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 COG2984 ABC transporter substrate binding protein -0.042267
2 COG1397 ADP-ribosylglycohydrolase 0.035334
3 COG1129 ABC transporter -0.034653
4 COG0732 type I restriction modification DNA specificity domain 0.034617
5 COG0003 Pfam Anion-transporting ATPase 0.034404
6 COG2843 Capsule synthesis protein 0.033639
7 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component 0.032396
8 COG0699 ATPase. Has a role at an early stage in the morphogenesis of the spore coat -0.031297
9 COG3158 transport of potassium into the cell -0.030387
10 COG2378 regulation of single-species biofilm formation 0.030204
11 COG0153 Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P) -0.030116
12 33CY4 CarboxypepD_reg-like domain 0.029805
13 COG0111 D-isomer specific 2-hydroxyacid dehydrogenase 0.029695
14 COG4866 Psort location Cytoplasmic, score 0.029397
15 COG2301 Belongs to the HpcH HpaI aldolase family -0.029393
16 33TIW -0.029264
17 COG4942 peptidase -0.029078
18 339JU 0.028656
19 COG1024 Enoyl-CoA hydratase -0.028412
20 COG3274 enterobacterial common antigen metabolic process -0.028146
21 COG3314 Sporulation integral membrane protein YlbJ -0.028075
22 32RMG Arsenical resistance operon trans-acting repressor arsD 0.028005
23 COG0451 ADP-glyceromanno-heptose 6-epimerase activity 0.027790
24 33VTB Sigma-70 region 2 0.027764
25 COG4181 ATPase activity -0.027514
26 COG0762 integral membrane protein -0.026911
27 COG4925 sulfurtransferase activity -0.026705
28 COG0403 The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor 0.026674
29 COG1146 Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions 0.026619
30 COG5627 protein ubiquitination -0.026061
31 COG1172 Belongs to the binding-protein-dependent transport system permease family -0.026010
32 COG1887 Glycosyl glycerophosphate transferases involved in teichoic acid biosynthesis TagF TagB EpsJ RodC 0.025996
33 COG4659 FMN binding 0.025976
34 COG1694 Mazg nucleotide pyrophosphohydrolase 0.025852
35 COG0686 Belongs to the AlaDH PNT family 0.025747
36 COG3386 PFAM SMP-30 Gluconolaconase -0.025436
37 33PKE Concanavalin A-like lectin/glucanases superfamily -0.025164
38 COG0757 Catalyzes a trans-dehydration via an enolate intermediate -0.024868
39 COG4213 ABC transporter substrate-binding protein -0.024586
40 COG0710 3-dehydroquinate dehydratase activity 0.024543
41 COG2452 N-4 methylation of cytosine -0.024527
42 COG3967 Belongs to the short-chain dehydrogenases reductases (SDR) family -0.024461
43 COG0383 alpha-mannosidase activity 0.024432
44 COG1943 Transposase -0.024276
45 32YCK Stress responsive A/B Barrel Domain 0.024247
46 COG1106 Psort location Cytoplasmic, score 0.024246
47 COG2461 Hemerythrin HHE cation binding domain protein -0.024178
48 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein -0.024106
49 COG1897 L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine -0.023901
50 2Z85F Domain of unknown function (4846) 0.023438
51 COG3958 Transketolase 0.023422
52 COG0390 transport system, permease component -0.023341
53 COG1556 Lactate utilization protein 0.023299
54 319M2 Conserved hypothetical protein (Lin0512_fam) 0.023250
55 COG0154 amidase activity -0.023169
56 COG3579 cysteine-type endopeptidase activity 0.023100
57 COG3344 reverse transcriptase -0.022834
58 COG0064 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) -0.022828
59 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) -0.022828
60 COG2271 Major facilitator Superfamily 0.022811
61 COG3589 Outer surface protein 0.022606
62 COG1331 Highly conserved protein containing a thioredoxin domain 0.022409
63 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 -0.022368
64 COG4198 Conserved Protein 0.022300
65 COG3935 DnaD domain protein -0.022173
66 32RF3 Plasmid recombination enzyme -0.022170
67 COG3877 Protein conserved in bacteria -0.022141
68 COG0790 COG0790 FOG TPR repeat, SEL1 subfamily 0.022096
69 COG2087 Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate 0.022027
70 COG3697 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase -0.021975
71 COG0725 ABC transporter, periplasmic molybdate-binding protein -0.021877
72 COG2835 tetraacyldisaccharide 4'-kinase activity -0.021740
73 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) 0.021646
74 COG5640 endopeptidase activity 0.021632
75 33XR9 Psort location Cytoplasmic, score 8.96 0.021612
76 COG0368 Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate 0.021608
77 COG2972 Histidine kinase 0.021599
78 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid 0.021597
79 COG3199 ATP-NAD kinase 0.021489
80 2ZAUF -0.021451
81 COG0404 The glycine cleavage system catalyzes the degradation of glycine 0.021340
82 COG1135 Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system -0.021233
83 COG1464 Belongs to the NlpA lipoprotein family -0.021233
84 COG4886 Leucine-rich repeat (LRR) protein -0.021194
85 COG0521 Mo-molybdopterin cofactor biosynthetic process -0.021182
86 COG0656 L-ascorbic acid biosynthetic process -0.021060
87 COG5338 Protein conserved in bacteria -0.021054
88 COG3345 alpha-galactosidase -0.020842
89 2Z80J Psort location Cytoplasmic, score 8.87 -0.020821
90 COG3959 Transketolase, thiamine diphosphate binding domain 0.020673
91 3432Z Domain of unknown function (DUF4153) -0.020659
92 COG2011 ABC-type metal ion transport system permease component -0.020565
93 COG2008 Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde 0.020559
94 COG3942 CHAP domain -0.020480
95 COG1956 GAF domain-containing protein 0.020475
96 COG0575 Belongs to the CDS family -0.020441
97 COG0711 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) -0.020411
98 COG2315 Protein conserved in bacteria 0.020387
99 COG0113 porphobilinogen synthase activity 0.020379
100 COG2210 Belongs to the sulfur carrier protein TusA family -0.020371
101 COG0743 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity 0.020273
102 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.020245
103 COG1905 PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit -0.020221
104 COG5280 Phage tail tape measure protein TP901 0.020212
105 COG0476 Involved in molybdopterin and thiamine biosynthesis, family 2 -0.020193
106 30NZ2 0.020171
107 COG4149 molybdate abc transporter -0.020112
108 COG2386 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes -0.020078
109 2ZAF1 Domain of unknown function (DUF4374) 0.020019
110 33U5H -0.019840
111 335CS 0.019788
112 COG1444 tRNA N-acetyltransferase activity 0.019781
113 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 0.019689
114 COG0551 DNA topoisomerase type I activity -0.019637
115 33X8T 0.019627
116 COG3635 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity 0.019610
117 COG0342 Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA -0.019570
118 COG1484 DNA-dependent DNA replication -0.019556
119 32UGM -0.019551
120 COG0248 Ppx GppA phosphatase -0.019547
121 COG1758 RNA polymerase activity -0.019505
122 33E1I Domain of unknown function (DUF1858) -0.019496
123 COG4843 Uncharacterized protein conserved in bacteria (DUF2179) 0.019454
124 COG3379 PFAM type I phosphodiesterase nucleotide pyrophosphatase 0.019311
125 COG5435 protein kinase activity -0.019290
126 2ZBES -0.019259
127 COG0386 Belongs to the glutathione peroxidase family 0.019252
128 COG4948 Mandelate Racemase Muconate Lactonizing 0.019192
129 33UKF 0.019180
130 COG1277 ABC-type transport system involved in multi-copper enzyme maturation permease component -0.019146
131 COG0105 UTP biosynthetic process -0.019111
132 2ZIMS 0.019070
133 COG5001 Diguanylate cyclase -0.018950
134 COG0432 Pfam Uncharacterised protein family UPF0047 -0.018918
135 COG1453 Aldo Keto reductase 0.018878
136 COG4963 Pilus assembly protein -0.018809
137 2ZDC8 0.018771
138 COG3426 butyrate kinase activity 0.018746
139 33P14 FIVAR domain 0.018712
140 COG3641 Membrane 0.018698
141 32HTK Protein of unknown function (DUF3788) 0.018691
142 32U37 PKD-like domain 0.018676
143 COG1288 antiporter activity -0.018659
144 COG1763 Mo-molybdopterin cofactor biosynthetic process -0.018658
145 2Z8IC Protein of unknown function (DUF4003) 0.018611
146 33GDE This gene contains a nucleotide ambiguity which may be the result of a sequencing error 0.018609
147 COG1237 beta-lactamase domain protein 0.018600
148 30WI8 0.018587
149 COG0694 Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins 0.018581
150 2ZGPA PspA/IM30 family -0.018552
151 COG3774 pathogenesis 0.018531
152 COG3052 prosthetic group binding -0.018516
153 COG3051 citrate lyase alpha subunit -0.018516
154 COG0255 Belongs to the universal ribosomal protein uL29 family -0.018514
155 COG0863 Belongs to the N(4) N(6)-methyltransferase family -0.018498
156 2Z9BC Protein of unknown function (DUF4876) 0.018496
157 COG2957 Belongs to the agmatine deiminase family 0.018486
158 COG3786 Protein conserved in bacteria 0.018472
159 31QNY Winged helix DNA-binding domain 0.018430
160 33J2G Control of competence regulator ComK, YlbF/YmcA 0.018403
161 COG3973 AAA domain -0.018337
162 COG3576 pyridoxamine 5-phosphate -0.018321
163 COG3031 protein transport across the cell outer membrane -0.018305
164 2Z7N5 Psort location Cytoplasmic, score 8.96 0.018282
165 2ZX47 Psort location Cytoplasmic, score 8.96 0.018282
166 32TUP O-Antigen ligase 0.018235
167 344BH -0.018197
168 COG3023 N-Acetylmuramoyl-L-alanine amidase 0.018177
169 COG3456 conserved protein contains FHA domain -0.018158
170 33A7H Putative auto-transporter adhesin, head GIN domain 0.018156
171 334TS -0.018152
172 348PX -0.018152
173 COG1219 ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP -0.018143
174 32TQR Psort location Cytoplasmic, score 0.018118
175 32RP7 Domain of unknown function (DUF1911) -0.018109
176 338EI 0.018058
177 30J24 Protein of unknown function (DUF2442) 0.018055
178 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.018047
179 COG0538 isocitrate dehydrogenase activity -0.018038
180 COG3619 membrane -0.017972
181 COG1506 peptidase 0.017945
182 COG3315 Exhibits S-adenosyl-L-methionine-dependent methyltransferase activity 0.017943
183 COG3549 Plasmid maintenance system killer 0.017895
184 COG2017 converts alpha-aldose to the beta-anomer -0.017862
185 3025Y Psort location Cytoplasmic, score 0.017842
186 325AS CarboxypepD_reg-like domain 0.017839
187 COG2365 Tyrosine phosphatase family 0.017835
188 COG3728 DNA packaging 0.017833
189 COG1525 nuclease -0.017822
190 COG3682 Transcriptional regulator -0.017811
191 COG1230 cation diffusion facilitator family transporter -0.017758
192 COG0235 Class ii aldolase -0.017749
193 COG1346 cytolysis -0.017736
194 COG1380 Effector of murein hydrolase LrgA -0.017736
195 COG3758 protein conserved in bacteria -0.017707
196 32TGW 0.017706
197 COG3280 synthase -0.017682
198 COG2273 Hydrolase Family 16 0.017657
199 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 -0.017623
200 COG0356 it plays a direct role in the translocation of protons across the membrane -0.017623
201 2Z8G6 Conjugative transposon TraJ protein 0.017616
202 2ZJSA 0.017609
203 COG0169 Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA) -0.017601
204 339J8 Protein of unknown function (DUF3098) 0.017587
205 COG0546 phosphoglycolate phosphatase activity -0.017574
206 338D2 -0.017569
207 31Y7J 0.017533
208 COG1252 NADH dehydrogenase -0.017531
209 COG2356 endonuclease I -0.017524
210 33ECV 0.017492
211 COG3469 chitinase activity 0.017481
212 34CH1 Helix-turn-helix 0.017474
213 COG2318 DinB family -0.017460
214 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 -0.017448
215 COG4211 Belongs to the binding-protein-dependent transport system permease family -0.017420
216 COG1501 Belongs to the glycosyl hydrolase 31 family -0.017387
217 COG0161 adenosylmethionine-8-amino-7-oxononanoate transaminase activity -0.017379
218 COG1894 NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain -0.017345
219 33CJ8 0.017301
220 COG2149 membrane -0.017295
221 30CC5 TIGRFAM C_GCAxxG_C_C family protein 0.017288
222 COG4970 Tfp pilus assembly protein FimT -0.017283
223 32QT8 Psort location Cytoplasmic, score 0.017264
224 COG3108 Peptidase M15 -0.017184
225 COG3408 Glycogen debranching enzyme 0.017179
226 32VYT T5orf172 0.017178
227 COG3442 glutamine amidotransferase -0.017154
228 COG1234 tRNA 3'-trailer cleavage 0.017115
229 COG2367 Beta-lactamase -0.017081
230 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates 0.017079
231 COG0413 3-methyl-2-oxobutanoate hydroxymethyltransferase activity 0.017050
232 30I07 Bacterial mobilisation protein (MobC) 0.016980
233 COG3404 Formiminotransferase-cyclodeaminase 0.016961
234 COG3240 lipase activity -0.016944
235 COG1672 PFAM Archaeal ATPase 0.016904
236 338V0 -0.016900
237 COG1979 alcohol dehydrogenase 0.016900
238 COG1457 Belongs to the purine-cytosine permease (2.A.39) family -0.016891
239 COG3747 phage terminase small subunit -0.016879
240 2ZC4W 0.016847
241 2ZRCG -0.016804
242 COG1002 Type II restriction enzyme, methylase subunits -0.016797
243 COG0295 cytidine deaminase activity 0.016766
244 COG1077 Cell shape determining protein MreB Mrl 0.016762
245 32ZQF 0.016761
246 30PMP -0.016754
247 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding 0.016731
248 COG1803 Methylglyoxal synthase -0.016722
249 COG1213 nucleotidyl transferase 0.016722
250 COG1607 acyl-coa hydrolase -0.016715