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 COG4794 Type iii secretion 0.073872
2 COG4791 protein targeting 0.073566
3 COG4790 Type iii secretion 0.072966
4 COG4792 protein secretion 0.072269
5 COG4669 (LipO)protein 0.071699
6 COG4789 Type iii secretion 0.068549
7 COG1450 Type ii and iii secretion system protein 0.040786
8 COG5613 Secretion system effector C (SseC) like family 0.034382
9 307NE Inner membrane component of T3SS, periplasmic domain 0.032869
10 COG2032 superoxide dismutase activity 0.027745
11 32SWF 0.024530
12 COG5435 protein kinase activity 0.022577
13 3153I 0.021876
14 COG4335 DNA alkylation repair -0.021612
15 COG0367 asparagine synthase 0.021197
16 COG1635 Involved in the biosynthesis of the thiazole moiety of thiamine. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylate (ADT), an adenylated thiazole intermediate, using free sulfide as a source of sulfur -0.021147
17 32VH1 HrpJ-like domain 0.021116
18 33E8X protein secretion 0.021116
19 COG0699 ATPase. Has a role at an early stage in the morphogenesis of the spore coat -0.021086
20 2ZBVJ Type iii secretion 0.020866
21 COG1412 self proteolysis 0.020428
22 COG2323 membrane -0.020416
23 COG2390 Transcriptional regulator 0.020305
24 COG3794 PFAM blue (type 1) copper domain protein 0.020103
25 31RN5 Bacterial regulatory proteins, tetR family 0.019750
26 COG2378 regulation of single-species biofilm formation -0.019659
27 COG3143 Plays an important role in bacterial chemotaxis signal transduction pathway by accelerating the dephosphorylation of phosphorylated CheY (CheY-P) 0.019481
28 COG3232 5-carboxymethyl-2-hydroxymuconate isomerase 0.019397
29 COG1366 Belongs to the anti-sigma-factor antagonist family 0.019316
30 COG3133 Outer membrane lipoprotein 0.019262
31 COG2873 o-acetylhomoserine -0.019236
32 334XN 0.018946
33 COG0612 Peptidase, M16 -0.018944
34 COG2723 6-phospho-beta-galactosidase activity 0.018853
35 32Y7R -0.018776
36 COG4700 PFAM Protein kinase domain 0.018752
37 3448G 'Pfam Bacterial regulatory proteins, tetR family 0.018439
38 COG4638 Rieske (2fe-2S) 0.018411
39 COG3836 Belongs to the HpcH HpaI aldolase family 0.018342
40 COG0475 glutathione-regulated potassium exporter activity -0.018002
41 COG1448 Aminotransferase 0.017989
42 COG2358 TRAP transporter, solute receptor (TAXI family -0.017970
43 COG0330 HflC and HflK could -0.017813
44 COG2073 Cobalamin biosynthesis protein cbiG 0.017784
45 COG3524 carbohydrate:proton symporter activity -0.017725
46 COG1929 Belongs to the glycerate kinase type-1 family 0.017709
47 COG0154 amidase activity -0.017479
48 COG3265 gluconokinase activity 0.017328
49 2ZAF8 Type III secretion 0.017267
50 COG5517 Aromatic-ring-hydroxylating dioxygenase beta subunit 0.017245
51 COG2133 pyrroloquinoline quinone binding -0.017171
52 COG5599 Phosphatase 0.017028
53 34APG 0.017022
54 COG3919 ATP-grasp 0.016927
55 COG1237 beta-lactamase domain protein -0.016837
56 COG0700 Nucleoside recognition 0.016786
57 COG0716 FMN binding -0.016783
58 COG0595 An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay -0.016777
59 COG5437 major tail protein TP901-1 family -0.016755
60 COG3153 acetyltransferase 0.016678
61 COG5238 GTPase activator activity 0.016668
62 COG2303 Involved in the biosynthesis of the osmoprotectant glycine betaine. Catalyzes the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine at the same rate -0.016593
63 COG3597 protein domain associated with -0.016494
64 COG3673 conserved protein 0.016488
65 COG0858 One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA -0.016474
66 COG4928 KAP family P-loop domain -0.016435
67 COG1683 Conserved Protein 0.016424
68 COG3518 anti-sigma factor antagonist activity 0.016385
69 COG1573 uracil-dna glycosylase -0.016329
70 COG3121 Chaperone 0.016321
71 COG0760 Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation -0.016282
72 2Z91M NolX protein 0.016205
73 COG2301 Belongs to the HpcH HpaI aldolase family -0.016047
74 COG4875 SnoaL-like domain 0.016025
75 COG5516 Conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding 0.015939
76 COG4517 Domain of unknown function (DUF1820) 0.015933
77 COG2317 Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues -0.015893
78 COG1268 BioY protein 0.015864
79 COG1025 Belongs to the peptidase M16 family 0.015851
80 COG4115 mRNA cleavage -0.015722
81 COG5410 chromosome segregation -0.015696
82 COG3519 Type VI secretion system, TssF 0.015692
83 COG4665 TRAP-type mannitol chloroaromatic compound transport system small permease component -0.015657
84 COG4315 Pfam Secreted repeat of 0.015608
85 COG3386 PFAM SMP-30 Gluconolaconase -0.015592
86 COG1134 teichoic acid transport -0.015443
87 COG1637 Cleaves both 3' and 5' ssDNA extremities of branched DNA structures -0.015442
88 COG0500 methyltransferase 0.015364
89 COG1113 amino acid transport 0.015360
90 32UW3 -0.015346
91 COG2513 Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate 0.015303
92 COG2747 anti-sigma28 factor FlgM 0.015268
93 316UM TonB C terminal -0.015263
94 COG1305 Transglutaminase-like -0.015249
95 COG3062 negative regulation of establishment of protein localization 0.015248
96 342R0 Trypsin-like peptidase domain -0.015200
97 COG1881 PFAM PEBP family protein 0.015137
98 COG3126 Type III secretion system lipoprotein chaperone (YscW) 0.015135
99 COG4222 Protein conserved in bacteria 0.015121
100 COG4244 Membrane -0.015112
101 31W2T Universal stress protein family -0.014977
102 342NJ -0.014968
103 33U39 Methyltransferase domain 0.014947
104 COG0053 Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family -0.014935
105 33HH1 0.014915
106 COG3159 Protein conserved in bacteria 0.014911
107 COG0669 Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate -0.014847
108 COG2208 phosphoserine phosphatase activity 0.014843
109 COG3011 Protein conserved in bacteria 0.014837
110 COG3511 phospholipase C 0.014812
111 COG2240 Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP 0.014796
112 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) -0.014773
113 COG3228 Belongs to the MtfA family 0.014753
114 COG2898 Catalyzes the transfer of a lysyl group from L-lysyl- tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), a major component of the bacterial membrane with a positive net charge. LPG synthesis contributes to bacterial virulence as it is involved in the resistance mechanism against cationic antimicrobial peptides (CAMP) produces by the host's immune system (defensins, cathelicidins) and by the competing microorganisms 0.014727
115 COG4456 Virulence-associated protein 0.014715
116 COG0027 Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate 0.014703
117 COG5621 secreted hydrolase -0.014665
118 COG2509 5-formyltetrahydrofolate cyclo-ligase activity -0.014628
119 COG1208 COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon 0.014602
120 COG5164 cell wall organization 0.014582
121 COG3467 pyridoxamine 5'-phosphate 0.014541
122 3330U Type iii secretion 0.014530
123 COG0674 pyruvate-flavodoxin oxidoreductase activity -0.014526
124 COG1181 Belongs to the D-alanine--D-alanine ligase family -0.014523
125 COG3484 -0.014444
126 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 0.014432
127 2Z9AA Protein of unknown function (DUF3034) 0.014416
128 COG0837 glucose binding 0.014400
129 COG4239 (ABC) transporter, permease 0.014369
130 COG2150 ACT domain -0.014345
131 COG3844 kynureninase activity 0.014341
132 COG2350 Protein conserved in bacteria 0.014300
133 COG2206 PFAM metal-dependent phosphohydrolase, HD sub domain 0.014288
134 COG2175 clavaminate synthase activity 0.014281
135 COG3450 Protein of unknown function (DUF861) 0.014279
136 COG1520 Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane -0.014269
137 COG0797 Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides -0.014265
138 32ZB3 0.014243
139 COG1521 Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis -0.014225
140 33T8K -0.014221
141 31QMZ 0.014210
142 COG5459 Ribosomal small subunit Rsm22 0.014204
143 COG4287 PhoPQ-activated pathogenicity-related protein 0.014193
144 COG5448 Glycoside hydrolase family 24 -0.014161
145 COG1762 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.014160
146 COG2184 nucleotidyltransferase activity -0.014108
147 COG3659 wide pore channel activity 0.014059
148 33B37 0.014059
149 COG3125 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor 0.014048
150 COG3204 pilus organization 0.014024
151 COG3134 Outer membrane lipoprotein 0.014014
152 COG3342 major pilin protein fima 0.013981
153 COG2138 Cobalamin (vitamin B12) biosynthesis CbiX protein -0.013955
154 COG4305 rare lipoprotein A 0.013950
155 2ZGGU -0.013930
156 33AZD 0.013888
157 COG2940 SET domain 0.013857
158 31EBN Bacterial regulatory proteins, tetR family -0.013855
159 COG1694 Mazg nucleotide pyrophosphohydrolase -0.013850
160 COG0796 Provides the (R)-glutamate required for cell wall biosynthesis -0.013802
161 30HV0 Family of unknown function (DUF5375) 0.013759
162 COG1669 hydrolase activity, acting on ester bonds -0.013747
163 2ZTY5 Protein of unknown function (DUF1804) 0.013713
164 COG0757 Catalyzes a trans-dehydration via an enolate intermediate -0.013696
165 COG3005 denitrification pathway 0.013693
166 COG2165 general secretion pathway protein 0.013693
167 2ZQPU Outer membrane efflux protein -0.013689
168 COG2109 Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids 0.013675
169 COG4934 collagen metabolic process 0.013655
170 COG0606 chelatase, subunit chli -0.013651
171 COG3367 COGs COG3367 conserved -0.013626
172 COG3784 Protein of unknown function (DUF1318) -0.013595
173 COG0849 cell division -0.013594
174 3375A Domain of unknown function (DUF4123) 0.013592
175 COG2077 Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides 0.013585
176 COG3138 arginine N-succinyltransferase 0.013508
177 33ARA COG0526, thiol-disulfide isomerase and thioredoxins 0.013506
178 COG2171 N-acyltransferase activity -0.013504
179 COG0732 type I restriction modification DNA specificity domain 0.013495
180 2Z87K COG0666 FOG Ankyrin repeat 0.013450
181 COG1205 dead DEAH box helicase 0.013441
182 3359J PhoP regulatory network protein YrbL 0.013416
183 COG2964 Protein conserved in bacteria 0.013414
184 COG3651 Uncharacterized protein conserved in bacteria (DUF2237) -0.013386
185 COG2421 Acetamidase/Formamidase family -0.013378
186 COG4254 PFAM FecR protein -0.013367
187 COG0333 Belongs to the bacterial ribosomal protein bL32 family -0.013333
188 COG0474 ATPase, P-type transporting, HAD superfamily, subfamily IC -0.013332
189 COG1484 DNA-dependent DNA replication -0.013327
190 334KG Replication regulatory protein RepB 0.013325
191 COG4420 membrane -0.013287
192 COG1159 An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism -0.013268
193 COG3136 membrane protein required for alginate biosynthesis 0.013258
194 COG5449 Phage conserved hypothetical protein BR0599 -0.013257
195 COG3225 cell adhesion -0.013227
196 342TQ -0.013223
197 COG3241 Transfers electrons from cytochrome c551 to cytochrome oxidase 0.013208
198 COG3293 Transposase 0.013196
199 COG3043 anaerobic respiration 0.013195
200 COG3739 integral membrane protein -0.013183
201 COG1304 FMN binding -0.013181
202 COG2928 Conserved Protein 0.013165
203 COG3042 response to heat 0.013164
204 337DD FlgN protein 0.013156
205 32PGZ helix_turn_helix multiple antibiotic resistance protein 0.013153
206 2ZIWH General secretion pathway protein H 0.013146
207 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 -0.013134
208 COG4271 nucleotide-binding Protein -0.013098
209 COG0336 Belongs to the RNA methyltransferase TrmD family -0.013063
210 COG1262 PFAM Formylglycine-generating sulfatase enzyme -0.013061
211 COG3913 Uncharacterized protein conserved in bacteria (DUF2094) 0.013045
212 COG4718 Minor tail 0.013041
213 33AQ3 0.013029
214 COG3491 Belongs to the iron ascorbate-dependent oxidoreductase family 0.013026
215 COG0701 Predicted permease -0.013023
216 COG3710 Transcriptional regulator 0.013000
217 COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain 0.012998
218 2Z9EN PDDEXK-like domain of unknown function (DUF3799) -0.012976
219 34B3W 0.012968
220 33PMM -0.012968
221 COG1314 P-P-bond-hydrolysis-driven protein transmembrane transporter activity -0.012956
222 COG1385 rRNA (uridine-N3-)-methyltransferase activity -0.012945
223 COG0806 An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes -0.012945
224 COG4666 Tripartite ATP-independent periplasmic transporter, DctM component -0.012930
225 COG5639 conserved small protein 0.012925
226 COG1286 toxin biosynthetic process -0.012915
227 COG2335 COG2335, Secreted and surface protein containing fasciclin-like repeats -0.012908
228 COG3724 N-succinylarginine dihydrolase activity 0.012904
229 COG1161 Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity -0.012896
230 COG3666 COG3666 Transposase and inactivated derivatives -0.012896
231 COG1556 Lactate utilization protein -0.012886
232 COG1942 4-Oxalocrotonate Tautomerase -0.012835
233 2ZABZ Type iii secretion 0.012813
234 COG1988 membrane-bound metal-dependent 0.012808
235 COG4176 ABC-type proline glycine betaine transport system permease component 0.012801
236 COG4240 helicase activity -0.012796
237 COG4962 Type ii secretion system protein e -0.012775
238 34B0R 0.012771
239 COG1744 ABC transporter substrate-binding protein PnrA-like -0.012761
240 COG3164 Protein of unknown function 0.012759
241 COG0741 lytic transglycosylase activity 0.012736
242 COG3132 Protein of unknown function, DUF480 0.012714
243 COG3190 flagellar 0.012709
244 COG1074 ATP-dependent DNA helicase activity -0.012695
245 COG2828 Protein conserved in bacteria 0.012693
246 COG4643 DNA integration 0.012686
247 33CTH MORN repeat variant 0.012667
248 COG3527 Alpha-acetolactate decarboxylase -0.012665
249 COG0077 Prephenate dehydratase -0.012663
250 348VI Type III secretion protein 0.012648