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 COG3152 Membrane 0.046729
2 COG3645 SOS response -0.044426
3 COG3077 Addiction module antitoxin, RelB DinJ family 0.044060
4 COG0562 UDP-galactopyranose mutase -0.043311
5 COG2235 arginine 0.043108
6 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.041993
7 COG0116 Belongs to the methyltransferase superfamily -0.041952
8 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.041499
9 COG1752 Esterase of the alpha-beta hydrolase superfamily -0.040058
10 COG0464 growth -0.039882
11 COG4767 VanZ like family 0.039272
12 33TG4 -0.039216
13 COG1979 alcohol dehydrogenase -0.037966
14 COG5039 Polysaccharide pyruvyl transferase -0.037682
15 COG0526 COG0526, thiol-disulfide isomerase and thioredoxins 0.037608
16 COG3886 PLD-like domain -0.037114
17 COG1823 symporter activity 0.036667
18 COG5002 protein histidine kinase activity -0.036419
19 COG4198 Conserved Protein -0.036268
20 COG4099 phospholipase Carboxylesterase -0.036210
21 COG0753 catalase activity 0.035970
22 COG1898 dTDP-4-dehydrorhamnose 3,5-epimerase activity -0.035766
23 COG1015 Phosphotransfer between the C1 and C5 carbon atoms of pentose 0.035489
24 COG2771 luxR family -0.035200
25 COG3864 Putative metallopeptidase domain 0.035034
26 30A8Q Bacterial regulatory proteins, tetR family -0.034999
27 COG3707 response regulator 0.034901
28 COG0402 S-adenosylhomocysteine deaminase activity 0.034573
29 COG4115 mRNA cleavage 0.034467
30 COG3560 Nitroreductase -0.033959
31 2ZSRR Psort location Cytoplasmic, score 8.87 0.033916
32 COG3764 Sortase (surface protein transpeptidase) 0.033844
33 COG1989 Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue 0.033437
34 COG4941 Belongs to the sigma-70 factor family -0.033066
35 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 0.032861
36 COG1620 l-lactate permease 0.032755
37 COG4570 Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC -0.032685
38 COG2985 domain, Protein -0.032266
39 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 0.032216
40 COG2873 o-acetylhomoserine -0.032127
41 COG5441 Belongs to the UPF0261 family -0.032061
42 COG1392 Phosphate transport regulator 0.032008
43 COG0679 Auxin Efflux Carrier -0.031954
44 COG5283 actin binding -0.031873
45 COG4700 PFAM Protein kinase domain 0.031696
46 COG3647 Membrane 0.031542
47 COG2071 gamma-glutamyl-gamma-aminobutyrate hydrolase activity 0.031137
48 32X0X ERF superfamily -0.031127
49 COG2030 dehydratase 0.030985
50 COG3250 beta-galactosidase activity 0.030896
51 32YS4 Helix-turn-helix domain -0.030892
52 COG0622 Phosphoesterase 0.030801
53 COG0827 DNA restriction-modification system 0.030654
54 COG2368 4-hydroxyphenylacetate -0.030470
55 2Z8UY Domain of unknown function (DUF4874) 0.030410
56 COG2876 3-deoxy-7-phosphoheptulonate synthase activity -0.030304
57 COG2080 2 iron, 2 sulfur cluster binding -0.030293
58 COG2073 Cobalamin biosynthesis protein cbiG 0.030049
59 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 -0.030027
60 COG3436 PFAM IS66 Orf2 family protein 0.029807
61 COG0748 coenzyme F420 binding 0.029599
62 COG2842 Transposition protein -0.029558
63 31BMY 0.029540
64 COG4172 Belongs to the ABC transporter superfamily -0.029534
65 COG2311 Membrane -0.029155
66 COG1387 Histidinol phosphatase and related hydrolases of the PHP family -0.029128
67 341CM Bacterial regulatory proteins, tetR family -0.029042
68 COG0391 Required for morphogenesis under gluconeogenic growth conditions -0.028931
69 COG2105 PFAM AIG2 family protein -0.028856
70 COG2855 membrane 0.028781
71 COG0405 Gamma-glutamyltransferase -0.028658
72 COG4235 cytochrome complex assembly 0.028590
73 COG1775 2-hydroxyglutaryl-CoA dehydratase, D-component -0.028232
74 COG4857 Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate -0.028003
75 COG0025 NhaP-type Na H and K H 0.027983
76 COG4564 Single Cache domain 2 0.027982
77 COG2110 phosphatase homologous to the C-terminal domain of histone macroH2A1 -0.027820
78 COG1089 Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose 0.027776
79 COG1760 l-serine dehydratase 0.027729
80 COG3086 response to oxidative stress -0.027701
81 COG4154 Belongs to the RbsD FucU family 0.027597
82 COG2945 thiolester hydrolase activity -0.027553
83 COG1022 Amp-dependent synthetase and ligase -0.027545
84 COG4976 Methyltransferase -0.027442
85 COG0394 Belongs to the low molecular weight phosphotyrosine protein phosphatase family 0.027385
86 COG5184 regulator of chromosome condensation, RCC1 -0.027246
87 COG3727 T/G mismatch-specific endonuclease activity -0.027195
88 COG4720 Psort location CytoplasmicMembrane, score 0.027112
89 COG0813 purine-nucleoside phosphorylase activity 0.027049
90 COG0631 protein serine/threonine phosphatase activity 0.026975
91 COG1585 Membrane protein implicated in regulation of membrane protease activity -0.026960
92 COG0535 radical SAM domain protein -0.026950
93 COG3892 5-dehydro-2-deoxygluconokinase -0.026928
94 COG1661 DNA-binding protein with PD1-like DNA-binding motif -0.026659
95 COG3682 Transcriptional regulator -0.026626
96 COG0836 Belongs to the mannose-6-phosphate isomerase type 2 family 0.026487
97 COG0277 FAD linked oxidase domain protein -0.026397
98 32H4Q Bacterial regulatory proteins, tetR family -0.026359
99 COG0392 lysyltransferase activity -0.026307
100 COG5627 protein ubiquitination 0.026281
101 COG4989 oxidoreductase activity 0.026252
102 COG3851 Histidine kinase 0.026125
103 COG3835 regulator 0.026015
104 32YHG Putative adhesin 0.025816
105 COG0409 Hydrogenase expression formation protein 0.025640
106 COG2894 cell division 0.025610
107 COG2126 Ion transport protein 0.025454
108 COG1129 ABC transporter -0.025436
109 31EGY 0.025418
110 COG5036 VTC domain 0.025407
111 COG0503 Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis -0.025325
112 COG2211 Major facilitator Superfamily 0.025229
113 2ZS9D 0.025212
114 COG1454 alcohol dehydrogenase 0.025179
115 COG0428 transporter 0.025175
116 COG0295 cytidine deaminase activity -0.025174
117 33EZ9 ECF transporter, substrate-specific component -0.025169
118 COG4200 ABC-2 family transporter protein -0.025081
119 COG0547 Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA) 0.025052
120 COG0225 Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine 0.024927
121 COG0646 methionine synthase -0.024921
122 COG2372 response to copper ion -0.024897
123 COG1266 CAAX protease self-immunity -0.024807
124 COG1401 restriction endodeoxyribonuclease activity -0.024752
125 COG4653 Phage capsid family 0.024657
126 COG3428 Bacterial PH domain -0.024613
127 COG3231 kanamycin kinase activity 0.024591
128 COG3616 Alanine racemase, N-terminal domain -0.024544
129 COG4545 Glutaredoxin-related protein 0.024468
130 COG1393 Belongs to the ArsC family -0.024463
131 COG3041 Addiction module toxin RelE StbE family 0.024447
132 COG2239 Acts as a magnesium transporter -0.024437
133 32YHS 0.024416
134 COG3836 Belongs to the HpcH HpaI aldolase family 0.024339
135 COG1012 belongs to the aldehyde dehydrogenase family -0.024231
136 COG2259 Doxx family -0.024176
137 COG0001 glutamate-1-semialdehyde 2,1-aminomutase activity 0.024160
138 COG3605 phosphoenolpyruvate-protein phosphotransferase activity 0.024106
139 339UG -0.024062
140 COG2268 Band 7 protein 0.024033
141 COG5505 Protein of unknown function (DUF819) -0.023980
142 33QAR Baseplate J-like protein -0.023967
143 COG3311 Transcriptional regulator -0.023944
144 COG3739 integral membrane protein -0.023895
145 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin -0.023884
146 COG1010 Tetrapyrrole (Corrin/Porphyrin) Methylases 0.023868
147 COG1131 (ABC) transporter 0.023832
148 COG1937 Protein conserved in bacteria 0.023800
149 COG1035 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus -0.023783
150 COG4221 oxidoreductase activity -0.023650
151 COG3223 Belongs to the PsiE family 0.023563
152 COG3597 protein domain associated with 0.023551
153 COG5416 Lipopolysaccharide assembly protein A domain -0.023544
154 COG1099 with the TIM-barrel fold -0.023507
155 COG0800 Aldolase 0.023490
156 COG0163 prenyltransferase activity -0.023477
157 33A5I Psort location CytoplasmicMembrane, score -0.023475
158 32G2T helix_turn_helix, Arsenical Resistance Operon Repressor -0.023419
159 COG2848 UPF0210 protein 0.023345
160 COG3396 Phenylacetate-CoA oxygenase 0.023222
161 2ZBWT Glycine/sarcosine/betaine reductase selenoprotein B (GRDB) 0.023220
162 COG2222 sugar isomerase 0.023092
163 COG3711 transcriptional antiterminator 0.023086
164 COG2189 Belongs to the N(4) N(6)-methyltransferase family 0.023078
165 COG0395 ABC-type sugar transport system, permease component 0.023075
166 COG3384 dioxygenase -0.023068
167 COG0288 reversible hydration of carbon dioxide 0.022990
168 COG0803 Belongs to the bacterial solute-binding protein 9 family 0.022988
169 32RV1 Domain of Unknown Function with PDB structure (DUF3862) -0.022985
170 COG0847 DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease 0.022972
171 COG0511 ligase activity, forming carbon-carbon bonds -0.022946
172 COG0589 response to stress -0.022925
173 COG4300 Cadmium resistance transporter 0.022915
174 32TGG -0.022848
175 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine 0.022847
176 COG2843 Capsule synthesis protein 0.022727
177 COG2824 Alkylphosphonate utilization operon protein PhnA 0.022667
178 COG1083 cytidylyl-transferase 0.022638
179 COG1124 (ABC) transporter -0.022578
180 COG0281 malic enzyme -0.022550
181 COG0125 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis -0.022545
182 COG3465 dGTPase activity -0.022531
183 COG1226 (belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family) -0.022507
184 34BNT Protein of unknown function (DUF806) -0.022457
185 COG3378 Phage plasmid primase P4 family 0.022457
186 COG4123 Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC) 0.022448
187 COG2143 COG2143 Thioredoxin-related protein -0.022437
188 COG1573 uracil-dna glycosylase 0.022435
189 COG1208 COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon -0.022413
190 COG0549 Belongs to the carbamate kinase family 0.022412
191 COG3688 RNA-binding protein containing a PIN domain 0.022392
192 COG5305 Membrane -0.022372
193 COG0643 Histidine kinase 0.022343
194 COG1857 crispr-associated protein 0.022323
195 COG2351 hydroxyisourate hydrolase activity 0.022214
196 COG1203 CRISPR-associated helicase, Cas3 -0.022060
197 COG0695 Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins 0.022000
198 COG1070 Carbohydrate kinase 0.021957
199 33JI9 PFAM FeoA family protein -0.021914
200 33T8K -0.021905
201 COG0159 tryptophan synthase activity 0.021881
202 COG4990 cell redox homeostasis 0.021880
203 316Z5 Universal stress protein family 0.021827
204 COG3122 Protein conserved in bacteria 0.021823
205 COG2210 Belongs to the sulfur carrier protein TusA family 0.021821
206 2ZGYA -0.021745
207 COG3950 AAA domain, putative AbiEii toxin, Type IV TA system 0.021688
208 COG0298 carbon dioxide binding 0.021637
209 COG2867 negative regulation of translational initiation -0.021620
210 2ZI4Y PAAR motif -0.021583
211 2Z7J7 0.021528
212 COG1230 cation diffusion facilitator family transporter 0.021519
213 COG0176 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway 0.021495
214 COG3460 Phenylacetate-CoA oxygenase 0.021485
215 COG4656 Part of a membrane complex involved in electron transport -0.021460
216 COG4533 DNA binding -0.021458
217 COG1977 Involved in sulfur transfer in the conversion of molybdopterin precursor Z to molybdopterin 0.021438
218 COG1502 Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol -0.021430
219 COG0859 PFAM glycosyl transferase family 9 -0.021326
220 COG2094 Belongs to the DNA glycosylase MPG family 0.021325
221 COG0367 asparagine synthase -0.021314
222 COG2031 fatty acid transporter 0.021306
223 COG5545 protein tyrosine phosphatase activity -0.021302
224 COG4467 Involved in initiation control of chromosome replication 0.021284
225 COG2361 Protein of unknown function DUF86 0.021226
226 COG4135 transport system, permease component 0.021218
227 2ZS4Q ankyrin repeats -0.021202
228 COG3464 Transposase 0.021147
229 COG1206 Catalyzes the folate-dependent formation of 5-methyl- uridine at position 54 (M-5-U54) in all tRNAs 0.021141
230 COG2109 Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids 0.021139
231 COG4290 ribonuclease -0.021075
232 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity -0.021045
233 COG0321 lipoyl(octanoyl) transferase activity -0.021012
234 COG2519 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA -0.020975
235 COG5217 Protein of unknown function (DUF3086) 0.020928
236 COG2768 binding domain, Protein -0.020898
237 3304N Replication initiator protein A (RepA) N-terminus 0.020860
238 COG4845 Chloramphenicol acetyltransferase -0.020827
239 COG4898 Protein conserved in bacteria 0.020824
240 COG1085 galactose-1-phosphate uridylyltransferase 0.020757
241 330BC Siphovirus Gp157 -0.020751
242 COG2327 Polysaccharide pyruvyl transferase -0.020698
243 33JN2 -0.020688
244 COG2068 MobA-Related Protein -0.020684
245 COG4558 Periplasmic binding protein -0.020619
246 2ZNS7 -0.020606
247 COG0604 alcohol dehydrogenase -0.020581
248 COG1649 PFAM Uncharacterised BCR, COG1649 -0.020545
249 2Z7IK Protein of unknown function (DUF1861) -0.020542
250 COG2169 Transcriptional regulator 0.020530