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 ENOG4105FUY alpha subunit 0.024906
2 ENOG4105VQD rieske 2fe-2S domain-containing protein 0.024539
3 ENOG4105DPT Diguanylate cyclase phosphodiesterase -0.019103
4 ENOG4105HS6 binding-protein-dependent transport systems inner membrane Component 0.018959
5 ENOG4108Q89 anthranilate 1,2-dioxygenase large subunit 0.018023
6 ENOG4107RGD Major Facilitator superfamily 0.017022
7 ENOG4105IKQ hydratase 0.016595
8 ENOG4105KJF protein tyrosine phosphatase 0.016581
9 ENOG4105NN7 muconolactone delta-isomerase 0.016194
10 ENOG4108T58 Mg2 transport protein CorA -0.015682
11 ENOG4108HNC Extracellular solute-binding protein, family 5 -0.015449
12 ENOG4107SBP chromosomal replication initiator -0.015318
13 ENOG4108UKV benzoate 1,2-dioxygenase 0.014961
14 ENOG4108WUH Transcriptional regulator, TetR family 0.014842
15 ENOG4105T1S Transposase 0.014739
16 ENOG4105CQZ Histidine kinase 0.014661
17 ENOG4105EQJ Nitrous-oxide reductase is part of a bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide (By similarity) 0.014613
18 ENOG4107R8Z faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.014236
19 ENOG4105Y36 Binding-protein-dependent transport systems, inner membrane component 0.014229
20 ENOG4107QVT Binding-protein-dependent transport systems, inner membrane component 0.014151
21 ENOG4107GHC outer membrane autotransporter -0.014099
22 ENOG4105KRJ gCN5-related N-acetyltransferase 0.013864
23 ENOG4105WAS NUDIX hydrolase -0.013691
24 ENOG4106B1D glycosyl transferase group 1 -0.013671
25 ENOG4108Z90 colanic acid biosynthesis acetyltransferase wcaF -0.013628
26 ENOG4107XJ7 Short-chain dehydrogenase reductase Sdr -0.013618
27 ENOG4105EJ9 Membrane 0.013490
28 ENOG4105Q1B NA 0.013387
29 ENOG4107T7X Aminotransferase -0.013372
30 ENOG4107SY8 Glycosyl transferase, family 2 -0.013279
31 ENOG4108UMN azlc family 0.013273
32 ENOG4108EQM faD-dependent pyridine nucleotide-disulfide oxidoreductase 0.013268
33 ENOG4108KWI Transcriptional regulator 0.013230
34 ENOG4105CSV Glutaminase 0.013222
35 ENOG4105DTQ mandelate racemase muconate lactonizing 0.013208
36 ENOG4107SEV 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 0.013163
37 ENOG41069NU Nitroreductase 0.013105
38 ENOG4105E09 nadh pyrophosphatase 0.013086
39 ENOG4108VTW Thioesterase -0.013083
40 ENOG4105HD9 Alpha Beta Hydrolase 0.013037
41 ENOG4108SVZ Methyltransferase, type 11 0.012916
42 ENOG4107QP7 CoA-transferase subunit A 0.012908
43 ENOG4108S7S Transglutaminase family protein cysteine peptidase, btlcp -0.012876
44 ENOG4108KYP polysaccharide deacetylase 0.012784
45 ENOG4108QJ2 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase 0.012783
46 ENOG4105E9V Periplasmic binding protein LacI transcriptional regulator 0.012625
47 ENOG4105CRS phenylacetate-CoA oxygenase PaaG subunit 0.012531
48 ENOG4108R85 Short chain dehydrogenase 0.012526
49 ENOG4105CBP Major Facilitator 0.012517
50 ENOG4108Q7I Sn-glycerol-3-phosphate ABC transporter, permease protein -0.012496
51 ENOG4105C7Z Conserved Protein 0.012425
52 ENOG4107TJP Alcohol dehydrogenase GroES-like domain 0.012425
53 ENOG410626B catechol 1,2-dioxygenase 0.012414
54 ENOG4105D12 Protein of unknown function (DUF1355) 0.012354
55 ENOG4107RJI Alcohol dehydrogenase zinc-binding domain protein 0.012351
56 ENOG4105KTQ flagellar basal-body rod protein 0.012329
57 ENOG4107TVJ ,Oxidoreductase FAD NAD(P)-binding 0.012315
58 ENOG4106CD9 glycosyl transferase group 1 -0.012229
59 ENOG4108PXT Sensor hybrid histidine kinase 0.012150
60 ENOG41081SP polysaccharide biosynthesis protein -0.012102
61 ENOG4105UK9 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity (By similarity) 0.012048
62 ENOG4106254 transglutaminase domain protein 0.012038
63 ENOG4105TIT NA -0.012016
64 ENOG4105ZXK Dehydrogenase -0.011940
65 ENOG4105KV2 Protein of unknown function (DUF983) -0.011923
66 ENOG4105ET1 Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate (By similarity) 0.011861
67 ENOG4105C1F The M ring may be actively involved in energy transduction (By similarity) -0.011807
68 ENOG4105DKT Transcriptional regulator -0.011795
69 ENOG410685W NA -0.011788
70 ENOG4105CB4 tonB-dependent siderophore receptor -0.011773
71 ENOG4105ENB ATPase involved in DNA replication initiation 0.011732
72 ENOG4108K5C ABC transporter, permease 0.011695
73 ENOG4105EFA 4-hydroxyphenylacetate 0.011646
74 ENOG4105EQQ protein containing aminopeptidase domain -0.011632
75 ENOG4107QR9 Iron-sulfur cluster binding protein 0.011591
76 ENOG4108MAM abc transporter permease protein 0.011589
77 ENOG4108W5M transcriptional regulator 0.011574
78 ENOG4105FEQ ParB domain protein nuclease 0.011538
79 ENOG41086G8 propeptide, pepSY amd peptidase M4 -0.011436
80 ENOG4105C9A Phoh family 0.011367
81 ENOG4108SC4 )-transporter 0.011365
82 ENOG4107V89 outer membrane autotransporter 0.011324
83 ENOG4108ZXM Esterase 0.011317
84 ENOG4105GAV receptor -0.011299
85 ENOG4105D9S phenylacetate-CoA oxygenase PaaI subunit 0.011286
86 ENOG4106AF3 Conserved protein CoxF -0.011276
87 ENOG4105K5X acetyltransferase -0.011258
88 ENOG4105D2X ABC transporter substrate-binding protein 0.011249
89 ENOG4105F2Z 3-oxoadipate enol-lactonase 0.011226
90 ENOG4105EZ2 Haloacid dehalogenase type II 0.011224
91 ENOG4106IX6 NA -0.011195
92 ENOG4108SBK dioxygenase, subunit beta 0.011164
93 ENOG4105C85 amino acid -0.011133
94 ENOG4105K7A Phage prohead protease, HK97 family 0.011121
95 ENOG4105F38 ABC transporter, permease -0.011120
96 ENOG410629J Glycosyl transferase (Group 1 -0.011116
97 ENOG4105WQX Branched-chain amino acid transport 0.011112
98 ENOG4105C65 Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism (By similarity) 0.005533
98 ENOG4105CM0 Catalyzes the synthesis of GMP from XMP (By similarity) 0.005533
99 ENOG4107THA Transketolase -0.011060
100 ENOG4105MQ6 Disulfide Bond Formation Protein 0.011035
101 ENOG4107ZEA Replication protein c 0.011021
102 ENOG4108V7B Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide (By similarity) 0.011004
103 ENOG4106PI4 Pfam:DUF894 0.010963
104 ENOG4107XQ1 cobalamin (vitamin B12) biosynthesis CbiM protein 0.010961
105 ENOG4105C25 Primosomal protein n' 0.010956
106 ENOG4108YG1 Transposition protein -0.010947
107 ENOG4107TY8 binding-protein-dependent transport systems inner membrane Component 0.010928
108 ENOG4105SYT Methylenetetrahydrofolate reductase 0.010912
109 ENOG4105C3I Nad-dependent epimerase dehydratase 0.010884
110 ENOG4105DF3 Catalyzes the retro-aldol cleavage of 4-hydroxy-2- oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds (By similarity) 0.010878
111 ENOG4105C7N Xanthine uracil vitamin C permease 0.010877
112 ENOG4105X60 secreted 0.010845
113 ENOG4108033 Ammonia monooxygenase -0.010791
114 ENOG4105DGF epimerase dehydratase -0.010790
115 ENOG4105F4E fad dependent oxidoreductase 0.010778
116 ENOG4105DTK saccharopine dehydrogenase 0.010754
117 ENOG41066P7 Transposase -0.010709
118 ENOG4105VE0 acetyltransferase 0.010709
119 ENOG4108TUY outer membrane protein PgaA 0.010698
120 ENOG4107N1Q ErfK YbiS YcfS YnhG family protein -0.010693
121 ENOG4108TSK Binding-protein-dependent transport systems, inner membrane component 0.010693
122 ENOG4105DIK (ABC) transporter 0.010690
123 ENOG4105CZE histidine utilization repressor -0.010672
124 ENOG4108ZA2 phenylacetate-CoA oxygenase PaaJ subunit 0.010652
125 ENOG4105XUA cytochrome c -0.010646
126 ENOG4108HGT Histidine kinase -0.010643
127 ENOG4108YEZ Glycosyl transferase (Group 1 -0.010627
128 ENOG4105DJN thiJ pfpI -0.010623
129 ENOG4108R86 Transcriptional regulator 0.010613
130 ENOG4105EAM Na Pi-cotransporter 0.010607
131 ENOG4105QDQ NA 0.010563
132 ENOG410906J NA -0.010559
133 ENOG4105GWP tricarboxylate transport protein TctB -0.010553
134 ENOG41069T8 NA 0.010551
135 ENOG4105UCB Gene transfer agent 0.010540
136 ENOG4107QQG Dehydrogenase 0.010505
137 ENOG4105EZ7 amino acid ABC transporter -0.010482
138 ENOG4105K46 50S ribosomal protein l27 0.010473
139 ENOG410759R Inherit from COG: Nad-dependent epimerase dehydratase -0.002618
139 ENOG4107CT2 Penicillin amidase -0.002618
139 ENOG4107JW7 Inherit from NOG: autotransporter-associated beta strand repeat protein -0.002618
139 ENOG4107VGC Glycosyl transferase family 4 -0.002618
140 ENOG4105VVR NA -0.010469
141 ENOG4105DXM phenylacetic acid degradation protein 0.010460
142 ENOG4105DIV Catalyzes the conversion of acetaldehyde to acetyl-CoA, using NAD( ) and coenzyme A. Is the final enzyme in the meta- cleavage pathway for the degradation of aromatic compounds (By similarity) 0.010460
143 ENOG4108MPW TRANSCRIPTIONal REGULATOR, lysR family 0.010458
144 ENOG4108EU9 Aminotransferase 0.010427
145 ENOG41079N1 Bacterial extracellular solute-binding proteins, family 3 0.003473
145 ENOG4107M8S SH3 type 3 domain protein 0.003473
145 ENOG41085HW flagellar FlbD family protein 0.003473
146 ENOG4105DIJ Phosphoethanolamine transferase -0.010418
147 ENOG41082YX Transcriptional regulator, arsr family 0.010416
148 ENOG4105R5S Transcriptional regulator (XRE family 0.010400
149 ENOG4106F5P sh3 type 3 domain-containing protein -0.010387
150 ENOG4108N94 Nad-dependent epimerase dehydratase -0.010383
151 ENOG4105C5E polysaccharide biosynthesis protein 0.010353
152 ENOG4105CV6 ABC transporter, permease 0.010337
153 ENOG4107YET SMP-30/Gluconolaconase/LRE-like region -0.010335
154 ENOG41063Y4 Major Facilitator superfamily 0.010309
155 ENOG4105IGJ Zn-dependent Hydrolase of the beta-lactamase fold protein 0.010272
156 ENOG4105DEF Extracellular solute-binding protein, family 5 -0.010268
157 ENOG4106WDZ NA -0.010266
158 ENOG4106U5A One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity) 0.010263
159 ENOG4105GN1 Diguanylate cyclase -0.010232
160 ENOG4108NA5 Inherit from COG: DNA primase -0.010216
161 ENOG4105CWD Nad-dependent epimerase dehydratase 0.010204
162 ENOG4108T0C Pepsy-associated tm helix 0.010196
163 ENOG4105F53 2,3-dioxygenase 0.010187
164 ENOG4105DZS Phenylacetate-CoA ligase 0.010122
165 ENOG4106C1J NA 0.010120
166 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.010118
167 ENOG4108TW8 Uncharacterized alpha/beta hydrolase domain (DUF2235) 0.010089
168 ENOG4105CMM transposase 0.010044
169 ENOG4105QZM nudix hydrolase 0.010038
170 ENOG4105CH5 extracellular solute-binding protein, family 7 0.010029
171 ENOG4105SA9 Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides (By similarity) 0.010027
172 ENOG4106KQD abc transporter atp-binding protein -0.010021
173 ENOG4107QVR glycerophosphoryl diester phosphodiesterase -0.010014
174 ENOG4105F9F transposase 0.009999
175 ENOG4108VDS Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) -0.009978
176 ENOG4106IUB NA 0.009975
177 ENOG4105WKU brancheD-chain amino acid aminotransferase 0.009973
178 ENOG41069KQ Phage regulatory protein 0.009966
179 ENOG4105YBG Phage head-tail adaptor 0.009962
180 ENOG4105CHG glycolate oxidase (iron-sulfur subunit) 0.009928
181 ENOG41068UE Type iv pilus assembly 0.009919
182 ENOG4105DQ4 alcohol dehydrogenase -0.009907
183 ENOG4105IS1 Rieske 2Fe-2S 0.009897
184 ENOG4108RIS Recombinase -0.009896
185 ENOG4107R0D fad dependent oxidoreductase -0.009812
186 ENOG4107VYK Polysaccharide pyruvyl transferase -0.009810
187 ENOG41075VP Bacterial Ig-like domain (group 1) -0.009810
188 ENOG4108SGR YheO domain-containing protein 0.009789
189 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.009725
190 ENOG41090AG Bacteriophage protein 0.009685
191 ENOG4105D3Q Sugar transferase 0.009673
192 ENOG41067WK Transcriptional regulator -0.009663
193 ENOG4107QR4 Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity (By similarity) 0.009628
194 ENOG4105CF4 DegT DnrJ EryC1 StrS aminotransferase 0.009624
195 ENOG41061TZ Short-chain dehydrogenase reductase Sdr 0.009607
196 ENOG4108E27 acetoacetyl-CoA synthetase 0.009607
197 ENOG4105TJN NA -0.009599
198 ENOG4107R0K CoA transferase having broad substrate specificity for short-chain acyl-CoA thioesters with the activity decreasing when the length of the carboxylic acid chain exceeds four carbons (By similarity) -0.009591
199 ENOG4107UGJ Glycosyl transferase, family 2 -0.009571
200 ENOG4105N76 Phenylacetate-CoA oxygenase, subunit 0.009547
201 ENOG4105DAB fumarate reductase succinate dehydrogenase flavoprotein domain protein 0.009491
202 ENOG4105CQM Urea amidohydrolase subunit alpha 0.009489
203 ENOG4108ZTR Glyoxalase Bleomycin resistance protein (Dioxygenase 0.009438
204 ENOG4107E2E PKHD-type hydroxylase 0.009419
205 ENOG4105CKD glutathione-regulated potassium-efflux system protein -0.009414
206 ENOG41067AN NA 0.009412
207 ENOG4106Y7X Peptide synthase -0.009412
208 ENOG4108UAJ Transcriptional regulator 0.009394
209 ENOG4105ES9 amino acid 0.009387
210 ENOG4105E45 Histidinol-phosphate aminotransferase 0.009358
211 ENOG4105D3H Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol (By similarity) -0.009352
212 ENOG4106V33 NA -0.009350
213 ENOG4105J6C DUF218 domain -0.009350
214 ENOG4107SA5 Trap dicarboxylate transporter, dctm subunit 0.009316
215 ENOG4107EI0 non-ribosomal peptide synthetase -0.009292
216 ENOG4107YWI protein tyrosine phosphatase -0.009263
217 ENOG4105G0T bifunctional deaminase-reductase domain protein 0.009253
218 ENOG4108EFE Potassium efflux system protein 0.009245
219 ENOG4108QN8 LysR family transcriptional regulator 0.009188
220 ENOG4105FAG bacteriophage protein 0.009169
221 ENOG4107QQF RND efflux system, outer membrane lipoprotein -0.009120
222 ENOG4105DSE periplasmic solute binding protein 0.009120
223 ENOG4107ZQ5 Phage-associated protein, HI1409 family 0.009118
224 ENOG4107BX4 Diguanylate cyclase 0.009117
225 ENOG4107HZC Pfam:YadA 0.009083
226 ENOG4105DJ2 Major Facilitator Superfamily -0.009073
227 ENOG4107ZAE 6-carboxy-5,6,7,8-tetrahydropterin synthase 0.009055
228 ENOG4105DNH Major Facilitator -0.009047
229 ENOG4105J3T Histidine kinase 0.009037
230 ENOG4105CH2 amidohydrolase 0.009024
231 ENOG4105GQR Chaperone -0.009011
232 ENOG4108FGK plasmid partitioning protein -0.008995
233 ENOG4105Q0R Chorismate mutase 0.008993
234 ENOG4106HF6 NA -0.008979
235 ENOG4105FT1 Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I (By similarity) -0.008961
236 ENOG4105TNG K13735 adhesin invasin -0.008918
237 ENOG4105CTX dehydratase 0.008905
238 ENOG4105EV5 Peptidase, M16 -0.008900
239 ENOG4107HJ1 Sel1 domain protein repeat-containing protein 0.008898
240 ENOG4108P5J Membrane 0.008890
241 ENOG4106BC2 transposase, IS3 IS911 family protein 0.008865
242 ENOG4105MI0 Catalyzes the non-heme iron(II)-dependent oxidative cleavage of 2,3-dihydroxyphenylpropionic acid and 2,3- dihydroxicinnamic acid into 2-hydroxy-6-ketononadienedioate and 2- hydroxy-6-ketononatrienedioate, respectively (By similarity) 0.008862
243 ENOG41082PI Sel1 domain protein repeat-containing protein -0.008858
244 ENOG4105H44 NA -0.008849