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 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 -0.043883
2 COG4564 Single Cache domain 2 0.041056
3 COG2206 PFAM metal-dependent phosphohydrolase, HD sub domain 0.039503
4 COG2703 oxygen carrier activity 0.038754
5 COG0526 COG0526, thiol-disulfide isomerase and thioredoxins -0.035851
6 COG1516 flagellar protein fliS 0.034743
7 COG3152 Membrane -0.034505
8 COG2329 Antibiotic biosynthesis monooxygenase 0.034176
9 COG1477 protein flavinylation -0.033870
10 COG1835 transferase activity, transferring acyl groups other than amino-acyl groups -0.033432
11 COG3345 alpha-galactosidase -0.032966
12 COG0835 chemotaxis 0.032137
13 COG2200 EAL domain 0.031479
14 COG2314 TM2 domain -0.031276
15 COG0861 Integral membrane protein TerC family -0.030779
16 COG5340 Psort location Cytoplasmic, score -0.030308
17 COG3447 MASE1 domain protein 0.029877
18 COG1118 Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system 0.029256
19 COG4988 ABC transporter -0.029083
20 COG1090 epimerase -0.028604
21 COG1352 Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP 0.028467
22 COG1222 aaa ATPase -0.028331
23 COG0123 including yeast histone deacetylase and acetoin utilization protein 0.028290
24 COG1670 COG1670 acetyltransferases, including N-acetylases of ribosomal proteins -0.028161
25 COG1014 Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin 0.027933
26 31SDF 0.027827
27 COG4146 Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family -0.027560
28 COG3381 protein complex oligomerization 0.027445
29 COG3451 type IV secretory pathway VirB4 -0.027310
30 COG3144 bacterial-type flagellum assembly 0.027305
31 COG4993 Dehydrogenase -0.027181
32 COG1089 Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose 0.026995
33 COG0657 acetylesterase activity -0.026946
34 COG1462 curli production assembly transport component CsgG 0.026902
35 COG1846 Transcriptional regulator -0.026849
36 COG3366 ferrous iron transmembrane transporter activity 0.026841
37 COG4641 Protein conserved in bacteria -0.026800
38 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 0.026790
39 COG1937 Protein conserved in bacteria 0.026743
40 COG3774 pathogenesis -0.026733
41 COG2805 Type II/IV secretion system protein 0.026700
42 COG1536 FliG is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation 0.026679
43 COG2188 Transcriptional regulator -0.026561
44 COG0427 acetyl-CoA hydrolase 0.026438
45 COG1970 mechanosensitive ion channel activity -0.026335
46 COG2603 Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA 0.026271
47 COG1660 Displays ATPase and GTPase activities -0.026250
48 COG2146 nitrite reductase [NAD(P)H] activity -0.026192
49 COG0416 fatty acid biosynthetic process 0.026115
50 COG0303 'Molybdopterin 0.026055
51 COG2894 cell division 0.025976
52 COG0393 Putative heavy-metal-binding -0.025841
53 COG2907 Flavin containing amine oxidoreductase 0.025812
54 2ZGY7 -0.025649
55 COG2246 polysaccharide biosynthetic process -0.025611
56 COG1586 Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine 0.025513
57 COG1832 CoA-binding protein 0.025374
58 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC 0.025350
59 COG2365 Tyrosine phosphatase family -0.025341
60 COG1231 oxidoreductase activity -0.025335
61 COG1442 glycosyl transferase family 8 -0.025184
62 32STP -0.025003
63 COG5293 efflux transmembrane transporter activity 0.024942
64 30GAQ GDSL-like Lipase/Acylhydrolase family 0.024622
65 COG1419 protein localization to endoplasmic reticulum 0.024445
66 COG2115 Belongs to the xylose isomerase family 0.024429
67 COG0389 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII -0.024347
68 COG1957 nucleoside hydrolase -0.024148
69 COG4690 dipeptidase activity -0.024120
70 COG2026 Addiction module toxin, RelE StbE family 0.024057
71 COG0500 methyltransferase 0.024042
72 COG1843 Required for flagellar hook formation. May act as a scaffolding protein 0.024024
73 COG1943 Transposase -0.023922
74 COG0701 Predicted permease -0.023875
75 COG4206 TonB-dependent receptor -0.023804
76 COG3332 Transport and Golgi organisation 2 -0.023779
77 COG0398 Pfam SNARE associated Golgi protein 0.023745
78 COG1076 Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA 0.023666
79 COG1298 Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin 0.023598
80 COG0714 Associated with various cellular activities 0.023549
81 COG1868 FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation 0.023382
82 COG0219 Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide 0.023349
83 COG0863 Belongs to the N(4) N(6)-methyltransferase family -0.023207
84 COG2442 InterPro IPR007367 0.023176
85 COG0509 glycine decarboxylation via glycine cleavage system 0.023166
86 COG1140 nitrate reductase beta subunit 0.023164
87 COG0840 transmembrane signaling receptor activity 0.023098
88 COG1556 Lactate utilization protein -0.023082
89 COG0433 COG0433 Predicted ATPase -0.023065
90 COG4632 Exopolysaccharide biosynthesis protein -0.023030
91 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 0.023030
92 COG1541 Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA) -0.023029
93 30823 rifampin adp-ribosyl transferase 0.023026
94 COG4720 Psort location CytoplasmicMembrane, score 0.022994
95 COG0700 Nucleoside recognition 0.022973
96 COG2856 Zn peptidase -0.022943
97 COG3934 Belongs to the glycosyl hydrolase 5 (cellulase A) family 0.022883
98 COG4119 NUDIX hydrolase 0.022842
99 COG1321 iron dependent repressor -0.022687
100 COG1523 belongs to the glycosyl hydrolase 13 family -0.022635
101 COG3653 N-Acyl-D-aspartate D-glutamate deacylase -0.022608
102 COG0510 thiamine kinase activity 0.022588
103 COG3614 Histidine kinase -0.022535
104 COG3843 relaxase mobilization nuclease domain protein -0.022439
105 COG4787 bacterial-type flagellum-dependent cell motility 0.022413
106 COG4233 Disulphide bond corrector protein DsbC -0.022380
107 COG2005 Transcriptional regulator 0.022377
108 COG4833 Hydrolase -0.022367
109 COG3208 Thioesterase involved in non-ribosomal peptide biosynthesis -0.022349
110 COG1814 membrane -0.022346
111 COG0747 negative chemotaxis 0.022249
112 COG1699 Binds to the C-terminal region of flagellin, which is implicated in polymerization, and participates in the assembly of the flagellum 0.022106
113 2Z854 membrane 0.022086
114 COG1639 'signal transduction protein 0.022086
115 COG4807 Protein conserved in bacteria 0.022071
116 COG2113 Glycine betaine 0.022024
117 COG1720 tRNA m6t6A37 methyltransferase activity 0.021975
118 COG1724 mRNA binding 0.021955
119 COG1765 OsmC-like protein 0.021824
120 COG1322 Protein conserved in bacteria -0.021766
121 32X46 0.021765
122 COG2954 triphosphatase activity 0.021733
123 COG1734 Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters 0.021733
124 COG3367 COGs COG3367 conserved 0.021710
125 COG1551 Could accelerate the degradation of some genes transcripts potentially through selective RNA binding 0.021709
126 COG5516 Conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding -0.021706
127 COG1515 deoxyribonuclease V activity 0.021669
128 COG0301 tRNA thio-modification 0.021595
129 COG4544 Component of the SOS system and an inhibitor of cell division. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. In the presence of GTP, binds a polymerization-competent form of FtsZ in a 1 1 ratio, thus inhibiting FtsZ polymerization and therefore preventing it from participating in the assembly of the Z ring. This mechanism prevents the premature segregation of damaged DNA to daughter cells during cell division -0.021556
130 2Z84S 0.021508
131 COG1823 symporter activity 0.021488
132 COG3434 signal transduction protein containing EAL and modified HD-GYP domains 0.021372
133 COG4594 ABC-type Fe3 -citrate transport system, periplasmic component 0.021329
134 COG4132 (ABC) transporter, permease 0.021322
135 COG1247 -acetyltransferase -0.021297
136 COG1291 archaeal or bacterial-type flagellum-dependent cell motility 0.021287
137 COG0496 Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates 0.021280
138 COG3181 Tripartite tricarboxylate transporter family receptor -0.021273
139 COG2315 Protein conserved in bacteria 0.021226
140 COG2910 NAD(P)H-binding 0.021208
141 COG3021 interspecies interaction between organisms -0.021192
142 COG1279 arginine transmembrane transporter activity 0.021188
143 COG4385 Tail protein 0.021185
144 COG4246 protein conserved in bacteria -0.021164
145 COG3090 Trap-type c4-dicarboxylate transport system, small permease component 0.021054
146 COG4719 TIGRFAM conserved repeat domain -0.021011
147 COG3142 Participates in the control of copper homeostasis 0.020948
148 COG1276 copper resistance -0.020933
149 COG1335 isochorismatase -0.020899
150 348N2 -0.020807
151 COG3333 protein conserved in bacteria -0.020765
152 COG1520 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.020738
153 COG0343 queuine tRNA-ribosyltransferase activity -0.020622
154 COG3222 Protein conserved in bacteria -0.020601
155 COG1684 flagellar biosynthetic protein fliR 0.020599
156 COG3926 Glycosyl hydrolase 108 -0.020582
157 COG2132 Multicopper oxidase -0.020549
158 COG3167 carbon utilization 0.020479
159 33C2X -0.020478
160 COG4030 Protein of unknown function (DUF2961) 0.020454
161 COG1253 flavin adenine dinucleotide binding -0.020443
162 COG1558 bacterial-type flagellum-dependent cell motility 0.020425
163 COG1677 Flagellar hook-basal body complex protein FliE 0.020425
164 COG1815 bacterial-type flagellum-dependent cell motility 0.020425
165 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 0.020405
166 COG3378 Phage plasmid primase P4 family -0.020326
167 2Z7KX EcsC protein family -0.020315
168 COG2145 Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ) 0.020310
169 COG1942 4-Oxalocrotonate Tautomerase 0.020298
170 COG1987 bacterial-type flagellum assembly 0.020244
171 COG4103 Tellurite resistance protein TerB 0.020238
172 COG1256 bacterial-type flagellum assembly 0.020219
173 COG1209 Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis 0.020146
174 COG1161 Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity 0.020122
175 COG3682 Transcriptional regulator -0.020091
176 COG1664 Polymer-forming cytoskeletal -0.020071
177 COG4487 mechanosensitive ion channel activity 0.020029
178 COG0783 Belongs to the Dps family -0.020013
179 COG1749 Flagellar hook protein flgE 0.019913
180 COG2818 Glycosylase -0.019894
181 COG2896 Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate 0.019888
182 COG0748 coenzyme F420 binding 0.019879
183 COG3145 DNA-N1-methyladenine dioxygenase activity -0.019830
184 COG4191 Histidine kinase 0.019812
185 COG0396 ATPase activity 0.019749
186 COG0719 Fe-S assembly protein 0.019749
187 COG0069 glutamate synthase activity -0.019706
188 COG2861 carbohydrate metabolic process 0.019704
189 COG2021 Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine -0.019665
190 COG5010 COG0457 FOG TPR repeat 0.019649
191 COG1338 Plays a role in the flagellum-specific transport system 0.019645
192 COG4733 cellulase activity 0.019573
193 32P9E Crp-like helix-turn-helix domain 0.019497
194 COG0589 response to stress -0.019487
195 COG2201 protein-glutamate methylesterase activity 0.019467
196 COG4753 response regulator -0.019461
197 COG0448 Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans -0.019409
198 2ZAT4 Concanavalin A-like lectin/glucanases superfamily -0.019390
199 COG1344 Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella 0.019378
200 COG3607 glyoxalase bleomycin resistance protein dioxygenase 0.019352
201 COG0279 D-glycero-D-manno-heptose 7-phosphate biosynthetic process 0.019342
202 COG1443 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) -0.019316
203 COG0578 Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family -0.019161
204 COG1569 PIN domain -0.019138
205 COG1738 Involved in the import of queuosine (Q) precursors, required for Q precursor salvage -0.019137
206 COG2836 Biogenesis protein 0.019133
207 COG0836 Belongs to the mannose-6-phosphate isomerase type 2 family 0.019093
208 COG2808 Putative FMN-binding domain 0.019012
209 COG1157 protein secretion by the type III secretion system 0.019004
210 COG2882 bacterial-type flagellum organization 0.018945
211 COG1654 Acts both as a biotin-- acetyl-CoA-carboxylase ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio- 5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon -0.018926
212 COG5653 Protein involved in cellulose biosynthesis 0.018906
213 COG2859 Protein conserved in bacteria 0.018899
214 COG3727 T/G mismatch-specific endonuclease activity -0.018885
215 COG3128 pkhd-type hydroxylase -0.018869
216 COG4097 nitric oxide dioxygenase activity -0.018860
217 COG3713 MltA-interacting MipA family protein 0.018845
218 COG1166 arginine decarboxylase activity 0.018833
219 COG3907 PAP2 (Acid phosphatase) superfamily protein 0.018807
220 2Z7JT 2-keto-3-deoxygluconate:proton symporter activity 0.018802
221 339UG -0.018786
222 32XR9 Outer membrane efflux protein -0.018784
223 COG1067 ATP-dependent peptidase activity 0.018779
224 COG2180 nitrate reductase molybdenum cofactor assembly chaperone 0.018723
225 COG0236 Carrier of the growing fatty acid chain in fatty acid biosynthesis -0.018666
226 COG2721 sulfolactate sulfo-lyase activity 0.018656
227 COG2947 Ubiquinol--cytochrome c reductase -0.018638
228 COG0775 Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively 0.018628
229 COG3705 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine 0.018607
230 COG1821 Pfam ATP-grasp domain 0.018572
231 COG3230 heme oxygenase -0.018539
232 COG0814 amino acid 0.018517
233 COG0731 radical SAM domain protein 0.018487
234 COG4928 KAP family P-loop domain 0.018471
235 COG5581 Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)- dependent manner. Binds 1 c-di-GMP dimer per subunit. Increasing levels of c-di-GMP lead to decreased motility 0.018453
236 COG2391 methyltransferase activity -0.018441
237 COG5278 phosphoserine phosphatase activity 0.018424
238 COG5368 Putative glucoamylase 0.018401
239 COG0053 Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family 0.018362
240 COG4558 Periplasmic binding protein 0.018350
241 COG0502 Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism 0.018336
242 31FR9 MarR family -0.018323
243 32Y3Z -0.018308
244 COG0681 Belongs to the peptidase S26 family -0.018286
245 COG1735 metal-dependent hydrolase with the TIM-barrel fold -0.018283
246 COG0506 proline dehydrogenase activity 0.018278
247 32Z6W Protein of unknown function (DUF3126) 0.018277
248 COG3666 COG3666 Transposase and inactivated derivatives -0.018277
249 COG3239 Fatty acid desaturase -0.018275
250 COG1661 DNA-binding protein with PD1-like DNA-binding motif 0.018234