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 COG1030 water channel activity 0.023160
2 COG1613 Sulfate ABC transporter periplasmic sulfate-binding protein -0.023084
3 COG4967 type IV pilus modification protein PilV 0.022022
4 COG3505 Type IV secretory pathway VirD4 -0.019951
5 COG1982 Orn Lys Arg decarboxylase major -0.019714
6 COG0644 oxidoreductase 0.019600
7 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine -0.019478
8 COG4798 methyltransferase 0.019001
9 COG1610 YqeY-like protein 0.018992
10 COG1027 Aspartate ammonia-lyase -0.018969
11 COG0738 Major facilitator superfamily -0.018681
12 COG1292 Belongs to the BCCT transporter (TC 2.A.15) family 0.018640
13 COG4208 sulfate ABC transporter -0.018362
14 COG0698 ribose 5-phosphate isomerase -0.017987
15 COG4446 Protein conserved in bacteria 0.017954
16 COG3806 Anti-sigma factor 0.017829
17 COG0655 NAD(P)H dehydrogenase (quinone) activity 0.017825
18 COG0555 PFAM binding-protein-dependent transport systems inner membrane component -0.017576
19 COG1912 Pfam S-adenosyl-l-methionine hydroxide adenosyltransferase 0.017543
20 COG0340 biotin-[acetyl-CoA-carboxylase] ligase activity -0.017412
21 COG1515 deoxyribonuclease V activity 0.017075
22 COG3090 Trap-type c4-dicarboxylate transport system, small permease component 0.016968
23 COG1528 Iron-storage protein -0.016890
24 COG1089 Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose -0.016859
25 COG1983 PspC domain protein 0.016832
26 COG1525 nuclease -0.016797
27 COG1482 cell wall glycoprotein biosynthetic process -0.016757
28 COG1233 COG1233 Phytoene dehydrogenase and related 0.016730
29 COG0469 pyruvate kinase activity -0.016659
30 COG4559 Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system 0.016632
31 2Z7ZD Ion transport protein 0.016522
32 COG1272 protein, Hemolysin III 0.016488
33 COG0123 including yeast histone deacetylase and acetoin utilization protein 0.016383
34 COG2005 Transcriptional regulator -0.016250
35 COG0390 transport system, permease component 0.016240
36 COG3769 mannosylglycerate metabolic process 0.015683
37 COG2060 Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds and transports the potassium across the cytoplasmic membrane -0.015676
38 COG2156 Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit acts as a catalytic chaperone that increases the ATP- binding affinity of the ATP-hydrolyzing subunit KdpB by the formation of a transient KdpB KdpC ATP ternary complex -0.015530
39 COG4178 (ABC) transporter -0.015504
40 2ZBMT Protein of unknown function (DUF2959) 0.015492
41 COG4325 translation initiation factor activity 0.015423
42 COG3414 Phosphotransferase system galactitol-specific IIB component -0.015308
43 COG2216 Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system -0.015220
44 COG4993 Dehydrogenase 0.015185
45 COG3591 Belongs to the peptidase S1B family 0.015167
46 COG2948 multi-organism process -0.015111
47 COG0393 Putative heavy-metal-binding 0.015028
48 COG2721 sulfolactate sulfo-lyase activity -0.014984
49 COG0657 acetylesterase activity -0.014944
50 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component 0.014865
51 COG0822 iron-sulfur transferase activity -0.014826
52 COG5006 permease, DMT superfamily 0.014757
53 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 -0.014754
54 COG4717 serine-type aminopeptidase activity 0.014751
55 COG2945 thiolester hydrolase activity -0.014708
56 COG0622 Phosphoesterase -0.014579
57 COG4261 Acyltransferase -0.014555
58 COG2271 Major facilitator Superfamily -0.014449
59 COG4536 flavin adenine dinucleotide binding 0.014394
60 33ARA COG0526, thiol-disulfide isomerase and thioredoxins 0.014391
61 COG1914 H( )-stimulated, divalent metal cation uptake system -0.014341
62 COG4928 KAP family P-loop domain 0.014340
63 COG2128 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 0.014321
64 32RYR Domain of unknown function (DUF4112) 0.014290
65 COG0530 calcium, potassium:sodium antiporter activity 0.014250
66 COG1654 Acts both as a biotin-- acetyl-CoA-carboxylase ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio- 5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon 0.014230
67 COG0796 Provides the (R)-glutamate required for cell wall biosynthesis -0.014207
68 COG2733 membrane -0.014192
69 COG1490 D-aminoacyl-tRNA deacylase activity 0.014167
70 COG1063 alcohol dehydrogenase 0.014026
71 COG3119 arylsulfatase activity -0.013954
72 COG1162 GTPase activity -0.013777
73 COG1502 Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol -0.013714
74 COG3451 type IV secretory pathway VirB4 -0.013660
75 COG1732 Glycine betaine -0.013603
76 COG1970 mechanosensitive ion channel activity -0.013512
77 COG1035 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus 0.013506
78 COG1337 RAMP superfamily 0.013490
79 COG4104 PAAR repeat-containing protein -0.013416
80 COG1550 Protein conserved in bacteria 0.013401
81 COG3707 response regulator -0.013320
82 COG1462 curli production assembly transport component CsgG 0.013291
83 COG1585 Membrane protein implicated in regulation of membrane protease activity -0.013257
84 COG1074 ATP-dependent DNA helicase activity -0.013249
85 COG0672 )-iron permease -0.013247
86 COG1752 Esterase of the alpha-beta hydrolase superfamily 0.013237
87 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 -0.013194
88 32RM0 23S rRNA-intervening sequence protein 0.013159
89 COG0508 dehydrogenase complex catalyzes the overall conversion of -0.013096
90 COG0626 cystathionine gamma-synthase activity -0.013048
91 COG4912 Dna alkylation repair 0.012949
92 COG1621 beta-fructofuranosidase activity -0.012945
93 COG2859 Protein conserved in bacteria 0.012881
94 COG1624 Catalyzes the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP), a second messenger used to regulate differing processes in different bacteria -0.012835
95 COG5305 Membrane -0.012816
96 COG2234 aminopeptidase activity 0.012804
97 COG0179 Fumarylacetoacetate (FAA) hydrolase 0.012796
98 COG3193 protein, possibly involved in utilization of glycolate and propanediol -0.012791
99 COG1324 tolerance protein 0.012751
100 COG1284 Uncharacterised 5xTM membrane BCR, YitT family COG1284 -0.012681
101 COG3415 Transposase 0.012647
102 COG3453 Protein conserved in bacteria 0.012647
103 COG0639 Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP 0.012643
104 COG4103 Tellurite resistance protein TerB 0.012609
105 COG5652 VanZ like family 0.012560
106 COG1942 4-Oxalocrotonate Tautomerase -0.012555
107 COG0562 UDP-galactopyranose mutase -0.012548
108 COG0520 Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine -0.012504
109 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 0.012451
110 COG1757 Na H antiporter 0.012431
111 COG1509 lysine 2,3-aminomutase activity 0.012418
112 COG1975 Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family -0.012403
113 COG0241 D,D-heptose 1,7-bisphosphate phosphatase 0.012374
114 COG3640 PFAM CobQ CobB MinD ParA nucleotide binding domain 0.012347
115 COG1236 Exonuclease of the beta-lactamase fold involved in RNA processing 0.012347
116 COG2826 transposase and inactivated derivatives, IS30 family -0.012334
117 COG4132 (ABC) transporter, permease -0.012317
118 COG1638 TRAP-type C4-dicarboxylate transport system periplasmic component 0.012280
119 COG2501 S4 domain -0.012274
120 COG0733 neurotransmitter:sodium symporter activity 0.012232
121 COG1489 DNA binding 0.012212
122 COG1607 acyl-coa hydrolase 0.012193
123 COG4782 Protein conserved in bacteria 0.012190
124 COG1141 Ferredoxin -0.012178
125 COG4105 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.012166
126 COG0737 Belongs to the 5'-nucleotidase family -0.012157
127 COG0432 Pfam Uncharacterised protein family UPF0047 0.012124
128 COG3158 transport of potassium into the cell -0.012107
129 COG3245 cytochrome 0.012076
130 COG0500 methyltransferase 0.012068
131 COG1652 LysM domain -0.012064
132 COG4487 mechanosensitive ion channel activity -0.012036
133 COG2137 regulation of response to DNA damage stimulus 0.012033
134 COG1763 Mo-molybdopterin cofactor biosynthetic process -0.012023
135 COG1353 crispr-associated protein 0.012019
136 COG4537 Required for transformation and DNA binding 0.011943
137 COG2252 PERMEase -0.011927
138 COG3504 Conjugal transfer protein -0.011860
139 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 -0.011855
140 COG0204 Acyl-transferase -0.011849
141 COG0566 Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family -0.011849
142 COG0656 L-ascorbic acid biosynthetic process -0.011798
143 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid -0.011779
144 COG2968 Membrane 0.011775
145 COG4327 Domain of unknown function (DUF4212) 0.011704
146 COG3576 pyridoxamine 5-phosphate 0.011695
147 COG3450 Protein of unknown function (DUF861) -0.011666
148 COG2514 catechol 2,3-dioxygenase activity 0.011657
149 COG2366 antibiotic biosynthetic process 0.011646
150 COG3919 ATP-grasp 0.011627
151 COG2738 Putative neutral zinc metallopeptidase 0.011622
152 COG1918 ferrous iron import across plasma membrane -0.011541
153 32VXQ NUDIX domain 0.011541
154 COG5639 conserved small protein -0.011536
155 COG1122 ATPase activity -0.011526
156 COG2190 (PTS) system -0.011510
157 COG0609 Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily 0.011510
158 COG0791 NLP P60 protein -0.011473
159 COG1522 sequence-specific DNA binding 0.011459
160 COG1725 Transcriptional regulator -0.011448
161 COG0699 ATPase. Has a role at an early stage in the morphogenesis of the spore coat 0.011366
162 COG0707 Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II) -0.011362
163 32S6W 0.011348
164 COG1432 Conserved Protein 0.011307
165 COG3758 protein conserved in bacteria -0.011286
166 COG3228 Belongs to the MtfA family 0.011285
167 COG0435 Glutathione S-transferase 0.011247
168 COG0306 phosphate transporter -0.011244
169 COG3671 membrane 0.011236
170 COG1011 Hydrolase 0.011227
171 COG5551 CRISPR-associated protein Cas6 0.011226
172 COG1956 GAF domain-containing protein 0.011178
173 COG2893 phosphoenolpyruvate-dependent sugar phosphotransferase system -0.011175
174 COG1514 Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester 0.011153
175 COG2081 HI0933 family 0.011145
176 COG1720 tRNA m6t6A37 methyltransferase activity 0.011140
177 COG3263 regulation of cellular component size 0.011138
178 COG2975 iron-sulfur cluster assembly -0.011135
179 COG4619 ABC transporter 0.011127
180 COG2331 Regulatory protein, FmdB family 0.011126
181 COG0255 Belongs to the universal ribosomal protein uL29 family -0.011106
182 COG1780 Probably involved in ribonucleotide reductase function -0.011103
183 COG3860 Transcriptional regulator 0.011097
184 COG0314 molybdopterin synthase activity -0.011077
185 COG0670 Belongs to the BI1 family -0.011076
186 COG2509 5-formyltetrahydrofolate cyclo-ligase activity -0.011069
187 COG2358 TRAP transporter, solute receptor (TAXI family 0.011043
188 COG2864 formate dehydrogenase -0.011035
189 COG0218 Necessary for normal cell division and for the maintenance of normal septation -0.011014
190 COG2361 Protein of unknown function DUF86 0.010966
191 COG2002 toxin-antitoxin pair type II binding 0.010950
192 COG2907 Flavin containing amine oxidoreductase 0.010919
193 COG3464 Transposase 0.010898
194 COG0017 Asparaginyl-tRNA synthetase -0.010892
195 3279X protein transport 0.010889
196 COG0549 Belongs to the carbamate kinase family -0.010888
197 31W2T Universal stress protein family 0.010876
198 32YVH Bacterial inner membrane protein 0.010872
199 COG1505 serine-type exopeptidase activity 0.010847
200 COG3956 TIGRFAM MazG family protein 0.010824
201 338CY 0.010820
202 COG3378 Phage plasmid primase P4 family 0.010812
203 COG3861 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity 0.010794
204 COG1189 Ribosomal RNA methyltransferase RrmJ FtsJ -0.010777
205 COG3149 Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins 0.010758
206 COG0212 Belongs to the 5-formyltetrahydrofolate cyclo-ligase family -0.010753
207 COG1497 Winged helix-turn-helix DNA-binding 0.010751
208 COG4538 SnoaL-like domain 0.010729
209 COG0560 Phosphoserine phosphatase -0.010701
210 COG3568 Endonuclease Exonuclease Phosphatase 0.010698
211 COG3809 Transcription factor zinc-finger 0.010688
212 COG5377 YqaJ viral recombinase family -0.010661
213 COG2254 TIGRFAM CRISPR-associated helicase Cas3 -0.010658
214 COG4970 Tfp pilus assembly protein FimT 0.010653
215 COG4395 Tim44 -0.010630
216 COG5505 Protein of unknown function (DUF819) 0.010623
217 COG1208 COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon 0.010606
218 COG1445 protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity -0.010597
219 COG0611 Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1 0.010578
220 COG2519 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA -0.010572
221 COG4147 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family 0.010568
222 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 -0.010564
223 COG0579 oxidoreductase -0.010536
224 COG1127 ABC transporter -0.010521
225 COG0003 Pfam Anion-transporting ATPase 0.010509
226 COG0161 adenosylmethionine-8-amino-7-oxononanoate transaminase activity -0.010505
227 COG5592 hemerythrin HHE cation binding domain -0.010492
228 COG2017 converts alpha-aldose to the beta-anomer -0.010464
229 COG3585 molybdate ion transport -0.010453
230 COG3492 Protein of unknown function (DUF1244) 0.010443
231 COG3137 Salt-induced outer membrane protein 0.010427
232 COG5519 DNA primase 0.010410
233 COG3069 C4-dicarboxylate transmembrane transporter activity -0.010401
234 COG1115 amino acid carrier protein 0.010378
235 COG0631 protein serine/threonine phosphatase activity -0.010324
236 COG0282 Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction -0.010319
237 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family -0.010313
238 COG2193 ferroxidase activity 0.010305
239 COG0668 transmembrane transport 0.010281
240 COG0602 queuosine metabolic process -0.010278
241 COG2246 polysaccharide biosynthetic process -0.010268
242 COG2192 nodulation -0.010251
243 COG1371 PFAM Archease protein family (DUF101 UPF0211) 0.010247
244 COG0035 Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate -0.010232
245 COG2321 neutral zinc metallopeptidase -0.010226
246 COG5581 Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)- dependent manner. Binds 1 c-di-GMP dimer per subunit. Increasing levels of c-di-GMP lead to decreased motility -0.010226
247 33XV7 Protein of unknown function (DUF3450) 0.010215
248 COG1804 L-carnitine dehydratase bile acid-inducible protein F 0.010204
249 345S6 0.010198
250 32TUN 0.010179