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 COG1024 Enoyl-CoA hydratase 0.047074
2 COG1250 3-hydroxyacyl-CoA dehydrogenase 0.041921
3 COG1960 acyl-CoA dehydrogenase activity 0.039203
4 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.035059
5 COG2025 fatty acid beta-oxidation using acyl-CoA dehydrogenase 0.029253
6 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit 0.027918
7 COG2057 Acyl CoA acetate 3-ketoacid CoA transferase beta subunit 0.027918
8 COG0074 Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit -0.027510
9 COG2086 electron transfer activity 0.027377
10 COG0599 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity -0.027079
11 COG4769 heptaprenyl diphosphate synthase component I 0.026474
12 COG4624 Iron only hydrogenase large subunit, C-terminal domain 0.026436
13 COG2059 Chromate 0.026320
14 COG0833 amino acid -0.025757
15 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 -0.025664
16 COG2033 superoxide reductase activity 0.025533
17 COG3475 LICD family -0.025087
18 COG0427 acetyl-CoA hydrolase 0.024715
19 COG0402 S-adenosylhomocysteine deaminase activity 0.024704
20 COG1539 Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin -0.024527
21 COG1477 protein flavinylation 0.024515
22 COG0286 site-specific DNA-methyltransferase (adenine-specific) activity -0.024461
23 COG1114 Component of the transport system for branched-chain amino acids -0.024208
24 COG4536 flavin adenine dinucleotide binding 0.024139
25 COG1882 Formate acetyltransferase -0.023524
26 COG4980 gas vesicle protein -0.023370
27 COG0105 UTP biosynthetic process -0.023358
28 COG4566 intracellular signal transduction -0.022820
29 COG4934 collagen metabolic process -0.022800
30 COG1033 growth of symbiont in host cell 0.022793
31 COG2080 2 iron, 2 sulfur cluster binding 0.022498
32 COG3263 regulation of cellular component size 0.022365
33 COG2768 binding domain, Protein 0.022122
34 COG5341 Protein conserved in bacteria 0.022083
35 COG3862 protein with conserved CXXC pairs 0.022060
36 COG2878 Part of a membrane complex involved in electron transport 0.022048
37 COG4657 Part of a membrane complex involved in electron transport 0.021924
38 COG0636 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation 0.021750
39 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding 0.021720
40 COG0022 dehydrogenase e1 component -0.021666
41 32SGE Protein of unknown function (DUF3793) 0.021630
42 COG5495 nadp oxidoreductase, coenzyme f420-dependent 0.021621
43 COG0306 phosphate transporter -0.021574
44 2Z7N4 PFAM KilA, N-terminal APSES-type HTH, DNA-binding -0.021470
45 COG2088 sporulation resulting in formation of a cellular spore 0.021426
46 COG1064 alcohol dehydrogenase -0.021365
47 COG1982 Orn Lys Arg decarboxylase major 0.021329
48 COG0579 oxidoreductase 0.021291
49 COG0303 'Molybdopterin -0.021280
50 COG4715 Zinc finger, swim domain protein 0.021241
51 COG0799 negative regulation of ribosome biogenesis -0.021113
52 COG2731 YhcH YjgK YiaL family protein -0.021095
53 33JI9 PFAM FeoA family protein 0.020859
54 COG4660 Part of a membrane complex involved in electron transport 0.020793
55 COG3604 Transcriptional regulator 0.020747
56 COG0135 phosphoribosylanthranilate isomerase activity -0.020712
57 COG0399 UDP-4-amino-4-deoxy-L-arabinose aminotransferase -0.020611
58 COG1528 Iron-storage protein 0.020499
59 COG1225 Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.020376
60 COG4469 Competence protein -0.020317
61 COG0156 8-amino-7-oxononanoate synthase activity -0.020317
62 COG2008 Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde 0.020267
63 COG1647 Serine aminopeptidase, S33 0.020151
64 COG1071 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor -0.020136
65 COG4492 Belongs to the UPF0735 family 0.020062
66 COG0159 tryptophan synthase activity -0.019859
67 COG0732 type I restriction modification DNA specificity domain -0.019786
68 COG0078 Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline -0.019778
69 COG0338 D12 class N6 adenine-specific DNA methyltransferase -0.019719
70 COG0561 phosphatase activity -0.019712
71 COG1346 cytolysis 0.019649
72 COG1380 Effector of murein hydrolase LrgA 0.019649
73 COG3581 4 iron, 4 sulfur cluster binding 0.019627
74 COG1914 H( )-stimulated, divalent metal cation uptake system -0.019565
75 COG0302 gtp cyclohydrolase -0.019400
76 COG0626 cystathionine gamma-synthase activity -0.019259
77 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 -0.019239
78 COG3119 arylsulfatase activity -0.019232
79 COG1428 Deoxynucleoside kinase -0.019224
80 2Z9AE 0.019209
81 COG0785 Cytochrome C biogenesis protein 0.019203
82 COG0686 Belongs to the AlaDH PNT family -0.019138
83 COG1283 sodium-dependent phosphate transmembrane transporter activity 0.019130
84 COG1529 Aldehyde oxidase and xanthine dehydrogenase 0.019070
85 COG0508 dehydrogenase complex catalyzes the overall conversion of -0.018946
86 COG1957 nucleoside hydrolase -0.018868
87 COG0404 The glycine cleavage system catalyzes the degradation of glycine -0.018854
88 COG0547 Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA) -0.018831
89 COG1308 UBA TS-N domain 0.018735
90 COG1554 hydrolase, family 65, central catalytic -0.018716
91 COG3945 hemerythrin HHE cation binding domain 0.018715
92 COG0783 Belongs to the Dps family -0.018654
93 COG2129 metallophosphoesterase 0.018626
94 2ZJU3 -0.018576
95 33E1I Domain of unknown function (DUF1858) 0.018571
96 COG1445 protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity 0.018511
97 COG4658 electron transport chain 0.018445
98 COG4193 domain, Protein 0.018223
99 30J2J 0.018178
100 COG0280 phosphate acetyltransferase 0.018148
101 COG0077 Prephenate dehydratase -0.018076
102 COG2183 response to ionizing radiation -0.018021
103 COG0095 Lipoate-protein ligase -0.018009
104 COG2241 protein methyltransferase activity 0.017981
105 COG1078 dGTPase activity -0.017979
106 COG4651 solute:proton antiporter activity -0.017958
107 COG1132 (ABC) transporter 0.017952
108 COG4866 Psort location Cytoplasmic, score 0.017881
109 COG2607 Atpase (Aaa 0.017839
110 COG4747 ACT domain protein -0.017829
111 COG3878 Protein conserved in bacteria 0.017828
112 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 0.017785
113 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity -0.017773
114 COG2022 thiamine diphosphate biosynthetic process 0.017765
115 COG4512 PFAM Accessory gene regulator B 0.017670
116 COG1875 ATPase related to phosphate starvation-inducible protein PhoH 0.017650
117 COG5438 YibE/F-like protein 0.017622
118 COG3533 Beta-L-arabinofuranosidase, GH127 -0.017615
119 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 -0.017607
120 2ZDY4 Psort location Cytoplasmic, score -0.017605
121 COG0294 Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives -0.017594
122 COG0314 molybdopterin synthase activity -0.017556
123 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.017550
124 COG1705 Flagellar rod assembly protein muramidase FlgJ -0.017541
125 3322G Stage III sporulation protein AF (Spore_III_AF) 0.017506
126 COG2906 2 iron, 2 sulfur cluster binding 0.017497
127 COG3382 B3 4 domain protein -0.017335
128 COG0431 NADPH-dependent FMN reductase -0.017321
129 COG1149 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.017310
130 COG1151 hydroxylamine reductase activity 0.017294
131 COG0805 protein transport -0.017273
132 COG4990 cell redox homeostasis -0.017268
133 COG0610 Subunit R is required for both nuclease and ATPase activities, but not for modification -0.017261
134 2Z7XM TraX protein 0.017248
135 COG3246 L-lysine catabolic process to acetate 0.017232
136 COG4894 glucomannan catabolic process 0.017138
137 COG2315 Protein conserved in bacteria -0.017088
138 COG0393 Putative heavy-metal-binding -0.017038
139 COG1164 Oligoendopeptidase f 0.016984
140 COG0850 regulation of cytokinetic process 0.016921
141 COG2855 membrane 0.016916
142 COG1167 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs 0.016906
143 32TDJ Domain of unknown function (DUF4367) -0.016890
144 COG0378 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG -0.016889
145 COG4284 Utp--glucose-1-phosphate uridylyltransferase 0.016881
146 COG2246 polysaccharide biosynthetic process -0.016816
147 COG3668 Plasmid stabilization system -0.016801
148 2Z9TG -0.016801
149 COG1521 Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis 0.016766
150 COG1489 DNA binding 0.016751
151 COG1763 Mo-molybdopterin cofactor biosynthetic process -0.016662
152 COG3201 nicotinamide mononucleotide transporter -0.016649
153 COG4656 Part of a membrane complex involved in electron transport 0.016648
154 COG1305 Transglutaminase-like -0.016633
155 COG4770 biotin carboxylase activity -0.016631
156 COG1246 Belongs to the acetyltransferase family. ArgA subfamily -0.016624
157 COG2151 metal-sulfur cluster biosynthetic enzyme -0.016615
158 COG3177 Filamentation induced by cAMP protein fic -0.016614
159 COG0133 tryptophan synthase activity -0.016605
160 COG0595 An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay -0.016605
161 COG1426 Protein conserved in bacteria -0.016593
162 COG1011 Hydrolase -0.016559
163 COG4552 Acetyltransferase involved in intracellular survival and related 0.016548
164 COG1076 Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA -0.016539
165 COG2610 gluconate transmembrane transporter activity 0.016510
166 COG0369 Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH - FAD - FMN to the hemoprotein component -0.016471
167 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component -0.016460
168 COG4936 Histidine kinase 0.016386
169 COG0134 indole-3-glycerol-phosphate synthase activity -0.016332
170 COG4558 Periplasmic binding protein 0.016321
171 COG0616 signal peptide processing -0.016320
172 COG1480 7TM receptor with intracellular HD hydrolase 0.016287
173 COG1294 oxidase, subunit -0.016273
174 COG3459 Glycosyltransferase 36 associated 0.016258
175 COG1611 Belongs to the LOG family -0.016252
176 COG4481 Protein conserved in bacteria -0.016251
177 COG2936 dipeptidyl-peptidase activity -0.016251
178 COG1924 4 iron, 4 sulfur cluster binding 0.016211
179 COG0510 thiamine kinase activity -0.016209
180 COG1454 alcohol dehydrogenase 0.016182
181 2Z85F Domain of unknown function (4846) 0.016154
182 334G5 0.016098
183 COG0003 Pfam Anion-transporting ATPase 0.016096
184 3488M helix_turn_helix multiple antibiotic resistance protein 0.016080
185 COG0662 Cupin 2, conserved barrel domain protein -0.016065
186 COG4129 membrane 0.016043
187 COG0737 Belongs to the 5'-nucleotidase family -0.016005
188 COG1119 ATPase activity -0.015965
189 322UQ 0.015925
190 COG0483 inositol monophosphate 1-phosphatase activity -0.015891
191 COG4096 Type I site-specific restriction-modification system, R (Restriction) subunit and related -0.015837
192 COG3649 crispr-associated protein 0.015825
193 COG3410 Uncharacterized conserved protein (DUF2075) 0.015817
194 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity 0.015803
195 339FG -0.015782
196 COG0247 lactate metabolic process -0.015781
197 COG1218 3'(2'),5'-bisphosphate nucleotidase -0.015762
198 COG3911 COG3911 Predicted ATPase 0.015736
199 32S3C Stress responsive A/B Barrel Domain 0.015717
200 COG1040 competence protein -0.015709
201 COG3695 enzyme binding -0.015706
202 COG2856 Zn peptidase 0.015686
203 COG0539 negative regulation of cytoplasmic translation -0.015667
204 COG2348 transferase activity, transferring amino-acyl groups -0.015635
205 COG0386 Belongs to the glutathione peroxidase family -0.015607
206 COG0413 3-methyl-2-oxobutanoate hydroxymethyltransferase activity 0.015569
207 COG1496 oxidoreductase activity -0.015567
208 32RMG Arsenical resistance operon trans-acting repressor arsD 0.015524
209 COG0864 Transcriptional regulator -0.015489
210 COG2311 Membrane -0.015441
211 COG4735 regulation of single-species biofilm formation -0.015423
212 COG0659 secondary active sulfate transmembrane transporter activity 0.015421
213 COG4222 Protein conserved in bacteria -0.015391
214 342VC Cyclic nucleotide-monophosphate binding domain 0.015378
215 COG0600 ABC-type nitrate sulfonate bicarbonate transport system permease component 0.015287
216 COG4200 ABC-2 family transporter protein 0.015256
217 COG0657 acetylesterase activity -0.015249
218 33A8G YtxH-like protein 0.015218
219 COG3603 ACT domain 0.015208
220 30H51 Protein of unknown function (DUF551) -0.015180
221 COG3643 Formiminotransferase domain 0.015134
222 COG4824 toxin secretion phage lysis holin -0.015132
223 32V42 Immunity protein 70 -0.015126
224 33A63 Psort location Cytoplasmic, score 0.015096
225 COG1342 Belongs to the UPF0251 family 0.015089
226 COG0502 Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism 0.015085
227 COG1873 PFAM PRC-barrel domain -0.015084
228 COG3335 DDE superfamily endonuclease -0.015045
229 COG1619 proteins homologs of microcin C7 resistance protein MccF 0.015002
230 2ZCK6 Phage minor capsid protein 2 -0.014968
231 COG0384 phenazine biosynthesis protein PhzF 0.014947
232 COG1165 Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate (SEPHCHC) -0.014935
233 COG5279 protein involved in cytokinesis, contains TGc (transglutaminase protease-like) domain 0.014921
234 COG1720 tRNA m6t6A37 methyltransferase activity -0.014910
235 COG1669 hydrolase activity, acting on ester bonds 0.014903
236 COG1544 Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase -0.014895
237 32WQD Protein of unknown function (DUF3822) 0.014870
238 32REW Transglutaminase-like superfamily -0.014841
239 COG1702 phosphate starvation-inducible protein PhoH -0.014834
240 3360K Protein of unknown function (DUF3892) 0.014812
241 COG3800 Transcriptional regulator -0.014801
242 COG2807 transmembrane transport -0.014744
243 COG0414 Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate 0.014735
244 32AT1 0.014706
245 COG1738 Involved in the import of queuosine (Q) precursors, required for Q precursor salvage -0.014679
246 COG4479 Belongs to the UPF0346 family -0.014654
247 32YRT Maff2 family 0.014654
248 COG2805 Type II/IV secretion system protein 0.014634
249 COG0407 Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III -0.014628
250 COG0754 glutathionylspermidine amidase activity -0.014603