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 COG1398 Fatty acid desaturase 0.016419
2 COG3415 Transposase 0.014401
3 COG3335 DDE superfamily endonuclease 0.014347
4 COG0588 phosphoglycerate mutase activity 0.014313
5 COG1140 nitrate reductase beta subunit 0.014103
6 COG3002 Belongs to the UPF0753 family 0.014090
7 COG0701 Predicted permease -0.014007
8 COG2180 nitrate reductase molybdenum cofactor assembly chaperone 0.013986
9 COG2116 formate transmembrane transporter activity 0.013374
10 COG1832 CoA-binding protein -0.013226
11 COG2930 (twin-arginine translocation) pathway signal 0.013199
12 32VW1 0.013089
13 COG4398 FIST C domain 0.012839
14 COG2321 neutral zinc metallopeptidase 0.012820
15 COG1454 alcohol dehydrogenase -0.012733
16 COG1525 nuclease 0.012562
17 COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase 0.012493
18 COG1222 aaa ATPase 0.012333
19 COG1513 Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide 0.012302
20 3316G Protein of unknown function (DUF3386) 0.012270
21 COG0375 protein maturation -0.012217
22 COG4521 taurine ABC transporter -0.012213
23 COG2191 Formylmethanofuran dehydrogenase, subunit e -0.012182
24 COG2391 methyltransferase activity -0.012181
25 COG1402 creatininase -0.012136
26 COG0648 Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin -0.012121
27 COG0833 amino acid 0.011988
28 COG3237 CsbD-like 0.011972
29 COG1053 succinate dehydrogenase -0.011864
30 COG3676 manually curated 0.011368
31 COG3253 May function as heme-dependent peroxidase 0.011365
32 33AK9 Antitoxin Phd_YefM, type II toxin-antitoxin system 0.011300
33 COG0348 domain, Protein -0.011270
34 COG0661 Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis -0.011245
35 COG3182 Iron-regulated membrane protein 0.011209
36 COG4314 lipoprotein involved in nitrous oxide reduction -0.011173
37 COG1022 Amp-dependent synthetase and ligase -0.011071
38 2ZTJS Protein of unknown function (DUF2958) 0.010966
39 COG1301 dicarboxylic acid transport 0.010931
40 COG4096 Type I site-specific restriction-modification system, R (Restriction) subunit and related 0.010923
41 COG3883 PFAM NLP P60 protein 0.010850
42 COG0680 Initiates the rapid degradation of small, acid-soluble proteins during spore germination -0.010809
43 COG0395 ABC-type sugar transport system, permease component -0.010790
44 COG3587 Type III restriction enzyme, res subunit 0.010704
45 COG4258 3-demethylubiquinone-9 3-O-methyltransferase activity 0.010699
46 COG0374 Belongs to the NiFe NiFeSe hydrogenase large subunit family -0.010646
47 COG1740 oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor -0.010646
48 COG0298 carbon dioxide binding -0.010629
49 COG4715 Zinc finger, swim domain protein 0.010601
50 2Z7UJ Alginate export 0.010570
51 COG1924 4 iron, 4 sulfur cluster binding -0.010541
52 COG5555 FG-GAP repeat 0.010495
53 COG1966 Carbon starvation protein 0.010456
54 COG4637 Psort location Cytoplasmic, score -0.010383
55 COG0679 Auxin Efflux Carrier -0.010382
56 COG2186 Transcriptional regulator -0.010293
57 COG0230 Belongs to the bacterial ribosomal protein bL34 family -0.010263
58 COG1245 4Fe-4S binding domain 0.010192
59 COG3313 Fe-S protein -0.010186
60 COG1861 Spore coat polysaccharide biosynthesis protein F CMP-KDO synthetase 0.010136
61 COG3462 membrane protein (DUF2078) -0.010120
62 COG3746 phosphate-selective porin O and P 0.010113
63 2ZAF0 Rhamnogalacturonate lyase 0.010106
64 COG4233 Disulphide bond corrector protein DsbC 0.010078
65 COG5496 Thioesterase -0.010054
66 COG0334 Belongs to the Glu Leu Phe Val dehydrogenases family 0.010031
67 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family -0.010030
68 COG0543 2 iron, 2 sulfur cluster binding -0.010027
69 COG1171 Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA -0.010020
70 COG3004 Na( ) H( ) antiporter that extrudes sodium in exchange for external protons 0.010007
71 31W2T Universal stress protein family -0.010005
72 COG3108 Peptidase M15 0.009982
73 COG4627 Pfam Methyltransferase 0.009919
74 33B3Z 0.009894
75 COG1226 (belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family) -0.009886
76 COG3293 Transposase 0.009880
77 COG0397 Uncharacterized ACR, YdiU/UPF0061 family 0.009862
78 COG3320 Male sterility 0.009859
79 COG5617 Psort location CytoplasmicMembrane, score -0.009858
80 COG0411 ABC transporter -0.009855
81 33CEF Uncharacterised nucleotidyltransferase 0.009845
82 COG2608 mercury ion transmembrane transporter activity -0.009833
83 COG3225 cell adhesion 0.009780
84 30ZJ3 Gram-negative bacterial TonB protein C-terminal -0.009776
85 COG3957 D-xylulose 5-phosphate D-fructose 6-phosphate phosphoketolase 0.009745
86 COG4424 Sulfotransferase 0.009741
87 COG1433 Dinitrogenase iron-molybdenum cofactor -0.009735
88 COG2363 Small membrane protein 0.009691
89 COG2133 pyrroloquinoline quinone binding 0.009690
90 33FA9 O-antigen ligase like membrane protein -0.009679
91 COG1787 Restriction endonuclease -0.009605
92 COG3600 Phage-associated protein 0.009571
93 COG5426 von Willebrand factor, type A 0.009568
94 COG0175 sulfate reduction 0.009528
95 COG3795 YCII-related domain 0.009524
96 333E7 0.009520
97 COG0759 Could be involved in insertion of integral membrane proteins into the membrane -0.009506
98 2Z8T4 Carboxysome shell peptide mid-region 0.009503
99 2Z9V7 carboxysome shell 0.009503
100 COG4576 ethanolamine utilization protein EutN carboxysome structural protein Ccml 0.009503
101 COG4577 Carbon dioxide concentrating mechanism carboxysome shell protein 0.009503
102 COG1574 metal-dependent hydrolase with the TIM-barrel fold -0.009498
103 COG0437 4 iron, 4 sulfur cluster binding -0.009455
104 COG1858 cytochrome C peroxidase 0.009453
105 COG0060 amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) -0.009447
106 COG1620 l-lactate permease -0.009427
107 COG2329 Antibiotic biosynthesis monooxygenase 0.009417
108 COG0309 Hydrogenase expression formation protein (HypE) -0.009413
109 COG1775 2-hydroxyglutaryl-CoA dehydratase, D-component -0.009399
110 2ZIIW 0.009397
111 COG2146 nitrite reductase [NAD(P)H] activity 0.009397
112 2Z8M4 0.009395
113 COG2759 Belongs to the formate--tetrahydrofolate ligase family -0.009359
114 COG1412 self proteolysis 0.009344
115 COG0736 holo-[acyl-carrier-protein] synthase activity -0.009267
116 COG5621 secreted hydrolase 0.009261
117 310CC TonB C terminal 0.009256
118 COG1533 DNA photolyase activity 0.009253
119 COG0560 Phosphoserine phosphatase 0.009229
120 COG3221 ABC-type phosphate phosphonate transport system periplasmic component -0.009210
121 COG1213 nucleotidyl transferase 0.009204
122 32ZM7 0.009193
123 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component -0.009182
124 COG2945 thiolester hydrolase activity 0.009174
125 COG4638 Rieske (2fe-2S) -0.009162
126 COG2312 Erythromycin esterase 0.009141
127 COG3947 sequence-specific DNA binding -0.009139
128 COG1270 Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group -0.009139
129 COG3242 Uncharacterized protein conserved in bacteria (DUF2065) 0.009124
130 COG1820 Belongs to the metallo-dependent hydrolases superfamily. NagA family -0.009121
131 COG3247 response to pH 0.009102
132 COG0444 Belongs to the ABC transporter superfamily -0.009076
133 31KQ8 0.009073
134 COG1838 Catalyzes the reversible hydration of fumarate to (S)- malate -0.009056
135 COG0068 Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of NiFe -hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide -0.009046
136 COG2124 cytochrome p450 0.009012
137 COG3058 Necessary for formate dehydrogenase activity -0.009008
138 COG1023 phosphogluconate dehydrogenase (decarboxylating) activity 0.009001
139 COG4782 Protein conserved in bacteria 0.009000
140 COG2906 2 iron, 2 sulfur cluster binding 0.008982
141 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 0.008971
142 COG4555 ABC transporter -0.008961
143 COG1763 Mo-molybdopterin cofactor biosynthetic process 0.008957
144 COG1175 transmembrane transport -0.008954
145 COG1201 RNA secondary structure unwinding 0.008942
146 COG0132 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring 0.008930
147 COG1802 Transcriptional regulator -0.008903
148 2ZMK7 0.008886
149 2ZP2P 0.008886
150 334KX Proto-chlorophyllide reductase 57 kd subunit 0.008886
151 33MXU 0.008886
152 COG1937 Protein conserved in bacteria -0.008884
153 COG2920 part of a sulfur-relay system -0.008868
154 33AW2 0.008845
155 336WS Replication-relaxation 0.008845
156 33G8J 0.008845
157 COG3636 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 -0.008803
158 COG2354 Protein conserved in bacteria 0.008796
159 COG2991 Protein conserved in bacteria 0.008796
160 COG3222 Protein conserved in bacteria 0.008789
161 COG2192 nodulation 0.008758
162 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 -0.008732
163 COG1047 Peptidyl-prolyl cis-trans 0.008715
164 COG0518 GMP synthase (glutamine-hydrolyzing) activity -0.008701
165 COG0601 transmembrane transport -0.008682
166 COG1173 ABC-type dipeptide oligopeptide nickel transport systems, permease components -0.008682
167 COG1296 Branched-chain amino acid permease (Azaleucine resistance) -0.008681
168 COG2071 gamma-glutamyl-gamma-aminobutyrate hydrolase activity -0.008679
169 COG0665 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity -0.008663
170 COG3189 MarR family transcriptional regulator 0.008656
171 COG3748 Urate oxidase N-terminal 0.008653
172 COG1089 Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose 0.008653
173 COG3039 Transposase 0.008619
174 COG3832 glyoxalase III activity 0.008610
175 COG2091 lysine biosynthetic process via aminoadipic acid 0.008603
176 COG2113 Glycine betaine -0.008591
177 COG4175 Glycine betaine -0.008591
178 COG4176 ABC-type proline glycine betaine transport system permease component -0.008591
179 COG4453 Protein conserved in bacteria 0.008573
180 COG3385 transposase activity 0.008564
181 COG5433 transposase activity 0.008545
182 COG3615 Tellurite resistance protein tehB 0.008529
183 COG2605 GHMP kinase 0.008523
184 32VYT T5orf172 0.008501
185 COG2061 Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA 0.008493
186 COG2079 MmgE PrpD family protein -0.008492
187 COG1289 transmembrane transporter activity -0.008476
188 COG2764 glyoxalase bleomycin resistance protein dioxygenase 0.008471
189 COG1180 Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine -0.008458
190 COG2256 atpase related to the helicase subunit of the holliday junction resolvase -0.008446
191 COG3408 Glycogen debranching enzyme 0.008445
192 COG1034 ATP synthesis coupled electron transport -0.008439
193 COG0003 Pfam Anion-transporting ATPase -0.008437
194 COG0697 spore germination -0.008423
195 COG1797 cobyrinic acid a,c-diamide synthase activity -0.008402
196 COG0747 negative chemotaxis -0.008400
197 COG2847 Copper chaperone PCu(A)C -0.008398
198 336ZC Protein of unknown function (DUF2442) 0.008366
199 COG0709 Synthesizes selenophosphate from selenide and ATP -0.008329
200 COG1488 Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP -0.008321
201 COG5126 Ca2 -binding protein (EF-Hand superfamily -0.008317
202 3414V Macrocin-O-methyltransferase (TylF) 0.008314
203 COG4630 Xanthine dehydrogenase iron-sulfur cluster and FAD-binding subunit A -0.008292
204 COG4446 Protein conserved in bacteria 0.008286
205 COG2259 Doxx family 0.008282
206 2ZC6I 0.008281
207 32ZE4 Protein of unknown function (DUF3775) -0.008241
208 339JC MerR HTH family regulatory protein 0.008231
209 COG3577 Aspartyl protease 0.008230
210 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.008197
211 COG3119 arylsulfatase activity 0.008189
212 COG5006 permease, DMT superfamily -0.008162
213 COG0232 Belongs to the dGTPase family. Type 2 subfamily -0.008148
214 COG2873 o-acetylhomoserine -0.008130
215 COG4263 nitrous-oxide reductase activity -0.008126
216 COG0025 NhaP-type Na H and K H 0.008125
217 COG2239 Acts as a magnesium transporter 0.008121
218 COG0045 succinate-CoA ligase (ADP-forming) activity -0.008118
219 COG3673 conserved protein 0.008102
220 COG3622 Belongs to the hyi family -0.008101
221 COG2032 superoxide dismutase activity 0.008080
222 32ZSB Protein of unknown function (DUF3309) 0.008080
223 32RYR Domain of unknown function (DUF4112) 0.008079
224 3019X 0.008078
225 COG4584 PFAM Integrase catalytic 0.008068
226 COG1748 Saccharopine dehydrogenase 0.008054
227 COG2826 transposase and inactivated derivatives, IS30 family 0.008052
228 COG3845 ABC transporter -0.008042
229 COG0431 NADPH-dependent FMN reductase 0.008040
230 COG0626 cystathionine gamma-synthase activity -0.008036
231 COG3899 AAA ATPase domain -0.008031
232 COG2165 general secretion pathway protein -0.008022
233 COG3197 Cytochrome oxidase maturation protein -0.008012
234 COG1765 OsmC-like protein -0.008011
235 COG2855 membrane -0.008008
236 COG3215 Pilus assembly protein PilZ 0.007993
237 COG1350 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine -0.007983
238 COG4774 siderophore transport 0.007978
239 COG1742 UPF0060 membrane protein 0.007978
240 2ZBIP 0.007966
241 COG0381 UDP-N-acetylglucosamine 2-epimerase activity 0.007962
242 COG3698 Phosphodiester glycosidase 0.007958
243 COG1125 glycine betaine transport 0.007945
244 COG2322 membrane 0.007944
245 COG0554 Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate -0.007943
246 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the -0.007943
247 33DCB 0.007942
248 COG5083 PhoD-like phosphatase 0.007942
249 COG2355 Zn-dependent dipeptidase, microsomal dipeptidase -0.007941
250 2ZB8M 0.007938