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 ENOG4105NPC Membrane 0.011715
2 ENOG4105PJG NA 0.011498
3 ENOG4108I7E Sodium/hydrogen exchanger family 0.010426
4 ENOG41082I9 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) -0.010198
5 ENOG4108Z86 Glutamine amidotransferase 0.010135
6 ENOG4108HEQ Dinitrogenase iron-molybdenum cofactor 0.010115
7 ENOG4108N10 NA 0.009414
8 ENOG4106UYT NA 0.009333
9 ENOG4105E0A ABC, transporter -0.009122
10 ENOG4105CCY NADH flavin oxidoreductase, NADH oxidase 0.008966
11 ENOG4108HQ0 Exopolysaccharide biosynthesis protein -0.008550
12 ENOG4106IPI cyclase, family 0.008354
13 ENOG41069VG NA 0.008138
14 ENOG4107R2F nlpC P60 family protein -0.008130
15 ENOG4105EHG Permease protein -0.008093
16 ENOG4105H61 Nitroreductase -0.008064
17 ENOG4105XNJ branched-chain amino acid transport -0.008027
18 ENOG4105DCT glycerol dehydrogenase -0.008016
19 ENOG4105HHQ 6-phosphogluconolactonase (EC 3.1.1.31) -0.008015
20 ENOG4105CFI type iii restriction protein res subunit -0.007923
21 ENOG4108MG2 Transcriptional Regulator AraC Family 0.007808
22 ENOG4105GB1 bioY protein -0.007778
23 ENOG41090I7 cation diffusion facilitator family transporter 0.007773
24 ENOG4105KMR acetyltransferase, (GNAT) family 0.007633
25 ENOG4105IH9 NA 0.007632
26 ENOG4108YZK glyoxalase bleomycin resistance protein dioxygenase -0.007621
27 ENOG41073TP transcriptional regulator -0.007609
28 ENOG4108IQD Involved in the biosynthesis of D-alanyl-lipoteichoic acid (LTA). Catalyzes an ATP-dependent two-step reaction where it forms a high energy D-alanyl AMP intermediate and transfers the alanyl residues from AMP to Dcp (By similarity) -0.007500
29 ENOG4105RPU NA 0.007498
30 ENOG4105VAW lrga family -0.007468
31 ENOG4107S40 ABC, transporter 0.007464
32 ENOG4105PW4 Sugar fermentation stimulation protein homolog -0.007413
33 ENOG41080JN TipAS antibiotic-recognition domain 0.007371
34 ENOG4106AW5 NA 0.007340
35 ENOG4107T14 Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity) 0.007316
36 ENOG4108Z4T Peptidase M50 0.007272
37 ENOG4105K5W NA -0.007216
38 ENOG4105EC2 ftsk spoIIIe 0.007200
39 ENOG4108JJA ABC, transporter -0.007196
40 ENOG4105XKD NA 0.007161
41 ENOG4105QGU Siphovirus protein of unknown function (DUF859) 0.007148
42 ENOG4107T5V SNARE associated Golgi 0.007141
43 ENOG4105CM1 Catalyzes, together with MoaC, the conversion of 5'-GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.007113
44 ENOG4108IJ6 ABC transporter 0.007089
45 ENOG4105GW6 NA -0.007086
46 ENOG4105CZF Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism (By similarity) -0.007077
47 ENOG4105W71 Phosphopantetheine attachment site. (EC 6.1.1.13) -0.006978
48 ENOG41080E8 Transcriptional regulator, Spx MgsR family 0.006908
49 ENOG4105C36 SPFH domain, Band 7 family protein -0.006842
50 ENOG4108JD0 DUF218 domain 0.006834
51 ENOG41061UT Predicted membrane protein (DUF2085) 0.006823
52 ENOG410604Q amidohydrolase 0.006813
53 ENOG4105MFM RNA Polymerase 0.006753
54 ENOG4105D5B Sulfite reductase, subunit A -0.006727
55 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) 0.006711
56 ENOG4105WDG DNA-binding helix-turn-helix protein 0.006690
57 ENOG4107TXC Transcriptional regulator 0.006671
58 ENOG4108ZI8 NA 0.006663
59 ENOG4105PBZ NA 0.006657
60 ENOG4108NQ8 ATPase histidine kinase DNA gyrase B HSP90 domain protein 0.006657
61 ENOG4105Q38 Transcriptional Regulator AraC Family 0.006614
62 ENOG4105YNR glycerophosphoryl diester phosphodiesterase -0.006595
63 ENOG4105WJT transcriptional Regulator Cro CI 0.006594
64 ENOG4106ARX NA 0.006567
65 ENOG41068P3 sporulation protein YqfC 0.006550
66 ENOG4108JEI Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system (By similarity) 0.006547
67 ENOG4108ZI5 domain protein -0.006544
68 ENOG4106KTJ 3D domain protein -0.006513
69 ENOG4108V4U NA -0.006496
70 ENOG4105CPN adenine deaminase 0.006486
71 ENOG4105CMD Transcriptional regulator, GntR family -0.006466
72 ENOG4105CIN aminoacyl-histidine dipeptidase 0.006459
73 ENOG4105EPU Molybdenum cofactor synthesis domain protein 0.006457
74 ENOG41063I6 Protein of unknown function (DUF2752) 0.006428
75 ENOG4107YSK Glycerol-3-phosphate cytidylyltransferase 0.006413
76 ENOG4107SHJ sulfite reductase subunit b -0.006408
77 ENOG4108UGV hypoxanthine phosphoribosyltransferase 0.006407
78 ENOG4106JUT Streptomycin 3''-adenylyltransferase 0.006387
79 ENOG4105DMS mur ligase 0.006364
80 ENOG4107U2C Amino acid permease 0.006363
81 ENOG4106AJ6 F420-0:Gamma-glutamyl ligase 0.006361
82 ENOG4105TFI NA 0.006348
83 ENOG4107USE Diacylglycerol kinase -0.006341
84 ENOG4105KZ5 Nudix family -0.006341
85 ENOG4105ENI DNA helicase 0.006338
86 ENOG4105CYH conjugative transposon membrane protein -0.006332
87 ENOG4108REF Sporulation integral membrane protein ytvi 0.006306
88 ENOG4105WC9 nucleotidyltransferase substrate binding protein, HI0074 family 0.006292
89 ENOG4108IMY Transcriptional regulator 0.006284
90 ENOG4105DCV ABC transporter 0.006270
91 ENOG4105JZZ NA -0.006261
92 ENOG4108K17 NA -0.006257
93 ENOG4105PEF Hydrolase 0.006256
94 ENOG4105XV6 tcdA-E operon negative regulator 0.006245
95 ENOG41086WV sporulation protein YqfC -0.006230
96 ENOG4108H63 Lpxtg-motif cell wall anchor domain protein 0.006225
97 ENOG4107SZ1 shikimate 0.006217
98 ENOG41082UY Transcriptional regulator, arsr family 0.006206
99 ENOG4108UTU response regulator 0.006194
100 ENOG4105DVN RecA-family ATPase -0.001545
100 ENOG4105KYS endodeoxyribonuclease RusA -0.001545
100 ENOG41061N6 phage protein -0.001545
100 ENOG41078AV domain protein -0.001545
101 ENOG4105W8Z 4'-phosphopantetheinyl transferase -0.006155
102 ENOG4107RNY amino acid -0.006150
103 ENOG4105XRQ Xanthine dehydrogenase accessory factor 0.006150
104 ENOG41064M2 NA -0.006146
105 ENOG4108VR8 Branched-chain amino acid -0.006142
106 ENOG4107X93 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.006125
107 ENOG4108R80 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. The C subunit may be involved in assembly of the KDP complex (By similarity) 0.006105
108 ENOG4108JQ0 Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) 0.006098
109 ENOG4105K4H Nlp p60 protein -0.006095
110 ENOG4105KRY conjugative transposon protein -0.006093
111 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase 0.006074
112 ENOG4108QXE glycerophosphoryl diester phosphodiesterase -0.006073
113 ENOG4106FFB NA 0.006064
114 ENOG4105D9K One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions (By similarity) 0.006061
115 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) -0.006049
116 ENOG4105EH4 helicase -0.006030
117 ENOG4107WIA FMN-dependent alpha-hydroxy acid dehydrogenase 0.006010
118 ENOG4106319 transcriptional regulator), MarR family -0.005997
119 ENOG4105WJW Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S- specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX (By similarity) 0.005965
120 ENOG4106C35 abc transporter atp-binding protein 0.005963
121 ENOG4105CJ7 NA 0.005948
122 ENOG4107REE AICARFT/IMPCHase bienzyme -0.005941
123 ENOG41089H9 NA 0.005935
124 ENOG4107BU2 esterase 0.005931
125 ENOG4107RZY Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid (By similarity) -0.005892
126 ENOG4105DMU Mate efflux family protein 0.005885
127 ENOG4105E0C molybdate abc transporter 0.005878
128 ENOG4105Q9D Abortive infection protein AbiGI -0.005875
129 ENOG4105C28 cystathionine -0.005862
130 ENOG4108WGF NA 0.005859
131 ENOG4105K8R UPF0145 protein 0.005854
132 ENOG4105C08 Histidine kinase 0.005850
133 ENOG4105FD2 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) (By similarity) -0.005830
134 ENOG4105K56 Transcriptional regulator -0.005818
135 ENOG4105C90 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). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS (By similarity) 0.005807
136 ENOG4105HFY transporter, permease 0.005807
137 ENOG41084DV enzyme IIB component 0.005805
138 ENOG4105FDE NA 0.005798
139 ENOG4108S74 DNA-binding helix-turn-helix protein 0.005795
140 ENOG4105BZ6 Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides (By similarity) 0.005774
141 ENOG410903H NA 0.005774
142 ENOG4108ZWN Nitroreductase 0.005758
143 ENOG4105KPI PTS system sorbose subfamily IIB component 0.002869
143 ENOG4105PCG Inherit from COG: regulatoR 0.002869
144 ENOG4107YV7 response regulator -0.005727
145 ENOG4105XZ1 NA 0.005721
146 ENOG4108HQV tail tape measure protein 0.005709
147 ENOG4105D01 (LipO)protein 0.005707
148 ENOG4105KXX peptidase s58 dmpa 0.005701
149 ENOG4107HY1 Dehydrogenase 0.005689
150 ENOG4107QSK Phage infection protein -0.005682
151 ENOG41068FG NA 0.005676
152 ENOG4105WWN NA -0.005664
153 ENOG4108Z2X Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity) -0.005651
154 ENOG4108YXW Together with MoaA, is involved in the conversion of 5'- GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.005620
155 ENOG4107TPG myo-inositol catabolism -0.005618
156 ENOG4105F96 Transposase 0.005617
157 ENOG4108G4G portal protein 0.005605
158 ENOG4105CAR Terminase, large subunit 0.005603
159 ENOG4108XXK NUDIX hydrolase -0.005599
160 ENOG4106MVZ Membrane 0.005595
161 ENOG4108TXY site-specific recombinase, phage integrase family 0.005592
162 ENOG4107X73 Inherit from COG: 4Fe-4S Ferredoxin iron-sulfur binding domain protein 0.005590
163 ENOG4108V4M Cobalt abc transporter 0.005589
164 ENOG41064ZH Pfam:DUF1893 0.005576
165 ENOG4108R3I dna polymerase iii -0.005567
166 ENOG4105CI5 domain protein 0.005564
167 ENOG4108SWU Histidine kinase -0.005563
168 ENOG4108YYD acetyltransferase 0.005549
169 ENOG41076CZ activating enzyme -0.005548
170 ENOG4105XC8 protein, conserved in bacteria 0.005542
171 ENOG4107VHK HTH_XRE -0.005542
172 ENOG410607W Transposase 0.005535
173 ENOG4105CYX Short-chain dehydrogenase reductase Sdr 0.005530
174 ENOG4108052 hydrolase, Nudix family 0.005522
175 ENOG41081MC TRANSCRIPTIONAl REGULATOR GntR family 0.005521
176 ENOG4106R8B NA 0.005516
177 ENOG4108RU2 n-acetylmuramoyl-l-alanine amidase -0.005511
178 ENOG4105ENQ Alpha-L-fucosidase 0.005508
179 ENOG4105WUG Toxin-antitoxin system, antitoxin component, HicB family 0.005499
180 ENOG41083AA HTH_XRE 0.005487
181 ENOG4108Z5G NA -0.005485
182 ENOG4105PNH acetyltransferase, (GNAT) family 0.005477
183 ENOG4108RBZ Transcriptional regulator, Crp Fnr family 0.005472
184 ENOG41060V9 Cysteine-rich small domain protein 0.005471
185 ENOG4105WUA NA 0.005471
186 ENOG4108VWU Histidine kinase -0.005465
187 ENOG4105YJE holin, phage phi LC3 family 0.005456
188 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin 0.005445
189 ENOG4106E6N NA 0.005445
190 ENOG41067QW Transcriptional regulator 0.005438
191 ENOG410817Q Pentapeptide repeat protein 0.005434
192 ENOG4105MD7 metal-dependent hydrolase -0.005433
193 ENOG4107XYM Inherit from COG: Beta-lactamase 0.005426
194 ENOG4108M2T Binding Domain protein -0.005411
195 ENOG4105F1T DNA repair protein -0.005407
196 ENOG4105VIC PAP2 Family -0.005399
197 ENOG4105UG4 Inherit from COG: DNA recombination 0.005394
198 ENOG4107DES NA -0.005384
199 ENOG4107HJ6 Competence protein 0.005370
200 ENOG4107S00 Xylose isomerase domain protein TIM barrel -0.005349
201 ENOG4105BZW Glycerate kinase -0.005343
202 ENOG4105DTV traE protein -0.005328
203 ENOG41077EP Pfam:DUF2174 0.005324
204 ENOG410618W NA 0.005319
205 ENOG4108P49 AntiSigma factor 0.005310
206 ENOG4108SU4 UPF0309 protein 0.005306
207 ENOG4108RXB Transcriptional regulator (AraC family) 0.005304
208 ENOG4108KH6 NA 0.005304
209 ENOG4105Z6D NA 0.005294
210 ENOG41062KA polysaccharide biosynthesis protein 0.005289
211 ENOG4107MNJ NA 0.005276
212 ENOG4105CSX c4-dicarboxylate anaerobic carrier -0.005273
213 ENOG4105J2K Transcriptional regulator, MarR family -0.005272
214 ENOG4105XPD Periplasmic binding protein LacI transcriptional regulator 0.005270
215 ENOG4105FM6 NA 0.005269
216 ENOG41081FK Mediates zinc uptake. May also transport other divalent cations (By similarity) 0.005260
217 ENOG4107WXJ BadF BadG BcrA BcrD 0.005260
218 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) -0.005258
219 ENOG4107MIU NA 0.005253
220 ENOG410691Z NA 0.005253
221 ENOG41090A1 ferritin 0.005249
222 ENOG4105DEU major facilitator superfamily 0.005243
223 ENOG41061J0 Pyridoxamine 5'-phosphate oxidase 0.005230
224 ENOG4105DWU Membrane 0.005227
225 ENOG4105DKQ ROK family -0.005222
226 ENOG41084TV HAD-superfamily subfamily IB hydrolase -0.005215
227 ENOG4105WGC NA 0.005214
228 ENOG4108UMI ABC transporter, permease 0.005211
229 ENOG4108TM0 transcriptional regulator, RpiR family 0.005209
230 ENOG4105DBI uridine monophosphokinase -0.005207
231 ENOG4108R03 Major Facilitator superfamily -0.005206
232 ENOG4105CMG Carbohydrate kinase 0.005195
233 ENOG4105C6Q that is required for full activity and stability of the Y subunit. Could have a chaperone-like function for the proper and stable folding of 0.002595
233 ENOG4107XM4 PTS system sorbose subfamily IIB component 0.002595
234 ENOG4108Q1H PHP domain protein 0.005187
235 ENOG4108BII NA 0.005187
236 ENOG4105EIZ Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) -0.005183
237 ENOG4105EY8 ABC transporter 0.005180
238 ENOG4108927 Bacterial extracellular solute-binding protein 0.005169
239 ENOG4105NMU Transcriptional regulator 0.005167
240 ENOG41080KT Resistance protein 0.005160
241 ENOG4105FZN Glycosyl transferase (Group 1 -0.005157
242 ENOG4108JPM phospho-2-dehydro-3-deoxyheptonate aldolase 0.005150
243 ENOG4105SKP Gnat family 0.005149
244 ENOG4105H6D Gcn5-related n-acetyltransferase 0.005149
245 ENOG4105CV1 Transketolase (EC 2.2.1.1) -0.005146