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 ENOG4105CS3 FliG is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation (By similarity) 0.021808
2 ENOG4108KTQ Methyltransferase 0.019442
3 ENOG4105CBS Chea signal transduction histidine kinase 0.018791
4 ENOG4105CMP catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR (By similarity) 0.018734
5 ENOG4105DD5 Flagellar motor switch protein 0.018372
6 ENOG4105C1F The M ring may be actively involved in energy transduction (By similarity) 0.018340
7 ENOG4105D7B Flagellar biosynthesis protein flha 0.018329
8 ENOG4105CN7 Flagellar biosynthetic protein FliP 0.018032
9 ENOG4105D19 Role in flagellar biosynthesis (By similarity) 0.017969
10 ENOG4105KTQ flagellar basal-body rod protein 0.017682
11 ENOG4105DN4 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.016485
12 ENOG4108JIR Flagellum-specific ATP synthase 0.016400
13 ENOG4105E1Q flagellar hook-associated protein 0.016252
14 ENOG4105D24 FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation (By similarity) 0.016192
15 ENOG4105EPM Diguanylate phosphodiesterase 0.016008
16 ENOG4105I03 Flagellin 0.015301
17 ENOG4108ZC9 flagellar basal-body rod protein flgc 0.015123
18 ENOG4105D00 flagellar biosynthetic protein flhB 0.015088
19 ENOG4105FZW flagellar biosynthesis regulator FlhF 0.014555
20 ENOG4105CJ2 (LipO)protein -0.013605
21 ENOG4108URH decarboxylase -0.013502
22 ENOG4108RD3 chew protein 0.012632
23 ENOG4105VS8 Flagellar biosynthetic protein fliq 0.012539
24 ENOG4105D4I Uncharacterized protein conserved in bacteria (DUF2130) 0.012421
25 ENOG4108JJ9 ABC, transporter -0.012324
26 ENOG4105CGA flagellar basal-body rod protein FlgG 0.012122
27 ENOG4105M2E Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell (By similarity) -0.012012
28 ENOG4105CZX twitching motility protein 0.011996
29 ENOG410822I Flagellar hook capping protein 0.011919
30 ENOG4105EXC Acyl-transferase -0.011245
31 ENOG4105E14 MotA TolQ exbB proton channel 0.011137
32 ENOG4108Z4W Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis (By similarity) 0.011019
33 ENOG4105CQ3 Poorly processive error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. Exhibits no 3-5 exonuclease (proofreading) activity. May be involved in translesional synthesis in conjunction with the beta clamp from polIII (By similarity) -0.010993
34 ENOG4108SEK ompa motb domain protein 0.010918
35 ENOG4105CR7 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA (By similarity) 0.010863
36 ENOG4105BZE flagellar hook protein, FlgE 0.010862
37 ENOG4105KAF membrAne -0.010848
38 ENOG4105PXI polysaccharide deacetylase 0.010828
39 ENOG4105C8U phosphate abc transporter -0.010782
40 ENOG4105D58 Diguanylate phosphodiesterase 0.010637
41 ENOG4105C52 Atpase, p-type (Transporting), had superfamily, subfamily ic 0.010462
42 ENOG4105CNE Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane (By similarity) -0.010438
43 ENOG41067S9 phage shock protein C, PspC -0.010426
44 ENOG4105PSV Polysaccharide Biosynthesis Protein 0.010418
45 ENOG4108VYJ response regulator receiver protein 0.010326
46 ENOG4105C6B Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl- acyl-carrier-protein (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA (By similarity) 0.010243
47 ENOG4105XA0 heptosyltransferase ii 0.010178
48 ENOG4105BZH Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity) 0.010149
49 ENOG4105CVM Molybdenum cofactor synthesis domain protein 0.010119
50 ENOG4105CMW The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity) 0.010105
51 ENOG4105MQ3 flagellar protein FliS 0.010074
52 ENOG4105C93 Xylose Isomerase 0.010013
53 ENOG4105C0K Gdp-mannose 4,6-dehydratase 0.009995
54 ENOG4105D92 Assembles around the rod to form the L-ring and probably protects the motor basal body from shearing forces during rotation (By similarity) 0.009930
55 ENOG4107PHP CheC --inhibitor of MCP methylation 0.009914
56 ENOG4105VQ0 flagellar hook-basal body complex protein fliE 0.009877
57 ENOG4105DGU Histone deacetylase 0.009820
58 ENOG4105MN5 HAD-superfamily hydrolase subfamily IA variant 3 -0.009799
59 ENOG4107NQ8 LysR family Transcriptional regulator 0.009766
60 ENOG4105D4F Synthesizes selenophosphate from selenide and ATP (By similarity) 0.009720
61 ENOG4105N0J dUTPase 0.009677
62 ENOG41076HS cation diffusion facilitator family transporter 0.009666
63 ENOG4105DKS phage plasmid primase, p4 family -0.009604
64 ENOG4105JPG D-isomer specific 2-hydroxyacid dehydrogenase 0.009568
65 ENOG4105DSG hydrolase family 43 0.009490
66 ENOG4107S81 Nad-dependent epimerase dehydratase -0.009445
67 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase 0.009410
68 ENOG4108W15 Protein of unknown function (DUF1456) 0.009398
69 ENOG4105DAB fumarate reductase succinate dehydrogenase flavoprotein domain protein -0.009385
70 ENOG4105C21 Displays ATPase and GTPase activities (By similarity) -0.009346
71 ENOG4105CS2 ec 0.009328
72 ENOG4105C3X it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP (By similarity) -0.009289
73 ENOG4105D64 Mechanosensitive ion channel -0.009246
74 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.009236
75 ENOG4108KX3 Short-chain dehydrogenase reductase Sdr -0.009160
76 ENOG4109003 Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis (By similarity) 0.009154
77 ENOG4105C9B Cysteine desulfurase 0.009108
78 ENOG4108Z0A Cupin 2, conserved barrel domain protein -0.009084
79 ENOG4105F55 Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate (By similarity) 0.009075
80 ENOG4105CCY NADH flavin oxidoreductase, NADH oxidase 0.009062
81 ENOG4108RCM Nitroreductase 0.009058
82 ENOG4105DKB L-sorbosone dehydrogenase -0.009012
83 ENOG4105C3J Cysteine desulfurase -0.008997
84 ENOG4108J0Y Diguanylate cyclase 0.008972
85 ENOG4105EJ9 Membrane -0.008970
86 ENOG4108W5V epimerase dehydratase 0.008963
87 ENOG4107RKQ Methyl-accepting chemotaxis sensory transducer 0.008914
88 ENOG4105CM1 Catalyzes, together with MoaC, the conversion of 5'-GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity) 0.008914
89 ENOG4105JZI cytochrome P450 -0.008902
90 ENOG4105D6I beta-mannosidase EC 0.008857
91 ENOG4108IMY Transcriptional regulator -0.008845
92 ENOG4106KVQ PAP2 superfamily 0.008839
93 ENOG4105C9W Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity (By similarity) 0.008825
94 ENOG4105ED7 Catalyzes the specific phosphorylation of 1,6-anhydro-N- acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling (By similarity) -0.008775
95 ENOG4105CJT Mannose-1-phosphate guanylyltransferase 0.008768
96 ENOG4107Z7S Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity) 0.008735
97 ENOG4107SXU methyl-accepting chemotaxis 0.008676
98 ENOG4105C5G amine oxidase 0.008663
99 ENOG4108UH8 Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4- diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity) 0.008657
100 ENOG4105CC1 hydrolase, CocE NonD family protein 0.008642
101 ENOG4105VEQ Cold shock protein -0.008570
102 ENOG4105NG1 exported protein 0.008567
103 ENOG4105C5Z peptidase -0.008550
104 ENOG4108MJI response regulator -0.008531
105 ENOG4108C33 Resolvase -0.008516
106 ENOG4107J5X Diguanylate cyclase with PAS PAC sensor 0.008472
107 ENOG4105C1G acyl-Coa dehydrogenase 0.008470
108 ENOG4105DQ6 Transposase -0.008463
109 ENOG4108IYT Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity) -0.008451
110 ENOG4105QF1 response regulator 0.008421
111 ENOG4108KI7 Diguanylate cyclase 0.008390
112 ENOG4108DMZ Glutaredoxin -0.008382
113 ENOG4105C71 hydrolase family 65, central catalytic 0.008341
114 ENOG4105VM1 flagellar 0.008309
115 ENOG4106N3A copper homeostasis protein cutc 0.008299
116 ENOG4105W5T Binds to the C-terminal region of flagellin, which is implicated in polymerization, and participates in the assembly of the flagellum (By similarity) 0.008295
117 ENOG4105CYC Transferase 0.008284
118 ENOG4106D4I domain protein -0.008276
119 ENOG4105Y7X Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair (By similarity) 0.008242
120 ENOG4107EES Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide the precursor of murein (By similarity) -0.008212
121 ENOG4105C83 adenylosuccinate lyase 0.008211
122 ENOG4107TME TrkA-N domain protein 0.008203
123 ENOG4105EJZ Glucose-1-phosphate cytidylyltransferase 0.008186
124 ENOG4105KNA -acetyltransferase 0.008185
125 ENOG4105CH2 amidohydrolase -0.008184
126 ENOG4105D3H Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol (By similarity) 0.008172
127 ENOG4105DW3 Response regulator receiver modulated metal dependent phosphohydrolase 0.008153
128 ENOG4105C30 Nad-dependent epimerase dehydratase 0.008147
129 ENOG4108ZY0 Glyoxalase Bleomycin resistance protein (Dioxygenase -0.008110
130 ENOG4107RQP nicotinate phosphoribosyltransferase 0.008107
131 ENOG4105E9Q Acyl-transferase 0.008088
132 ENOG4105CYW agmatinase 0.008085
133 ENOG4105I3N Conserved Protein -0.008082
134 ENOG4105DV0 amidase (EC 0.008043
135 ENOG4105X3E Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine (By similarity) 0.008027
136 ENOG4105KUR CAAX amino terminal protease family protein 0.008025
137 ENOG4107RKD Uncharacterized protein family (UPF0051) 0.008017
138 ENOG4105H0T rifampin adp-ribosyl transferase 0.007984
139 ENOG4108HW5 amino acid AbC transporter 0.007981
140 ENOG4107R21 site-determining protein 0.007964
141 ENOG4105BZX nudix hydrolase -0.007933
142 ENOG4105KMR acetyltransferase, (GNAT) family -0.007930
143 ENOG4105DQQ Major facilitator superfamily MFS_1 0.007927
144 ENOG4105DFF Rod shape-determining protein mreb 0.007913
145 ENOG4108KHX Diguanylate cyclase 0.007905
146 ENOG4105EBR Carboxylesterase 0.007903
147 ENOG4105E0X reductase -0.007890
148 ENOG4108U05 Transcriptional regulator 0.007883
149 ENOG41090BB DNA mismatch endonuclease (vsr) -0.007866
150 ENOG4106TD9 Diguanylate cyclase 0.007864
151 ENOG4108Z1M DSBA oxidoreductase 0.007862
152 ENOG4105CRU nitrate reductase, alpha subunit 0.007817
153 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) 0.007805
154 ENOG4105DHQ Histidine kinase -0.007801
155 ENOG4108IF1 Methyl-accepting chemotaxis 0.007798
156 ENOG4109066 lysm domain bon superfamily protein -0.007784
157 ENOG4106FEU of the drug metabolite transporter, DMT superfamily 0.007772
158 ENOG4105J76 Periplasmic binding protein 0.007757
159 ENOG41082QR Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity) 0.007724
160 ENOG4105XZT Protein of unknown function (DUF2892) 0.007721
161 ENOG410667J hydrolase 0.007703
162 ENOG4105H0B Domain-Containing protein 0.007695
163 ENOG4105D5D udp-galactopyranose mutase -0.007686
164 ENOG4105ENI DNA helicase -0.007626
165 ENOG4108H18 Polysaccharide biosynthesis protein 0.007622
166 ENOG4105CEQ signal transduction histidine kinase regulating citrate malate metabolism 0.007617
167 ENOG4107QKV phosphomannomutase 0.007607
168 ENOG4105DJ2 Major Facilitator Superfamily -0.007607
169 ENOG4105EX6 NA -0.007594
170 ENOG4105WCN acetyltransferase 0.007572
171 ENOG4105HFZ Membrane -0.007568
172 ENOG4105CIS alcohol dehydrogenase 0.007560
173 ENOG41063Z6 transcriptional regulator, lysR family 0.007559
174 ENOG4107TCE N-acetyltransferase 0.007559
175 ENOG4106KZR phosphorylase -0.007555
176 ENOG4107R0U MotA TolQ exbB proton channel 0.007539
177 ENOG4105DW9 NA -0.007515
178 ENOG4108IQK o-acetylhomoserine 0.007502
179 ENOG4105IU9 (LipO)protein -0.007502
180 ENOG4105FEG PALM domain HD hydrolase domain and 0.007494
181 ENOG4105CYX Short-chain dehydrogenase reductase Sdr 0.007490
182 ENOG4105D89 Nucleotidyl transferase of unknown function (DUF1814) -0.007473
183 ENOG4105DAN ATP-dependent protease 0.007472
184 ENOG4105EKD Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism (By similarity) 0.007463
185 ENOG4105E41 Domain of unknown function(DUF2779) 0.007459
186 ENOG4105BZT Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA (By similarity) -0.007452
187 ENOG4107RW9 nh(3)-dependent nad( ) synthetase 0.007445
188 ENOG4105F9F transposase 0.007437
189 ENOG4105ER6 polysaccharide biosynthesis protein -0.007434
190 ENOG4105HKU nucleoside recognition domain-containing protein 0.007429
191 ENOG4105DW0 Catalyzes the ADP transfer to D-glycero-D-manno-heptose 1-phosphate, yielding ADP-D,D-heptose (By similarity) 0.007402
192 ENOG4105D9P serine threonine protein kinase -0.007395
193 ENOG4105D4E response regulator receiver modulated chew protein 0.007383
194 ENOG4105DBI uridine monophosphokinase 0.007367
195 ENOG4106H3J Lpxtg-motif cell wall anchor domain protein -0.007364
196 ENOG4105WMR Protein CrcB homolog -0.007357
197 ENOG4105WD6 Transposase 0.007324
198 ENOG4105C6A phenylalanyl-tRNA synthetase (beta subunit) -0.007321
199 ENOG4105ESD Protein of unknown function (DUF1611) 0.007314
200 ENOG4108JQ9 ABC transporter 0.007312
201 ENOG4105Q2H domain protein -0.007311
202 ENOG4105DQ5 transport system permease protein 0.007301
203 ENOG4108Z2G Membrane 0.007300
204 ENOG4105EQK -acetyltransferase 0.007298
205 ENOG4105C7Q Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity) -0.007287
206 ENOG4108JJ8 (ABC) transporter -0.007257
207 ENOG4105CK7 Sodium proline symporter -0.007250
208 ENOG4107W7W Assembles around the rod to form the L-ring and probably protects the motor basal body from shearing forces during rotation (By similarity) 0.007242
209 ENOG4105FFC UPF0187 protein 0.007230
210 ENOG4106JT2 Dehydrogenase 0.007210
211 ENOG4105S6R Iron-hydroxamate transporter permease subunit 0.007204
212 ENOG4107RDP Dehydrogenase 0.007204
213 ENOG4108ZAK Membrane -0.007203
214 ENOG4108K84 Inherit from NOG: glyoxalase bleomycin resistance protein dioxygenase -0.007194
215 ENOG4105CE1 Ferrous iron transport protein b 0.007186
216 ENOG4107S9S domain protein -0.007179
217 ENOG4108M15 ABC transporter 0.007171
218 ENOG4105XWN NA -0.007170
219 ENOG4108SGY acetyltransferase 0.007169
220 ENOG4107XRM Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine (By similarity) 0.007163
221 ENOG4105K4I Scp-like extracellular 0.007148
222 ENOG4105C1V Peptidase, M16 0.007144
223 ENOG4105E09 nadh pyrophosphatase 0.007143
224 ENOG4107Y49 methyltransferase -0.007134
225 ENOG4105VM8 Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity) 0.007130
226 ENOG4105C7W Xanthine dehydrogenase 0.007125
227 ENOG4105C6P ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner (By similarity) 0.007115
228 ENOG4107S4G oxidoreductase 0.007113
229 ENOG4105P3U 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 (By similarity) -0.007111
230 ENOG4105DSX permease -0.007106
231 ENOG4108TM9 integral membrane protein 0.007103
232 ENOG4105C4U 4-methyl-5-beta-hydroxyethylthiazole kinase 0.007092
233 ENOG4107G87 m6 family metalloprotease domain protein -0.007089
234 ENOG4105KNE Phosphatidate cytidylyltransferase -0.007081
235 ENOG4108Z0Z intracellular protease Pfpi family -0.007078
236 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.007068
237 ENOG41087PN heavy metal transport detoxification protein -0.007068
238 ENOG4107GFK fumarate -0.007063
239 ENOG4105FDK ABC transporter 0.007051
240 ENOG4105CE5 Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP) (By similarity) 0.007040
241 ENOG4105CAX The 2-keto-3-deoxygluconate permease transports the degraded pectin products into the bacterial cell, where they serve as carbon and energy sources. This is a hydrogen coupled transport system (By similarity) 0.007039
242 ENOG4105EPV lipolytic protein G-D-S-L family -0.007034
243 ENOG4108Q3G Methyltransferase 0.007024
244 ENOG4108JJA ABC, transporter 0.007022
245 ENOG4105DN3 alpha-2-macroglobulin domain protein -0.007021
246 ENOG4105F76 Sarcosine oxidase -0.007020
247 ENOG4107S75 HAD-superfamily hydrolase subfamily IA variant 3 0.007018
248 ENOG4105T4W Transcriptional regulator 0.007008
249 ENOG4107RJX Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) 0.007001
250 ENOG4105CCX Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor (By similarity) 0.006996