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 COG0413 3-methyl-2-oxobutanoate hydroxymethyltransferase activity 0.036016
2 COG0403 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.034072
3 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component 0.033635
4 COG3682 Transcriptional regulator -0.032497
5 COG3426 butyrate kinase activity 0.030359
6 COG3274 enterobacterial common antigen metabolic process -0.030313
7 3432Z Domain of unknown function (DUF4153) -0.030024
8 COG1003 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.029317
9 COG1397 ADP-ribosylglycohydrolase 0.028892
10 COG1146 Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions 0.028211
11 COG0154 amidase activity -0.027499
12 COG5496 Thioesterase -0.027356
13 COG1705 Flagellar rod assembly protein muramidase FlgJ 0.026356
14 COG0686 Belongs to the AlaDH PNT family 0.026042
15 COG4198 Conserved Protein 0.025810
16 COG2856 Zn peptidase -0.025485
17 COG0404 The glycine cleavage system catalyzes the degradation of glycine 0.025479
18 COG4626 Terminase -0.025360
19 COG3476 COG3476 Tryptophan-rich sensory protein (mitochondrial benzodiazepine receptor homolog) -0.025330
20 COG5545 protein tyrosine phosphatase activity -0.025054
21 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) -0.024938
22 COG0721 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) -0.024938
23 COG3504 Conjugal transfer protein -0.024680
24 COG3509 depolymerase -0.024544
25 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin 0.024510
26 COG1129 ABC transporter -0.024263
27 COG0509 glycine decarboxylation via glycine cleavage system 0.024017
28 COG2382 esterase 0.023824
29 COG3153 acetyltransferase -0.023684
30 COG1556 Lactate utilization protein 0.023235
31 COG1929 Belongs to the glycerate kinase type-1 family 0.023205
32 COG2240 Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP 0.023143
33 COG1135 Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system -0.023046
34 COG2115 Belongs to the xylose isomerase family -0.022977
35 COG3936 Protein involved in polysaccharide intercellular adhesin (PIA) synthesis biofilm formation 0.022831
36 COG1956 GAF domain-containing protein 0.022734
37 COG4963 Pilus assembly protein -0.022727
38 319M2 Conserved hypothetical protein (Lin0512_fam) 0.022683
39 335CG Psort location CytoplasmicMembrane, score 0.022590
40 COG1636 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) 0.022533
41 COG0390 transport system, permease component -0.022452
42 COG2461 Hemerythrin HHE cation binding domain protein -0.022451
43 COG2876 3-deoxy-7-phosphoheptulonate synthase activity 0.022431
44 COG1464 Belongs to the NlpA lipoprotein family -0.022243
45 COG2011 ABC-type metal ion transport system permease component -0.022243
46 COG0575 Belongs to the CDS family -0.022224
47 COG1451 nucleotide metabolic process -0.022179
48 COG4290 ribonuclease -0.021912
49 COG1075 acetyltransferases and hydrolases with the alpha beta hydrolase fold -0.021906
50 COG1995 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) 0.021856
51 COG2211 Major facilitator Superfamily -0.021841
52 COG5239 Endonuclease/Exonuclease/phosphatase family 0.021777
53 32RWC 23S rRNA-intervening sequence protein 0.021747
54 COG3747 phage terminase small subunit -0.021644
55 COG1250 3-hydroxyacyl-CoA dehydrogenase -0.021631
56 COG3345 alpha-galactosidase -0.021567
57 COG1754 DNA topoisomerase type I activity -0.021566
58 COG4667 esterase of the alpha-beta hydrolase superfamily -0.021526
59 COG0003 Pfam Anion-transporting ATPase 0.021506
60 32ERD Outer membrane protein beta-barrel domain 0.021379
61 COG1897 L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine -0.021350
62 COG1903 Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A 0.021349
63 COG1561 YicC-like family, N-terminal region 0.021098
64 COG4181 ATPase activity -0.021043
65 2Z8FC Psort location CytoplasmicMembrane, score 10.00 0.020777
66 33CJ8 0.020764
67 COG5627 protein ubiquitination -0.020665
68 COG1506 peptidase 0.020541
69 321KG Psort location CytoplasmicMembrane, score 0.020435
70 COG1249 Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family 0.020400
71 COG0550 Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone 0.020382
72 COG1687 branched-chain amino acid -0.020379
73 COG1505 serine-type exopeptidase activity 0.020330
74 COG2270 Major facilitator Superfamily 0.020286
75 COG0214 Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively 0.020254
76 COG0786 glutamate:sodium symporter activity 0.020233
77 3025Y Psort location Cytoplasmic, score 0.020231
78 COG1101 ABC transporter -0.020227
79 COG4120 Belongs to the binding-protein-dependent transport system permease family -0.020227
80 COG1145 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.020186
81 COG1141 Ferredoxin 0.020178
82 COG1480 7TM receptor with intracellular HD hydrolase 0.020166
83 COG4249 Peptidase C14 caspase catalytic subunit p20 0.020166
84 COG3385 transposase activity -0.020108
85 31HS3 -0.020030
86 COG0523 cobalamin synthesis protein -0.019991
87 COG0791 NLP P60 protein 0.019957
88 COG1304 FMN binding 0.019954
89 COG4227 nucleotidyltransferase activity -0.019871
90 COG4859 Psort location Cytoplasmic, score 0.019792
91 COG0414 Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate 0.019737
92 COG0732 type I restriction modification DNA specificity domain 0.019685
93 COG0790 COG0790 FOG TPR repeat, SEL1 subfamily 0.019610
94 32XR9 Outer membrane efflux protein -0.019609
95 COG2035 Membrane -0.019481
96 COG0432 Pfam Uncharacterised protein family UPF0047 -0.019447
97 COG0737 Belongs to the 5'-nucleotidase family 0.019411
98 COG2008 Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde 0.019382
99 2ZRS1 HTH-like domain -0.019351
100 COG3576 pyridoxamine 5-phosphate -0.019337
101 33C80 COG NOG35566 non supervised orthologous group 0.019330
102 COG0656 L-ascorbic acid biosynthetic process -0.019249
103 COG4194 SdpI/YhfL protein family 0.019216
104 2ZIC6 Helix-turn-helix XRE-family like proteins 0.019178
105 COG3910 aaa ATPase -0.019128
106 COG2366 antibiotic biosynthetic process -0.019091
107 COG0601 transmembrane transport -0.019065
108 COG1173 ABC-type dipeptide oligopeptide nickel transport systems, permease components -0.019065
109 COG4221 oxidoreductase activity -0.019052
110 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) -0.018848
111 COG1083 cytidylyl-transferase -0.018816
112 COG1069 ribulokinase activity -0.018765
113 COG3883 PFAM NLP P60 protein 0.018698
114 COG1666 GTP binding -0.018629
115 COG5338 Protein conserved in bacteria -0.018628
116 COG1373 ATPase (AAA superfamily -0.018606
117 COG4464 protein tyrosine phosphatase activity 0.018593
118 COG0663 COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily -0.018549
119 33JR4 -0.018502
120 COG0372 Belongs to the citrate synthase family 0.018338
121 COG0219 Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide -0.018296
122 COG4608 Belongs to the ABC transporter superfamily -0.018294
123 COG3579 cysteine-type endopeptidase activity 0.018173
124 COG3199 ATP-NAD kinase 0.018150
125 COG1925 phosphoenolpyruvate-dependent sugar phosphotransferase system -0.018143
126 COG4542 GHMP kinases N terminal domain 0.018101
127 COG1875 ATPase related to phosphate starvation-inducible protein PhoH 0.018035
128 COG5280 Phage tail tape measure protein TP901 0.018012
129 COG1518 maintenance of DNA repeat elements 0.017917
130 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 -0.017885
131 32RP7 Domain of unknown function (DUF1911) -0.017845
132 311B0 Fimbrillin-like 0.017783
133 COG3710 Transcriptional regulator -0.017773
134 COG1296 Branched-chain amino acid permease (Azaleucine resistance) -0.017770
135 COG0045 succinate-CoA ligase (ADP-forming) activity 0.017726
136 32YCK Stress responsive A/B Barrel Domain 0.017619
137 COG1530 ribonuclease E activity 0.017601
138 32T36 -0.017596
139 COG1495 Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein -0.017592
140 COG1921 L-seryl-tRNASec selenium transferase activity 0.017501
141 COG0311 Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS 0.017461
142 COG3442 glutamine amidotransferase -0.017452
143 COG1922 lipopolysaccharide N-acetylmannosaminouronosyltransferase activity 0.017380
144 COG1580 Controls the rotational direction of flagella during chemotaxis -0.017356
145 COG4413 Urea transporter -0.017292
146 2ZQU2 -0.017288
147 32Y88 VRR-NUC domain protein -0.017265
148 2ZCH9 -0.017255
149 COG3843 relaxase mobilization nuclease domain protein 0.017193
150 COG4641 Protein conserved in bacteria -0.017182
151 COG3938 Belongs to the proline racemase family 0.017050
152 33KKK -0.017047
153 COG0610 Subunit R is required for both nuclease and ATPase activities, but not for modification 0.017014
154 COG2017 converts alpha-aldose to the beta-anomer -0.017013
155 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity 0.017002
156 COG0410 ABC transporter -0.016945
157 COG0411 ABC transporter -0.016945
158 COG0559 Belongs to the binding-protein-dependent transport system permease family -0.016945
159 COG4177 L-phenylalanine transmembrane transporter activity -0.016945
160 COG1126 abc transporter atp-binding protein -0.016922
161 COG3958 Transketolase 0.016907
162 COG5423 Predicted metal-binding protein (DUF2284) 0.016901
163 32YH4 -0.016873
164 COG5527 Initiator Replication protein -0.016851
165 COG1796 DNA polymerase 0.016813
166 3397Y Lysine exporter LysO 0.016754
167 COG2186 Transcriptional regulator 0.016721
168 32RFD Protein of unknown function (DUF3867) 0.016700
169 33RRR -0.016691
170 30NZ2 0.016690
171 COG0639 Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP -0.016677
172 COG3955 Domain of unknown function (DUF1919) -0.016660
173 COG3158 transport of potassium into the cell -0.016657
174 COG0269 3-dehydro-L-gulonate-6-phosphate decarboxylase activity -0.016657
175 COG1024 Enoyl-CoA hydratase -0.016643
176 2ZJYW -0.016625
177 30MM0 -0.016625
178 COG2522 sequence-specific DNA binding -0.016610
179 COG2249 NAD(P)H dehydrogenase (quinone) activity 0.016482
180 COG2984 ABC transporter substrate binding protein -0.016419
181 34CH1 Helix-turn-helix 0.016416
182 COG0803 Belongs to the bacterial solute-binding protein 9 family -0.016403
183 COG1402 creatininase 0.016380
184 COG0483 inositol monophosphate 1-phosphatase activity -0.016356
185 COG0546 phosphoglycolate phosphatase activity -0.016342
186 COG4907 membrane protein (DUF2207) -0.016341
187 COG0744 Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors -0.016295
188 COG1715 Restriction endonuclease -0.016237
189 COG0855 Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) -0.016222
190 COG1048 Catalyzes the isomerization of citrate to isocitrate via cis-aconitate 0.016204
191 2ZFBU 0.016173
192 32I9F Domain of unknown function (DUF5067) 0.016173
193 33AWA 0.016173
194 33DZD 0.016173
195 33ITM Immunity protein 8 0.016173
196 COG1672 PFAM Archaeal ATPase 0.016173
197 COG1275 C4-dicarboxylate transporter malic acid transport protein 0.016169
198 COG0169 Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA) -0.016131
199 COG0342 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 -0.016121
200 COG3408 Glycogen debranching enzyme 0.016115
201 2Z7R3 CarboxypepD_reg-like domain 0.016101
202 COG0295 cytidine deaminase activity 0.016090
203 COG1122 ATPase activity -0.016036
204 32YHS 0.016036
205 33R57 -0.016021
206 30CRG Phosphopantetheine attachment site -0.015986
207 COG1045 serine acetyltransferase 0.015980
208 2Z86D Glycosyl transferase -0.015932
209 32T2Y -0.015930
210 COG3645 SOS response 0.015849
211 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.015840
212 32RQN Cna protein B-type domain 0.015821
213 COG2764 glyoxalase bleomycin resistance protein dioxygenase -0.015821
214 COG3959 Transketolase, thiamine diphosphate binding domain 0.015768
215 32S5I 0.015750
216 30G7E 0.015707
217 304BD -0.015706
218 30I06 Helix-turn-helix domain -0.015706
219 327GG -0.015679
220 338RU -0.015679
221 32STP 0.015642
222 32S46 Fe-S-cluster oxidoreductase 0.015638
223 COG4748 type I restriction enzyme 0.015595
224 30U0E Protein of unknown function (DUF3188) 0.015583
225 32Y7Q Protein of unknown function (Porph_ging) 0.015563
226 COG2194 sulfuric ester hydrolase activity 0.015535
227 COG0014 Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5- carboxylate -0.015525
228 COG0263 Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate -0.015525
229 COG0757 Catalyzes a trans-dehydration via an enolate intermediate -0.015475
230 2Z7RJ InterPro IPR011630 0.015475
231 COG3027 Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division -0.015471
232 COG1979 alcohol dehydrogenase 0.015468
233 COG5495 nadp oxidoreductase, coenzyme f420-dependent 0.015401
234 COG0711 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) -0.015397
235 COG1528 Iron-storage protein 0.015298
236 2ZB6F -0.015292
237 COG1492 cobalamin metabolic process 0.015264
238 COG3047 cAMP biosynthetic process 0.015258
239 COG3643 Formiminotransferase domain 0.015248
240 2Z800 Protein of unknown function (DUF1177) 0.015246
241 COG1061 Type III restriction enzyme res subunit -0.015244
242 338E7 -0.015216
243 32SEQ -0.015196
244 32H4Q Bacterial regulatory proteins, tetR family 0.015192
245 COG0037 tRNA processing -0.015175
246 COG3848 Pyruvate phosphate dikinase 0.015135
247 33DNC Psort location Cytoplasmic, score 0.015134
248 COG3404 Formiminotransferase-cyclodeaminase 0.015129
249 COG2972 Histidine kinase 0.015078
250 COG1473 amidohydrolase -0.015077