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 COG1620 l-lactate permease 0.054525
2 COG2837 iron assimilation 0.041748
3 COG1199 ATP-dependent helicase activity -0.039120
4 COG1283 sodium-dependent phosphate transmembrane transporter activity -0.028097
5 COG3663 DNA glycosylase 0.026918
6 COG4976 Methyltransferase -0.026884
7 COG0315 cyclic pyranopterin monophosphate synthase activity 0.026807
8 COG4753 response regulator 0.026794
9 COG3239 Fatty acid desaturase -0.026624
10 COG2314 TM2 domain -0.026469
11 COG0371 Dehydrogenase -0.026319
12 COG0510 thiamine kinase activity -0.026129
13 COG2704 Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane 0.026073
14 COG2180 nitrate reductase molybdenum cofactor assembly chaperone 0.025707
15 COG2040 homocysteine 0.025670
16 COG1191 sigma factor activity -0.025617
17 COG3620 sequence-specific DNA binding 0.025616
18 COG4283 Protein of unknown function (DUF1706) -0.025599
19 COG1275 C4-dicarboxylate transporter malic acid transport protein -0.025481
20 COG0785 Cytochrome C biogenesis protein -0.025021
21 COG2896 Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate 0.024985
22 COG2015 COG2015, Alkyl sulfatase and related hydrolases -0.024911
23 COG1887 Glycosyl glycerophosphate transferases involved in teichoic acid biosynthesis TagF TagB EpsJ RodC 0.024664
24 COG0696 Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate 0.024636
25 COG1600 Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr) -0.024351
26 COG3591 Belongs to the peptidase S1B family -0.024337
27 3381Y Antitoxin component of a toxin-antitoxin (TA) module 0.024089
28 COG2183 response to ionizing radiation -0.023836
29 2ZWWV ORF located using Blastx 0.023753
30 COG1182 Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity -0.023581
31 COG0715 COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components -0.023532
32 COG1951 Catalyzes the reversible hydration of fumarate to (S)- malate 0.023120
33 COG3378 Phage plasmid primase P4 family 0.023075
34 COG3376 Belongs to the NiCoT transporter (TC 2.A.52) family 0.023056
35 COG3668 Plasmid stabilization system 0.022930
36 COG0157 Belongs to the NadC ModD family -0.022717
37 COG0741 lytic transglycosylase activity -0.022291
38 COG1575 Belongs to the MenA family. Type 1 subfamily -0.022256
39 COG1742 UPF0060 membrane protein 0.022229
40 3448G 'Pfam Bacterial regulatory proteins, tetR family -0.022222
41 COG2879 small protein 0.022152
42 COG1853 conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family -0.022149
43 COG1903 Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A 0.021960
44 COG0520 Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine -0.021869
45 COG0400 carboxylic ester hydrolase activity -0.021824
46 COG1546 Belongs to the CinA family -0.021447
47 COG3475 LICD family 0.021197
48 COG1129 ABC transporter -0.021192
49 COG1010 Tetrapyrrole (Corrin/Porphyrin) Methylases 0.021128
50 COG2336 PFAM SpoVT AbrB -0.020993
51 COG2984 ABC transporter substrate binding protein 0.020968
52 COG0753 catalase activity 0.020942
53 COG4145 pantothenate transmembrane transporter activity -0.020893
54 COG2073 Cobalamin biosynthesis protein cbiG 0.020867
55 COG1211 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity -0.020632
56 COG0646 methionine synthase -0.020592
57 COG3610 response to peptide 0.020544
58 COG2056 Na+-H+ antiporter family 0.020436
59 COG1140 nitrate reductase beta subunit 0.020398
60 COG1364 Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate -0.020341
61 COG3942 CHAP domain -0.020280
62 COG4607 ABC-type enterochelin transport system periplasmic component -0.020267
63 COG1301 dicarboxylic acid transport 0.020258
64 COG0805 protein transport 0.020222
65 COG4260 virion core protein, lumpy skin disease virus -0.020134
66 COG0384 phenazine biosynthesis protein PhzF -0.020012
67 COG2820 Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis -0.019937
68 COG3250 beta-galactosidase activity 0.019889
69 COG3081 Nucleoid-associated protein 0.019760
70 2Z8PG -0.019733
71 COG1321 iron dependent repressor -0.019617
72 33JI9 PFAM FeoA family protein -0.019580
73 COG0717 Belongs to the dCTP deaminase family -0.019572
74 COG1363 Peptidase, m42 -0.019565
75 COG1826 Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes 0.019555
76 COG3174 membrane 0.019503
77 COG3303 Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process 0.019341
78 COG3426 butyrate kinase activity -0.019325
79 COG4907 membrane protein (DUF2207) 0.019267
80 COG2848 UPF0210 protein -0.019144
81 COG4213 ABC transporter substrate-binding protein 0.019120
82 COG5015 Pyridoxamine 5'-phosphate oxidase -0.019091
83 COG3944 biosynthesis protein 0.019064
84 COG2271 Major facilitator Superfamily 0.019007
85 COG0076 glutamate decarboxylase activity -0.018999
86 COG1006 Multisubunit Na H antiporter MnhC subunit -0.018968
87 33AEP Domain of unknown function (DUF4430) 0.018966
88 COG0464 growth -0.018913
89 COG4224 UPF0291 protein 0.018863
90 COG4565 transcriptional regulatory protein -0.018804
91 COG0523 cobalamin synthesis protein 0.018778
92 COG4768 protein containing a divergent version of the methyl-accepting chemotaxis-like domain -0.018743
93 COG2918 glutathione biosynthetic process -0.018726
94 COG2181 nitrate reductase activity 0.018715
95 COG0581 inorganic phosphate transmembrane transporter activity 0.018569
96 COG1775 2-hydroxyglutaryl-CoA dehydratase, D-component -0.018544
97 COG1605 Chorismate mutase -0.018533
98 COG3336 cytochrome c oxidase -0.018457
99 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin -0.018453
100 COG0398 Pfam SNARE associated Golgi protein -0.018449
101 COG1143 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 0.018422
102 COG1533 DNA photolyase activity 0.018384
103 COG0616 signal peptide processing -0.018384
104 COG0562 UDP-galactopyranose mutase -0.018370
105 COG0657 acetylesterase activity 0.018346
106 COG0610 Subunit R is required for both nuclease and ATPase activities, but not for modification 0.018315
107 30BKD Bacterial regulatory proteins, lacI family 0.018304
108 COG4336 lyase activity -0.018245
109 COG0145 ligase activity -0.018226
110 COG1528 Iron-storage protein -0.018174
111 COG3870 Protein conserved in bacteria 0.018158
112 COG1178 ABC-type Fe3 transport system permease component -0.018155
113 COG2184 nucleotidyltransferase activity -0.018130
114 COG1085 galactose-1-phosphate uridylyltransferase 0.018093
115 COG0427 acetyl-CoA hydrolase 0.018091
116 COG2113 Glycine betaine 0.018031
117 COG2199 diguanylate cyclase activity 0.018024
118 COG2173 Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide 0.018007
119 COG2875 Belongs to the precorrin methyltransferase family 0.017966
120 32Y15 Psort location CytoplasmicMembrane, score 0.017957
121 COG3921 Protein conserved in bacteria 0.017941
122 COG1135 Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system 0.017913
123 COG3585 molybdate ion transport -0.017909
124 32STP 0.017869
125 COG4540 Baseplate assembly protein -0.017856
126 COG0859 PFAM glycosyl transferase family 9 -0.017854
127 COG0346 lactoylglutathione lyase activity -0.017833
128 COG5036 VTC domain -0.017804
129 308P1 0.017766
130 COG4720 Psort location CytoplasmicMembrane, score 0.017742
131 COG1794 racemase activity, acting on amino acids and derivatives 0.017683
132 COG1735 metal-dependent hydrolase with the TIM-barrel fold -0.017623
133 COG3037 sugar-specific permease SgaT UlaA -0.017612
134 COG3755 Protein conserved in bacteria 0.017487
135 33CG9 GDSL-like Lipase/Acylhydrolase 0.017456
136 32RPZ Domain of unknown function (DUF4811) 0.017450
137 COG1443 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) -0.017428
138 COG0553 Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair -0.017397
139 COG2084 Dehydrogenase -0.017385
140 COG3440 Restriction endonuclease -0.017362
141 COG2365 Tyrosine phosphatase family 0.017295
142 COG3945 hemerythrin HHE cation binding domain -0.017288
143 COG4289 Protein conserved in bacteria 0.017281
144 32T36 0.017231
145 33CM8 0.017184
146 COG4454 pyrroloquinoline quinone binding 0.017173
147 COG2972 Histidine kinase -0.017093
148 COG0295 cytidine deaminase activity -0.017083
149 COG0379 Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate -0.017072
150 COG1954 Regulates expression of the glpD operon. In the presence of glycerol 3-phosphate (G3P) causes antitermination of transcription of glpD at the inverted repeat of the leader region to enhance its transcription. Binds and stabilizes glpD leader mRNA 0.017065
151 31W2T Universal stress protein family -0.017065
152 COG1804 L-carnitine dehydratase bile acid-inducible protein F -0.017064
153 COG1937 Protein conserved in bacteria 0.017047
154 COG2329 Antibiotic biosynthesis monooxygenase -0.017036
155 COG0521 Mo-molybdopterin cofactor biosynthetic process 0.017035
156 COG2368 4-hydroxyphenylacetate -0.017034
157 COG3682 Transcriptional regulator -0.017030
158 COG0780 Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) 0.017015
159 COG2227 3-demethylubiquinone-9 3-O-methyltransferase activity 0.017007
160 COG0341 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA -0.016990
161 COG2011 ABC-type metal ion transport system permease component 0.016968
162 COG0112 Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism 0.016935
163 32A7C GDSL-like Lipase/Acylhydrolase family 0.016912
164 COG2826 transposase and inactivated derivatives, IS30 family 0.016900
165 COG0560 Phosphoserine phosphatase -0.016819
166 COG1012 belongs to the aldehyde dehydrogenase family -0.016819
167 COG3973 AAA domain -0.016803
168 COG4670 ketone body catabolic process -0.016798
169 COG4185 zeta toxin -0.016772
170 COG3093 addiction module antidote protein HigA 0.016707
171 COG4464 protein tyrosine phosphatase activity 0.016695
172 COG0590 tRNA wobble adenosine to inosine editing -0.016677
173 COG1410 methionine synthase 0.016673
174 COG2030 dehydratase -0.016656
175 COG0605 Destroys radicals which are normally produced within the cells and which are toxic to biological systems -0.016618
176 COG1764 response to oxidative stress 0.016599
177 COG1186 Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA 0.016575
178 COG1104 cysteine desulfurase activity -0.016572
179 COG2898 Catalyzes the transfer of a lysyl group from L-lysyl- tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), a major component of the bacterial membrane with a positive net charge. LPG synthesis contributes to bacterial virulence as it is involved in the resistance mechanism against cationic antimicrobial peptides (CAMP) produces by the host's immune system (defensins, cathelicidins) and by the competing microorganisms 0.016494
180 32G2Z Lysin motif 0.016493
181 COG5578 integral membrane protein -0.016441
182 COG1442 glycosyl transferase family 8 0.016428
183 COG3059 membrane 0.016416
184 33J2G Control of competence regulator ComK, YlbF/YmcA 0.016407
185 2Z948 Psort location CytoplasmicMembrane, score 10.00 -0.016362
186 COG3039 Transposase 0.016346
187 COG1477 protein flavinylation -0.016264
188 COG0608 single-stranded DNA 5'-3' exodeoxyribonuclease activity -0.016258
189 COG1989 Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue 0.016246
190 COG3851 Histidine kinase 0.016156
191 COG4109 DRTGG domain -0.016150
192 COG4555 ABC transporter -0.016120
193 COG2706 6-phosphogluconolactonase activity -0.016095
194 COG0027 Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate -0.016084
195 COG3822 ABC-type sugar transport system, auxiliary component -0.016081
196 COG2856 Zn peptidase -0.016080
197 COG4403 Lanthionine synthetase C family protein -0.016069
198 COG5614 head-tail adaptor 0.016050
199 COG3328 transposase activity 0.016036
200 32QT1 -0.016015
201 COG0106 1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase -0.015973
202 COG0704 Plays a role in the regulation of phosphate uptake 0.015972
203 COG2035 Membrane -0.015951
204 32W8Q 0.015949
205 COG4641 Protein conserved in bacteria 0.015933
206 33D6A Nucleotidyltransferase substrate binding protein like 0.015927
207 COG1070 Carbohydrate kinase 0.015895
208 COG0814 amino acid 0.015888
209 COG2177 Part of the ABC transporter FtsEX involved in -0.015823
210 COG0122 3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase -0.015816
211 COG1715 Restriction endonuclease -0.015783
212 COG4615 Cyclic peptide transporter 0.015783
213 COG0314 molybdopterin synthase activity 0.015758
214 COG2976 Protein conserved in bacteria -0.015755
215 COG3369 Iron-binding zinc finger CDGSH type -0.015733
216 COG1007 ATP synthesis coupled electron transport 0.015643
217 COG3981 Acetyltransferase (GNAT) domain -0.015620
218 COG0671 phosphoesterase, PA-phosphatase related -0.015619
219 COG2352 Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle -0.015614
220 COG0662 Cupin 2, conserved barrel domain protein 0.015613
221 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 -0.015610
222 COG1464 Belongs to the NlpA lipoprotein family 0.015595
223 COG1556 Lactate utilization protein 0.015541
224 COG2963 transposase activity 0.015525
225 COG0820 rRNA (adenine-C2-)-methyltransferase activity -0.015517
226 COG1484 DNA-dependent DNA replication 0.015501
227 COG2370 cobalamin-transporting ATPase activity 0.015477
228 2ZGY7 0.015456
229 COG4465 DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor -0.015439
230 COG4485 Bacterial membrane protein, YfhO 0.015432
231 COG0645 Protein conserved in bacteria -0.015410
232 COG1177 transmembrane transport 0.015406
233 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC -0.015386
234 3058S 0.015355
235 COG4822 anaerobic cobalamin biosynthetic process 0.015338
236 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity -0.015337
237 30C2I -0.015335
238 COG2143 COG2143 Thioredoxin-related protein -0.015331
239 COG0175 sulfate reduction 0.015331
240 346DU GDSL-like Lipase/Acylhydrolase 0.015325
241 COG1785 Belongs to the alkaline phosphatase family -0.015325
242 33YTS -0.015274
243 COG5457 Domain of unknown function (DUF1127) 0.015271
244 COG0385 Bile acid 0.015268
245 COG2884 Cell division ATP-binding protein ftsE -0.015265
246 30584 0.015260
247 COG3883 PFAM NLP P60 protein -0.015242
248 COG4129 membrane -0.015239
249 COG1979 alcohol dehydrogenase -0.015194
250 COG2515 1-aminocyclopropane-1-carboxylate deaminase 0.015190