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 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit 0.039465
2 ENOG4107QIZ NADH dehydrogenase 0.037798
3 ENOG4107QHI -hydrogenase 0.032532
4 ENOG4108H1H hydrogenase) (Fe-only 0.031294
5 ENOG4107QW8 radical SAM domain protein 0.030171
6 ENOG4108DZZ K00336 NADH-quinone oxidoreductase subunit G EC 1.6.5.3 0.028872
7 ENOG4105F4F gtp-binding protein 0.026726
8 ENOG4105D1Q UPF0246 protein 0.020475
9 ENOG4105BZ8 glutamate synthase 0.020197
10 ENOG4108Z1H conserved protein domain typically associated with flavoprotein 0.019950
11 ENOG4105VF1 iron-only hydrogenase system regulator 0.019840
12 ENOG4105D7T ABC transporter 0.018985
13 ENOG4105NAX ABC-type nitrate sulfonate bicarbonate transport 0.018802
14 ENOG4105D41 biosynthesis protein thiH 0.018651
15 ENOG4107QYN fad dependent oxidoreductase 0.018646
16 ENOG4107VBT abc transporter permease protein 0.018526
17 ENOG4105DTT CRISPR-associated helicase, cas3 0.017872
18 ENOG4105CU9 asparagine synthetase A -0.017670
19 ENOG4105C8Y Acetylornithine aminotransferase 0.017337
20 ENOG4105E4Z Catalyzes the stereoinversion of LL-2,6- diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso- DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan (By similarity) 0.016930
21 ENOG4105CER acetyl-CoA carboxylase biotin carboxylase 0.016836
22 ENOG4107U2I Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol (By similarity) -0.016763
23 ENOG4107QPR SAICAR synthetase 0.016736
24 ENOG4105CE1 Ferrous iron transport protein b 0.016693
25 ENOG4105H2V Virulence-associated protein e -0.016563
26 ENOG4108UTW Plays a role in the regulation of phosphate uptake 0.016469
27 ENOG4106F1P AAA ATPase, central domain protein -0.016430
28 ENOG4105DYB Isoaspartyl dipeptidase 0.016296
29 ENOG4108R66 Conserved Protein -0.016123
30 ENOG4107H9G Necessary for formate dehydrogenase activity (By similarity) -0.016042
31 ENOG4107EEK Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide (By similarity) 0.015669
32 ENOG41060R1 head morphogenesis protein, SPP1 gp7 0.015342
33 ENOG4105X39 NA -0.015258
34 ENOG4106034 NA -0.015214
35 ENOG4108TXY site-specific recombinase, phage integrase family -0.014993
36 ENOG4105C53 Part of the ABC transporter complex PotABCD involved in spermidine putrescine import. Responsible for energy coupling to the transport system (By similarity) -0.014921
37 ENOG4105CEZ Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP) (By similarity) 0.014919
38 ENOG4108JSW Hydrolyase, Fe-S type, tartrate fumarate subfamily, alpha subunit 0.014702
39 ENOG4108VG5 DNA metabolism protein -0.014658
40 ENOG4107QHF type ii secretion system protein e 0.014561
41 ENOG4107XE3 adenine phosphoribosyltransferase -0.014504
42 ENOG4108R3E Dna-3-methyladenine glycosylase i 0.014383
43 ENOG4105F55 Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate (By similarity) 0.014374
44 ENOG4105ED0 Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates (By similarity) 0.014311
45 ENOG4105DBV ornithine carbamoyltransferase 0.014284
46 ENOG410757D NLPA lipoprotein 0.014258
47 ENOG41081MC TRANSCRIPTIONAl REGULATOR GntR family 0.014199
48 ENOG4108JPM phospho-2-dehydro-3-deoxyheptonate aldolase 0.014176
49 ENOG4105CPQ Dehydrogenase 0.014109
50 ENOG4105S4U addiction module toxin, RelE StbE family 0.014055
51 ENOG4108Z8I decarboxylase 0.013991
52 ENOG4108K9Z Histidine kinase -0.013969
53 ENOG4105GR3 Histidine kinase 0.013967
54 ENOG41067TZ transcriptional regulator, MarR family 0.013912
55 ENOG4105KM4 Acetyl-CoA carboxylase, biotin carboxyl carrier protein 0.013753
56 ENOG4105H3Q Primosomal protein, DnaI 0.013689
57 ENOG4105CH2 amidohydrolase 0.013674
58 ENOG4105M1A NADP-reducing hydrogenase, subunit B 0.013615
59 ENOG4105C4B ABC transporter, permease -0.013580
60 ENOG4108YZ4 nudix hydrolase 0.013522
61 ENOG41068B1 Cob-I-yrinic acid a,c-diamide adenosyltransferase 0.013462
62 ENOG4108W8W CRISPR-associated RAMP protein, Csm3 family -0.013449
63 ENOG4108UMB Flavodoxin -0.013439
64 ENOG4107JYE Terminase, large subunit 0.013436
65 ENOG4108759 YopX protein -0.013387
66 ENOG4105CBF Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction (By similarity) 0.013345
67 ENOG4108RB3 Capsular polysaccharide biosynthesis protein 0.013225
68 ENOG41076HS cation diffusion facilitator family transporter 0.013218
69 ENOG4105CDP Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA) (By similarity) 0.013180
70 ENOG4105C2W permease -0.013129
71 ENOG4108UT2 hemolysin iii 0.013104
72 ENOG4105C6Z Gluconate 0.013062
73 ENOG4108VZ1 Uncharacterised ACR, YkgG family COG1556 0.013058
74 ENOG4105CIG ABC transporter 0.013027
75 ENOG4105CIH Imidazole acetol-phosphate transaminase 0.012984
76 ENOG4108WWW Pyridoxamine 5-phosphate 0.012955
77 ENOG4105CEM UPF0597 protein 0.012922
78 ENOG4107WQQ Metallo-beta-lactamase superfamily -0.012899
79 ENOG41067QW Transcriptional regulator 0.012880
80 ENOG4105HMI Membrane 0.012879
81 ENOG4105DZ0 fad dependent oxidoreductase -0.012839
82 ENOG4108BFD Membrane 0.012795
83 ENOG4105ERH Fumarylacetoacetate hydrolase 0.012763
84 ENOG4105MK2 5-formyltetrahydrofolate cyclo-ligase -0.012729
85 ENOG4108ZK7 protein family UPF0029, Impact, N-terminal protein -0.012723
86 ENOG4105ECZ D12 class N6 adenine-specific DNA methyltransferase 0.012721
87 ENOG4107QTG Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA (By similarity) 0.012707
88 ENOG4105RPU NA 0.012631
89 ENOG4105E79 Binding Domain protein 0.012607
90 ENOG4105C6T cysteine synthase -0.012598
91 ENOG4107QYE Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.012590
92 ENOG4108C80 FliB family 0.012585
93 ENOG4108A1J transposase InsK for insertion sequence 0.012566
94 ENOG410683M YopX protein 0.012564
95 ENOG4105C7H Helicase, RecD TraA family -0.012549
96 ENOG4105SBU Peptidase m56 0.012501
97 ENOG4105CW3 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.012414
98 ENOG410622M DNA alkylation repair enzyme -0.012403
99 ENOG4105CVM Molybdenum cofactor synthesis domain protein -0.012369
100 ENOG4108RDQ ABC transporter -0.012231
101 ENOG4108PI2 O-Methyltransferase 0.012217
102 ENOG4105G7B Protein of unknown function (DUF2992) 0.012192
103 ENOG41090BB DNA mismatch endonuclease (vsr) 0.012188
104 ENOG4108JJ8 (ABC) transporter -0.012179
105 ENOG4105EH3 5-methylcytosine restriction system -0.012169
106 ENOG4106G6Z regulatoR -0.012159
107 ENOG4105CAS nag kinase 0.012142
108 ENOG4108KI7 Diguanylate cyclase 0.012109
109 ENOG4105DSQ Nitric oxide reductase 0.012091
110 ENOG4105CJV Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase 0.012046
111 ENOG4108URP Dtdp-4-dehydrorhamnose 3,5-epimerase -0.012004
112 ENOG4105CE7 Amidase, hydantoinase carbamoylase family 0.011987
113 ENOG4107US1 Cytosine-specific methyltransferase 0.011976
114 ENOG4105F9F transposase 0.011972
115 ENOG4105ITW cytosolic protein -0.011919
116 ENOG4105D5G Transposase 0.011915
117 ENOG4107UFQ TraG family -0.011868
118 ENOG41067US Addiction module antitoxin, RelB DinJ family -0.011788
119 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) -0.011786
120 ENOG4105EVN Prephenate dehydrogenase 0.011752
121 ENOG4105KEM Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation (By similarity) -0.011706
122 ENOG4105WUG Toxin-antitoxin system, antitoxin component, HicB family 0.011704
123 ENOG4108IM5 Binding-protein-dependent transport systems, inner membrane component 0.011702
124 ENOG4105C2C drug resistance transporter, Bcr CflA -0.011691
125 ENOG4107R6V ABC transporter, permease -0.011675
126 ENOG4107SNZ Competence protein 0.011673
127 ENOG4105VCQ rubredoxin 0.011667
128 ENOG4105E5H Transposase 0.011652
129 ENOG4105DZR Type I site-specific deoxyribonuclease 0.011632
130 ENOG4107W5F NA -0.011572
131 ENOG41066HC integral membrane protein -0.011569
132 ENOG41089BC DNA repair protein RadA domain -0.011560
133 ENOG4105DH3 ABC transporter -0.011526
134 ENOG4105WEF catalase 0.011513
135 ENOG4107UJ1 Ppx/GppA phosphatase family 0.011504
136 ENOG4107SFI Major Facilitator superfamily 0.011445
137 ENOG41080X2 domain protein -0.011439
138 ENOG4105G01 cobalamin (vitamin B12) biosynthesis CbiM protein 0.011425
139 ENOG4105D7Q type ii secretion system 0.011412
140 ENOG4107UEU restriction endonuclease 0.011411
141 ENOG4105PXR Erf family 0.011400
142 ENOG4106VEM tagatose-6-phosphate kinase -0.011373
143 ENOG4107YTV GtrA-like protein 0.011362
144 ENOG4105C6I Resolvase -0.011359
145 ENOG4105EW4 (LipO)protein 0.011340
146 ENOG4108K3T NA -0.011281
147 ENOG4105CJX Molecular chaperone. Has ATPase activity (By similarity) -0.011273
148 ENOG4105C0R drug resistance transporter emrb qaca subfamily 0.011266
149 ENOG4107QT3 pfkb domain protein 0.011232
150 ENOG4105E39 Enoyl-CoA hydratase -0.011186
151 ENOG4105PW2 ggdef family -0.011182
152 ENOG4107UX4 Carbohydrate kinase 0.011148
153 ENOG4107792 NA 0.011147
154 ENOG4107V4I ABC transporter, permease 0.011114
155 ENOG4105WGA ABC transporter substrate-binding protein 0.011100
156 ENOG4105C0W non-ribosomal peptide synthetase 0.011087
157 ENOG4108JYN Transketolase -0.011062
158 ENOG4108SMS transposase -0.011059
159 ENOG4107QU4 malate dehydrogenase (Oxaloacetate-decarboxylating) 0.011054
160 ENOG4105CMT Dihydroxyacetone kinase 0.011047
161 ENOG4105D2H Uronic isomerase 0.010993
162 ENOG4105DZW Dipeptidase -0.010990
163 ENOG4107GFK fumarate 0.010979
164 ENOG4108UXA Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA (By similarity) -0.010928
165 ENOG4105PI5 acetyltransferase, (GNAT) family 0.010925
166 ENOG4108SEJ sensor with hamp domain -0.010919
167 ENOG4108I3C Pfam:DapD_N 0.010915
168 ENOG4108JJ9 ABC, transporter -0.010867
169 ENOG4105DTC 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (air) carboxylase 0.010855
170 ENOG4108Z66 YbaK ebsC protein -0.010798
171 ENOG4105DU0 nucleoside hydrolase -0.010786
172 ENOG41072GB extracellular solute-binding protein 0.010772
173 ENOG4107RGE Inherit from COG: ATPase (AAA -0.010769
174 ENOG4105DA4 cytochrome c-type biogenesis protein -0.010755
175 ENOG4108KQY NA 0.010744
176 ENOG4105GA3 phage protein -0.010743
177 ENOG4107R95 Catalyzes the phosphorylation of pyruvate to phosphoenolpyruvate (By similarity) -0.010733
178 ENOG4105C03 ribonuclease 0.010732
179 ENOG4105CRZ Nucleotidyl transferase of unknown function (DUF1814) -0.010694
180 ENOG4108KN7 Removes 5-oxoproline from various penultimate amino acid residues except L-proline (By similarity) 0.010673
181 ENOG4105FSC abc transporter permease protein -0.010670
182 ENOG4105WC4 NA 0.010662
183 ENOG4105CG1 Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (By similarity) -0.010659
184 ENOG4108DGP K00336 NADH-quinone oxidoreductase subunit G EC 1.6.5.3 0.010619
185 ENOG4108T8Z NA 0.010603
186 ENOG4108IAA Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity) 0.010587
187 ENOG4105C48 Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (By similarity) 0.010580
188 ENOG410625Q Produces ATP from ADP in the presence of a proton gradient across the membrane (By similarity) -0.010578
189 ENOG41066S5 ORF6C domain 0.010574
190 ENOG4106FY5 NA -0.010571
191 ENOG4108PUM FMN-binding domain protein 0.010556
192 ENOG4105VRS hydrolase family 18 -0.010547
193 ENOG4107R5K X-X-X-Leu-X-X-Gly heptad repeats -0.010544
194 ENOG4105ZBD NA 0.010532
195 ENOG4105U4S restriction 0.010530
196 ENOG4105C9S Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) (By similarity) -0.010513
197 ENOG4105XEP YhcH YjgK YiaL family protein 0.010491
198 ENOG41087XI family Transcriptional regulator -0.010469
199 ENOG41083FC Inherit from COG: Membrane 0.010468
200 ENOG4108UYN gCN5-related N-acetyltransferase 0.010457
201 ENOG4106A8H NA -0.010454
202 ENOG41083CF Conserved repeat -0.010446
203 ENOG4108233 NA 0.010445
204 ENOG4105F4T Histidine kinase 0.010426
205 ENOG4107QXD PAS PAC sensor protein 0.010406
206 ENOG4108UX0 ABC transporter -0.010378
207 ENOG41061ZR Transcriptional regulator 0.010368
208 ENOG4107QXN Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate) (By similarity) 0.010361
209 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase -0.010326
210 ENOG4105JZC GHMP kinase -0.010311
211 ENOG41074XI NA 0.010285
212 ENOG4105XBY Regulates arginine biosynthesis genes (By similarity) -0.010284
213 ENOG4105DG4 malate L-lactate dehydrogenase 0.010271
214 ENOG4105D22 carbon starvation protein -0.010252
215 ENOG4107W2Q Inherit from COG: transposase 0.010249
216 ENOG4108HHM Glycosyl transferase, family 2 -0.010246
217 ENOG41063SB peptidase 0.010243
218 ENOG4108614 NA -0.010222
219 ENOG4107V8S c4-dicarboxylate transporter malic acid transport protein 0.010211
220 ENOG4105TRF Transcriptional regulator, TetR family 0.010205
221 ENOG4108T47 CRISPR-associated RAMP protein, Csm4 family -0.010203
222 ENOG4105DXN mazG family 0.010152
223 ENOG4105CY7 stage II sporulation protein E 0.010133
224 ENOG4107VBG transcriptional regulator, lysr family 0.010128
225 ENOG4107F32 Peptidoglycan-binding lysm -0.010128
226 ENOG4105FBX amino acid AbC transporter -0.010125
227 ENOG4108RUR transposase -0.010116
228 ENOG4105CHR reductase 0.010114
229 ENOG4108Z7S Single-stranded nucleic acid binding R3H domain-containing protein 0.010112
230 ENOG41082BK PAP2 Family 0.010104
231 ENOG4105MS2 ribosomal subunit Interface protein -0.010103
232 ENOG4108SBN RNA polymerase sigma factor, sigma-70 family -0.010101
233 ENOG41067R4 Phage tail tape measure protein, TP901 family 0.010095
234 ENOG4105E98 transcriptional regulator DeoR family -0.010092
235 ENOG41081C4 Toxic component of a toxin-antitoxin (TA) module (By similarity) 0.010092
236 ENOG4105H4G m50 family 0.010086
237 ENOG410690S NA -0.010075
238 ENOG4105CG5 Glycosyl transferase (Group 1 0.010055
239 ENOG410652G NA 0.010038
240 ENOG4107TNU Helix-turn-helix type 11 domain protein -0.010018
241 ENOG4106IQY NA -0.010014
242 ENOG41073MB NA 0.010013
243 ENOG4108KFT cyclic nucleotide-binding domain protein 0.010009
244 ENOG4107R1M 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) (By similarity) 0.010007
245 ENOG4108KPW sugar kinase 0.010003
246 ENOG4107R2A decarboxylase 0.009985
247 ENOG41061ZP NA 0.009983
248 ENOG4108REF Sporulation integral membrane protein ytvi 0.009982
249 ENOG4105DI7 Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs (By similarity) -0.009951
250 ENOG4105ES7 radical SAM domain protein -0.009948