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 COG0130 Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs 0.228171
2 COG1187 pseudouridine synthase activity 0.224135
3 COG0101 tRNA pseudouridine synthase activity 0.223922
4 COG0564 pseudouridine synthase activity 0.220204
5 COG0729 surface antigen -0.096443
6 32UTB -0.094707
7 33AGD -0.094707
8 33Z2K -0.094224
9 30YFD -0.094177
10 34AYS -0.091903
11 COG3590 peptidase -0.089289
12 COG3226 Transcriptional regulator -0.087331
13 COG1266 CAAX protease self-immunity -0.086023
14 COG1376 ErfK ybiS ycfS ynhG family protein -0.082616
15 COG4977 sequence-specific DNA binding -0.080644
16 COG3604 Transcriptional regulator -0.070647
17 COG4774 siderophore transport -0.067795
18 COG0580 Belongs to the MIP aquaporin (TC 1.A.8) family -0.066730
19 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) -0.056154
20 COG0329 Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA) -0.052014
21 COG0625 glutathione transferase activity -0.051192
22 COG0543 2 iron, 2 sulfur cluster binding -0.050868
23 32TDU -0.049390
24 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity -0.048172
25 COG3347 Dehydrogenase -0.045532
26 COG4638 Rieske (2fe-2S) -0.044809
27 COG3620 sequence-specific DNA binding 0.044798
28 COG0365 Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA -0.044449
29 COG5517 Aromatic-ring-hydroxylating dioxygenase beta subunit -0.042988
30 COG2514 catechol 2,3-dioxygenase activity -0.042212
31 COG2146 nitrite reductase [NAD(P)H] activity -0.041851
32 COG3917 2-hydroxychromene-2-carboxylate isomerase -0.041686
33 COG1080 General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) -0.041485
34 COG3239 Fatty acid desaturase -0.041377
35 2Z9D2 Psort location CytoplasmicMembrane, score -0.041062
36 COG5639 conserved small protein -0.040571
37 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family -0.040401
38 COG0135 phosphoribosylanthranilate isomerase activity -0.039511
39 COG0841 Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family -0.039345
40 COG3883 PFAM NLP P60 protein 0.039342
41 COG3324 translation initiation factor activity 0.038945
42 COG4581 dead DEAH box helicase 0.038363
43 COG1605 Chorismate mutase 0.038137
44 COG0692 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine 0.037801
45 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family 0.037141
46 COG1664 Polymer-forming cytoskeletal -0.036148
47 COG0596 Alpha beta hydrolase -0.035764
48 COG2337 Toxic component of a toxin-antitoxin (TA) module 0.035546
49 COG4105 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.035527
50 COG3835 regulator 0.035509
51 COG3442 glutamine amidotransferase 0.034340
52 COG4775 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.033922
53 COG4795 General secretion pathway protein -0.033620
54 COG2877 3-deoxy-8-phosphooctulonate synthase activity -0.033200
55 COG3546 catalase activity 0.033056
56 COG1004 Belongs to the UDP-glucose GDP-mannose dehydrogenase family -0.032789
57 COG3246 L-lysine catabolic process to acetate 0.032553
58 COG3634 alkyl hydroperoxide reductase activity -0.032481
59 COG1113 amino acid transport 0.032435
60 COG4585 Histidine kinase 0.032265
61 COG1324 tolerance protein -0.032121
62 COG1172 Belongs to the binding-protein-dependent transport system permease family -0.031963
63 COG1022 Amp-dependent synthetase and ligase -0.031870
64 COG1481 regulation of sporulation 0.031807
65 COG4913 Putative exonuclease SbcCD, C subunit 0.031752
66 COG3264 Mechanosensitive ion channel -0.031687
67 COG3608 succinylglutamate desuccinylase aspartoacylase -0.031673
68 COG4559 Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system -0.031393
69 COG1778 Involved in the biosynthesis of lipopolysaccharides (LPSs). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate -0.031363
70 COG1969 Ni Fe-hydrogenase, b-type cytochrome subunit -0.031205
71 COG0234 Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter -0.031159
72 32Y4N CotJB protein 0.031105
73 COG2199 diguanylate cyclase activity -0.030959
74 COG0632 four-way junction helicase activity -0.030889
75 COG1702 phosphate starvation-inducible protein PhoH 0.030752
76 COG1584 GPR1 FUN34 yaaH family protein -0.030534
77 COG2005 Transcriptional regulator 0.030526
78 345K5 -0.030422
79 2ZQPU Outer membrane efflux protein -0.030353
80 COG3610 response to peptide 0.030244
81 COG1983 PspC domain protein 0.029950
82 COG3688 RNA-binding protein containing a PIN domain 0.029878
83 COG1211 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity 0.029750
84 COG1597 lipid kinase activity 0.029744
85 COG1251 Belongs to the nitrite and sulfite reductase 4Fe-4S domain family -0.029556
86 COG0811 peptide transport -0.029548
87 30URY An automated process has identified a potential problem with this gene model -0.029517
88 COG1649 PFAM Uncharacterised BCR, COG1649 -0.029494
89 COG1011 Hydrolase 0.029455
90 COG1178 ABC-type Fe3 transport system permease component -0.029285
91 COG5435 protein kinase activity 0.029217
92 COG4752 Belongs to the RNA methyltransferase TrmD family -0.029203
93 COG5621 secreted hydrolase -0.029115
94 COG1082 Xylose isomerase domain protein TIM barrel 0.029061
95 COG3214 Protein conserved in bacteria 0.028992
96 COG2826 transposase and inactivated derivatives, IS30 family -0.028952
97 COG2313 pseudouridylate synthase activity -0.028883
98 COG1942 4-Oxalocrotonate Tautomerase -0.028858
99 COG0688 phosphatidylethanolamine metabolic process -0.028857
100 COG4232 protein-disulfide reductase activity -0.028770
101 31H4F Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily -0.028711
102 COG2358 TRAP transporter, solute receptor (TAXI family -0.028602
103 COG1234 tRNA 3'-trailer cleavage 0.028511
104 COG1971 Probably functions as a manganese efflux pump 0.028418
105 COG3653 N-Acyl-D-aspartate D-glutamate deacylase -0.028385
106 COG5577 PFAM Coat F domain 0.028347
107 COG2339 peptidase activity 0.028308
108 COG0531 amino acid 0.028177
109 COG1280 lysine exporter protein (LysE YggA) -0.028144
110 31XUS sporulation protein 0.028116
111 COG1077 Cell shape determining protein MreB Mrl -0.028104
112 COG0616 signal peptide processing -0.028060
113 33Y7F -0.028016
114 COG3412 dihydroxyacetone kinase, phosphotransfer subunit -0.027965
115 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) -0.027949
116 COG5506 Protein of unknown function (DUF1694) -0.027864
117 COG3851 Histidine kinase 0.027840
118 COG1017 nitric oxide dioxygenase activity 0.027803
119 COG3764 Sortase (surface protein transpeptidase) 0.027791
120 COG4941 Belongs to the sigma-70 factor family 0.027772
121 COG4667 esterase of the alpha-beta hydrolase superfamily 0.027759
122 COG5569 Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family -0.027742
123 COG1299 protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity 0.027732
124 COG3402 PFAM membrane-flanked domain 0.027618
125 COG4970 Tfp pilus assembly protein FimT -0.027446
126 COG4569 acetaldehyde dehydrogenase (acetylating) activity -0.027443
127 COG0330 HflC and HflK could -0.027433
128 COG2501 S4 domain 0.027290
129 32Z9Y DNA-templated transcription, termination 0.026901
130 COG3386 PFAM SMP-30 Gluconolaconase 0.026852
131 COG2986 histidine ammonia-lyase -0.026796
132 COG0795 lipopolysaccharide-transporting ATPase activity -0.026727
133 COG1799 cell septum assembly 0.026716
134 COG3504 Conjugal transfer protein -0.026714
135 COG1620 l-lactate permease 0.026692
136 COG4200 ABC-2 family transporter protein 0.026658
137 31RN5 Bacterial regulatory proteins, tetR family 0.026557
138 COG4841 protein insertion into membrane 0.026554
139 COG2948 multi-organism process -0.026457
140 COG1316 TRANSCRIPTIONal 0.026376
141 COG3021 interspecies interaction between organisms 0.026373
142 COG0741 lytic transglycosylase activity -0.026213
143 COG2303 Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine at the same rate 0.026167
144 COG2379 hydroxypyruvate reductase -0.026164
145 338TK 0.026144
146 COG2353 YceI-like domain -0.026138
147 3172B Bacterial PH domain 0.026131
148 COG0437 4 iron, 4 sulfur cluster binding -0.026087
149 COG2606 Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily 0.026053
150 COG1637 Cleaves both 3' and 5' ssDNA extremities of branched DNA structures 0.026004
151 324HC Sigma-70 region 2 -0.025965
152 COG1350 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine -0.025963
153 COG2267 carboxylic ester hydrolase activity 0.025871
154 COG3540 Alkaline phosphatase 0.025806
155 COG2376 Dihydroxyacetone kinase -0.025770
156 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component -0.025709
157 COG1450 Type ii and iii secretion system protein -0.025697
158 COG2966 Psort location CytoplasmicMembrane, score 0.025688
159 COG3702 type iv secretory pathway -0.025673
160 COG1076 Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA -0.025626
161 COG1452 involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane -0.025614
162 COG0459 protein refolding -0.025379
163 COG0817 Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group -0.025289
164 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) -0.025191
165 COG2346 COG2346, Truncated hemoglobins 0.025157
166 COG3600 Phage-associated protein -0.025125
167 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 0.025106
168 COG0859 PFAM glycosyl transferase family 9 -0.025093
169 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 -0.025093
170 339JQ Spore cortex biosynthesis protein YabQ 0.025036
171 COG3736 Type IV secretory pathway, component VirB8 -0.024945
172 2ZU9X Mut7-C ubiquitin 0.024941
173 COG3937 granule-associated protein 0.024935
174 33HRU -0.024904
175 COG0037 tRNA processing -0.024904
176 COG3475 LICD family 0.024831
177 COG3601 Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the 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. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins 0.024808
178 COG2312 Erythromycin esterase 0.024808
179 COG2169 Transcriptional regulator 0.024756
180 COG1032 radical SAM domain protein -0.024754
181 COG3643 Formiminotransferase domain -0.024713
182 COG0144 Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA -0.024651
183 COG4388 Caudovirus prohead serine protease 0.024601
184 2Z7YI Psort location Cytoplasmic, score -0.024593
185 32SBU Tryptophan transporter 0.024577
186 COG5504 Zn-dependent protease 0.024576
187 COG1804 L-carnitine dehydratase bile acid-inducible protein F 0.024540
188 349CY COG1670 acetyltransferases, including N-acetylases of ribosomal proteins -0.024493
189 COG2364 Membrane 0.024470
190 330YS 0.024460
191 COG1523 belongs to the glycosyl hydrolase 13 family -0.024352
192 COG1560 Kdo2-lipid A biosynthetic process -0.024338
193 COG2825 PFAM Outer membrane chaperone Skp (OmpH) -0.024296
194 COG3311 Transcriptional regulator -0.024289
195 COG3002 Belongs to the UPF0753 family -0.024255
196 COG1363 Peptidase, m42 0.024250
197 COG0388 Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source -0.024228
198 COG0486 Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34 -0.024222
199 COG2268 Band 7 protein 0.024125
200 COG4572 Cation transport regulator 0.024117
201 COG0389 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII 0.024051
202 COG0848 biopolymer transport protein -0.024024
203 COG4670 ketone body catabolic process -0.024016
204 COG2020 methyltransferase activity -0.023950
205 333DA 0.023917
206 334N1 0.023853
207 COG4651 solute:proton antiporter activity -0.023773
208 COG1735 metal-dependent hydrolase with the TIM-barrel fold 0.023715
209 32RKH 0.023582
210 COG3164 Protein of unknown function -0.023559
211 33BU4 0.023527
212 COG0523 cobalamin synthesis protein 0.023484
213 COG1212 Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria -0.023481
214 COG1115 amino acid carrier protein 0.023466
215 COG0849 cell division -0.023460
216 32YI8 0.023439
217 COG1691 (AIR) carboxylase 0.023431
218 COG3119 arylsulfatase activity 0.023429
219 33160 -0.023408
220 COG4688 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 0.023379
221 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates -0.023365
222 COG2949 membrane -0.023353
223 COG3328 transposase activity 0.023332
224 COG4924 0.023278
225 COG4668 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.023272
226 COG0573 inorganic phosphate transmembrane transporter activity 0.023196
227 2ZQ9P 0.023144
228 33IIW 0.023131
229 COG3577 Aspartyl protease -0.023127
230 COG0702 epimerase 0.023114
231 COG2367 Beta-lactamase 0.023102
232 30A7P 0.023078
233 COG1242 4 iron, 4 sulfur cluster binding 0.023065
234 COG5266 PFAM Nickel transport complex, NikM subunit, transmembrane -0.023055
235 337A1 -0.023001
236 COG2094 Belongs to the DNA glycosylase MPG family 0.022936
237 32YQ0 -0.022908
238 COG1754 DNA topoisomerase type I activity -0.022872
239 COG0672 )-iron permease 0.022866
240 COG0466 ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner -0.022853
241 2ZITU Cupin domain -0.022852
242 31S9P sporulation protein YtxC 0.022847
243 335XQ sh3 domain protein 0.022839
244 33EHP 0.022807
245 3454B Mannose-6-phosphate isomerase -0.022790
246 COG0154 amidase activity -0.022788
247 COG1904 glucuronate isomerase -0.022757
248 COG2964 Protein conserved in bacteria -0.022692
249 COG1366 Belongs to the anti-sigma-factor antagonist family 0.022677
250 COG1099 with the TIM-barrel fold 0.022659