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 COG1063 alcohol dehydrogenase -0.060357
2 COG3711 transcriptional antiterminator 0.055179
3 COG1757 Na H antiporter -0.052681
4 COG3775 system Galactitol-specific IIC component 0.050069
5 COG1322 Protein conserved in bacteria 0.049710
6 COG3633 Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system) 0.049460
7 COG5586 Nucleotidyl transferase AbiEii toxin, Type IV TA system -0.048192
8 31EGY 0.047542
9 COG0562 UDP-galactopyranose mutase -0.047273
10 COG2378 regulation of single-species biofilm formation -0.045144
11 COG2116 formate transmembrane transporter activity 0.044467
12 COG3465 dGTPase activity -0.044063
13 COG0655 NAD(P)H dehydrogenase (quinone) activity 0.044008
14 2Z8AD Carbohydrate-binding domain-containing protein Cthe_2159 0.043516
15 2ZSRR Psort location Cytoplasmic, score 8.87 0.042664
16 COG3560 Nitroreductase -0.042487
17 COG4587 transport system, permease component 0.042293
18 COG1794 racemase activity, acting on amino acids and derivatives -0.042152
19 COG3247 response to pH 0.041678
20 COG2818 Glycosylase -0.041022
21 COG1479 Protein of unknown function DUF262 0.041021
22 COG1619 proteins homologs of microcin C7 resistance protein MccF 0.040353
23 COG2827 Endonuclease containing a URI domain -0.039899
24 33P14 FIVAR domain 0.039659
25 COG4245 von Willebrand factor, type A 0.038789
26 COG5360 Heparinase II/III-like protein 0.038619
27 COG4225 unsaturated rhamnogalacturonyl hydrolase activity 0.038504
28 COG3513 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9 crRNA tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer -0.038422
29 COG4559 Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system -0.038250
30 COG0615 ADP-L-glycero-beta-D-manno-heptose biosynthetic process -0.038166
31 COG3589 Outer surface protein 0.037908
32 COG3191 aminopeptidase activity -0.037898
33 COG3263 regulation of cellular component size -0.037785
34 COG1233 COG1233 Phytoene dehydrogenase and related -0.037550
35 COG0846 NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form -0.037416
36 COG1053 succinate dehydrogenase -0.037108
37 COG3221 ABC-type phosphate phosphonate transport system periplasmic component -0.036944
38 32TBR Protein of unknown function (DUF2974) 0.036866
39 COG3275 phosphorelay sensor kinase activity 0.036770
40 2ZIYW Psort location Cytoplasmic, score 0.036712
41 COG0584 glycerophosphoryl diester phosphodiesterase -0.036173
42 COG4642 MORN repeat 0.036079
43 COG3408 Glycogen debranching enzyme 0.035924
44 COG4095 Psort location CytoplasmicMembrane, score -0.035659
45 COG5340 Psort location Cytoplasmic, score -0.035439
46 COG1680 COG1680 Beta-lactamase class C and other penicillin binding -0.035427
47 COG1971 Probably functions as a manganese efflux pump 0.035420
48 COG1882 Formate acetyltransferase 0.035199
49 COG5499 transcription regulator containing HTH domain 0.034952
50 2Z8ZV ABC-2 family transporter protein -0.034918
51 COG4720 Psort location CytoplasmicMembrane, score 0.034850
52 COG0785 Cytochrome C biogenesis protein -0.034532
53 COG0715 COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components 0.034479
54 32XKY ECF transporter, substrate-specific component -0.034442
55 COG0471 metal ion transport -0.034377
56 COG0794 Belongs to the SIS family. GutQ KpsF subfamily -0.034274
57 COG5485 Ester cyclase 0.033959
58 COG1748 Saccharopine dehydrogenase 0.033923
59 COG3833 ABC-type maltose transport systems, permease component 0.033795
60 COG1916 peptidoglycan binding 0.033773
61 COG1080 General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) 0.033403
62 COG0390 transport system, permease component 0.033318
63 33CG9 GDSL-like Lipase/Acylhydrolase 0.033314
64 COG4915 5-bromo-4-chloroindolyl phosphate hydrolysis protein -0.033277
65 COG0801 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 0.033156
66 COG1180 Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine 0.033010
67 COG3459 Glycosyltransferase 36 associated 0.032881
68 COG3967 Belongs to the short-chain dehydrogenases reductases (SDR) family -0.032862
69 32RYJ Domain of unknown function (DUF4186) 0.032846
70 COG0210 DNA helicase 0.032799
71 COG3618 amidohydrolase 0.032680
72 COG1429 ligase activity, forming nitrogen-metal bonds -0.032669
73 COG1669 hydrolase activity, acting on ester bonds 0.032624
74 COG2129 metallophosphoesterase -0.032614
75 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 0.032442
76 COG1989 Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue -0.032432
77 COG1917 Cupin 2, conserved barrel domain protein -0.032398
78 COG1278 Cold shock -0.032188
79 COG3257 ureidoglycine aminohydrolase activity 0.031884
80 COG4221 oxidoreductase activity 0.031883
81 303R9 -0.031817
82 COG4824 toxin secretion phage lysis holin -0.031810
83 COG1508 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding -0.031782
84 COG1442 glycosyl transferase family 8 -0.031767
85 COG1074 ATP-dependent DNA helicase activity -0.031763
86 COG2509 5-formyltetrahydrofolate cyclo-ligase activity -0.031712
87 COG4284 Utp--glucose-1-phosphate uridylyltransferase 0.031703
88 COG3393 -acetyltransferase -0.031669
89 338B2 0.031639
90 COG3639 organic phosphonate transmembrane transporter activity -0.031534
91 32U4Y helix_turn_helix, Lux Regulon 0.031507
92 COG0063 ADP-dependent NAD(P)H-hydrate dehydratase activity -0.031391
93 COG1652 LysM domain -0.031370
94 COG3830 Belongs to the UPF0237 family 0.031363
95 342R0 Trypsin-like peptidase domain -0.031275
96 COG5337 Spore coat protein CotH 0.031149
97 COG2113 Glycine betaine 0.031142
98 COG5617 Psort location CytoplasmicMembrane, score -0.031095
99 COG1636 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) -0.030956
100 COG3757 hydrolase, family 25 0.030916
101 COG1922 lipopolysaccharide N-acetylmannosaminouronosyltransferase activity -0.030893
102 COG1062 S-(hydroxymethyl)glutathione dehydrogenase activity 0.030820
103 COG2964 Protein conserved in bacteria 0.030782
104 COG0393 Putative heavy-metal-binding 0.030778
105 COG1741 Belongs to the pirin family -0.030770
106 COG2271 Major facilitator Superfamily -0.030745
107 2Z7TS Domain of unknown function (DUF4317) 0.030726
108 COG2452 N-4 methylation of cytosine -0.030719
109 COG5566 PFAM Mor transcription activator -0.030654
110 COG4886 Leucine-rich repeat (LRR) protein 0.030635
111 COG3037 sugar-specific permease SgaT UlaA 0.030614
112 2ZYY6 Bacterial regulatory proteins, tetR family -0.030606
113 COG3598 Psort location Cytoplasmic, score 0.030530
114 COG3740 Phage prohead protease, HK97 family -0.030506
115 COG3290 protein histidine kinase activity 0.030438
116 32S7G Excisionase 0.030372
117 COG1477 protein flavinylation -0.030354
118 COG0235 Class ii aldolase 0.030337
119 COG1827 regulation of RNA biosynthetic process 0.030232
120 COG1038 Catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second -0.030168
121 COG3707 response regulator 0.030150
122 COG2845 Protein of unknown function (DUF459) -0.030115
123 30TEW Ribosomal protein L33 0.030073
124 32AMX -0.029744
125 COG4694 Protein conserved in bacteria -0.029714
126 COG4235 cytochrome complex assembly 0.029650
127 COG0351 phosphomethylpyrimidine kinase 0.029649
128 COG1416 DNA-binding transcription factor activity 0.029571
129 COG2227 3-demethylubiquinone-9 3-O-methyltransferase activity -0.029443
130 COG0557 exoribonuclease II activity -0.029386
131 COG5016 pyruvate 0.029155
132 COG1541 Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA) 0.029141
133 COG0174 glutamine synthetase 0.029063
134 COG2030 dehydratase -0.028997
135 COG3878 Protein conserved in bacteria -0.028943
136 COG0395 ABC-type sugar transport system, permease component 0.028921
137 COG4302 ethanolamine ammonia-lyase activity 0.028909
138 COG2876 3-deoxy-7-phosphoheptulonate synthase activity -0.028895
139 COG3304 Inner membrane component domain 0.028875
140 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein -0.028794
141 COG3272 Protein of unknown function (DUF1722) 0.028790
142 COG1380 Effector of murein hydrolase LrgA -0.028789
143 312PY Cro/C1-type HTH DNA-binding domain -0.028787
144 COG1864 DNA RNA non-specific endonuclease -0.028663
145 COG2862 Uncharacterized protein family, UPF0114 -0.028647
146 COG1328 CTP reductase activity -0.028370
147 COG3576 pyridoxamine 5-phosphate 0.028252
148 COG1132 (ABC) transporter -0.028174
149 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) -0.028164
150 COG3467 pyridoxamine 5'-phosphate -0.028058
151 COG2524 Domain in cystathionine beta-synthase and other proteins. -0.028051
152 COG3226 Transcriptional regulator 0.028032
153 340N5 0.027998
154 COG1041 phosphinothricin N-acetyltransferase activity 0.027950
155 COG0616 signal peptide processing -0.027883
156 COG2972 Histidine kinase 0.027879
157 COG2235 arginine -0.027870
158 COG1525 nuclease -0.027866
159 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 -0.027863
160 33A5I Psort location CytoplasmicMembrane, score 0.027858
161 COG4894 glucomannan catabolic process 0.027857
162 2ZGPA PspA/IM30 family 0.027826
163 COG0176 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway 0.027810
164 COG4702 Belongs to the UPF0303 family 0.027766
165 33CTH MORN repeat variant -0.027761
166 33BGI Parallel beta-helix repeats 0.027747
167 30GAQ GDSL-like Lipase/Acylhydrolase family -0.027719
168 COG1305 Transglutaminase-like -0.027627
169 COG0154 amidase activity -0.027569
170 COG0741 lytic transglycosylase activity 0.027528
171 COG2267 carboxylic ester hydrolase activity 0.027512
172 COG3328 transposase activity -0.027492
173 COG4187 Peptidase family M20/M25/M40 -0.027464
174 COG5546 COG5546 Small integral membrane protein 0.027462
175 COG3433 isochorismatase activity 0.027427
176 33E24 Helix-turn-helix XRE-family like proteins -0.027399
177 COG2364 Membrane -0.027385
178 COG4626 Terminase -0.027352
179 COG3525 Glycosyl hydrolase, family 20, catalytic domain 0.027196
180 COG4965 Type ii secretion system 0.027144
181 33PG8 Psort location Cytoplasmic, score 8.96 -0.027116
182 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 -0.027103
183 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 0.027080
184 32W9S -0.027009
185 COG1182 Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity -0.027006
186 COG3412 dihydroxyacetone kinase, phosphotransfer subunit 0.026983
187 COG1879 ABC-type sugar transport system periplasmic component -0.026947
188 COG1510 regulation of RNA biosynthetic process 0.026942
189 COG0402 S-adenosylhomocysteine deaminase activity -0.026928
190 COG0526 COG0526, thiol-disulfide isomerase and thioredoxins 0.026912
191 2ZC3Y family 11 -0.026864
192 COG2382 esterase 0.026828
193 31FR9 MarR family 0.026794
194 COG1286 toxin biosynthetic process -0.026763
195 COG1329 Transcriptional regulator 0.026745
196 COG1297 OPT oligopeptide transporter protein -0.026734
197 COG1142 4fe-4S ferredoxin, iron-sulfur binding domain protein 0.026708
198 COG2896 Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate -0.026681
199 COG0420 3'-5' exonuclease activity -0.026658
200 COG5017 Glycosyltransferase family 28 C-terminal domain -0.026654
201 COG2431 L-lysine efflux transmembrane transporter activity -0.026622
202 COG4927 Acyl-coenzyme A 6-aminopenicillanic acid acyl-transferase -0.026607
203 342VC Cyclic nucleotide-monophosphate binding domain -0.026566
204 COG0161 adenosylmethionine-8-amino-7-oxononanoate transaminase activity -0.026556
205 COG0672 )-iron permease -0.026550
206 COG1023 phosphogluconate dehydrogenase (decarboxylating) activity 0.026532
207 COG1116 anion transmembrane transporter activity 0.026515
208 2ZD1U 0.026495
209 32RP2 Psort location CytoplasmicMembrane, score 0.026482
210 COG3254 rhamnose metabolic process 0.026439
211 COG5602 Belongs to the OprB family 0.026408
212 COG3728 DNA packaging -0.026392
213 COG3731 PTS system glucitol sorbitol-specific IIA component -0.026378
214 COG1473 amidohydrolase -0.026331
215 33REM Sigma-70 region 2 -0.026318
216 COG2160 L-arabinose isomerase activity 0.026275
217 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) -0.026208
218 COG0779 Required for maturation of 30S ribosomal subunits -0.026200
219 COG4346 Dolichyl-phosphate-mannose--protein O-mannosyl transferase -0.026177
220 COG2723 6-phospho-beta-galactosidase activity 0.026135
221 COG4096 Type I site-specific restriction-modification system, R (Restriction) subunit and related -0.026123
222 33S26 HNH nucleases -0.026119
223 COG0312 modulator of DNA gyrase 0.026070
224 COG3710 Transcriptional regulator 0.026058
225 COG4303 Ethanolamine ammonia lyase large subunit 0.026018
226 COG0674 pyruvate-flavodoxin oxidoreductase activity -0.025983
227 COG1072 (Pantothenic acid kinase)) -0.025965
228 COG1640 4-alpha-glucanotransferase 0.025960
229 COG3394 polysaccharide catabolic process 0.025900
230 COG0294 Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives 0.025874
231 COG2819 hydrolase of the alpha beta superfamily 0.025840
232 COG5018 Exonuclease 0.025820
233 COG1203 CRISPR-associated helicase, Cas3 0.025737
234 COG3807 Bacterial SH3 domain -0.025693
235 COG1394 ATPase activity, coupled to movement of substances -0.025678
236 COG2894 cell division 0.025670
237 COG0447 Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoyl-CoA (DHNA-CoA) -0.025660
238 COG3541 Predicted nucleotidyltransferase -0.025614
239 COG5627 protein ubiquitination -0.025590
240 COG2706 6-phosphogluconolactonase activity -0.025534
241 COG1869 D-ribose catabolic process 0.025471
242 COG3682 Transcriptional regulator -0.025432
243 COG2146 nitrite reductase [NAD(P)H] activity -0.025393
244 COG2313 pseudouridylate synthase activity -0.025382
245 COG0001 glutamate-1-semialdehyde 2,1-aminomutase activity 0.025355
246 COG0830 nickel cation binding -0.025326
247 COG0144 Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA -0.025321
248 COG4744 Conserved Protein -0.025319
249 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 -0.025267
250 308PC Domain of unknown function (DUF4956) 0.025264