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 COG3451 type IV secretory pathway VirB4 0.041949
2 COG3736 Type IV secretory pathway, component VirB8 0.037692
3 COG3505 Type IV secretory pathway VirD4 0.034467
4 COG3702 type iv secretory pathway 0.033708
5 COG3504 Conjugal transfer protein 0.031977
6 COG2948 multi-organism process 0.030743
7 COG1125 glycine betaine transport 0.028581
8 COG5627 protein ubiquitination 0.026818
9 COG0420 3'-5' exonuclease activity -0.025404
10 COG3481 metal-dependent phosphohydrolase, HD sub domain 0.025383
11 COG1397 ADP-ribosylglycohydrolase -0.025291
12 COG1174 glycine betaine transport 0.025039
13 COG3021 interspecies interaction between organisms -0.024732
14 COG0800 Aldolase 0.023642
15 COG0618 3'(2'),5'-bisphosphate nucleotidase activity -0.023468
16 COG2239 Acts as a magnesium transporter -0.023419
17 COG0648 Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin -0.023034
18 COG3295 Protein conserved in bacteria 0.023029
19 COG1032 radical SAM domain protein -0.022830
20 COG0630 type IV secretory pathway, VirB11 components, and related ATPases involved in Archaeal flagella biosynthesis 0.022774
21 COG3704 protein secretion by the type IV secretion system 0.022768
22 COG0393 Putative heavy-metal-binding -0.022673
23 COG3319 amino acid activation for nonribosomal peptide biosynthetic process 0.022569
24 COG0423 glycine-tRNA ligase activity -0.022423
25 COG1220 this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis 0.022298
26 COG1022 Amp-dependent synthetase and ligase -0.021971
27 COG2761 dithiol-disulfide isomerase involved in polyketide biosynthesis -0.021713
28 COG1368 sulfuric ester hydrolase activity 0.021633
29 COG3285 dna ligase 0.021418
30 COG2210 Belongs to the sulfur carrier protein TusA family -0.021372
31 COG3651 Uncharacterized protein conserved in bacteria (DUF2237) -0.021295
32 COG0727 PFAM Uncharacterised protein family (UPF0153) 0.021230
33 COG0741 lytic transglycosylase activity 0.021197
34 COG1495 Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein 0.021151
35 COG3886 PLD-like domain -0.021140
36 COG0025 NhaP-type Na H and K H -0.020624
37 COG2217 Heavy metal translocating P-type atpase -0.020475
38 COG2070 2-Nitropropane dioxygenase 0.020328
39 COG2094 Belongs to the DNA glycosylase MPG family 0.020111
40 COG2326 polyphosphate kinase activity -0.020032
41 COG2873 o-acetylhomoserine -0.019797
42 COG3001 Fructosamine kinase -0.019687
43 COG2222 sugar isomerase 0.019675
44 COG1968 undecaprenyl-diphosphatase activity -0.019632
45 COG0007 Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme -0.019551
46 COG4391 Protein conserved in bacteria 0.019478
47 COG1965 Belongs to the frataxin family 0.019470
48 COG3707 response regulator -0.019459
49 COG1732 Glycine betaine 0.019427
50 COG0469 pyruvate kinase activity -0.019426
51 COG5012 cobalamin binding -0.019411
52 COG4658 electron transport chain -0.019361
53 COG1521 Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis -0.019282
54 COG1324 tolerance protein 0.019199
55 COG3545 Serine hydrolase 0.019189
56 COG0644 oxidoreductase -0.019168
57 COG3125 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor 0.019160
58 COG2348 transferase activity, transferring amino-acyl groups -0.019146
59 COG4249 Peptidase C14 caspase catalytic subunit p20 -0.018939
60 COG3654 -0.018914
61 COG0086 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates -0.018905
62 COG0002 Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde -0.018840
63 COG1288 antiporter activity 0.018782
64 COG1161 Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity -0.018698
65 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 -0.018696
66 COG0079 Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily -0.018525
67 COG0561 phosphatase activity -0.018472
68 COG3443 Belongs to the bacterial solute-binding protein 9 family 0.018410
69 COG2857 Cytochrome c1 0.018410
70 COG0425 Belongs to the sulfur carrier protein TusA family -0.018392
71 COG0569 domain protein -0.018364
72 COG2975 iron-sulfur cluster assembly 0.018312
73 COG3412 dihydroxyacetone kinase, phosphotransfer subunit 0.018304
74 COG4890 Cyd operon protein YbgT 0.018279
75 COG2148 undecaprenyl-phosphate glucose phosphotransferase activity -0.018278
76 COG1115 amino acid carrier protein 0.018276
77 COG0205 6-phosphofructokinase activity -0.018264
78 COG0366 Alpha amylase catalytic -0.018243
79 COG0435 Glutathione S-transferase 0.018176
80 COG0440 acetolactate synthase activity -0.018114
81 COG1012 belongs to the aldehyde dehydrogenase family -0.018106
82 COG1490 D-aminoacyl-tRNA deacylase activity -0.018094
83 COG4129 membrane 0.018081
84 COG3339 Conserved Protein 0.018070
85 COG0518 GMP synthase (glutamine-hydrolyzing) activity 0.017944
86 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 -0.017909
87 COG1178 ABC-type Fe3 transport system permease component -0.017857
88 COG3496 Conserved Protein -0.017828
89 COG2932 Transcriptional regulator 0.017825
90 COG1426 Protein conserved in bacteria -0.017709
91 COG3555 Aspartyl Asparaginyl beta-hydroxylase 0.017697
92 COG0282 Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction -0.017666
93 COG0687 Required for the activity of the bacterial periplasmic transport system of putrescine -0.017590
94 COG3450 Protein of unknown function (DUF861) 0.017577
95 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein -0.017569
96 COG5351 Uncharacterized protein conserved in bacteria (DUF2169) 0.017513
97 COG4191 Histidine kinase 0.017500
98 COG0798 PFAM Bile acid sodium symporter -0.017479
99 COG5405 Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery 0.017449
100 COG3164 Protein of unknown function 0.017418
101 COG2184 nucleotidyltransferase activity 0.017409
102 COG0733 neurotransmitter:sodium symporter activity -0.017400
103 COG2257 FlhB HrpN YscU SpaS Family 0.017377
104 COG1539 Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin 0.017375
105 COG1605 Chorismate mutase 0.017342
106 COG1284 Uncharacterised 5xTM membrane BCR, YitT family COG1284 -0.017309
107 COG2938 An FAD assembly protein, which accelerates covalent attachment of the cofactor into other proteins. Plays an essential role in the assembly of succinate dehydrogenase (SDH, respiratory complex II), an enzyme complex that is a component of both the tricarboxylic acid cycle and the electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit SdhA of SDH 0.017288
108 COG0017 Asparaginyl-tRNA synthetase -0.017253
109 COG2876 3-deoxy-7-phosphoheptulonate synthase activity -0.017198
110 COG3668 Plasmid stabilization system 0.017163
111 COG4651 solute:proton antiporter activity 0.017154
112 COG2309 aminopeptidase activity 0.017104
113 COG3597 protein domain associated with -0.017095
114 COG4487 mechanosensitive ion channel activity 0.017071
115 COG0855 Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) -0.017020
116 COG3568 Endonuclease Exonuclease Phosphatase 0.017019
117 COG1703 isobutyryl-CoA mutase activity -0.016966
118 COG2867 negative regulation of translational initiation 0.016941
119 COG3456 conserved protein contains FHA domain -0.016939
120 COG0166 Belongs to the GPI family -0.016860
121 COG3843 relaxase mobilization nuclease domain protein 0.016830
122 COG2271 Major facilitator Superfamily 0.016808
123 COG2308 Evidence 4 Homologs of previously reported genes of -0.016764
124 COG2369 cell adhesion 0.016762
125 COG1774 PSP1 C-terminal conserved region -0.016745
126 COG4908 Psort location Cytoplasmic, score -0.016743
127 COG2989 Protein conserved in bacteria -0.016718
128 COG3508 Involved in the catabolism of homogentisate (2,5- dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the aromatic ring of homogentisate to yield maleylacetoacetate 0.016698
129 COG4976 Methyltransferase 0.016661
130 COG0500 methyltransferase 0.016646
131 COG4656 Part of a membrane complex involved in electron transport -0.016581
132 COG5383 Protein conserved in bacteria 0.016580
133 COG0106 1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase -0.016578
134 COG1660 Displays ATPase and GTPase activities -0.016537
135 COG3484 -0.016506
136 COG2710 Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein -0.016490
137 COG1520 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.016489
138 COG1233 COG1233 Phytoene dehydrogenase and related -0.016459
139 COG1462 curli production assembly transport component CsgG -0.016449
140 COG5649 Domain of unknown function (DU1801) 0.016420
141 COG0802 atpase or kinase -0.016415
142 COG1468 defense response to virus -0.016262
143 COG2208 phosphoserine phosphatase activity -0.016236
144 COG1054 Belongs to the UPF0176 family 0.016232
145 COG2884 Cell division ATP-binding protein ftsE 0.016200
146 COG4088 5-carbamoylmethyl uridine residue modification 0.016162
147 COG3838 Conjugal transfer protein Trbc 0.016104
148 COG4520 surface antigen 0.016082
149 COG5270 sulfate reduction 0.015972
150 COG3737 Protein of unknown function (DUF498/DUF598) 0.015943
151 COG0693 protein deglycase activity -0.015924
152 COG5185 Phage-related minor tail protein 0.015917
153 COG2142 Succinate dehydrogenase hydrophobic membrane anchor 0.015912
154 COG2032 superoxide dismutase activity 0.015906
155 COG4653 Phage capsid family 0.015884
156 COG3708 Transcriptional regulator 0.015882
157 COG1274 phosphoenolpyruvate carboxykinase (GTP) activity -0.015876
158 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 0.015861
159 COG1806 Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the 0.015852
160 COG0040 Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of hisG enzymatic activity -0.015835
161 COG0107 imidazoleglycerol-phosphate synthase activity -0.015835
162 COG0131 Imidazoleglycerol-phosphate dehydratase -0.015835
163 COG4735 regulation of single-species biofilm formation 0.015814
164 COG0751 glycine-tRNA ligase activity 0.015798
165 COG3544 Protein conserved in bacteria -0.015754
166 2Z7S1 adenylyltransferase 0.015747
167 COG3663 DNA glycosylase -0.015723
168 COG0141 Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine -0.015694
169 COG1480 7TM receptor with intracellular HD hydrolase -0.015692
170 COG2718 Belongs to the UPF0229 family 0.015626
171 COG0139 Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP -0.015624
172 COG0313 Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA -0.015595
173 COG1154 Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) -0.015570
174 COG3382 B3 4 domain protein 0.015555
175 COG0613 PHP domain protein -0.015539
176 COG5553 Cysteine dioxygenase type I 0.015532
177 COG1187 pseudouridine synthase activity -0.015511
178 COG0722 Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP) 0.015507
179 COG0697 spore germination -0.015499
180 31DNS K COG5665 CCR4-NOT transcriptional regulation complex, NOT5 subunit -0.015405
181 COG3511 phospholipase C 0.015388
182 COG3917 2-hydroxychromene-2-carboxylate isomerase -0.015343
183 COG5441 Belongs to the UPF0261 family 0.015337
184 COG1273 With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD 0.015327
185 COG0297 glycogen (starch) synthase activity -0.015311
186 COG3835 regulator 0.015266
187 2Z7QR Membrane 0.015245
188 COG3436 PFAM IS66 Orf2 family protein 0.015242
189 COG3884 Acyl-ACP thioesterase -0.015222
190 COG2055 Belongs to the LDH2 MDH2 oxidoreductase family 0.015208
191 COG1071 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor 0.015176
192 COG1366 Belongs to the anti-sigma-factor antagonist family -0.015162
193 COG2960 long-chain fatty acid transporting porin activity 0.015157
194 COG2959 enzyme of heme biosynthesis 0.015113
195 COG1045 serine acetyltransferase -0.015099
196 COG4421 COG4421 Capsular polysaccharide biosynthesis protein -0.015076
197 COG2838 Isocitrate dehydrogenase -0.015066
198 COG0118 IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of IGP and AICAR -0.015030
199 COG2151 metal-sulfur cluster biosynthetic enzyme 0.015010
200 COG3846 protein secretion by the type IV secretion system 0.014999
201 COG0067 glutamate synthase -0.014951
202 COG1565 acr, cog1565 0.014936
203 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein -0.014878
204 COG0575 Belongs to the CDS family -0.014827
205 COG3705 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine -0.014825
206 COG3040 lipid binding -0.014816
207 COG3376 Belongs to the NiCoT transporter (TC 2.A.52) family 0.014806
208 COG0545 Peptidyl-prolyl cis-trans isomerase -0.014718
209 COG4694 Protein conserved in bacteria 0.014699
210 33WG4 Nucleoside 2-deoxyribosyltransferase like 0.014668
211 COG3937 granule-associated protein -0.014668
212 COG1348 The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex which has 2 components the iron protein and the molybdenum-iron protein -0.014653
213 COG0595 An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay -0.014589
214 COG3623 hexulose-6-phosphate isomerase 0.014578
215 COG3610 response to peptide -0.014564
216 COG2907 Flavin containing amine oxidoreductase -0.014563
217 COG1950 PFAM Membrane protein of -0.014523
218 COG3320 Male sterility -0.014490
219 COG1783 phage Terminase large subunit 0.014489
220 COG3946 virulence factor family protein 0.014453
221 COG3930 Protein conserved in bacteria 0.014390
222 COG1232 Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX -0.014381
223 COG4781 glycerophosphoryl diester phosphodiesterase 0.014371
224 COG0708 Exodeoxyribonuclease III 0.014347
225 COG0156 8-amino-7-oxononanoate synthase activity 0.014300
226 COG2764 glyoxalase bleomycin resistance protein dioxygenase 0.014284
227 33Y7F -0.014275
228 COG2828 Protein conserved in bacteria 0.014252
229 COG2254 TIGRFAM CRISPR-associated helicase Cas3 -0.014200
230 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 -0.014182
231 COG0831 urea catabolic process 0.014127
232 COG1385 rRNA (uridine-N3-)-methyltransferase activity 0.014109
233 COG3161 chorismate lyase activity 0.014071
234 COG3047 cAMP biosynthetic process 0.014058
235 COG1540 5-oxoprolinase (ATP-hydrolyzing) activity -0.013995
236 COG2860 membrane 0.013987
237 COG0362 Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH -0.013946
238 COG5402 Protein of unknown function (DUF1214) 0.013924
239 COG5436 integral membrane protein 0.013924
240 COG0132 Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring 0.013894
241 COG2602 Beta-lactamase 0.013881
242 COG4143 (ABC) transporter -0.013873
243 COG2967 ApaG domain 0.013867
244 COG2223 nitrite transmembrane transporter activity 0.013862
245 30AT0 0.013810
246 COG3719 Belongs to the RNase T2 family 0.013784
247 COG3614 Histidine kinase 0.013781
248 COG4723 tail assembly 0.013781
249 COG2731 YhcH YjgK YiaL family protein 0.013777
250 COG0804 urea catabolic process 0.013766