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 COG1702 phosphate starvation-inducible protein PhoH -0.014517
2 COG0799 negative regulation of ribosome biogenesis -0.013804
3 COG1932 Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine -0.013356
4 2ZAUC 0.011399
5 COG0705 Rhomboid family -0.011075
6 COG3247 response to pH -0.010622
7 COG1775 2-hydroxyglutaryl-CoA dehydratase, D-component 0.010513
8 COG0782 Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus -0.010426
9 COG4152 abc transporter atp-binding protein -0.010426
10 COG1983 PspC domain protein -0.010365
11 COG3270 Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA -0.010264
12 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 0.010090
13 COG5426 von Willebrand factor, type A -0.009953
14 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 -0.009923
15 COG0396 ATPase activity -0.009914
16 COG0719 Fe-S assembly protein -0.009914
17 COG1399 metal-binding, possibly nucleic acid-binding protein -0.009904
18 COG0546 phosphoglycolate phosphatase activity -0.009809
19 COG1825 This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance -0.009715
20 COG4566 intracellular signal transduction -0.009694
21 COG1475 DNA binding -0.009607
22 COG1539 Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin -0.009572
23 COG4485 Bacterial membrane protein, YfhO -0.009492
24 COG0593 it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids -0.009433
25 COG4992 N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity -0.009326
26 COG1243 radical SAM domain protein 0.009261
27 COG1623 Has also diadenylate cyclase activity, catalyzing the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP). c- di-AMP acts as a signaling molecule that couples DNA integrity with progression of sporulation. The rise in c-di-AMP level generated by DisA while scanning the chromosome, operates as a positive signal that advances sporulation 0.009261
28 COG5438 YibE/F-like protein 0.009148
29 3204A 0.009096
30 COG0590 tRNA wobble adenosine to inosine editing -0.009038
31 COG0174 glutamine synthetase -0.009002
32 COG2084 Dehydrogenase -0.008880
33 COG0428 transporter -0.008867
34 COG1494 fructose-1,6-bisphosphatase 0.008830
35 COG1785 Belongs to the alkaline phosphatase family -0.008809
36 COG0828 Belongs to the bacterial ribosomal protein bS21 family -0.008802
37 COG2843 Capsule synthesis protein -0.008772
38 COG1748 Saccharopine dehydrogenase -0.008752
39 COG0372 Belongs to the citrate synthase family -0.008705
40 COG0385 Bile acid -0.008538
41 COG3201 nicotinamide mononucleotide transporter -0.008487
42 COG0620 Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation -0.008469
43 COG2151 metal-sulfur cluster biosynthetic enzyme -0.008440
44 COG1297 OPT oligopeptide transporter protein -0.008367
45 COG0819 Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway -0.008328
46 COG1583 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) 0.008306
47 COG3250 beta-galactosidase activity -0.008290
48 COG2261 transglycosylase associated protein -0.008289
49 COG0205 6-phosphofructokinase activity -0.008262
50 COG1954 Regulates expression of the glpD operon. In the presence of glycerol 3-phosphate (G3P) causes antitermination of transcription of glpD at the inverted repeat of the leader region to enhance its transcription. Binds and stabilizes glpD leader mRNA 0.008202
51 COG0483 inositol monophosphate 1-phosphatase activity -0.008196
52 33J3F the current gene model (or a revised gene model) may contain a frame shift 0.008127
53 COG0021 Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate -0.008087
54 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 -0.008045
55 COG2214 Heat shock protein DnaJ domain protein 0.008016
56 33QJ0 0.007977
57 COG1329 Transcriptional regulator -0.007936
58 COG0369 Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH - FAD - FMN to the hemoprotein component -0.007905
59 COG0530 calcium, potassium:sodium antiporter activity -0.007889
60 COG4555 ABC transporter -0.007876
61 COG1296 Branched-chain amino acid permease (Azaleucine resistance) -0.007874
62 COG1522 sequence-specific DNA binding -0.007858
63 COG0731 radical SAM domain protein 0.007856
64 COG2081 HI0933 family -0.007830
65 COG4399 Belongs to the UPF0754 family 0.007828
66 COG2246 polysaccharide biosynthetic process -0.007792
67 COG1587 Uroporphyrinogen-III synthase -0.007780
68 COG2050 protein possibly involved in aromatic compounds catabolism -0.007743
69 COG2169 Transcriptional regulator -0.007737
70 COG5340 Psort location Cytoplasmic, score -0.007638
71 COG3395 kinase activity 0.007564
72 COG2088 sporulation resulting in formation of a cellular spore 0.007560
73 COG4748 type I restriction enzyme -0.007556
74 COG0026 Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR) -0.007504
75 32YHG Putative adhesin -0.007478
76 COG0623 enoyl-[acyl-carrier-protein] reductase (NADH) activity -0.007476
77 COG1680 COG1680 Beta-lactamase class C and other penicillin binding -0.007439
78 COG1433 Dinitrogenase iron-molybdenum cofactor 0.007436
79 COG0586 Pfam SNARE associated Golgi protein -0.007391
80 COG3493 citrate carrier protein 0.007367
81 COG1004 Belongs to the UDP-glucose GDP-mannose dehydrogenase family -0.007362
82 COG3976 FMN-binding domain protein 0.007346
83 COG0394 Belongs to the low molecular weight phosphotyrosine protein phosphatase family -0.007342
84 COG0276 Catalyzes the ferrous insertion into protoporphyrin IX -0.007338
85 COG3980 spore coat polysaccharide biosynthesis protein 0.007333
86 COG3883 PFAM NLP P60 protein -0.007318
87 COG0232 Belongs to the dGTPase family. Type 2 subfamily -0.007305
88 COG2884 Cell division ATP-binding protein ftsE -0.007302
89 COG0214 Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively 0.007295
90 33YTS 0.007286
91 30FW8 0.007255
92 32SQE Psort location CytoplasmicMembrane, score 0.007255
93 32YCW Domain of unknown function (DUF4363) 0.007255
94 32ZH6 Small, acid-soluble spore protein Tlp 0.007255
95 33BU4 0.007255
96 33HSY 0.007255
97 33NPR 4Fe-4S single cluster domain of Ferredoxin I 0.007255
98 COG2604 Protein of unknown function DUF115 0.007255
99 COG2836 Biogenesis protein 0.007255
100 COG2179 HAD superfamily (subfamily IIIA) phosphatase, TIGR01668 -0.007254
101 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 -0.007241
102 COG0538 isocitrate dehydrogenase activity -0.007228
103 COG3576 pyridoxamine 5-phosphate 0.007226
104 COG0737 Belongs to the 5'-nucleotidase family -0.007211
105 COG2807 transmembrane transport -0.007204
106 COG2089 acid synthase 0.007193
107 COG1861 Spore coat polysaccharide biosynthesis protein F CMP-KDO synthetase 0.007184
108 COG4734 Psort location Cytoplasmic, score -0.007150
109 COG0176 Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway -0.007142
110 COG0266 class I DNA-(apurinic or apyrimidinic site) endonuclease activity -0.007134
111 COG2951 lytic endotransglycosylase activity -0.007132
112 COG0610 Subunit R is required for both nuclease and ATPase activities, but not for modification -0.007121
113 COG0710 3-dehydroquinate dehydratase activity -0.007111
114 COG5305 Membrane 0.007065
115 COG3581 4 iron, 4 sulfur cluster binding 0.007054
116 COG2992 FlgJ-related protein 0.007037
117 2Z7IF 0.007037
118 2Z81M 0.007037
119 2Z8JZ 0.007037
120 2ZANH 0.007037
121 2ZB1T 0.007037
122 2ZB2U 0.007037
123 2ZB4K 0.007037
124 2ZBE8 SIR2-like domain 0.007037
125 2ZCBC 0.007037
126 2ZI92 0.007037
127 2ZN7A 0.007037
128 2ZNS3 0.007037
129 3059E 0.007037
130 30I98 0.007037
131 311NS 0.007037
132 31WHG 0.007037
133 32R07 0.007037
134 32TDI 0.007037
135 32TJ3 Domain of unknown function (DUF4911) 0.007037
136 32WIG 0.007037
137 32XIJ L,D-transpeptidase catalytic domain 0.007037
138 32Y2K Hydrid cluster protein-associated redox disulfide domain protein 0.007037
139 32YZT 0.007037
140 331VG 0.007037
141 33KNY Type IV leader peptidase family 0.007037
142 COG4752 Belongs to the RNA methyltransferase TrmD family 0.007037
143 COG3451 type IV secretory pathway VirB4 -0.007029
144 33MNE Domain of unknown function (DUF1904) 0.007021
145 COG4185 zeta toxin 0.007015
146 COG4492 Belongs to the UPF0735 family 0.007011
147 COG2860 membrane -0.007006
148 COG4533 DNA binding 0.006998
149 COG4604 ABC transporter, ATP-binding protein 0.006988
150 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) 0.006977
151 COG0850 regulation of cytokinetic process 0.006956
152 2Z7V1 0.006946
153 COG0378 Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG 0.006940
154 COG3878 Protein conserved in bacteria 0.006929
155 COG3872 metal-dependent enzyme 0.006927
156 COG0504 CTP synthase activity -0.006926
157 COG2129 metallophosphoesterase -0.006907
158 COG4892 Cytochrome b5 0.006869
159 COG3682 Transcriptional regulator -0.006856
160 COG3274 enterobacterial common antigen metabolic process -0.006804
161 COG0794 Belongs to the SIS family. GutQ KpsF subfamily 0.006802
162 COG0365 Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA -0.006795
163 COG0524 Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway -0.006790
164 COG3478 Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082) 0.006764
165 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 -0.006742
166 COG0135 phosphoribosylanthranilate isomerase activity -0.006741
167 32TBR Protein of unknown function (DUF2974) -0.006724
168 COG4990 cell redox homeostasis -0.006720
169 COG1322 Protein conserved in bacteria -0.006696
170 32ZT4 0.006690
171 2Z8TW 0.006690
172 30H27 0.006690
173 30U2T Psort location Cytoplasmic, score 0.006690
174 32ZVE 0.006690
175 COG0667 Aldo Keto reductase -0.006672
176 COG0611 Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1 -0.006662
177 COG4211 Belongs to the binding-protein-dependent transport system permease family 0.006649
178 COG0320 Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives -0.006647
179 COG0509 glycine decarboxylation via glycine cleavage system -0.006629
180 COG1244 Elongator protein 3, MiaB family, Radical SAM 0.006619
181 2ZCKR 0.006618
182 COG0741 lytic transglycosylase activity -0.006607
183 COG1668 transmembrane transport -0.006603
184 COG0738 Major facilitator superfamily -0.006595
185 COG3331 DNA recombination -0.006579
186 3471B Helix-turn-helix XRE-family like proteins 0.006574
187 2Z9AH 0.006564
188 COG3807 Bacterial SH3 domain 0.006563
189 COG1194 a g-specific adenine glycosylase -0.006557
190 COG2771 luxR family -0.006534
191 COG3276 selenocysteine insertion sequence binding 0.006532
192 32RV1 Domain of Unknown Function with PDB structure (DUF3862) 0.006523
193 COG2915 High frequency lysogenization protein hflD homolog -0.006523
194 COG2365 Tyrosine phosphatase family -0.006520
195 COG3326 Membrane -0.006510
196 COG0851 Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell 0.006477
197 COG2870 Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose 0.006474
198 COG2926 Belongs to the UPF0265 family 0.006474
199 COG4807 Protein conserved in bacteria 0.006474
200 COG0374 Belongs to the NiFe NiFeSe hydrogenase large subunit family 0.006468
201 COG1740 oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor 0.006468
202 COG5337 Spore coat protein CotH -0.006444
203 COG0112 Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism -0.006438
204 COG4545 Glutaredoxin-related protein 0.006430
205 COG2166 iron-sulfur cluster assembly -0.006427
206 COG1001 Belongs to the metallo-dependent hydrolases superfamily. Adenine deaminase family 0.006426
207 COG3246 L-lysine catabolic process to acetate 0.006425
208 COG0062 Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration -0.006425
209 COG4980 gas vesicle protein -0.006421
210 COG4392 branched-chain amino acid -0.006383
211 COG1342 Belongs to the UPF0251 family 0.006379
212 COG1808 Membrane -0.006359
213 COG0328 RNA-DNA hybrid ribonuclease activity -0.006347
214 COG1516 flagellar protein fliS 0.006338
215 COG0599 Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity -0.006331
216 COG1893 Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid -0.006327
217 COG0134 indole-3-glycerol-phosphate synthase activity -0.006324
218 COG1362 aminopeptidase activity 0.006322
219 COG1712 Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L- tetrahydrodipicolinate, to generate the meso compound, D,L-2,6- diaminopimelate -0.006320
220 COG3525 Glycosyl hydrolase, family 20, catalytic domain -0.006318
221 COG2259 Doxx family -0.006291
222 2Z7T7 Psort location CytoplasmicMembrane, score -0.006287
223 COG0002 Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde -0.006277
224 COG0548 Belongs to the acetylglutamate kinase family. ArgB subfamily -0.006277
225 COG0159 tryptophan synthase activity -0.006277
226 COG0547 Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA) -0.006277
227 COG3862 protein with conserved CXXC pairs 0.006274
228 COG3152 Membrane -0.006272
229 COG2073 Cobalamin biosynthesis protein cbiG 0.006267
230 COG2082 Precorrin-8x methylmutase 0.006267
231 COG2099 Precorrin-6x reductase 0.006267
232 COG0392 lysyltransferase activity -0.006258
233 COG1574 metal-dependent hydrolase with the TIM-barrel fold -0.006234
234 2Z974 Psort location Cytoplasmic, score 0.006224
235 COG1754 DNA topoisomerase type I activity -0.006216
236 COG5002 protein histidine kinase activity -0.006211
237 COG3935 DnaD domain protein -0.006206
238 COG3620 sequence-specific DNA binding -0.006191
239 COG2813 Specifically methylates the guanine in position -0.006187
240 COG1197 Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site -0.006166
241 COG4915 5-bromo-4-chloroindolyl phosphate hydrolysis protein -0.006164
242 COG2221 Nitrite and sulphite reductase 4Fe-4S 0.006157
243 COG3086 response to oxidative stress 0.006142
244 COG1961 COG1961 Site-specific recombinases, DNA invertase Pin homologs -0.006125
245 33E6K 0.006116
246 COG4936 Histidine kinase 0.006103
247 COG3710 Transcriptional regulator -0.006088
248 COG1253 flavin adenine dinucleotide binding -0.006080
249 32UC7 Glycosyltransferase family 52 0.006074
250 COG1266 CAAX protease self-immunity -0.006064