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 COG0603 Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)) -0.038407
2 COG2184 nucleotidyltransferase activity 0.034181
3 COG2862 Uncharacterized protein family, UPF0114 0.033718
4 COG1523 belongs to the glycosyl hydrolase 13 family 0.033709
5 30S7H 0.033702
6 COG0381 UDP-N-acetylglucosamine 2-epimerase activity -0.033579
7 COG1120 ATPase activity -0.033570
8 COG2945 thiolester hydrolase activity -0.033137
9 COG0213 The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis 0.032503
10 COG4552 Acetyltransferase involved in intracellular survival and related -0.031804
11 COG2089 acid synthase -0.031591
12 COG3345 alpha-galactosidase 0.031483
13 COG2017 converts alpha-aldose to the beta-anomer 0.031021
14 COG0407 Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III -0.030843
15 COG1070 Carbohydrate kinase 0.030743
16 COG1022 Amp-dependent synthetase and ligase 0.030083
17 COG0451 ADP-glyceromanno-heptose 6-epimerase activity -0.029655
18 COG1476 TRANSCRIPTIONal 0.029499
19 COG3412 dihydroxyacetone kinase, phosphotransfer subunit 0.029403
20 COG0352 thiamine-phosphate diphosphorylase activity -0.029310
21 COG1335 isochorismatase -0.028907
22 COG2503 HAD superfamily, subfamily IIIB (Acid phosphatase) -0.028902
23 COG4869 propanediol catabolic process 0.028848
24 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 0.028291
25 COG5426 von Willebrand factor, type A 0.028073
26 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 -0.027707
27 COG3855 fructose 1,6-bisphosphate 1-phosphatase activity 0.026971
28 COG0372 Belongs to the citrate synthase family 0.026842
29 COG0413 3-methyl-2-oxobutanoate hydroxymethyltransferase activity -0.026646
30 COG1640 4-alpha-glucanotransferase 0.026533
31 COG1606 tRNA processing 0.026528
32 COG0518 GMP synthase (glutamine-hydrolyzing) activity 0.026371
33 COG0055 Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits 0.026272
34 COG0627 Serine hydrolase involved in the detoxification of formaldehyde 0.025870
35 COG4200 ABC-2 family transporter protein -0.025656
36 COG1168 Bifunctional PLP-dependent enzyme with beta-cystaTHIonase and maltose regulon repressor activities 0.025406
37 COG2966 Psort location CytoplasmicMembrane, score 0.025321
38 COG4784 Peptidase m48 ste24p -0.025305
39 COG1494 fructose-1,6-bisphosphatase -0.025051
40 COG2358 TRAP transporter, solute receptor (TAXI family -0.024800
41 2Z7PD Psort location CytoplasmicMembrane, score -0.024779
42 COG1713 HD superfamily hydrolase involved in NAD metabolism 0.024400
43 COG2021 Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine 0.024369
44 COG4099 phospholipase Carboxylesterase 0.024168
45 COG3949 Membrane 0.023721
46 COG1655 Protein conserved in bacteria -0.023684
47 COG2152 Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man- Glc) to mannose 1-phosphate (Man1P) and glucose 0.023667
48 33GDE This gene contains a nucleotide ambiguity which may be the result of a sequencing error 0.023619
49 COG4823 Abi-like protein -0.023605
50 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 -0.023408
51 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component -0.023256
52 COG1858 cytochrome C peroxidase -0.023250
53 COG0248 Ppx GppA phosphatase -0.023245
54 COG2186 Transcriptional regulator 0.023174
55 COG3048 D-serine ammonia-lyase activity 0.023024
56 COG1994 Peptidase M50 -0.022997
57 COG3837 Cupin domain -0.022987
58 COG0657 acetylesterase activity 0.022880
59 COG1343 CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease. Involved in the integration of spacer DNA into the CRISPR cassette -0.022787
60 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) 0.022755
61 COG2944 sequence-specific DNA binding -0.022656
62 COG1721 protein (some members contain a von Willebrand factor type A (vWA) domain 0.022645
63 COG0388 Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source -0.022356
64 COG2213 PTS system mannitol-specific 0.022282
65 COG0561 phosphatase activity 0.022168
66 COG1015 Phosphotransfer between the C1 and C5 carbon atoms of pentose 0.022065
67 COG4268 DNA restriction-modification system 0.022013
68 33VFH -0.022001
69 COG0300 oxidoreductase activity 0.021910
70 COG1544 Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase 0.021801
71 COG1934 Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane. May form a bridge between the inner membrane and the outer membrane, via interactions with LptC and LptD, thereby facilitating LPS transfer across the periplasm -0.021772
72 COG2364 Membrane -0.021659
73 COG1304 FMN binding -0.021632
74 COG1063 alcohol dehydrogenase -0.021609
75 COG0675 Transposase, IS605 OrfB family 0.021587
76 COG4757 Alpha beta hydrolase 0.021584
77 COG2301 Belongs to the HpcH HpaI aldolase family -0.021553
78 COG0390 transport system, permease component -0.021533
79 COG0711 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) 0.021507
80 COG3610 response to peptide 0.021498
81 COG5164 cell wall organization 0.021413
82 COG4575 ribosome binding -0.021329
83 COG0712 F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation 0.021271
84 COG1859 Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP- ribose 1''-2''-cyclic phosphate (APPR P). May function as an ADP- ribosylase 0.021249
85 COG4587 transport system, permease component 0.021184
86 COG0720 synthase -0.021179
87 COG0114 fumarate hydratase activity -0.021178
88 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis 0.021175
89 COG1670 COG1670 acetyltransferases, including N-acetylases of ribosomal proteins 0.021066
90 COG1979 alcohol dehydrogenase -0.021021
91 COG4145 pantothenate transmembrane transporter activity -0.021011
92 COG0402 S-adenosylhomocysteine deaminase activity -0.020963
93 COG4729 Domain of unknown function (DUF1850) -0.020948
94 COG3279 Response regulator of the LytR AlgR family 0.020935
95 COG3055 Converts alpha-N-acetylneuranimic acid (Neu5Ac) to the beta-anomer, accelerating the equilibrium between the alpha- and beta-anomers. Probably facilitates sialidase-negative bacteria to compete sucessfully for limited amounts of extracellular Neu5Ac, which is likely taken up in the beta-anomer. In addition, the rapid removal of sialic acid from solution might be advantageous to the bacterium to damp down host responses 0.020821
96 COG4758 membrane 0.020814
97 COG1788 Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit -0.020805
98 COG2057 Acyl CoA acetate 3-ketoacid CoA transferase beta subunit -0.020805
99 COG0683 leucine binding 0.020793
100 COG0383 alpha-mannosidase activity 0.020783
101 COG2828 Protein conserved in bacteria -0.020780
102 COG1714 RDD family 0.020773
103 COG0176 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway -0.020753
104 COG1333 cytochrome c biogenesis protein 0.020740
105 COG0618 3'(2'),5'-bisphosphate nucleotidase activity 0.020721
106 328RQ -0.020694
107 COG3324 translation initiation factor activity 0.020692
108 COG1733 regulation of RNA biosynthetic process -0.020665
109 COG5006 permease, DMT superfamily -0.020661
110 COG1787 Restriction endonuclease -0.020653
111 COG1977 Involved in sulfur transfer in the conversion of molybdopterin precursor Z to molybdopterin -0.020618
112 COG4302 ethanolamine ammonia-lyase activity 0.020610
113 COG4303 Ethanolamine ammonia lyase large subunit 0.020610
114 COG0643 Histidine kinase -0.020572
115 COG4938 AAA ATPase domain 0.020534
116 COG1940 carbohydrate kinase activity 0.020524
117 COG4824 toxin secretion phage lysis holin 0.020495
118 COG2861 carbohydrate metabolic process -0.020485
119 2ZSRR Psort location Cytoplasmic, score 8.87 -0.020478
120 COG0252 asparaginase activity -0.020449
121 COG1762 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.020431
122 COG2005 Transcriptional regulator -0.020414
123 COG0058 SHG alpha-glucan phosphorylase activity 0.020361
124 COG0191 fructose-bisphosphate aldolase activity 0.020322
125 COG1830 Aldolase -0.020320
126 COG1112 Superfamily I DNA and RNA helicases and helicase subunits -0.020288
127 COG4132 (ABC) transporter, permease 0.020238
128 333PH -0.020202
129 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin -0.020174
130 COG5545 protein tyrosine phosphatase activity 0.020174
131 COG0647 UMP catabolic process 0.020141
132 COG5001 Diguanylate cyclase -0.020131
133 COG0751 glycine-tRNA ligase activity -0.020128
134 33EGG -0.020085
135 COG1613 Sulfate ABC transporter periplasmic sulfate-binding protein 0.020041
136 COG1393 Belongs to the ArsC family 0.020020
137 COG0686 Belongs to the AlaDH PNT family 0.019981
138 COG3585 molybdate ion transport -0.019962
139 COG0539 negative regulation of cytoplasmic translation 0.019952
140 COG0356 it plays a direct role in the translocation of protons across the membrane 0.019950
141 COG0725 ABC transporter, periplasmic molybdate-binding protein -0.019923
142 COG1194 a g-specific adenine glycosylase -0.019899
143 COG0723 plastoquinol--plastocyanin reductase activity -0.019891
144 COG2813 Specifically methylates the guanine in position -0.019836
145 COG0246 Mannitol dehydrogenase 0.019775
146 COG2214 Heat shock protein DnaJ domain protein -0.019673
147 31TVC -0.019630
148 COG1012 belongs to the aldehyde dehydrogenase family -0.019625
149 327NZ Heavy-metal-associated domain -0.019550
150 COG3366 ferrous iron transmembrane transporter activity -0.019547
151 COG1199 ATP-dependent helicase activity -0.019538
152 COG1618 nucleotide phosphatase activity, acting on free nucleotides -0.019494
153 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 0.019483
154 COG1593 TRAP-type C4-dicarboxylate transport system, large permease component -0.019478
155 2ZING LPXTG cell wall anchor motif -0.019451
156 COG1518 maintenance of DNA repeat elements -0.019401
157 COG3201 nicotinamide mononucleotide transporter -0.019307
158 COG4576 ethanolamine utilization protein EutN carboxysome structural protein Ccml 0.019294
159 COG4577 Carbon dioxide concentrating mechanism carboxysome shell protein 0.019294
160 COG4832 Psort location Cytoplasmic, score -0.019246
161 COG0355 proton-transporting ATP synthase activity, rotational mechanism 0.019160
162 COG0428 transporter 0.019153
163 COG4208 sulfate ABC transporter 0.019140
164 COG1254 Belongs to the acylphosphatase family 0.019117
165 33AHG Protein of unknown function (DUF1659) -0.019111
166 COG0056 Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit 0.019094
167 345XZ -0.019067
168 COG2050 protein possibly involved in aromatic compounds catabolism -0.019064
169 COG0220 tRNA (guanine-N7-)-methyltransferase activity 0.019060
170 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 -0.019031
171 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the -0.019028
172 COG2761 dithiol-disulfide isomerase involved in polyketide biosynthesis -0.018952
173 COG3288 NAD(P)+ transhydrogenase (AB-specific) activity -0.018888
174 COG3620 sequence-specific DNA binding 0.018767
175 COG2190 (PTS) system 0.018758
176 30A8Q Bacterial regulatory proteins, tetR family 0.018747
177 33CCV Protein of unknown function (Tiny_TM_bacill) -0.018720
178 COG1252 NADH dehydrogenase 0.018689
179 32H4Q Bacterial regulatory proteins, tetR family -0.018674
180 33AH5 Gram-negative bacterial TonB protein C-terminal -0.018614
181 COG1820 Belongs to the metallo-dependent hydrolases superfamily. NagA family 0.018579
182 COG1691 (AIR) carboxylase 0.018553
183 COG1390 Produces ATP from ADP in the presence of a proton gradient across the membrane -0.018531
184 COG4224 UPF0291 protein 0.018511
185 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine 0.018507
186 32TNY Domain of unknown function (DUF1992) -0.018488
187 2Z8Z7 Protein of unknown function (DUF3298) -0.018487
188 COG2610 gluconate transmembrane transporter activity 0.018474
189 COG1666 GTP binding -0.018425
190 COG1533 DNA photolyase activity 0.018412
191 COG4781 glycerophosphoryl diester phosphodiesterase 0.018398
192 COG0754 glutathionylspermidine amidase activity -0.018297
193 COG3835 regulator 0.018198
194 32ZJK Nitrous oxide-stimulated promoter -0.018155
195 COG4559 Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system -0.018141
196 COG0448 Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans 0.018133
197 COG1668 transmembrane transport -0.018122
198 2ZDJ6 -0.018121
199 COG0775 Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively 0.018109
200 COG1834 amidinotransferase -0.018098
201 COG5658 integral membrane protein 0.018084
202 COG4668 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.018069
203 32YHS -0.018063
204 COG0247 lactate metabolic process -0.018061
205 33JYB -0.018043
206 COG2065 Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant 0.018003
207 COG1527 subunit (C -0.018001
208 32RZW -0.017988
209 COG0236 Carrier of the growing fatty acid chain in fatty acid biosynthesis 0.017957
210 COG3311 Transcriptional regulator -0.017943
211 32YCI DNA topological change 0.017937
212 COG3953 SLT domain -0.017930
213 2Z80D Crispr-associated cxxc_cxxc protein Cst1 -0.017929
214 COG2151 metal-sulfur cluster biosynthetic enzyme 0.017927
215 COG3053 Acetylation of prosthetic group (2-(5''-phosphoribosyl)- 3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase -0.017895
216 COG1832 CoA-binding protein -0.017878
217 COG4607 ABC-type enterochelin transport system periplasmic component -0.017874
218 COG3442 glutamine amidotransferase 0.017866
219 COG0622 Phosphoesterase 0.017865
220 COG1875 ATPase related to phosphate starvation-inducible protein PhoH 0.017758
221 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family 0.017672
222 COG1155 Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit -0.017665
223 COG0224 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex 0.017626
224 COG0031 Belongs to the cysteine synthase cystathionine beta- synthase family 0.017596
225 COG5351 Uncharacterized protein conserved in bacteria (DUF2169) -0.017595
226 COG3884 Acyl-ACP thioesterase 0.017595
227 COG2015 COG2015, Alkyl sulfatase and related hydrolases -0.017576
228 2Z8AD Carbohydrate-binding domain-containing protein Cthe_2159 -0.017573
229 33XFG Universal stress protein family -0.017523
230 COG2329 Antibiotic biosynthesis monooxygenase -0.017516
231 COG3405 Belongs to the glycosyl hydrolase 8 (cellulase D) family -0.017515
232 COG4819 ethanolamine utilization protein 0.017509
233 COG4942 peptidase -0.017459
234 COG2327 Polysaccharide pyruvyl transferase -0.017458
235 COG5650 phosphatidylinositol metabolic process 0.017454
236 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 -0.017451
237 COG0504 CTP synthase activity -0.017442
238 COG1162 GTPase activity 0.017437
239 2ZQ34 Antibiotic biosynthesis monooxygenase -0.017433
240 COG2226 methyltransferase 0.017424
241 COG4325 translation initiation factor activity -0.017374
242 COG1193 negative regulation of DNA recombination 0.017371
243 COG5616 cAMP biosynthetic process 0.017367
244 COG1737 Transcriptional regulator 0.017359
245 COG2878 Part of a membrane complex involved in electron transport -0.017330
246 COG2124 cytochrome p450 -0.017312
247 COG5512 Zn-ribbon-containing possibly RNA-binding protein and truncated derivatives 0.017240
248 COG2602 Beta-lactamase 0.017232
249 COG4670 ketone body catabolic process -0.017207
250 COG4637 Psort location Cytoplasmic, score 0.017177