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 COG4608 Belongs to the ABC transporter superfamily -0.016943
2 2Z96N monooxygenase activity 0.016232
3 COG1126 abc transporter atp-binding protein -0.016141
4 COG0627 Serine hydrolase involved in the detoxification of formaldehyde -0.016077
5 2Z9T7 Ammonia monooxygenase methane monooxygenase, subunit C 0.015958
6 32213 0.015919
7 32TB9 Catalyzes the oxidation of primary alcohols including methanol 0.015919
8 COG1795 PFAM Formaldehyde-activating enzyme (Fae) 0.015919
9 COG3252 Catalyzes the hydrolysis of methenyl-H(4)MPT( ) to 5- formyl-H(4)MPT 0.015919
10 30I3V 0.015794
11 COG0444 Belongs to the ABC transporter superfamily -0.015430
12 COG2457 Protein of unknown function (DUF447) 0.015008
13 32RK9 Protein of unknown function (DUF4242) 0.014953
14 COG1907 transferase activity, transferring glycosyl groups 0.014289
15 COG4213 ABC transporter substrate-binding protein -0.013941
16 COG1620 l-lactate permease -0.013915
17 COG1070 Carbohydrate kinase -0.013838
18 COG1454 alcohol dehydrogenase -0.013469
19 COG4943 cyclic-guanylate-specific phosphodiesterase activity -0.013396
20 COG0010 Belongs to the arginase family -0.013369
21 2Z9FM monooxygenase activity 0.013359
22 COG1767 triphosphoribosyl-dephospho-CoA synthase activity 0.013043
23 32RK3 0.012978
24 COG0534 Mate efflux family protein -0.012804
25 COG0426 domain, Protein -0.012709
26 COG2993 Cytochrome C oxidase, mono-heme subunit/FixO 0.012679
27 COG1720 tRNA m6t6A37 methyltransferase activity -0.012538
28 COG1695 Transcriptional regulator -0.012450
29 COG0765 amino acid transport -0.012207
30 2Z8CH SIR2-like domain 0.011813
31 2ZBN7 nitrogen fixation protein 0.011813
32 327FW molybdenum ion binding 0.011813
33 COG5554 nitrogen fixation 0.011813
34 COG1029 Formylmethanofuran dehydrogenase, subunit B 0.011737
35 COG1229 Formylmethanofuran dehydrogenase subunit A 0.011737
36 COG1411 Belongs to the HisA HisF family 0.011737
37 COG1548 H4MPT-linked C1 transfer pathway protein 0.011737
38 COG2037 Catalyzes the transfer of a formyl group from 5-formyl tetrahydromethanopterin (5-formyl-H(4)MPT) to methanofuran (MFR) so as to produce formylmethanofuran (formyl-MFR) and tetrahydromethanopterin (H(4)MPT) 0.011737
39 COG4409 exo-alpha-(2->6)-sialidase activity 0.011735
40 COG4742 methyltransferase activity 0.011712
41 COG1304 FMN binding -0.011681
42 COG1538 Outer membrane efflux protein 0.011668
43 COG0471 metal ion transport -0.011507
44 COG1279 arginine transmembrane transporter activity -0.011449
45 COG0619 Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates -0.011424
46 COG1122 ATPase activity -0.011424
47 COG5501 0.011373
48 COG0736 holo-[acyl-carrier-protein] synthase activity -0.011267
49 334BZ 0.011110
50 COG3937 granule-associated protein -0.011092
51 COG0295 cytidine deaminase activity -0.011080
52 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family -0.011056
53 COG2218 PFAM glutamate synthase alpha subunit domain protein 0.011038
54 COG0190 Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate -0.011015
55 COG2249 NAD(P)H dehydrogenase (quinone) activity -0.010892
56 330W8 May protect the nitrogenase Fe-Mo protein from oxidative damage 0.010864
57 COG4244 Membrane 0.010857
58 COG1237 beta-lactamase domain protein -0.010714
59 COG0420 3'-5' exonuclease activity -0.010648
60 331JP Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter 0.010636
61 COG5424 Ring cyclization and eight-electron oxidation of 3a-(2- amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline- 7,9-dicarboxylic-acid to PQQ 0.010630
62 COG0395 ABC-type sugar transport system, permease component -0.010581
63 COG3256 nitric oxide reductase 0.010581
64 COG0846 NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form -0.010499
65 COG3448 diguanylate cyclase activity -0.010472
66 COG4301 Catalyzes the SAM-dependent triple methylation of the alpha-amino group of histidine to form hercynine, a step in the biosynthesis pathway of ergothioneine 0.010466
67 COG3435 Gentisate 1,2-dioxygenase 0.010448
68 COG5472 Small integral membrane protein 0.010425
69 COG2011 ABC-type metal ion transport system permease component -0.010406
70 COG0518 GMP synthase (glutamine-hydrolyzing) activity -0.010383
71 COG0232 Belongs to the dGTPase family. Type 2 subfamily -0.010317
72 COG1489 DNA binding -0.010277
73 COG1464 Belongs to the NlpA lipoprotein family -0.010264
74 COG1275 C4-dicarboxylate transporter malic acid transport protein -0.010197
75 2ZDJ6 0.010163
76 COG2317 Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues -0.010085
77 COG2832 Protein of unknown function (DUF454) -0.010085
78 COG1172 Belongs to the binding-protein-dependent transport system permease family -0.010084
79 330AH Protein of unknown function (DUF3455) 0.010035
80 COG1908 Methyl-viologen-reducing hydrogenase, delta subunit -0.010021
81 COG0668 transmembrane transport -0.009996
82 32VX7 0.009980
83 COG0753 catalase activity -0.009979
84 COG1414 Transcriptional regulator -0.009879
85 COG2176 DNA-directed DNA polymerase activity -0.009873
86 COG5573 PIN domain -0.009749
87 COG2008 Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde -0.009745
88 COG1368 sulfuric ester hydrolase activity -0.009728
89 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity -0.009725
90 COG0591 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.009713
91 COG1282 The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane 0.009700
92 COG3288 NAD(P)+ transhydrogenase (AB-specific) activity 0.009700
93 COG2054 PFAM Aspartate glutamate uridylate kinase 0.009655
94 COG1925 phosphoenolpyruvate-dependent sugar phosphotransferase system -0.009653
95 COG1560 Kdo2-lipid A biosynthetic process -0.009607
96 COG3071 HemY protein -0.009590
97 COG1612 heme a metabolic process 0.009584
98 COG0601 transmembrane transport -0.009571
99 COG0427 acetyl-CoA hydrolase -0.009532
100 COG1737 Transcriptional regulator -0.009532
101 COG1576 Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA -0.009489
102 COG4258 3-demethylubiquinone-9 3-O-methyltransferase activity 0.009473
103 COG0069 glutamate synthase activity -0.009422
104 COG2842 Transposition protein -0.009418
105 COG1251 Belongs to the nitrite and sulfite reductase 4Fe-4S domain family 0.009410
106 COG1607 acyl-coa hydrolase -0.009407
107 COG0696 Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate -0.009396
108 COG1999 signal sequence binding 0.009366
109 COG1022 Amp-dependent synthetase and ligase -0.009364
110 COG0011 TIGRFAM Protein of -0.009344
111 COG1513 Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide 0.009341
112 COG1941 NADH ubiquinone oxidoreductase 20 kDa subunit 0.009338
113 COG3259 Nickel-dependent hydrogenase 0.009338
114 329NG CAAX protease self-immunity 0.009308
115 2Z9F8 -0.009285
116 COG1476 TRANSCRIPTIONal -0.009251
117 COG2048 Heterodisulfide reductase, subunit B -0.009182
118 COG2516 radical SAM -0.009162
119 334TW Small metal-binding protein 0.009143
120 COG4558 Periplasmic binding protein -0.009139
121 COG2979 Protein of unknown function (DUF533) -0.009111
122 COG3619 membrane -0.009106
123 COG0694 Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins -0.009102
124 COG2860 membrane -0.009101
125 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for 0.009095
126 COG2220 Zn-dependent hydrolases of the beta-lactamase fold -0.009092
127 COG1178 ABC-type Fe3 transport system permease component -0.009076
128 32RUH 0.009042
129 COG0330 HflC and HflK could -0.009032
130 COG1346 cytolysis -0.008976
131 COG1380 Effector of murein hydrolase LrgA -0.008976
132 COG0626 cystathionine gamma-synthase activity -0.008973
133 COG1913 serine-type endopeptidase activity -0.008973
134 COG3104 oligopeptide transport 0.008949
135 33YJY 0.008947
136 COG3383 formate dehydrogenase (NAD+) activity 0.008945
137 COG1150 heterodisulfide reductase subunit C -0.008905
138 COG1609 Transcriptional regulator -0.008871
139 COG1502 Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol -0.008869
140 COG1926 phosphoribosyltransferase 0.008868
141 COG2137 regulation of response to DNA damage stimulus -0.008810
142 COG0121 glutamine amidotransferase -0.008809
143 2ZAZ5 0.008789
144 COG1740 oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor 0.008786
145 COG4564 Single Cache domain 2 -0.008718
146 COG4277 radical SAM -0.008701
147 COG3021 interspecies interaction between organisms -0.008690
148 COG3658 cytochrome 0.008631
149 COG4255 Protein conserved in bacteria -0.008617
150 COG0796 Provides the (R)-glutamate required for cell wall biosynthesis -0.008616
151 COG1113 amino acid transport -0.008614
152 32AZ4 Winged helix-turn-helix domain (DUF2582) 0.008608
153 COG5426 von Willebrand factor, type A 0.008607
154 COG0168 Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA -0.008601
155 COG5006 permease, DMT superfamily -0.008598
156 COG5607 PFAM CHAD domain containing protein 0.008591
157 COG1036 PFAM Flavoprotein 0.008585
158 COG3439 Domain of unknown function DUF302 0.008585
159 COG0025 NhaP-type Na H and K H -0.008529
160 COG1418 mRNA catabolic process -0.008519
161 327K1 0.008503
162 COG3883 PFAM NLP P60 protein -0.008478
163 COG1175 transmembrane transport -0.008460
164 COG1556 Lactate utilization protein -0.008458
165 COG3395 kinase activity -0.008433
166 COG1524 type I phosphodiesterase nucleotide pyrophosphatase -0.008399
167 COG2333 competence protein COMEC -0.008371
168 COG2355 Zn-dependent dipeptidase, microsomal dipeptidase -0.008360
169 COG4188 dienelactone hydrolase -0.008337
170 COG2936 dipeptidyl-peptidase activity -0.008319
171 32YM4 0.008301
172 COG0327 Belongs to the GTP cyclohydrolase I type 2 NIF3 family -0.008295
173 COG3108 Peptidase M15 0.008244
174 32Z86 NADH-dependant formate dehydrogenase delta subunit FdsD 0.008240
175 COG1981 membrane 0.008233
176 COG0857 belongs to the CobB CobQ family -0.008230
177 2ZWNP 0.008219
178 3359W 0.008219
179 337FK 0.008219
180 33AM3 0.008219
181 COG1444 tRNA N-acetyltransferase activity -0.008219
182 2Z7UJ Alginate export 0.008218
183 COG1886 FliN is one of three proteins (FliG, FliN, FliM) that form 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 -0.008217
184 COG4149 molybdate abc transporter 0.008214
185 COG1120 ATPase activity -0.008213
186 COG2411 cytidine deaminase activity 0.008190
187 33CDK 0.008186
188 COG3508 Involved in the catabolism of homogentisate (2,5- dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the aromatic ring of homogentisate to yield maleylacetoacetate 0.008185
189 COG1891 lyase activity 0.008184
190 COG5622 Protein required for attachment to host cells 0.008169
191 COG2372 response to copper ion 0.008167
192 COG4798 methyltransferase 0.008151
193 2ZPSX MmoB/DmpM family 0.008138
194 30P72 Methane monooxygenase, hydrolase gamma chain 0.008138
195 335AI 0.008138
196 333E5 -0.008133
197 COG3404 Formiminotransferase-cyclodeaminase 0.008129
198 COG1351 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NAD(P)H and FADH(2) as the reductant -0.008106
199 COG3474 cytochrome 0.008074
200 32ZJ3 -0.008066
201 COG3864 Putative metallopeptidase domain -0.008051
202 COG1847 R3H domain protein -0.008050
203 COG4774 siderophore transport 0.008045
204 COG3971 2-oxopent-4-enoate hydratase activity -0.008042
205 33B0D Type II secretion system protein B 0.008036
206 COG2233 PERMEase -0.008034
207 COG3842 ATPase activity -0.008022
208 336SP 0.008012
209 COG0126 phosphoglycerate kinase activity -0.007992
210 33K6G 0.007978
211 3493B 0.007972
212 COG0803 Belongs to the bacterial solute-binding protein 9 family -0.007958
213 32VK6 Protein of unknown function (DUF1523) -0.007944
214 COG1564 THIamine pyrophosphokinase -0.007933
215 COG0401 homolog of Blt101 -0.007928
216 COG0598 Magnesium transport protein CorA -0.007919
217 COG3744 PilT protein domain protein 0.007918
218 2ZV1D 0.007915
219 COG2365 Tyrosine phosphatase family -0.007903
220 COG1230 cation diffusion facilitator family transporter -0.007891
221 COG3615 Tellurite resistance protein tehB -0.007890
222 COG1135 Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system -0.007890
223 32WHM 0.007883
224 COG2095 MarC family integral membrane protein -0.007867
225 COG0708 Exodeoxyribonuclease III -0.007866
226 33DM8 0.007859
227 COG3749 Protein conserved in bacteria 0.007847
228 COG1448 Aminotransferase -0.007842
229 COG1813 peptidyl-tyrosine sulfation -0.007830
230 COG3961 Belongs to the TPP enzyme family 0.007808
231 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 -0.007792
232 COG1203 CRISPR-associated helicase, Cas3 0.007783
233 3367I 0.007782
234 COG5217 Protein of unknown function (DUF3086) 0.007771
235 COG2031 fatty acid transporter -0.007766
236 COG1076 Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA -0.007763
237 COG4891 PFAM Polyketide cyclase dehydrase 0.007730
238 COG0317 In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance -0.007699
239 COG3909 cytochrome 0.007698
240 COG0566 Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family -0.007694
241 32Y66 0.007665
242 COG3568 Endonuclease Exonuclease Phosphatase -0.007663
243 339QE 0.007656
244 COG1204 response to ionizing radiation -0.007643
245 COG3634 alkyl hydroperoxide reductase activity -0.007632
246 31R3P 0.007629
247 33P45 HNH nucleases 0.007629
248 COG0349 Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides 0.007625
249 COG2186 Transcriptional regulator -0.007604
250 30GRY Cytochrome P460 0.007591