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 COG1720 tRNA m6t6A37 methyltransferase activity 0.023790
2 COG2842 Transposition protein 0.022884
3 COG2046 Belongs to the sulfate adenylyltransferase family 0.022296
4 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 0.021227
5 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 0.021227
6 COG1200 Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA) -0.021019
7 COG1940 carbohydrate kinase activity -0.021007
8 COG1053 succinate dehydrogenase 0.020945
9 339S5 Putative regulatory protein 0.020283
10 COG1900 Homocysteine biosynthesis enzyme, sulfur-incorporation 0.020125
11 COG1035 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus 0.019817
12 COG3505 Type IV secretory pathway VirD4 0.019766
13 COG4087 Haloacid dehalogenase domain protein hydrolase 0.019499
14 COG1916 peptidoglycan binding 0.019342
15 COG5561 CGGC domain 0.019024
16 COG0578 Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family 0.018809
17 COG1489 DNA binding 0.018714
18 COG2122 PFAM ApbE family 0.018622
19 COG2873 o-acetylhomoserine -0.018613
20 COG0857 belongs to the CobB CobQ family 0.018407
21 337H4 0.018334
22 COG0785 Cytochrome C biogenesis protein -0.018169
23 COG0555 PFAM binding-protein-dependent transport systems inner membrane component -0.018166
24 32TNY Domain of unknown function (DUF1992) 0.018149
25 COG2104 thiamine diphosphate biosynthetic process -0.018049
26 COG3833 ABC-type maltose transport systems, permease component -0.017973
27 COG3705 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine -0.017972
28 COG0855 Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) -0.017964
29 COG0276 Catalyzes the ferrous insertion into protoporphyrin IX -0.017666
30 COG0230 Belongs to the bacterial ribosomal protein bL34 family -0.017577
31 COG2920 part of a sulfur-relay system 0.017344
32 COG4536 flavin adenine dinucleotide binding -0.017300
33 COG2043 Uncharacterised ArCR, COG2043 0.017214
34 COG3933 PFAM sigma-54 factor interaction domain-containing protein -0.017150
35 COG2145 Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ) 0.017034
36 COG0248 Ppx GppA phosphatase -0.016675
37 COG2998 abc-type tungstate transport system, permease component 0.016533
38 COG3127 ABC-type transport system involved in lysophospholipase L1, biosynthesis, permease component -0.016502
39 COG3418 PFAM FlgN family protein -0.016492
40 COG2221 Nitrite and sulphite reductase 4Fe-4S 0.016469
41 COG1578 Protein of unknown function DUF89 0.016393
42 COG1359 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity 0.016337
43 32RXU RsbT co-antagonist protein rsbRD N-terminal domain 0.016311
44 32SEM 0.016311
45 COG3857 The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the chi site generating a DNA molecule suitable for the initiation of homologous recombination -0.016275
46 32S9W Protein of unknown function (DUF3189) -0.016269
47 COG1105 Belongs to the carbohydrate kinase PfkB family -0.016082
48 COG0534 Mate efflux family protein -0.016080
49 COG4951 DNA primase small subunit 0.015997
50 COG2232 ATP-grasp domain 0.015853
51 COG2362 D-Aminopeptidase -0.015838
52 COG0308 aminopeptidase N -0.015762
53 COG2972 Histidine kinase -0.015635
54 COG3808 pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for -0.015627
55 COG1906 membrane 0.015620
56 COG0475 glutathione-regulated potassium exporter activity 0.015489
57 COG0661 Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis -0.015448
58 COG1908 Methyl-viologen-reducing hydrogenase, delta subunit 0.015428
59 COG3271 cysteine-type peptidase activity 0.015368
60 COG4129 membrane 0.015296
61 3224Y Universal stress protein family 0.015275
62 COG3075 Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses fumarate or nitrate as electron acceptor 0.015272
63 COG2107 Catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2) 0.015257
64 32SDN 0.015181
65 32VSP 0.015123
66 COG0693 protein deglycase activity 0.014961
67 COG1683 Conserved Protein 0.014933
68 COG1351 Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NAD(P)H and FADH(2) as the reductant -0.014925
69 COG0646 methionine synthase -0.014828
70 COG2189 Belongs to the N(4) N(6)-methyltransferase family -0.014808
71 COG1136 (ABC) transporter -0.014785
72 33AT3 Sulfurtransferase TusA 0.014764
73 COG0031 Belongs to the cysteine synthase cystathionine beta- synthase family -0.014730
74 COG0220 tRNA (guanine-N7-)-methyltransferase activity -0.014706
75 COG2864 formate dehydrogenase -0.014683
76 COG1741 Belongs to the pirin family -0.014645
77 COG1803 Methylglyoxal synthase -0.014617
78 COG0314 molybdopterin synthase activity 0.014553
79 COG4812 Cobalamin adenosyltransferase 0.014552
80 COG3655 Transcriptional regulator 0.014518
81 COG1573 uracil-dna glycosylase -0.014497
82 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid -0.014393
83 COG0257 Belongs to the bacterial ribosomal protein bL36 family -0.014299
84 COG1737 Transcriptional regulator -0.014222
85 32TK9 0.014167
86 COG3173 Aminoglycoside phosphotransferase 0.014075
87 COG5350 Protein tyrosine phosphatase 0.014059
88 COG2956 Modulates cellular lipopolysaccharide (LPS) levels by regulating LpxC, which is involved in lipid A biosynthesis. May act by modulating the proteolytic activity of FtsH towards LpxC. May also coordinate assembly of proteins involved in LPS synthesis at the plasma membrane -0.014047
89 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component 0.014013
90 307WW 0.013988
91 COG4822 anaerobic cobalamin biosynthetic process 0.013983
92 COG4766 ethanolamine catabolic process 0.013958
93 COG1434 Gram-negative-bacterium-type cell wall biogenesis -0.013954
94 COG1323 Belongs to the UPF0348 family -0.013907
95 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 -0.013906
96 COG2876 3-deoxy-7-phosphoheptulonate synthase activity -0.013806
97 33P2T 0.013803
98 31CNF 0.013800
99 33IU2 0.013726
100 COG4917 ethanolamine utilization protein 0.013647
101 COG4637 Psort location Cytoplasmic, score -0.013625
102 COG0626 cystathionine gamma-synthase activity -0.013613
103 COG0281 malic enzyme -0.013591
104 COG2014 Putative heavy-metal chelation 0.013550
105 COG1386 Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves -0.013502
106 COG4012 pyruvate format-lyase activating enzyme 0.013453
107 COG0511 ligase activity, forming carbon-carbon bonds -0.013452
108 COG0070 glutamate synthase -0.013382
109 COG3192 ethanolamine utilization protein 0.013313
110 COG4174 ABC transporter (Permease) 0.013307
111 COG0209 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides -0.013261
112 COG0145 ligase activity 0.013251
113 31H63 0.013216
114 32SHU Domain of unknown function (DUF2760) 0.013215
115 COG0337 Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ) -0.013203
116 COG1691 (AIR) carboxylase 0.013187
117 COG2895 sulfate adenylyltransferase (ATP) activity -0.013172
118 COG0471 metal ion transport 0.013113
119 2ZK16 Histidine Phosphotransfer domain 0.013094
120 2ZXZV Outer membrane efflux protein -0.013087
121 COG2193 ferroxidase activity -0.013075
122 32CXY phospholipase C 0.013075
123 2ZHJE Cyclic nucleotide-binding domain -0.013065
124 COG4820 ethanolamine utilization protein (EutJ) 0.013047
125 COG2868 ribosomal protein -0.013035
126 2Z9T8 Domain of unknown function (DUF4405) 0.013027
127 32U1K 0.012993
128 32TGZ 0.012992
129 33CDW 0.012992
130 COG1350 The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine -0.012973
131 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 -0.012960
132 2ZVPG 0.012939
133 30F9Z 0.012927
134 COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit, (S4 paralog)) -0.012890
135 COG0302 gtp cyclohydrolase -0.012864
136 32ZJH Domain of unknown function (DUF4363) 0.012858
137 COG1641 Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2 ), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is thus probably required for the activation of nickel-pincer cofactor- dependent enzymes 0.012854
138 COG3426 butyrate kinase activity 0.012832
139 33ASE 0.012831
140 32SN5 0.012826
141 2ZCJT 0.012815
142 COG1427 Catalyzes the dehydration of chorismate into 3- (1- carboxyvinyl)oxy benzoate, a step in the biosynthesis of menaquinone (MK, vitamin K2) 0.012813
143 COG4745 4-amino-4-deoxy-L-arabinose transferase activity -0.012769
144 COG2132 Multicopper oxidase -0.012757
145 COG1058 Belongs to the CinA family -0.012741
146 COG4810 utilization protein 0.012702
147 33191 PFAM Dissimilatory sulfite reductase D 0.012665
148 COG3836 Belongs to the HpcH HpaI aldolase family -0.012628
149 COG0761 Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)- butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP MEP pathway for isoprenoid precursor biosynthesis -0.012586
150 COG1150 heterodisulfide reductase subunit C 0.012527
151 2Z9E1 PFAM TnsA endonuclease 0.012523
152 COG3108 Peptidase M15 0.012481
153 COG4108 Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP 0.012479
154 33EUU 0.012441
155 COG1301 dicarboxylic acid transport -0.012431
156 COG3688 RNA-binding protein containing a PIN domain 0.012423
157 COG2048 Heterodisulfide reductase, subunit B 0.012415
158 3482A -0.012406
159 COG1512 COG1512 Beta-propeller domains of methanol dehydrogenase type -0.012383
160 COG0757 Catalyzes a trans-dehydration via an enolate intermediate -0.012365
161 COG3328 transposase activity -0.012321
162 COG2151 metal-sulfur cluster biosynthetic enzyme -0.012266
163 COG1928 C-terminal four TMM region of protein-O-mannosyltransferase 0.012258
164 COG5266 PFAM Nickel transport complex, NikM subunit, transmembrane 0.012249
165 310ZN Protein of unknown function (DUF3795) 0.012194
166 33MTN 0.012171
167 COG1612 heme a metabolic process -0.012171
168 COG4665 TRAP-type mannitol chloroaromatic compound transport system small permease component 0.012167
169 COG4936 Histidine kinase 0.012137
170 COG1825 This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance -0.012133
171 COG4619 ABC transporter 0.012114
172 COG4548 von Willebrand factor, type A 0.012088
173 COG3454 Phosphonate metabolism 0.012060
174 COG4799 Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta -0.012057
175 COG1329 Transcriptional regulator 0.012048
176 COG3848 Pyruvate phosphate dikinase 0.012010
177 33JWE 0.011991
178 COG2274 protein secretion by the type I secretion system -0.011989
179 COG4302 ethanolamine ammonia-lyase activity 0.011975
180 33WYX 0.011972
181 COG3593 DNA synthesis involved in DNA repair 0.011962
182 COG1704 LemA family -0.011961
183 COG1598 PFAM Uncharacterised protein family UPF0150 0.011916
184 COG4963 Pilus assembly protein 0.011897
185 33BA1 0.011896
186 COG0428 transporter -0.011869
187 30SQC PFAM UspA 0.011861
188 COG1610 YqeY-like protein -0.011859
189 COG1253 flavin adenine dinucleotide binding 0.011855
190 COG1310 metal-dependent protease of the Pad1 Jab1 superfamily -0.011806
191 COG2080 2 iron, 2 sulfur cluster binding -0.011798
192 303FQ TIGRFAM C_GCAxxG_C_C family protein 0.011792
193 COG3087 Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides -0.011760
194 COG0433 COG0433 Predicted ATPase -0.011728
195 33A63 Psort location Cytoplasmic, score -0.011715
196 2ZDT8 0.011714
197 COG2259 Doxx family -0.011705
198 31G01 TniQ 0.011704
199 337E4 YvrJ protein family 0.011699
200 COG0423 glycine-tRNA ligase activity -0.011673
201 COG1582 Flagellar protein (FlbD) -0.011657
202 2Z7K0 0.011631
203 334IY Domain of unknown function (DUF1844) 0.011630
204 3312Z 0.011629
205 COG0853 Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine -0.011611
206 32WU5 Class III cytochrome C family 0.011601
207 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) -0.011588
208 COG0684 Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions -0.011583
209 COG1477 protein flavinylation -0.011573
210 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component -0.011560
211 COG1606 tRNA processing 0.011549
212 COG0046 Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL -0.011527
213 COG1034 ATP synthesis coupled electron transport -0.011520
214 2Z852 0.011519
215 31X2N 0.011519
216 COG4303 Ethanolamine ammonia lyase large subunit 0.011505
217 COG3316 Transposase and inactivated derivatives 0.011504
218 COG0520 Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine -0.011475
219 COG3944 biosynthesis protein 0.011464
220 COG0422 Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction -0.011407
221 32SJ1 0.011393
222 COG1237 beta-lactamase domain protein 0.011393
223 COG2818 Glycosylase 0.011388
224 COG0334 Belongs to the Glu Leu Phe Val dehydrogenases family -0.011332
225 33AYK -0.011323
226 COG4589 Belongs to the CDS family -0.011313
227 31H6C Type I restriction enzyme R protein N terminus (HSDR_N) 0.011310
228 COG0328 RNA-DNA hybrid ribonuclease activity -0.011310
229 COG2166 iron-sulfur cluster assembly -0.011309
230 COG2358 TRAP transporter, solute receptor (TAXI family 0.011307
231 COG3270 Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA -0.011306
232 COG0624 Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls -0.011291
233 COG5416 Lipopolysaccharide assembly protein A domain 0.011284
234 33IJI 0.011273
235 3056W 0.011266
236 COG2414 aldehyde ferredoxin oxidoreductase 0.011251
237 2ZAQ1 Arylsulfotransferase Ig-like domain 0.011250
238 33BFJ 0.011239
239 2ZQKN 0.011231
240 COG3366 ferrous iron transmembrane transporter activity 0.011206
241 COG2816 NAD+ diphosphatase activity -0.011193
242 COG3862 protein with conserved CXXC pairs -0.011158
243 33ATC Domain of unknown function (DUF4352) 0.011156
244 COG0407 Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III -0.011150
245 COG4147 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family 0.011130
246 COG2369 cell adhesion 0.011120
247 COG4676 Protein conserved in bacteria 0.011103
248 COG3067 Na( ) H( ) antiporter that extrudes sodium in exchange for external protons 0.011093
249 COG1234 tRNA 3'-trailer cleavage 0.011063
250 33T1G 0.011057