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 COG1442 glycosyl transferase family 8 -0.038277
2 COG1541 Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA) 0.037629
3 COG0277 FAD linked oxidase domain protein -0.037053
4 COG1479 Protein of unknown function DUF262 0.035154
5 COG3274 enterobacterial common antigen metabolic process 0.032884
6 COG3941 tape measure 0.032741
7 COG3041 Addiction module toxin RelE StbE family 0.031627
8 COG2358 TRAP transporter, solute receptor (TAXI family 0.030397
9 COG1297 OPT oligopeptide transporter protein 0.030147
10 COG1368 sulfuric ester hydrolase activity 0.029959
11 COG0790 COG0790 FOG TPR repeat, SEL1 subfamily -0.029160
12 COG3598 Psort location Cytoplasmic, score 0.028369
13 COG0836 Belongs to the mannose-6-phosphate isomerase type 2 family 0.027228
14 COG2005 Transcriptional regulator -0.026794
15 COG2519 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA -0.026458
16 COG1116 anion transmembrane transporter activity 0.025981
17 COG3331 DNA recombination -0.025910
18 33VTB Sigma-70 region 2 0.025903
19 COG1027 Aspartate ammonia-lyase 0.025726
20 COG1293 RNA-binding protein homologous to eukaryotic snRNP -0.025608
21 COG1959 2 iron, 2 sulfur cluster binding -0.025597
22 33MT9 -0.025559
23 COG1484 DNA-dependent DNA replication -0.025539
24 334F6 Winged helix-turn helix 0.025334
25 COG0095 Lipoate-protein ligase -0.025169
26 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family -0.024939
27 COG1282 The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane 0.024900
28 COG3837 Cupin domain 0.024761
29 COG1253 flavin adenine dinucleotide binding -0.024724
30 COG0608 single-stranded DNA 5'-3' exodeoxyribonuclease activity 0.024621
31 COG0647 UMP catabolic process -0.024434
32 COG1533 DNA photolyase activity -0.024195
33 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit -0.024167
34 COG2057 Acyl CoA acetate 3-ketoacid CoA transferase beta subunit -0.024167
35 COG2871 sodium ion transport 0.023946
36 341CM Bacterial regulatory proteins, tetR family -0.023943
37 COG0125 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis -0.023821
38 COG0479 Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family 0.023636
39 COG3683 transport system, periplasmic component -0.023609
40 COG1832 CoA-binding protein -0.023503
41 COG0450 alkyl hydroperoxide reductase 0.023478
42 31EGY 0.023245
43 COG3288 NAD(P)+ transhydrogenase (AB-specific) activity 0.023163
44 COG1034 ATP synthesis coupled electron transport -0.023159
45 COG1118 Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system -0.023091
46 COG4188 dienelactone hydrolase -0.023036
47 COG4823 Abi-like protein 0.022936
48 2ZYY6 Bacterial regulatory proteins, tetR family -0.022908
49 COG2851 Citrate transporter -0.022719
50 COG4346 Dolichyl-phosphate-mannose--protein O-mannosyl transferase -0.022673
51 COG3247 response to pH 0.022630
52 COG1086 Polysaccharide biosynthesis protein 0.022569
53 COG5188 Subtilase family 0.022556
54 COG2856 Zn peptidase -0.022406
55 COG0015 Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily -0.022382
56 COG3323 Protein of unknown function (DUF1653) -0.022350
57 COG1022 Amp-dependent synthetase and ligase 0.022322
58 COG2020 methyltransferase activity 0.022217
59 COG4785 May be involved in cell division 0.022067
60 COG4665 TRAP-type mannitol chloroaromatic compound transport system small permease component 0.021981
61 COG1105 Belongs to the carbohydrate kinase PfkB family -0.021979
62 COG2949 membrane 0.021906
63 COG1720 tRNA m6t6A37 methyltransferase activity -0.021890
64 COG4199 Single-strand DNA-specific exonuclease, C terminal domain -0.021849
65 COG5660 integral membrane protein -0.021835
66 COG1124 (ABC) transporter -0.021832
67 COG0209 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides 0.021751
68 COG2860 membrane 0.021740
69 COG4186 nucleotidyltransferase activity -0.021675
70 COG0757 Catalyzes a trans-dehydration via an enolate intermediate 0.021615
71 COG0421 Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine 0.021547
72 COG3153 acetyltransferase -0.021488
73 COG2314 TM2 domain 0.021169
74 COG0332 Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched- chain and or straight-chain of fatty acids -0.021130
75 COG0395 ABC-type sugar transport system, permease component 0.021105
76 COG0651 ATP synthesis coupled electron transport -0.021034
77 COG0288 reversible hydration of carbon dioxide -0.020993
78 COG2086 electron transfer activity -0.020960
79 COG0554 Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate -0.020935
80 COG0427 acetyl-CoA hydrolase -0.020781
81 COG3774 pathogenesis -0.020679
82 COG3386 PFAM SMP-30 Gluconolaconase -0.020651
83 COG4690 dipeptidase activity -0.020651
84 COG3535 Protein of unknown function (DUF917) 0.020633
85 COG2350 Protein conserved in bacteria 0.020613
86 COG2253 Psort location Cytoplasmic, score 0.020551
87 COG3004 Na( ) H( ) antiporter that extrudes sodium in exchange for external protons 0.020436
88 COG5001 Diguanylate cyclase 0.020381
89 COG0416 fatty acid biosynthetic process -0.020347
90 COG4225 unsaturated rhamnogalacturonyl hydrolase activity -0.020342
91 COG1328 CTP reductase activity 0.020336
92 COG1222 aaa ATPase 0.020297
93 COG5006 permease, DMT superfamily -0.020186
94 COG1683 Conserved Protein -0.020183
95 COG3016 Iron-regulated protein 0.020178
96 COG1125 glycine betaine transport -0.020150
97 COG1319 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM -0.020119
98 COG2035 Membrane -0.020112
99 COG1506 peptidase 0.020074
100 COG0704 Plays a role in the regulation of phosphate uptake -0.019954
101 COG2872 Ser-tRNA(Ala) hydrolase activity 0.019939
102 COG3059 membrane 0.019918
103 COG1802 Transcriptional regulator -0.019866
104 COG2964 Protein conserved in bacteria -0.019851
105 30BKD Bacterial regulatory proteins, lacI family -0.019809
106 COG0405 Gamma-glutamyltransferase -0.019784
107 COG2027 D-alanyl-D-alanine carboxypeptidase 0.019771
108 COG0398 Pfam SNARE associated Golgi protein -0.019764
109 COG2240 Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP -0.019726
110 3381Y Antitoxin component of a toxin-antitoxin (TA) module -0.019706
111 COG4235 cytochrome complex assembly 0.019704
112 2ZA26 Psort location CytoplasmicMembrane, score 10.00 0.019591
113 COG2897 thiosulfate sulfurtransferase activity -0.019585
114 COG4149 molybdate abc transporter -0.019570
115 COG3921 Protein conserved in bacteria -0.019499
116 COG4233 Disulphide bond corrector protein DsbC -0.019419
117 COG1288 antiporter activity 0.019374
118 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine 0.019359
119 COG2251 uridine kinase activity -0.019297
120 COG1939 Involved in correct processing of both the 5' and 3' ends of 23S rRNA precursor. Processes 30S rRNA precursor transcript even in absence of ribonuclease 3 (Rnc) -0.019283
121 COG1937 Protein conserved in bacteria -0.019252
122 336HV 0.019248
123 COG1347 NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol 0.019205
124 COG2209 NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol 0.019205
125 COG2999 glutathione oxidoreductase activity 0.019194
126 COG0710 3-dehydroquinate dehydratase activity -0.019157
127 COG3568 Endonuclease Exonuclease Phosphatase 0.019111
128 COG4569 acetaldehyde dehydrogenase (acetylating) activity 0.019085
129 COG3250 beta-galactosidase activity 0.019071
130 2Z7PD Psort location CytoplasmicMembrane, score -0.019034
131 COG3842 ATPase activity 0.019008
132 COG4763 Acyl-transferase -0.018985
133 COG1285 pathogenesis 0.018944
134 COG2869 NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol 0.018882
135 COG1244 Elongator protein 3, MiaB family, Radical SAM 0.018863
136 COG3257 ureidoglycine aminohydrolase activity 0.018855
137 COG1827 regulation of RNA biosynthetic process -0.018854
138 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid -0.018847
139 32XR9 Outer membrane efflux protein -0.018819
140 COG1726 NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol 0.018785
141 COG3617 BRO family, N-terminal domain 0.018773
142 COG3716 PTS system mannose fructose sorbose family IID component -0.018751
143 COG4799 Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta -0.018728
144 COG4555 ABC transporter -0.018726
145 COG5433 transposase activity 0.018694
146 COG3302 dmso reductase anchor subunit 0.018650
147 COG2520 Methyltransferase fkbm family -0.018611
148 32RP9 Psort location CytoplasmicMembrane, score 0.018548
149 337JB 0.018536
150 COG2133 pyrroloquinoline quinone binding 0.018535
151 COG0031 Belongs to the cysteine synthase cystathionine beta- synthase family -0.018534
152 COG1525 nuclease -0.018532
153 2ZSRR Psort location Cytoplasmic, score 8.87 0.018491
154 COG0673 inositol 2-dehydrogenase activity 0.018470
155 COG4545 Glutaredoxin-related protein 0.018430
156 COG2333 competence protein COMEC 0.018372
157 COG1686 Belongs to the peptidase S11 family -0.018363
158 COG2859 Protein conserved in bacteria 0.018347
159 COG2033 superoxide reductase activity -0.018346
160 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 0.018344
161 COG3543 Protein of unknown function (DUF1284) 0.018340
162 COG1045 serine acetyltransferase -0.018338
163 COG1363 Peptidase, m42 -0.018310
164 COG4926 Phage minor structural protein 0.018308
165 COG4640 response to antibiotic 0.018303
166 COG2327 Polysaccharide pyruvyl transferase -0.018273
167 COG2302 S4 RNA-binding domain -0.018246
168 COG1443 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) -0.018170
169 COG0175 sulfate reduction 0.018155
170 COG0717 Belongs to the dCTP deaminase family -0.018120
171 COG2067 long-chain fatty acid transport protein 0.018087
172 COG0054 6,7-dimethyl-8-ribityllumazine synthase activity -0.018080
173 COG0110 maltose O-acetyltransferase activity -0.018079
174 COG4123 Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC) 0.018044
175 COG1175 transmembrane transport 0.018014
176 COG0388 Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source -0.017947
177 COG5499 transcription regulator containing HTH domain 0.017917
178 COG0760 Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation -0.017914
179 COG4193 domain, Protein -0.017900
180 COG0730 response to heat -0.017852
181 COG4319 ketosteroid isomerase -0.017820
182 COG1985 Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate -0.017799
183 COG3679 Belongs to the UPF0342 family -0.017761
184 COG2113 Glycine betaine 0.017743
185 COG1054 Belongs to the UPF0176 family -0.017691
186 COG3442 glutamine amidotransferase 0.017668
187 COG1556 Lactate utilization protein -0.017622
188 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 -0.017595
189 COG0715 COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components 0.017581
190 COG2072 flavoprotein involved in K transport -0.017579
191 COG0154 amidase activity -0.017550
192 COG0475 glutathione-regulated potassium exporter activity 0.017512
193 COG3452 CHASE 0.017506
194 330GJ 0.017480
195 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component 0.017458
196 COG3950 AAA domain, putative AbiEii toxin, Type IV TA system 0.017448
197 COG4826 Belongs to the serpin family 0.017440
198 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.017412
199 COG2273 Hydrolase Family 16 0.017384
200 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 0.017349
201 COG2334 A protein kinase that phosphorylates Ser and Thr residues. Probably acts to suppress the effects of stress linked to accumulation of reactive oxygen species. Probably involved in the extracytoplasmic stress response 0.017328
202 COG3475 LICD family 0.017313
203 COG4126 flavin adenine dinucleotide binding 0.017303
204 COG3319 amino acid activation for nonribosomal peptide biosynthetic process -0.017253
205 COG1119 ATPase activity 0.017241
206 COG1301 dicarboxylic acid transport -0.017214
207 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.017188
208 COG2873 o-acetylhomoserine -0.017188
209 COG0539 negative regulation of cytoplasmic translation 0.017176
210 COG1139 Iron-sulfur cluster binding protein -0.017170
211 2Z9WA Psort location Cytoplasmic, score 0.017137
212 33ACP 0.017067
213 COG0375 protein maturation -0.017053
214 COG2301 Belongs to the HpcH HpaI aldolase family -0.017041
215 COG1459 type II secretion system -0.017039
216 2Z92J 0.017032
217 COG1113 amino acid transport -0.017029
218 2Z7J7 0.017019
219 COG2372 response to copper ion -0.016981
220 COG5627 protein ubiquitination 0.016966
221 COG1984 allophanate hydrolase subunit 2 0.016934
222 COG2359 stage V sporulation protein S 0.016886
223 COG4845 Chloramphenicol acetyltransferase -0.016870
224 COG1453 Aldo Keto reductase 0.016861
225 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 0.016849
226 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 -0.016846
227 COG3641 Membrane -0.016837
228 32SNM Psort location Cytoplasmic, score 0.016821
229 COG1554 hydrolase, family 65, central catalytic 0.016791
230 COG2184 nucleotidyltransferase activity 0.016787
231 COG1803 Methylglyoxal synthase 0.016785
232 COG4283 Protein of unknown function (DUF1706) 0.016760
233 COG1307 EDD domain protein, DegV family -0.016760
234 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) -0.016734
235 COG0777 Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA -0.016723
236 COG2026 Addiction module toxin, RelE StbE family 0.016702
237 COG4574 serine-type endopeptidase inhibitor activity -0.016687
238 COG1038 Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second -0.016670
239 COG1004 Belongs to the UDP-glucose GDP-mannose dehydrogenase family -0.016660
240 COG1189 Ribosomal RNA methyltransferase RrmJ FtsJ -0.016651
241 COG0160 Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family 0.016650
242 COG0685 methylenetetrahydrofolate reductase (NAD(P)H) activity -0.016647
243 COG0391 Required for morphogenesis under gluconeogenic growth conditions -0.016645
244 COG0747 negative chemotaxis -0.016624
245 COG1501 Belongs to the glycosyl hydrolase 31 family 0.016614
246 COG0476 Involved in molybdopterin and thiamine biosynthesis, family 2 0.016568
247 2ZD7J 4Fe-4S single cluster domain of Ferredoxin I 0.016548
248 COG3191 aminopeptidase activity -0.016540
249 COG2013 TIGRFAM TIGR00266 family protein -0.016539
250 COG2017 converts alpha-aldose to the beta-anomer 0.016532