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 ENOG4105CQM Urea amidohydrolase subunit alpha 0.022310
2 ENOG4108F09 Urease subunit gamma beta 0.022060
3 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase -0.015099
4 ENOG4105HFU Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) 0.014698
5 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.014652
6 ENOG4107S5F Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG (By similarity) 0.013926
7 ENOG4105CM9 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG (By similarity) 0.013047
8 ENOG4105P8G Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) 0.006402
8 ENOG4108EI5 Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.006402
9 ENOG4108XNJ Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.012680
10 ENOG4108S0R Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.012556
11 ENOG4105E80 TraG TraD family protein -0.012269
12 ENOG4105FNP Molybdopterin-guanine dinucleotide biosynthesis protein b -0.011959
13 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) -0.011371
14 ENOG4105MME Sugar o-acyltransferase, sialic acid o-acetyltransferase neud family -0.011359
15 ENOG4105FAW cDP-glucose 4,6-dehydratase -0.011011
16 ENOG4107ZAZ Oligosaccharyl transferase, STT3 subunit -0.010894
17 ENOG4105K85 Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) in DNA. Repairs alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated (By similarity) -0.010717
18 ENOG4105Z0F Cytochrome 0.010494
19 ENOG4105CH2 amidohydrolase -0.010368
20 ENOG4107ZMC HAD-superfamily hydrolase, subfamily IA -0.010247
21 ENOG4105DCY Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide (By similarity) 0.010210
22 ENOG4105D3Q Sugar transferase -0.010122
23 ENOG4105EP1 Efflux transporter rnd family, mfp subunit 0.010072
24 ENOG4106ZQ9 Helicobacter outer membrane protein 0.004959
24 ENOG4108RUX type 1 capsular polysaccharide biosynthesis protein 0.004959
25 ENOG4105IW1 AmiS UreI transporter 0.009918
26 ENOG4105EJX conjugal transfer ATPase -0.009896
27 ENOG4108YH3 Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.009789
28 ENOG4107QWZ Heavy metal efflux pump, CzcA 0.009715
29 ENOG410833W Hemolysin-type calcium binding protein -0.009531
30 ENOG4108PH6 NA -0.009463
31 ENOG4107ZYR domain protein 0.009420
32 ENOG4105YQQ NA -0.009405
33 ENOG4105ETV Phytanoyl-CoA dioxygenase -0.009255
34 ENOG4107RZC phospholipase d 0.009202
35 ENOG4105QPS Monooxygenase 0.008881
36 ENOG4105ECX polysaccharide export -0.008783
37 ENOG4105FBQ ATPase associated with various cellular activities aaa_5 0.008726
38 ENOG4105DWY Agmatine deiminase -0.008668
39 ENOG4108RCM Nitroreductase -0.008668
40 ENOG4106EBS Plasmid stabilization system -0.008622
41 ENOG4105C4M (Ubiquinol oxidase) subunit I -0.008588
42 ENOG4106G5I response regulator receiver modulated diguanylate cyclase -0.008581
43 ENOG4107T5V SNARE associated Golgi -0.008568
44 ENOG4108S3N antar domain-containing protein 0.008524
45 ENOG4105K8Q radical SAM domain protein -0.008507
46 ENOG4108MPT abc transporter 0.008485
47 ENOG4107Z84 sensor protein -0.008398
48 ENOG4107PCP NA 0.008297
49 ENOG4105CFB Gamma-glutamyltranspeptidase (EC 2.3.2.2) 0.008232
50 ENOG4105EGJ LysR family Transcriptional regulator 0.008207
51 ENOG4105D3S 4Fe-4S Ferredoxin, iron-sulfur binding domain protein -0.008203
52 ENOG4105CZN Potassium uptake protein 0.008174
53 ENOG4105EY8 ABC transporter -0.008160
54 ENOG4105QAX Iron-sulfur -0.008123
55 ENOG4108Z6K Catalyzes the circularization of gamma-N-acetyl- alpha,gamma-diaminobutyric acid (ADABA) to ectoine (1,4,5,6- tetrahydro-2-methyl-4-pyrimidine carboxylic acid), which is an excellent osmoprotectant (By similarity) 0.008085
56 ENOG4105CA0 peroxidase 0.008053
57 ENOG4105Y3C ABC, transporter 0.008028
58 ENOG41087W6 Protein slyX homolog -0.008011
59 ENOG4108XEJ methyl-accepting chemotaxis protein -0.008002
60 ENOG4105CQU Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner (By similarity) -0.007971
61 ENOG4108IEF Nitrate reductase -0.007968
62 ENOG4108UHE carbonic anhydrase 0.007942
63 ENOG4105CUY Mechanosensitive ion channel 0.007927
64 ENOG4106538 saf domain-containing protein 0.007914
65 ENOG4105CNZ decarboxylase family -0.007910
66 ENOG4105EHG Permease protein -0.007883
67 ENOG4105EA4 abc transporter atp-binding protein 0.003935
67 ENOG4107QZR ABC, transporter 0.003935
68 ENOG4105C3U ABC transporter -0.007863
69 ENOG4105C8U phosphate abc transporter -0.007855
70 ENOG4107TRK Transposase 0.007850
71 ENOG4105CFM UPF0317 protein 0.007845
72 ENOG4105C0N N-acetylglutamate semialdehyde dehydrogenase -0.007841
73 ENOG4105C08 Histidine kinase 0.007832
74 ENOG4107TCT Histidine kinase -0.007790
75 ENOG4105EAU Plays a role in nitrite reduction (By similarity) -0.007784
76 ENOG4108SUJ Ompa motb domain protein -0.007784
77 ENOG4107TSX ABC branched chain amino acid family transporter periplasmic ligand binding protein 0.007766
78 ENOG41065CV thiol peroxidase -0.007700
79 ENOG4107RWC DNA helicase 0.007694
80 ENOG4108V7X Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters -0.007693
81 ENOG4105P15 Prepilin-type N-terminal cleavage methylation domain-containing protein -0.007675
82 ENOG4105I9H NA 0.007663
83 ENOG4108ZPB UPF0306 protein -0.007661
84 ENOG4107WGV tail tape measure protein 0.007654
85 ENOG4105KPN Aminoglycoside phosphotransferase 0.003817
85 ENOG4107XQX choline ethanolamine kinase 0.003817
86 ENOG4107SRD 5-methylcytosine restriction system 0.007610
87 ENOG4107RB5 abc transporter permease protein 0.007579
88 ENOG4108IV0 ABC, transporter -0.007566
89 ENOG4105C0Z ABC transporter -0.007566
90 ENOG4105D4U had-superfamily hydrolase, subfamily iia -0.007563
91 ENOG4105F3Y NA 0.007531
92 ENOG4105EBD Amidase 0.007489
93 ENOG4105S9P Major Facilitator superfamily 0.007470
94 ENOG4107U5Q Coproporphyrinogen iii oxidase -0.007431
95 ENOG4106GIV Protein of unknown function DUF262 0.007414
96 ENOG4107QNW Aldolase 0.007337
97 ENOG4108IUY abc transporter atp-binding protein 0.007337
98 ENOG4108UIN ybak prolyl-trna synthetase associated region 0.007320
99 ENOG4106NDE Ammonium Transporter Family -0.007289
100 ENOG4107DKY pseudaminic acid biosynthesis-associated protein PseG -0.007288
101 ENOG4105EHA HipA domain protein 0.007272
102 ENOG4105E1T DNA ligase -0.007241
103 ENOG4105DAQ Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2) (By similarity) 0.007240
104 ENOG4105EMW 4Fe-4S ferredoxin, iron-sulfur binding -0.007238
105 ENOG4105DXZ ribonuclease BN -0.007237
106 ENOG4106CBV Inherit from COG: Fe-S-cluster oxidoreductase 0.007229
107 ENOG41061E2 NA -0.007220
108 ENOG4105QYF Glycosyl transferase (Group 1 0.007183
109 ENOG41077EP Pfam:DUF2174 0.007165
110 ENOG4107QPK )-transporter 0.007164
111 ENOG4105C0K Gdp-mannose 4,6-dehydratase 0.007138
112 ENOG4107TE2 basic membrane 0.007133
113 ENOG4105CEE C4-dicarboxylate transporter -0.007122
114 ENOG4105PXI polysaccharide deacetylase -0.007121
115 ENOG4107RYC LysR family transcriptional regulator -0.007116
116 ENOG4105GF5 General glycosylation pathway protein -0.007112
117 ENOG4105VXN addiction module toxin, RelE StbE family -0.007111
118 ENOG4106RRX NA 0.007107
119 ENOG4105BZY Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system (By similarity) -0.007082
120 ENOG4106C2P NA 0.007051
121 ENOG4108JQ6 ABC transporter 0.007047
122 ENOG4105CVA phosphate -0.007001
123 ENOG4105G5W regulator Fur family -0.006985
124 ENOG4108NFT Short-chain dehydrogenase reductase Sdr -0.006960
125 ENOG4108VPT UPF0234 protein -0.006948
126 ENOG41060HE NA -0.006934
127 ENOG4105XJC Two component transcriptional regulator (Winged helix family -0.006918
128 ENOG4108DEY Inherit from COG: acetyltransferase 0.006915
129 ENOG4105K9M phosphoribosyltransferase -0.006909
130 ENOG4105VR9 phosphoribosylformylglycinamidine synthase -0.006908
131 ENOG4105DF8 Transketolase -0.006902
132 ENOG41064PH Sporulation related domain -0.006901
133 ENOG41090FP flagellin -0.006898
134 ENOG4105GR3 Histidine kinase -0.006898
135 ENOG41065UY NA -0.006895
136 ENOG4107F67 NA 0.006874
137 ENOG4107U8W Helicase 0.006857
138 ENOG4105E0A ABC, transporter -0.006851
139 ENOG4105YXJ CopG domain protein DNA-binding domain protein -0.006851
140 ENOG4105CBB PepSY-associated TM helix domain protein 0.006842
141 ENOG4108I67 Catalyzes the synthesis of activated sulfate (By similarity) -0.006840
142 ENOG41076YT nitrate reductase, gamma subunit -0.006839
143 ENOG4108F0V Aminotransferase 0.006824
144 ENOG4106050 phage regulatory protein, rha family -0.006798
145 ENOG4105EEX Two component transcriptional regulator (Winged helix family 0.006795
146 ENOG4108SEU NA -0.006794
147 ENOG4106SE9 helicase 0.006794
148 ENOG4108UE5 NA 0.006792
149 ENOG4105VFU Rna-binding protein 0.006780
150 ENOG4107T1N adenine specific DNA methylase -0.006778
151 ENOG41065Q1 NA -0.006769
152 ENOG4105K6D phospholipase d 0.006764
153 ENOG4105DBF Periplasmic binding protein -0.006762
154 ENOG4108RM5 Nad-dependent epimerase dehydratase 0.006755
155 ENOG4105YR8 GlcG protein 0.006753
156 ENOG4108Z24 l-2,4-diaminobutyric acid acetyltransferase 0.006736
157 ENOG4105C1D Membrane 0.006732
158 ENOG4105CSJ Enoyl- acyl-carrier-protein reductase NADH -0.006731
159 ENOG4105NNK integral membrane protein 0.006726
160 ENOG4108EFQ Molybdopterin oxidoreductase Fe4S4 domain -0.006711
161 ENOG4105D13 transposase 0.006694
162 ENOG4105C80 Catalyzes the reversible oxidation of malate to oxaloacetate (By similarity) -0.006675
163 ENOG4108QRP hydrolase, carbon-nitrogen family -0.006670
164 ENOG4108UHC Glycosyl transferase, wecb taga cpsf family -0.006658
165 ENOG410800C AAA -0.006646
166 ENOG4108MZ7 Receptor -0.006642
167 ENOG4105CAR Terminase, large subunit -0.006641
168 ENOG4105CYW agmatinase 0.006628
169 ENOG4105CAN Short-chain dehydrogenase reductase Sdr 0.006625
170 ENOG4105CUZ uba thif-type nad fad binding protein -0.006624
171 ENOG4107QR6 type I restriction-modification system -0.006613
172 ENOG4105MP8 (LipO)protein -0.006595
173 ENOG4108Q56 NA 0.006588
174 ENOG4105CP2 von willebrand factor, type a 0.006577
175 ENOG4106X9B Helicobacter outer membrane protein 0.006564
176 ENOG4108P1X synthase -0.006495
177 ENOG4106ENA NA -0.006491
178 ENOG4108ZJN RNA Polymerase 0.006470
179 ENOG4105DKB L-sorbosone dehydrogenase 0.006466
180 ENOG4107QUV Domain protein -0.006466
181 ENOG4105EN6 Membrane -0.006462
182 ENOG4108IJ8 ABC transporter 0.006453
183 ENOG4106BKB NA -0.006442
184 ENOG4106A8U NA 0.006439
185 ENOG4106E8F NA -0.006438
186 ENOG4108VFE Methyltransferase 0.006417
187 ENOG4105CWZ Pfam:DUF395 -0.006386
188 ENOG4107RQ6 Dehydrogenase 0.006386
189 ENOG4106AG3 NA -0.006374
190 ENOG4108UV0 sigma 54 modulation protein ribosomal protein S30EA -0.006374
191 ENOG4105CFI type iii restriction protein res subunit 0.006366
192 ENOG4106BRS NA 0.003183
192 ENOG4106FE7 Outer membrane efflux protein 0.003183
193 ENOG4108W8F Acetyltransferase GNAT Family 0.006361
194 ENOG4105DC0 Membrane 0.006361
195 ENOG4105C2S Catalyzes the NADPH dependent reduction of L-gamma- glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate (By similarity) -0.006357
196 ENOG4108N8Q NA 0.006341
197 ENOG4108VHC Short-chain dehydrogenase reductase Sdr -0.006320
198 ENOG4105J5G Transferase hexapeptide repeat containing protein 0.006302
199 ENOG4107Z2H Phosphoesterase, PA-phosphatase related 0.006301
200 ENOG41063ZB Formyl transferase domain protein -0.006298
201 ENOG4105CHU acetyl-coa acetyltransferase 0.006293
202 ENOG4107R16 Multicopper oxidase 0.006284
203 ENOG4105F2K FkbH Like Protein 0.006276
204 ENOG4105H0B Domain-Containing protein 0.006276
205 ENOG4107S6Z Na H antiporter -0.006269
206 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) 0.006258
207 ENOG4106YKS NA -0.006257
208 ENOG4105EWI Short-chain dehydrogenase reductase Sdr 0.006255
209 ENOG4108UAU isochorismatase 0.006252
210 ENOG4105DS2 Anaerobic c4-dicarboxylate transporter -0.006252
211 ENOG4108V9Q carbonic anhydrase 0.006240
212 ENOG410859Q Plasmid stabilisation system protein -0.006220
213 ENOG4108EV4 Bile acid sodium symporter 0.006215
214 ENOG4105CD5 CoA-binding domain protein 0.006206
215 ENOG41068NY NA -0.006201
216 ENOG41061I7 NA -0.006200
217 ENOG41062ZG ion transport 2 domain protein 0.006195
218 ENOG4105NF4 modulator of drug activity -0.006193
219 ENOG410715Z Restriction endonuclease 0.006189
220 ENOG410679F NA 0.000772
220 ENOG4106KM6 Hof-family outer membrane protein 0.000772
220 ENOG4106UJ4 Helicobacter outer membrane protein 0.000772
220 ENOG4106WRC Membrane 0.000772
220 ENOG4106XV7 NA 0.000772
220 ENOG4106Y3B NA 0.000772
220 ENOG41070KB Membrane 0.000772
220 ENOG41079KP NA 0.000772
221 ENOG4107TXZ fad dependent oxidoreductase -0.006173
222 ENOG4105DEM Methyltransferase -0.006170
223 ENOG4107M53 biosynthesis protein -0.006148
224 ENOG4108J4X sugar efflux transporter -0.006140
225 ENOG4108XQC type IV secretion system protein VirB10 -0.006135
226 ENOG4105K90 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 -0.006128
227 ENOG4105ZHV NA 0.000764
227 ENOG4106QKH Hof-family outer membrane protein 0.000764
227 ENOG4106Y20 motility protein 0.000764
227 ENOG410740W NA 0.000764
227 ENOG4107A0K Helicobacter outer membrane protein 0.000764
227 ENOG4107V40 secretion protein, HlyD family 0.000764
227 ENOG4108MUS ABC-2 type transporter 0.000764
227 ENOG4108PE5 Outer membrane efflux protein 0.000764
228 ENOG4105DWR Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin (By similarity) -0.006114
229 ENOG4108VS5 CheC, inhibitor of MCP methylation -0.006106
230 ENOG4105DNP FAD linked oxidase domain protein 0.006104
231 ENOG4105FBA Phospholipase Carboxylesterase -0.006100