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 ENOG4108U47 catalase 0.243751
2 ENOG4105EVZ LysR family transcriptional regulator 0.196545
3 ENOG4107V4P Lytic transglycosylase catalytic 0.195110
4 ENOG4105EKN Major Facilitator -0.191978
5 ENOG4105K6X Protein of unknown function (DUF3014) 0.181471
6 ENOG410703R Inherit from COG: Tape measure protein 0.179511
7 ENOG410819Q NA 0.176388
8 ENOG4105DY3 RNA polymerase sigma-24 subunit, ECF subfamily 0.175414
9 ENOG4107D31 NA 0.168643
10 ENOG4108P4K tonB-dependent Receptor 0.161651
11 ENOG4107R0M Integrase 0.157713
12 ENOG4107QMP dna polymerase iii subunits gamma and tau 0.142631
13 ENOG4105S2J secreted protein 0.140935
14 ENOG4106B0M NA 0.139202
15 ENOG4108EMJ S-(hydroxymethyl)glutathione dehydrogenase class III alcohol dehydrogenase 0.137265
16 ENOG4105TW2 LysR substrate binding domain 0.134695
17 ENOG4105CW0 outer membrane usher protein 0.134312
18 ENOG4107X2G Diacylglycerol kinase -0.132567
19 ENOG4105Y4E Stress-induced bacterial acidophilic repeat motif -0.128172
20 ENOG4108IMY Transcriptional regulator 0.127870
21 ENOG4108VYX Potassium channel protein 0.125577
22 ENOG4105CVR type I restriction-modification system 0.121413
23 ENOG4105MEP Peptidase S24-like 0.118731
24 ENOG4108PXA Replication Protein 0.117244
25 ENOG4105F57 Anthranilate dioxygenase reductase -0.117000
26 ENOG4108YS2 small subunit -0.117000
27 ENOG410632Y Sel1 repeat protein -0.116375
28 ENOG4105MQX spore coat U domain-containing protein 0.116004
29 ENOG4106W0T fimbrial subunit 0.115848
30 ENOG4108R0M Aminoglycoside 0.115327
31 ENOG4105KHW NA 0.114736
32 ENOG41072A3 NA 0.113509
33 ENOG4108ITA resolvase 0.113051
34 ENOG4106VZ8 ribosomal rna methyltransferase 0.110030
35 ENOG4107D8W NA 0.109173
36 ENOG41083XP Transcriptional regulator, ModE family -0.108315
37 ENOG41089J0 NA 0.107823
38 ENOG4107RI2 phosphate transporter 0.106486
39 ENOG4105KMS anti-termination protein 0.105015
40 ENOG4105ZRH Transcriptional regulator 0.104937
41 ENOG4105GM0 NA -0.103865
42 ENOG4108HJ1 Uncharacterized conserved protein (DUF2303) 0.102408
43 ENOG410816G NA -0.102099
44 ENOG4106DCC NA 0.100631
45 ENOG41064TV Transcriptional regulator, IclR family 0.100272
46 ENOG4105SG0 Membrane 0.099851
47 ENOG4108W5M transcriptional regulator 0.099851
48 ENOG4106BXS Phage conjugal plasmid C-4 type zinc finger protein, TraR family -0.099537
49 ENOG4108H4G Sugar-specific transcriptional regulator TrmB -0.097431
50 ENOG4105MVB thioesterase Superfamily protein -0.097417
51 ENOG4105H40 NA 0.096730
52 ENOG4108RCU Transposase 0.096667
53 ENOG4105D2U Inherit from NOG: KH domain containing 3-like, subcortical maternal complex member -0.096325
54 ENOG41061SC NA -0.048120
54 ENOG410854N MerR family regulatory protein -0.048120
55 ENOG4108HZZ GGDEF 0.096172
56 ENOG4108R8X outer membrane lipoprotein 0.096172
57 ENOG4105X0D Fimbrial protein 0.095731
58 ENOG4108KHX Diguanylate cyclase -0.095067
59 ENOG4105ZCR Pilus assembly protein TraF 0.095047
60 ENOG4105ZPE Inherit from NOG: GCN5-related N-acetyltransferase 0.094953
61 ENOG410685M Sel1 domain protein repeat-containing protein 0.094030
62 ENOG4107X8T Terminase-like family 0.093587
63 ENOG4105X4P TolA protein -0.092897
64 ENOG4107U79 DNA Methylase 0.092224
65 ENOG4108K2X pilus assembly 0.090701
66 ENOG4105SA9 Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides (By similarity) 0.089755
67 ENOG4105IV8 Amino acid permease -0.089501
68 ENOG4105VNG YcgL domain-containing protein 0.044573
68 ENOG4107CX4 NA 0.044573
69 ENOG4108ENZ D-isomer specific 2-hydroxyacid dehydrogenase 0.088842
70 ENOG41064TI NA -0.088561
71 ENOG410684T prevent-host-death family 0.087879
72 ENOG4105HVM Type-F conjugative transfer system protein TraW 0.014560
72 ENOG41061TX Type-F conjugative transfer system pilin assembly protein TrbC 0.014560
72 ENOG4106X0T NA 0.014560
72 ENOG4107AVK NA 0.014560
72 ENOG4107MWI NA 0.014560
72 ENOG4108FEU Pfam:CxxC_CxxC_SSSS 0.014560
73 ENOG4108M3P Membrane 0.086689
74 ENOG4105F4G Membrane 0.086379
75 ENOG4105T79 Putative membrane peptidase family (DUF2324) 0.085501
76 ENOG41068YX NA -0.085302
77 ENOG4105CB6 ATPase associated with various cellular activities aaa_5 0.084810
78 ENOG41061PY Histidine kinase -0.084647
79 ENOG4108CRP domain protein 0.084527
80 ENOG4108UUF peptidase C13, legumain asparaginyl peptidase 0.084291
81 ENOG4105CBM Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12 (By similarity) 0.012042
81 ENOG4105DJV ribulose-phosphate 3-epimerase 0.012042
81 ENOG4105FFN Specifically methylates the guanosine in position 1516 of 16S rRNA (By similarity) 0.012042
81 ENOG4105XJ4 Uncharacterized protein conserved in bacteria (DUF2218) 0.012042
81 ENOG41067SS Bacterioferritin-associated ferredoxin 0.012042
81 ENOG4108UQY Iron-storage protein 0.012042
81 ENOG4108YSG O-Antigen polymerase 0.012042
82 ENOG4108UWZ 4-Carboxymuconolactone decarboxylase 0.084291
83 ENOG4105EJX conjugal transfer ATPase 0.083852
84 ENOG41076RF NA -0.083432
85 ENOG4105ZIE Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides (By similarity) 0.081022
86 ENOG4107CJ6 NA 0.080848
87 ENOG4106RT0 NA -0.080086
88 ENOG4105C4W S-formylglutathione hydrolase 0.079955
89 ENOG4108C1Q NA 0.077800
90 ENOG4106NC8 ngn domaiN-containing protein 0.076907
91 ENOG4105IQ7 Transposase -0.076899
92 ENOG4105VGH gCN5-related N-acetyltransferase 0.076895
93 ENOG4106E05 NA -0.076477
94 ENOG4106KWJ NA -0.076309
95 ENOG4107P6H NA 0.075917
96 ENOG41071TN NA -0.018872
96 ENOG41071V2 NA -0.018872
96 ENOG4108FD4 NA -0.018872
96 ENOG4108T3H DNA exonuclease X -0.018872
97 ENOG4105SDG bluf domain-containing protein 0.075487
98 ENOG4105YGM Outer membrane efflux protein 0.037744
98 ENOG4107835 probably involved in intracellular septation (By similarity) 0.037744
99 ENOG4105WTV NA -0.075238
100 ENOG410760B NA -0.075238
101 ENOG4108Y1E p-loop domain protein 0.074233
102 ENOG41090DD ISPg5 transposase Orf1 -0.074022
103 ENOG4107WKS Macrolide 2'-phosphotransferase -0.073886
104 ENOG41082PI Sel1 domain protein repeat-containing protein 0.073718
105 ENOG4108JU3 Alkyl hydroperoxide reductase 0.073088
106 ENOG4105FTC Lytic transglycosylase catalytic 0.018110
106 ENOG410659M TraK protein 0.018110
106 ENOG4106DQF type IV conjugative transfer system protein TraV 0.018110
106 ENOG4107JC1 NA 0.018110
107 ENOG4107TYW Glycosyltransferase, group 1 family protein 0.072304
108 ENOG4105IFT aminoglycoside N(6')acetyltransferase 0.071952
109 ENOG4108JFQ HTH_XRE -0.071605
110 ENOG4106VET NA -0.071279
111 ENOG4106249 Membrane -0.070760
112 ENOG41072UF Tape measure protein 0.070363
113 ENOG4108Z4X TRANSCRIPTIONal 0.070064
114 ENOG4105NM1 Replication Protein -0.070052
115 ENOG4106XAI NA 0.069666
116 ENOG4106D2X NA 0.069462
117 ENOG4105MGN Hnh endonuclease -0.069240
118 ENOG4107PHU transfer protein TraU 0.068524
119 ENOG4105EPA Major Facilitator superfamily 0.068386
120 ENOG41090VG NA 0.068177
121 ENOG410692I NA 0.068066
122 ENOG4105IDF Transposase -0.067179
123 ENOG4105R9F Fimbrial protein -0.066387
124 ENOG4105PXY Tetr family transcriptional regulator 0.066128
125 ENOG4108ZA9 Transcriptional regulator, TetR family 0.065566
126 ENOG4108Z51 anti-termination protein 0.065404
127 ENOG41066RG NA 0.065108
128 ENOG41068PG O-Antigen polymerase 0.064630
129 ENOG4107JVJ NA -0.064397
130 ENOG4105ZKY NA 0.064171
131 ENOG4105TFC spore coat U domain-containing protein -0.063909
132 ENOG4105DXV Long-chain fatty acid 0.063119
133 ENOG41066YE NA 0.063097
134 ENOG4106G26 NA -0.062584
135 ENOG41077UX NA -0.061487
136 ENOG4108QU8 NA -0.061313
137 ENOG4105XJI Host specificity protein -0.061302
138 ENOG4105WXW Antirepressor 0.061250
139 ENOG4108V2F protein ybcN in lambdoid DLP12 prophage regi 0.061209
140 ENOG41073E1 NA -0.061132
141 ENOG4108Y6M peptidase c39, bacteriocin processing -0.060545
142 ENOG4105CMA conjugation trbi family protein 0.060519
143 ENOG4106QJ8 Stress protein 0.060253
144 ENOG41063K6 NA 0.060056
145 ENOG4108WIJ Two component transcriptional regulator (Winged helix family 0.059549
146 ENOG4107VS1 KR domain 0.029707
146 ENOG4108K4C ec 3.1.3.12 0.029707
147 ENOG41078FZ NA 0.059282
148 ENOG4105HHQ 6-phosphogluconolactonase (EC 3.1.1.31) 0.058954
149 ENOG4105ZG6 NA -0.058798
150 ENOG4108TUF Acyl-coenzyme A 6-aminopenicillanic acid acyl-transferase -0.058774
151 ENOG4108EFE Potassium efflux system protein 0.058668
152 ENOG4108RGV mercury transport protein MerC -0.058301
153 ENOG4108R6E NA -0.057780
154 ENOG4105F8B mobA MobL family protein 0.057334
155 ENOG4107Y46 Protein of unknown function DUF86 0.057191
156 ENOG4105DXA Outer membrane porin -0.057128
157 ENOG4105Y68 type VI secretion system, lysozyme-related protein -0.056865
158 ENOG4108I0N Transporter, RarD family, DMT superfamily protein 0.055778
159 ENOG4106AG5 NA 0.055444
160 ENOG4105RAH Domain of unknown function (DUF1833) -0.055225
161 ENOG4105ECZ D12 class N6 adenine-specific DNA methyltransferase 0.055204
162 ENOG4108TYY NA 0.055171
163 ENOG41061KY NA 0.054641
164 ENOG4108DPU AMP-binding enzyme -0.054560
165 ENOG410711X NA 0.054060
166 ENOG4108R52 Type VI secretion protein, VC_A0107 family -0.053947
167 ENOG4105F9F transposase 0.053774
168 ENOG4108WT8 Hnh endonuclease 0.053511
169 ENOG4106A6I hemolysin 0.053403
170 ENOG4105VTN Protein of unknown function (DUF1311) -0.053276
171 ENOG41089BX ABC branched chain amino acid transporter, inner membrane subunit -0.053202
172 ENOG4108DKD HemX -0.053054
173 ENOG4107YH7 Beta-lactamase (EC 3.5.2.6) 0.053050
174 ENOG4107Q2X Protein of unknown function (DUF1064) -0.052670
175 ENOG4105VQU rdd domain containing protein 0.051861
176 ENOG4108C33 Resolvase 0.051704
177 ENOG4108RAE type VI secretion system effector, hcp1 family -0.051629
178 ENOG4107PYX Inherit from NOG: integron integrase 0.051478
179 ENOG4105DGK type VI secretion protein, EvpB VC_A0108 family -0.051378
180 ENOG4108QWJ Diguanylate phosphodiesterase -0.051232
181 ENOG4105S96 SEC-C motif domain protein 0.051114
182 ENOG4107W0A Histidine kinase 0.050814
183 ENOG41070HZ Transcription termination factor nusG 0.050472
184 ENOG41081PS Methyltransferase -0.050443
185 ENOG4108ZKD AraC Family Transcriptional Regulator 0.050288
186 ENOG4108N3Y NA 0.050131
187 ENOG4105XT9 zeta toxin -0.049550
188 ENOG4107GS8 Cobyrinic acid ac-diamide synthase -0.049440
189 ENOG4108JS3 KR domain 0.024713
189 ENOG41090CJ transposase 0.024713
190 ENOG4106QAA NA 0.049278
191 ENOG4108T2T NA -0.048889
192 ENOG4105CI5 domain protein 0.048813
193 ENOG41060YD NA 0.006087
193 ENOG41068IM transcriptional regulator, copG family 0.006087
193 ENOG410705U Transglutaminase-like superfamily 0.006087
193 ENOG4107NVD NA 0.006087
193 ENOG4107U6T NA 0.006087
193 ENOG41086B1 Bacterial protein of unknown function (DUF896) 0.006087
193 ENOG41088UI Sodium hydrogen exchanger 0.006087
193 ENOG4108M0H Extracellular lipase 0.006087
194 ENOG4105KUW Hnh endonuclease 0.048599
195 ENOG4107T2H Integrase, catalytic region 0.048591
196 ENOG4108MXF Alpha Beta Hydrolase 0.048537
197 ENOG4106SG4 NA 0.048434
198 ENOG4105CTX dehydratase 0.048349
199 ENOG4105DJB Major Facilitator Superfamily 0.016116
199 ENOG4105UVJ 5-dehydro-4-deoxyglucarate dehydratase 0.016116
199 ENOG4107EG7 GntR Family Transcriptional Regulator 0.016116
200 ENOG41066S5 ORF6C domain -0.047585
201 ENOG4108C6S NfeD-like C-terminal, partner-binding 0.047538
202 ENOG41069Q1 NA -0.046842
203 ENOG4107FAD NA -0.046739
204 ENOG4105TZD TrbL VirB6 plasmid conjugal transfer protein 0.046621
205 ENOG4108ND8 Dehydratase 0.046609
206 ENOG4105FJ8 phage repressor 0.046546
207 ENOG4108RMP Prophage Lp2 protein 4 0.046371
208 ENOG4105F1S paraquat-inducible protein a -0.046306
209 ENOG4105NUM transcriptional regulator AsnC family 0.046159
210 ENOG4106C17 NA -0.046071
211 ENOG4106A6K transfer protein -0.045621
212 ENOG4105D4K integrase catalytic -0.045459
213 ENOG410893F Alpha beta hydrolase -0.045325
214 ENOG4108KTA Periplasmic protein-like protein -0.045202
215 ENOG41086QX Protein of unknown function (DUF1311) 0.044859
216 ENOG410658P NA 0.044835
217 ENOG4105NI8 Cytosine-specific methyltransferase -0.044549
218 ENOG4107IHG Aminoglycoside-2''-adenylyltransferase 0.044191
219 ENOG4105S5T dihydrodipicolinate 0.044090