Metamenu

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 COG3033 Beta-eliminating lyase 0.074063
2 COG0393 Putative heavy-metal-binding -0.035280
3 COG0175 sulfate reduction -0.035105
4 COG2020 methyltransferase activity -0.034896
5 COG2978 secondary active p-aminobenzoyl-glutamate transmembrane transporter activity 0.034653
6 COG1429 ligase activity, forming nitrogen-metal bonds 0.033263
7 COG3681 Belongs to the UPF0597 family 0.031606
8 COG2211 Major facilitator Superfamily 0.031415
9 COG0631 protein serine/threonine phosphatase activity -0.029965
10 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit 0.029366
11 COG2057 Acyl CoA acetate 3-ketoacid CoA transferase beta subunit 0.029366
12 COG1132 (ABC) transporter -0.029163
13 COG1861 Spore coat polysaccharide biosynthesis protein F CMP-KDO synthetase 0.028322
14 32ZT3 Thioredoxin domain 0.027971
15 COG3142 Participates in the control of copper homeostasis 0.027536
16 COG0174 glutamine synthetase -0.027448
17 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family -0.027219
18 COG4823 Abi-like protein -0.027203
19 COG2185 Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly 0.027061
20 COG3051 citrate lyase alpha subunit 0.026969
21 COG1533 DNA photolyase activity 0.026941
22 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.026611
23 COG3226 Transcriptional regulator -0.026241
24 COG3481 metal-dependent phosphohydrolase, HD sub domain -0.026203
25 COG3267 Type II secretory pathway component ExeA -0.026189
26 COG0560 Phosphoserine phosphatase -0.026099
27 COG2819 hydrolase of the alpha beta superfamily -0.026092
28 COG3382 B3 4 domain protein -0.026001
29 COG2035 Membrane 0.025943
30 COG1346 cytolysis 0.025719
31 COG1380 Effector of murein hydrolase LrgA 0.025719
32 COG1819 glycosyl -0.025483
33 COG2271 Major facilitator Superfamily -0.025075
34 COG5280 Phage tail tape measure protein TP901 0.024889
35 COG0863 Belongs to the N(4) N(6)-methyltransferase family -0.024858
36 COG1916 peptidoglycan binding 0.024747
37 COG4717 serine-type aminopeptidase activity -0.024677
38 COG1021 2,3-dihydroxybenzoate-AMP ligase -0.024448
39 COG5627 protein ubiquitination 0.024399
40 COG4715 Zinc finger, swim domain protein 0.024334
41 COG4383 Mu-like prophage protein gp29 0.024247
42 COG5340 Psort location Cytoplasmic, score -0.024113
43 COG1321 iron dependent repressor -0.024044
44 COG3618 amidohydrolase -0.023961
45 COG0684 Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions -0.023658
46 COG4975 Glucose uptake -0.023594
47 COG4770 biotin carboxylase activity -0.023536
48 COG1250 3-hydroxyacyl-CoA dehydrogenase 0.023257
49 COG0270 DNA (cytosine-5-)-methyltransferase activity -0.023073
50 COG4744 Conserved Protein 0.022862
51 345AV Cyclic nucleotide-monophosphate binding domain 0.022854
52 COG2807 transmembrane transport -0.022790
53 COG0025 NhaP-type Na H and K H -0.022736
54 COG2856 Zn peptidase 0.022484
55 COG0373 Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA) 0.022475
56 COG3456 conserved protein contains FHA domain -0.022309
57 COG0526 COG0526, thiol-disulfide isomerase and thioredoxins -0.022243
58 COG2355 Zn-dependent dipeptidase, microsomal dipeptidase -0.022163
59 2Z8BH DNA N-6-adenine-methyltransferase 0.022129
60 COG3500 Late control gene D protein 0.021969
61 COG0741 lytic transglycosylase activity -0.021899
62 COG1226 (belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family) 0.021576
63 COG1231 oxidoreductase activity -0.021541
64 COG3448 diguanylate cyclase activity -0.021504
65 COG3807 Bacterial SH3 domain 0.021488
66 COG2957 Belongs to the agmatine deiminase family -0.021402
67 COG2610 gluconate transmembrane transporter activity 0.021371
68 COG2272 Belongs to the type-B carboxylesterase lipase family -0.021348
69 COG0753 catalase activity 0.021084
70 COG1164 Oligoendopeptidase f -0.020820
71 COG4925 sulfurtransferase activity -0.020819
72 COG1649 PFAM Uncharacterised BCR, COG1649 0.020700
73 COG0615 ADP-L-glycero-beta-D-manno-heptose biosynthetic process 0.020688
74 COG4832 Psort location Cytoplasmic, score -0.020472
75 COG2604 Protein of unknown function DUF115 -0.020466
76 COG0371 Dehydrogenase 0.020450
77 31YMS TIGRFAM Porphyromonas gingivalis paralogous family TIGR01200 -0.020447
78 COG1823 symporter activity 0.020396
79 COG0462 Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P) -0.020363
80 COG4221 oxidoreductase activity 0.020335
81 COG2818 Glycosylase 0.020331
82 COG3049 Linear amide C-N hydrolases, choloylglycine hydrolase family -0.020302
83 COG0730 response to heat 0.020229
84 COG3504 Conjugal transfer protein -0.020192
85 COG1794 racemase activity, acting on amino acids and derivatives -0.020133
86 COG0162 Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) -0.020090
87 COG2320 Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A -0.020034
88 2ZBW2 Psort location Cytoplasmic, score 8.96 0.020026
89 COG3016 Iron-regulated protein -0.019920
90 30MF4 0.019917
91 COG3981 Acetyltransferase (GNAT) domain -0.019917
92 COG1119 ATPase activity -0.019905
93 COG1257 Belongs to the HMG-CoA reductase family -0.019854
94 COG3774 pathogenesis -0.019798
95 COG1875 ATPase related to phosphate starvation-inducible protein PhoH 0.019641
96 COG2423 ornithine cyclodeaminase activity -0.019638
97 COG4849 Protein conserved in bacteria -0.019608
98 COG1381 Involved in DNA repair and RecF pathway recombination -0.019599
99 COG3883 PFAM NLP P60 protein -0.019565
100 COG1509 lysine 2,3-aminomutase activity 0.019527
101 33A5I Psort location CytoplasmicMembrane, score 0.019438
102 333FT 0.019422
103 COG2076 Multidrug Resistance protein -0.019418
104 33EHP -0.019380
105 COG2015 COG2015, Alkyl sulfatase and related hydrolases -0.019310
106 COG3472 conserved protein (DUF2081) 0.019222
107 COG3886 PLD-like domain -0.019165
108 COG1712 Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L- tetrahydrodipicolinate, to generate the meso compound, D,L-2,6- diaminopimelate 0.019165
109 COG0303 'Molybdopterin -0.019143
110 COG0277 FAD linked oxidase domain protein 0.019112
111 32ZJ3 0.019078
112 COG2963 transposase activity -0.019075
113 COG2066 Belongs to the glutaminase family 0.019038
114 COG4660 Part of a membrane complex involved in electron transport 0.018891
115 32XPT -0.018863
116 32WQD Protein of unknown function (DUF3822) 0.018780
117 COG2348 transferase activity, transferring amino-acyl groups 0.018741
118 COG1883 Na -transporting methylmalonyl-CoA oxaloacetate decarboxylase, beta subunit 0.018707
119 COG1066 DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function -0.018614
120 COG1069 ribulokinase activity 0.018601
121 COG3589 Outer surface protein -0.018544
122 COG3614 Histidine kinase 0.018512
123 2Z82M 0.018501
124 COG3311 Transcriptional regulator -0.018476
125 COG2208 phosphoserine phosphatase activity -0.018462
126 COG2514 catechol 2,3-dioxygenase activity -0.018437
127 COG5523 integral membrane protein -0.018355
128 COG3086 response to oxidative stress 0.018334
129 COG1610 YqeY-like protein -0.018276
130 COG2126 Ion transport protein -0.018253
131 COG0452 Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine -0.018238
132 COG0105 UTP biosynthetic process -0.018219
133 COG3935 DnaD domain protein -0.018202
134 COG2910 NAD(P)H-binding 0.018189
135 COG3919 ATP-grasp -0.018169
136 COG0507 A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD -0.018159
137 COG1744 ABC transporter substrate-binding protein PnrA-like -0.018126
138 COG1704 LemA family 0.018116
139 COG0804 urea catabolic process 0.018103
140 COG0831 urea catabolic process 0.018103
141 COG0829 nickel cation binding 0.018103
142 COG3345 alpha-galactosidase -0.018101
143 COG0499 May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine -0.017992
144 COG1486 melibiose metabolic process 0.017952
145 COG2110 phosphatase homologous to the C-terminal domain of histone macroH2A1 -0.017930
146 COG2212 antiporter activity -0.017909
147 COG3559 Exporter of polyketide antibiotics 0.017889
148 2Z9AE 0.017836
149 COG1514 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester -0.017829
150 COG4222 Protein conserved in bacteria -0.017813
151 COG2273 Hydrolase Family 16 -0.017809
152 33BGI Parallel beta-helix repeats -0.017772
153 COG0832 Belongs to the urease beta subunit family 0.017756
154 COG1151 hydroxylamine reductase activity 0.017706
155 32XR9 Outer membrane efflux protein -0.017699
156 COG1453 Aldo Keto reductase -0.017675
157 COG4552 Acetyltransferase involved in intracellular survival and related 0.017659
158 COG3010 Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P) 0.017654
159 COG4191 Histidine kinase -0.017637
160 COG3395 kinase activity 0.017601
161 COG1748 Saccharopine dehydrogenase -0.017582
162 COG2176 DNA-directed DNA polymerase activity -0.017540
163 COG1446 asparaginase -0.017530
164 COG0154 amidase activity -0.017516
165 COG0714 Associated with various cellular activities 0.017506
166 32U7V -0.017468
167 33GDE This gene contains a nucleotide ambiguity which may be the result of a sequencing error 0.017446
168 COG2377 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 0.017435
169 COG0799 negative regulation of ribosome biogenesis -0.017423
170 COG5499 transcription regulator containing HTH domain -0.017422
171 COG3303 Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process 0.017324
172 COG2966 Psort location CytoplasmicMembrane, score 0.017317
173 COG1638 TRAP-type C4-dicarboxylate transport system periplasmic component 0.017289
174 COG0129 dihydroxy-acid dehydratase activity -0.017285
175 COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain -0.017276
176 COG1680 COG1680 Beta-lactamase class C and other penicillin binding -0.017275
177 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.017266
178 COG0520 Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine -0.017233
179 COG2270 Major facilitator Superfamily -0.017231
180 COG3972 protein homooligomerization 0.017214
181 2ZA86 -0.017197
182 COG2312 Erythromycin esterase 0.017188
183 COG3075 Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses fumarate or nitrate as electron acceptor 0.017160
184 2Z8G6 Conjugative transposon TraJ protein 0.017139
185 COG0274 Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate 0.017129
186 COG1479 Protein of unknown function DUF262 0.017102
187 COG3757 hydrolase, family 25 0.017068
188 COG0716 FMN binding -0.017043
189 COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase -0.017011
190 COG2329 Antibiotic biosynthesis monooxygenase -0.016996
191 COG1651 Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process -0.016965
192 2ZA26 Psort location CytoplasmicMembrane, score 10.00 0.016954
193 COG0524 Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway -0.016937
194 COG2258 MOSC domain -0.016918
195 COG2246 polysaccharide biosynthetic process -0.016884
196 32ZVE 0.016873
197 COG4819 ethanolamine utilization protein 0.016870
198 33XR9 Psort location Cytoplasmic, score 8.96 0.016837
199 COG1331 Highly conserved protein containing a thioredoxin domain -0.016836
200 COG4105 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane 0.016834
201 2ZUJX -0.016833
202 COG2524 Domain in cystathionine beta-synthase and other proteins. -0.016826
203 COG3392 D12 class N6 adenine-specific DNA methyltransferase 0.016824
204 COG2146 nitrite reductase [NAD(P)H] activity -0.016809
205 COG3714 YhhN family 0.016790
206 33DEB Helix-turn-helix domain 0.016789
207 COG4335 DNA alkylation repair 0.016769
208 COG5580 Activator of Hsp90 ATPase 0.016697
209 COG1252 NADH dehydrogenase -0.016692
210 COG1145 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.016667
211 33EZ9 ECF transporter, substrate-specific component 0.016649
212 COG0852 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 -0.016648
213 30456 Domain of unknown function (DUF4276) -0.016645
214 COG0794 Belongs to the SIS family. GutQ KpsF subfamily 0.016626
215 COG3955 Domain of unknown function (DUF1919) 0.016625
216 COG3052 prosthetic group binding 0.016566
217 COG4615 Cyclic peptide transporter -0.016536
218 30NZ2 0.016492
219 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity 0.016490
220 COG5185 Phage-related minor tail protein 0.016483
221 COG3491 Belongs to the iron ascorbate-dependent oxidoreductase family -0.016477
222 COG0433 COG0433 Predicted ATPase 0.016471
223 COG2942 2-epimerase -0.016449
224 COG4810 utilization protein 0.016430
225 COG1981 membrane -0.016423
226 COG2301 Belongs to the HpcH HpaI aldolase family 0.016395
227 COG0460 homoserine dehydrogenase -0.016387
228 COG2311 Membrane 0.016377
229 COG0464 growth -0.016373
230 33F90 BNR Asp-box repeat -0.016370
231 COG0775 Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively 0.016352
232 COG4166 transmembrane transport -0.016329
233 COG2964 Protein conserved in bacteria 0.016286
234 COG0064 Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) -0.016224
235 COG2109 Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids 0.016224
236 COG1682 transport, permease protein -0.016222
237 2ZAQ1 Arylsulfotransferase Ig-like domain 0.016205
238 301GQ COG NOG30732 non supervised orthologous group 0.016184
239 COG2987 Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate 0.016184
240 COG4262 Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine -0.016171
241 COG1024 Enoyl-CoA hydratase 0.016168
242 COG2227 3-demethylubiquinone-9 3-O-methyltransferase activity 0.016151
243 COG2839 Protein conserved in bacteria 0.016114
244 COG0079 Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily -0.016104
245 COG0431 NADPH-dependent FMN reductase -0.016090
246 32V48 -0.016086
247 COG0386 Belongs to the glutathione peroxidase family 0.016055
248 COG4942 peptidase 0.016028
249 COG0095 Lipoate-protein ligase -0.016011
250 2ZBSZ 0.015995