasmic membrane, delivering Glc2-DAG as a substrate for LTA synthesis, thereby generating glycolipid-anchored LTA. Appears to play an important role in virulence 0.004014