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 COG1882 Formate acetyltransferase 0.023545
2 COG1525 nuclease -0.023396
3 COG1304 FMN binding -0.023316
4 COG2135 peptidase activity -0.022740
5 COG0155 Belongs to the nitrite and sulfite reductase 4Fe-4S domain family 0.022070
6 COG0499 May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine -0.021786
7 COG1858 cytochrome C peroxidase -0.021567
8 COG3593 DNA synthesis involved in DNA repair 0.021158
9 COG4781 glycerophosphoryl diester phosphodiesterase 0.020977
10 COG2364 Membrane -0.020796
11 COG1319 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM -0.020779
12 COG0623 enoyl-[acyl-carrier-protein] reductase (NADH) activity -0.020771
13 COG1438 arginine binding 0.020473
14 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 -0.020197
15 COG4261 Acyltransferase 0.020146
16 COG4096 Type I site-specific restriction-modification system, R (Restriction) subunit and related 0.020027
17 COG2214 Heat shock protein DnaJ domain protein -0.019916
18 COG1739 Uncharacterized protein family UPF0029 0.019693
19 COG0800 Aldolase 0.019658
20 COG3602 ACT domain -0.019632
21 COG2211 Major facilitator Superfamily 0.019394
22 COG0637 HAD-superfamily hydrolase subfamily IA, variant 3 0.019254
23 30BKD Bacterial regulatory proteins, lacI family 0.019158
24 COG0005 The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate -0.019106
25 COG1004 Belongs to the UDP-glucose GDP-mannose dehydrogenase family -0.018908
26 COG5005 Phage virion morphogenesis -0.018792
27 COG2103 Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate 0.018723
28 COG3412 dihydroxyacetone kinase, phosphotransfer subunit 0.018718
29 COG4946 Tricorn protease homolog -0.018555
30 COG4475 Protein of unknown function (DUF436) 0.018523
31 COG3641 Membrane 0.018400
32 339UG -0.018389
33 COG1322 Protein conserved in bacteria 0.018382
34 COG1194 a g-specific adenine glycosylase -0.018310
35 COG0405 Gamma-glutamyltransferase -0.018293
36 COG0851 Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell 0.018161
37 COG2425 protein containing a von Willebrand factor type A (vWA) domain 0.018082
38 COG1168 Bifunctional PLP-dependent enzyme with beta-cystaTHIonase and maltose regulon repressor activities 0.018057
39 COG4555 ABC transporter -0.017981
40 COG1526 Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH -0.017958
41 COG4260 virion core protein, lumpy skin disease virus 0.017956
42 COG1519 Transferase 0.017888
43 COG2246 polysaccharide biosynthetic process 0.017863
44 COG2808 Putative FMN-binding domain -0.017753
45 COG1850 ribulose-bisphosphate carboxylase activity 0.017682
46 COG0296 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position 0.017682
47 COG4227 nucleotidyltransferase activity -0.017673
48 COG1544 Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase 0.017662
49 COG3586 endonuclease activity -0.017604
50 COG1523 belongs to the glycosyl hydrolase 13 family 0.017386
51 COG1368 sulfuric ester hydrolase activity 0.017281
52 COG2230 cyclopropane-fatty-acyl-phospholipid synthase 0.017264
53 COG0561 phosphatase activity 0.017216
54 COG2771 luxR family -0.017163
55 COG1737 Transcriptional regulator 0.017151
56 COG4638 Rieske (2fe-2S) -0.017149
57 2ZGPA PspA/IM30 family 0.017117
58 COG1288 antiporter activity 0.017087
59 COG2852 Protein conserved in bacteria -0.016951
60 COG3323 Protein of unknown function (DUF1653) -0.016890
61 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) 0.016861
62 COG1854 S-ribosylhomocysteine lyase activity 0.016843
63 COG1013 pyruvate-flavodoxin oxidoreductase activity -0.016753
64 COG2050 protein possibly involved in aromatic compounds catabolism -0.016715
65 COG1390 Produces ATP from ADP in the presence of a proton gradient across the membrane -0.016517
66 COG2985 domain, Protein 0.016517
67 COG0220 tRNA (guanine-N7-)-methyltransferase activity 0.016488
68 COG1134 teichoic acid transport -0.016487
69 COG4224 UPF0291 protein 0.016434
70 COG1228 amidohydrolase -0.016374
71 3310N Protein of unknown function (DUF3054) -0.016302
72 COG1284 Uncharacterised 5xTM membrane BCR, YitT family COG1284 0.016182
73 COG2519 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA -0.016151
74 COG1556 Lactate utilization protein 0.016123
75 COG2148 undecaprenyl-phosphate glucose phosphotransferase activity -0.016077
76 COG2180 nitrate reductase molybdenum cofactor assembly chaperone 0.016038
77 COG4290 ribonuclease 0.016036
78 COG2190 (PTS) system 0.016010
79 COG0572 uridine kinase 0.016002
80 COG2017 converts alpha-aldose to the beta-anomer 0.015969
81 COG1275 C4-dicarboxylate transporter malic acid transport protein -0.015941
82 COG5164 cell wall organization 0.015910
83 2Z7WH CRISPR-associated protein, Csd1 family -0.015909
84 2Z82V maintenance of DNA repeat elements -0.015909
85 COG4461 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process -0.015901
86 COG4382 Mu-like prophage protein Gp16 -0.015867
87 COG1144 Oxidoreductase -0.015832
88 COG1482 cell wall glycoprotein biosynthetic process 0.015802
89 COG0207 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis 0.015769
90 COG3387 PFAM Glycoside hydrolase 15-related -0.015761
91 COG1250 3-hydroxyacyl-CoA dehydrogenase -0.015749
92 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 0.015746
93 COG2723 6-phospho-beta-galactosidase activity 0.015727
94 COG0063 ADP-dependent NAD(P)H-hydrate dehydratase activity -0.015692
95 COG0535 radical SAM domain protein -0.015466
96 COG3456 conserved protein contains FHA domain -0.015447
97 COG2140 Oxalate decarboxylase 0.015406
98 COG4146 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family 0.015379
99 COG1741 Belongs to the pirin family -0.015373
100 COG1541 Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA) -0.015348
101 COG1140 nitrate reductase beta subunit 0.015323
102 COG5305 Membrane 0.015304
103 COG2327 Polysaccharide pyruvyl transferase -0.015136
104 COG1820 Belongs to the metallo-dependent hydrolases superfamily. NagA family 0.015130
105 COG3711 transcriptional antiterminator 0.015128
106 COG1834 amidinotransferase -0.015097
107 2Z7JT 2-keto-3-deoxygluconate:proton symporter activity 0.015009
108 COG1091 dTDP-4-dehydrorhamnose reductase activity 0.014995
109 339ZJ Bacterial Ig-like domain (group 2) -0.014974
110 COG2240 Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP 0.014866
111 COG1058 Belongs to the CinA family 0.014825
112 COG0160 Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family -0.014790
113 COG2068 MobA-Related Protein -0.014775
114 COG1732 Glycine betaine -0.014770
115 COG0239 Important for reducing fluoride concentration in the cell, thus reducing its toxicity -0.014751
116 COG3320 Male sterility -0.014716
117 COG0591 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family 0.014690
118 COG4373 Mu-like prophage FluMu protein gp28 -0.014674
119 33YJW Ankyrin repeat -0.014598
120 COG0376 Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity -0.014576
121 COG2971 BadF BadG BcrA BcrD 0.014564
122 COG0588 phosphoglycerate mutase activity 0.014540
123 COG1018 Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress 0.014534
124 COG2041 Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide -0.014462
125 COG2957 Belongs to the agmatine deiminase family -0.014461
126 COG3142 Participates in the control of copper homeostasis 0.014453
127 COG1264 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity 0.014445
128 COG2218 PFAM glutamate synthase alpha subunit domain protein -0.014428
129 COG4106 trans-aconitate 2-methyltransferase activity -0.014420
130 COG1897 L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine 0.014393
131 COG3620 sequence-specific DNA binding 0.014375
132 COG3585 molybdate ion transport -0.014372
133 COG0607 Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS -0.014340
134 COG0504 CTP synthase activity -0.014316
135 COG0702 epimerase -0.014308
136 COG1462 curli production assembly transport component CsgG -0.014296
137 COG0643 Histidine kinase -0.014236
138 COG4552 Acetyltransferase involved in intracellular survival and related -0.014211
139 COG1940 carbohydrate kinase activity 0.014211
140 COG3824 Protein conserved in bacteria -0.014202
141 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 0.014191
142 COG1560 Kdo2-lipid A biosynthetic process 0.014151
143 COG2221 Nitrite and sulphite reductase 4Fe-4S -0.014150
144 COG1957 nucleoside hydrolase 0.014116
145 COG3475 LICD family 0.014106
146 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin -0.014076
147 COG3723 Recombinational DNA repair protein, rece pathway 0.014043
148 327NZ Heavy-metal-associated domain -0.014041
149 COG1872 DUF167 -0.014022
150 COG0059 Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol- acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3- dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3- hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate -0.013992
151 COG1397 ADP-ribosylglycohydrolase 0.013971
152 COG0646 methionine synthase -0.013967
153 COG1468 defense response to virus -0.013938
154 COG1247 -acetyltransferase 0.013934
155 COG3859 Proton-coupled thiamine transporter YuaJ 0.013913
156 COG0677 UDP-N-acetyl-D-mannosamine dehydrogenase activity -0.013884
157 33PN1 Protein of unknown function (DUF1460) 0.013876
158 COG2603 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA -0.013861
159 COG2996 Protein conserved in bacteria 0.013805
160 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 -0.013801
161 COG3505 Type IV secretory pathway VirD4 -0.013786
162 2ZBES 0.013718
163 COG2856 Zn peptidase -0.013709
164 33BFA -0.013658
165 COG4806 L-rhamnose isomerase 0.013655
166 COG1586 Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine 0.013576
167 COG1793 dna ligase -0.013572
168 COG1630 NurA -0.013571
169 COG1785 Belongs to the alkaline phosphatase family 0.013557
170 COG3137 Salt-induced outer membrane protein 0.013543
171 COG2045 Belongs to the ComB family -0.013542
172 COG2071 gamma-glutamyl-gamma-aminobutyrate hydrolase activity -0.013527
173 COG2501 S4 domain 0.013519
174 COG2308 Evidence 4 Homologs of previously reported genes of -0.013489
175 COG1015 Phosphotransfer between the C1 and C5 carbon atoms of pentose 0.013467
176 COG3222 Protein conserved in bacteria -0.013465
177 COG3392 D12 class N6 adenine-specific DNA methyltransferase -0.013426
178 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 0.013416
179 COG2160 L-arabinose isomerase activity 0.013398
180 COG1193 negative regulation of DNA recombination 0.013379
181 COG3449 Inhibits the supercoiling activity of DNA gyrase. Acts by inhibiting DNA gyrase at an early step, prior to (or at the step of) binding of DNA by the gyrase. It protects cells against toxins that target DNA gyrase, by inhibiting activity of these toxins and reducing the formation of lethal double-strand breaks in the cell 0.013379
182 COG4768 protein containing a divergent version of the methyl-accepting chemotaxis-like domain 0.013361
183 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates -0.013355
184 COG1924 4 iron, 4 sulfur cluster binding 0.013340
185 32VTS Protein of unknown function (DUF2861) -0.013339
186 COG2176 DNA-directed DNA polymerase activity 0.013328
187 COG0175 sulfate reduction 0.013296
188 COG4340 2OG-Fe dioxygenase 0.013294
189 3292A -0.013293
190 COG0502 Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism -0.013282
191 COG1828 Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL -0.013281
192 COG1024 Enoyl-CoA hydratase -0.013262
193 COG1950 PFAM Membrane protein of -0.013258
194 COG3214 Protein conserved in bacteria -0.013231
195 COG3576 pyridoxamine 5-phosphate 0.013230
196 2Z8PZ -0.013227
197 COG0667 Aldo Keto reductase 0.013226
198 COG1212 Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria 0.013166
199 COG1984 allophanate hydrolase subunit 2 -0.013163
200 COG3274 enterobacterial common antigen metabolic process -0.013126
201 COG3509 depolymerase 0.013114
202 COG2080 2 iron, 2 sulfur cluster binding -0.013100
203 COG1869 D-ribose catabolic process 0.013097
204 COG1929 Belongs to the glycerate kinase type-1 family 0.013079
205 32TUP O-Antigen ligase -0.013075
206 COG0437 4 iron, 4 sulfur cluster binding -0.013072
207 COG1613 Sulfate ABC transporter periplasmic sulfate-binding protein 0.013064
208 COG4200 ABC-2 family transporter protein -0.013054
209 COG2183 response to ionizing radiation 0.013045
210 COG1428 Deoxynucleoside kinase 0.013025
211 COG3547 Transposase (IS116 IS110 IS902 family) -0.012992
212 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) 0.012976
213 COG3941 tape measure 0.012970
214 COG3807 Bacterial SH3 domain 0.012913
215 COG5512 Zn-ribbon-containing possibly RNA-binding protein and truncated derivatives 0.012890
216 COG5566 PFAM Mor transcription activator -0.012890
217 COG4829 muconolactone delta-isomerase -0.012884
218 COG3087 Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides 0.012856
219 COG4154 Belongs to the RbsD FucU family 0.012835
220 COG0672 )-iron permease -0.012822
221 COG3649 crispr-associated protein -0.012817
222 33VTB Sigma-70 region 2 0.012806
223 COG3332 Transport and Golgi organisation 2 -0.012786
224 COG5646 InterPro IPR014922 -0.012763
225 COG0505 Belongs to the CarA family 0.012759
226 32YHS -0.012741
227 COG1597 lipid kinase activity 0.012730
228 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 -0.012718
229 COG4578 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.012707
230 COG0276 Catalyzes the ferrous insertion into protoporphyrin IX -0.012649
231 COG1416 DNA-binding transcription factor activity -0.012638
232 COG1280 lysine exporter protein (LysE YggA) -0.012633
233 COG3730 PTS system glucitol sorbitol-specific 0.012629
234 COG3731 PTS system glucitol sorbitol-specific IIA component 0.012629
235 COG1054 Belongs to the UPF0176 family 0.012619
236 COG4915 5-bromo-4-chloroindolyl phosphate hydrolysis protein -0.012619
237 COG4388 Caudovirus prohead serine protease -0.012610
238 COG4443 Transcriptional Coactivator p15 (PC4) 0.012609
239 COG4869 propanediol catabolic process 0.012596
240 33MT9 -0.012591
241 COG2877 3-deoxy-8-phosphooctulonate synthase activity 0.012587
242 COG3855 fructose 1,6-bisphosphate 1-phosphatase activity 0.012586
243 COG4732 ThiW protein 0.012583
244 COG0189 ligase activity -0.012551
245 2Z7HS Psort location CytoplasmicMembrane, score -0.012547
246 COG5658 integral membrane protein -0.012536
247 COG4235 cytochrome complex assembly 0.012528
248 COG1659 Linocin_M18 bacteriocin protein -0.012526
249 COG3732 PTS system glucitol sorbitol-specific 0.012512
250 COG2001 Belongs to the MraZ family 0.012512