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 ENOG4105MT7 Arsenical resistance operon tranS-acting repressor 0.037522
2 ENOG4107R5R arsenical pump membrane protein 0.032300
3 ENOG4105D0U Arsenite-activated ATPase (ArsA) 0.028544
4 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.024689
5 ENOG41080I8 transcriptional regulator), MarR family -0.024546
6 ENOG410821Y ec 3.6.3.16 0.021183
7 ENOG4106NDE Ammonium Transporter Family 0.021094
8 ENOG4108S3Y transcriptional regulator -0.020330
9 ENOG4105CPK Glycosyl transferase (Group 1 0.020288
10 ENOG4106HJE NA -0.019420
11 ENOG41066FG Protein of unknown function (DUF2759) -0.017657
12 ENOG4108ZXY Glycosyl transferase, family 2 -0.017382
13 ENOG41085GI NA -0.016894
14 ENOG4107YAG Inherit from COG: sulfurtransferase activity 0.016754
15 ENOG4105KVH Transcriptional regulator 0.016505
16 ENOG4107W03 Inherit from COG: cell filamentation protein 0.016490
17 ENOG4106HIM NA -0.016463
18 ENOG4105DYV ABC transporter 0.016364
19 ENOG4105DTT CRISPR-associated helicase, cas3 -0.016340
20 ENOG4105CVP deoxyribo-dipyrimidine photolyase 0.016117
21 ENOG4106G3M NA -0.016031
22 ENOG4108SMS transposase -0.015943
23 ENOG4105CS2 ec 3.2.1.21 -0.015830
24 ENOG4106MJ4 NA 0.015809
25 ENOG41078RD helix-turn-helix type 11 domain-containing protein -0.015678
26 ENOG4107FFF Protein of unknown function (DUF2970) 0.015640
27 ENOG4107B5U Transposase 0.015636
28 ENOG4105HA6 Glycosyl transferase, family 2 -0.015560
29 ENOG4106WSA NA -0.015560
30 ENOG4107CVH NA -0.015500
31 ENOG4108BWS Protein of unknown function (DUF466) -0.015483
32 ENOG4107QJZ Glycosyl transferase, family 2 -0.015393
33 ENOG4107R9Y phosphoglycerol transferase alkaline phosphatase superfamily protein -0.015247
34 ENOG41079VA NA -0.015195
35 ENOG410732S Sporulation inhibitor A -0.015119
36 ENOG4106CT7 NA -0.015099
37 ENOG4108S4N thiJ PfpI domain-containing protein -0.015070
38 ENOG4105VTR Integrase 0.014943
39 ENOG41069JV NA 0.014836
40 ENOG4106DF4 Sigma-70, region 4 0.014828
41 ENOG41074I7 NA -0.014801
42 ENOG4105KTU Transcriptional regulator, arsr family 0.014705
43 ENOG4107343 NA -0.014694
44 ENOG4105D85 methylase 0.014592
45 ENOG4105KDA Transcriptional regulator, GntR family 0.014541
46 ENOG4106H2G NA -0.014512
47 ENOG41074GR NA -0.014483
48 ENOG4108KI7 Diguanylate cyclase 0.014402
49 ENOG4108IY0 amino acid ABC transporter substrate-binding protein, PAAT family 0.014348
50 ENOG4107RMT Osmosensitive K channel His kinase sensor 0.014324
51 ENOG4105KT7 mgtC SapB transporter -0.014265
52 ENOG41077X5 conserved protein, contains two CXXC motifs -0.014063
53 ENOG41063CS Replication Protein 0.014007
54 ENOG4105U9X Bacterial regulatory proteins, tetR family -0.013910
55 ENOG41069F9 Pfam:TRF2 0.013886
56 ENOG4105EXW epimerase dehydratase -0.013845
57 ENOG4108FK9 symporter YidK 0.013787
58 ENOG4105MJN Transcriptional regulator, TetR family 0.013785
59 ENOG41069JC NA -0.013774
60 ENOG4105XJR Branched-chain amino acid 0.013766
61 ENOG41079HZ NA -0.013731
62 ENOG4105Y9H NA 0.013722
63 ENOG41086DA Protein of unknown function (DUF1272) -0.013710
64 ENOG41077IC NA -0.013647
65 ENOG4107R8B 5'-nucleotidase 0.013640
66 ENOG4106BBM NA -0.013636
67 ENOG4105JGP host cell surface-exposed lipoprotein 0.013631
68 ENOG4105D3Q Sugar transferase 0.013630
69 ENOG41077C5 NA -0.013626
70 ENOG4106WZ2 NA -0.013601
71 ENOG4108T0D glyoxalase 0.013599
72 ENOG4108Y1Q NA 0.013576
73 ENOG4108UXE Protein tyrosine phosphatase 0.013549
74 ENOG4105DB1 molybdopterin oxidoreductase 0.013527
75 ENOG4107RHI Cytosine-specific methyltransferase 0.013514
76 ENOG4106I7V NA -0.013485
77 ENOG4106Z2Q NA -0.006676
77 ENOG4107YJ4 chain length determinant protein -0.006676
78 ENOG410608E NA 0.013314
79 ENOG4105IE8 Alpha-ketoglutarate permease -0.013313
80 ENOG4108P7G capsid protein 0.013306
81 ENOG4106WUS NA 0.013278
82 ENOG4105ZMF Domain of Unknown Function (DUF1540) -0.013243
83 ENOG4107FK9 PbH1 0.013220
84 ENOG4107BZP NA -0.013169
85 ENOG410797K NA -0.013151
86 ENOG41069NG NA 0.001877
86 ENOG4107HPM Transposase 0.001877
86 ENOG4107JH8 NA 0.001877
86 ENOG4107WF7 NA 0.001877
86 ENOG410811X Methylamine utilization protein mauE 0.001877
86 ENOG4108BUS alpha/beta hydrolase fold 0.001877
86 ENOG4108C9F Poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit 0.001877
87 ENOG4105F6A helicase 0.013142
88 ENOG4108SEW NA 0.013135
89 ENOG4107CQ5 Flagellar hook-length control protein FliK -0.013109
90 ENOG4108V5C ABC transporter 0.013108
91 ENOG4106GWE NA -0.013062
92 ENOG41063G6 hmm pf04634 -0.013061
93 ENOG4106AWE NA 0.013051
94 ENOG41062BC Acetyltransferase (GNAT) family -0.013036
95 ENOG4105DID DevR family -0.006493
95 ENOG4108QCZ crispr-associated cxxc_cxxc protein cst1 -0.006493
96 ENOG4105CKK Glycosyl transferase, family 2 -0.012958
97 ENOG4105GR3 Histidine kinase 0.012953
98 ENOG41070YR NA 0.012917
99 ENOG41069V1 NA -0.006447
99 ENOG4108PG8 lipolytic protein G-D-S-L family -0.006447
100 ENOG4108RS2 oxidoreductase 0.012879
101 ENOG4105CIS alcohol dehydrogenase 0.012856
102 ENOG4105Z63 transport integral membrane protein 0.012840
103 ENOG4107C9S Inherit from COG: YD repeat protein -0.012810
104 ENOG4105MD7 metal-dependent hydrolase 0.012744
105 ENOG41065IU NA -0.012692
106 ENOG4106A74 NA 0.012683
107 ENOG4108GYP domain protein 0.012671
108 ENOG4107SPW HsdM N-terminal domain 0.012662
109 ENOG4108KJY Inherit from NOG: Family with sequence similarity 115, member -0.012647
110 ENOG41073DR NA -0.012641
111 ENOG4106959 NA -0.012632
112 ENOG4108NNA glycosyl transferase group 1 -0.012603
113 ENOG4105J10 restriction modification system DNA specificity domain 0.012581
114 ENOG4106VCP S4 -0.012581
115 ENOG4105DST XRE family Transcriptional regulator 0.012546
116 ENOG4107991 NA 0.012519
117 ENOG4106X7S NA -0.012502
118 ENOG4108WIN Transcriptional regulator 0.012456
119 ENOG4107AM5 NA 0.012453
120 ENOG4107DCA NA -0.012451
121 ENOG4105YHT Collagen triple helix 0.012449
122 ENOG4107R2D transcriptional regulator 0.012438
123 ENOG4106BJ1 NA 0.012391
124 ENOG4105MFV ABC-2 type transporter 0.012378
125 ENOG4105E92 Erythromycin esterase -0.012354
126 ENOG4105EP0 Glycosyl transferase (Group 1 -0.012340
127 ENOG41077KT NA 0.012334
128 ENOG4107C4X NA -0.012311
129 ENOG4107A28 NA -0.012270
130 ENOG4105VCD cytoplasmic protein 0.012267
131 ENOG4108YU6 Domain-Containing protein -0.012247
132 ENOG4106HNU NA -0.012218
133 ENOG4107DCE Haemolysin XhlA 0.012206
134 ENOG4106B51 transposase 0.012179
135 ENOG4108AEB Calcineurin-like phosphoesterase -0.012177
136 ENOG4107D3H Probable sporulation protein (Bac_small_yrzI) -0.012154
137 ENOG41073DP NA 0.012143
138 ENOG4105VJZ Helix-turn-helix domain protein 0.012123
139 ENOG4105HFU Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) -0.012123
140 ENOG4108BT1 NA -0.012111
141 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase 0.012099
142 ENOG4105DBZ Dtdp-4-dehydrorhamnose reductase -0.012098
143 ENOG4105N09 integral membrane protein 0.003011
143 ENOG4105TD6 Protein of unknown function (DUF2812) 0.003011
143 ENOG4107F5N Uncharacterized protein conserved in bacteria (DUF2065) 0.003011
143 ENOG4108C8K HTH_ARAC 0.003011
144 ENOG4107UC5 Glycosyl transferase, family 4 -0.012006
145 ENOG4107BQ5 NA -0.011994
146 ENOG4105CCN Peptidase M56 -0.011992
147 ENOG4107U4Y signal transduction Histidine kinase 0.011942
148 ENOG4107414 GntR family transcriptional regulator -0.011929
149 ENOG41069U5 Protein of unknown function (DUF2602) -0.011907
150 ENOG4105XXU Phage terminase small subunit -0.011905
151 ENOG4108R80 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. The C subunit may be involved in assembly of the KDP complex (By similarity) 0.011897
152 ENOG41081WK N-acetylmuramoyl-L-alanine amidase -0.011891
153 ENOG4106CB4 NA -0.011886
154 ENOG4108P83 ParB domain protein nuclease -0.011883
155 ENOG4105P13 Inherit from COG: Serine Threonine protein kinase -0.000791
155 ENOG4105VDG NA -0.000791
155 ENOG4105YFY Tic20-like protein -0.000791
155 ENOG41066M5 NA -0.000791
155 ENOG4106NKK NA -0.000791
155 ENOG41072X6 NA -0.000791
155 ENOG41073ZG NA -0.000791
155 ENOG4107D1H NA -0.000791
155 ENOG4107FE7 Multiple resistance and ph regulation protein f -0.000791
155 ENOG4107HIR Inherit from NOG: filamentous hemagglutinin -0.000791
155 ENOG41085EY HTH_XRE -0.000791
155 ENOG41087UR O-Antigen ligase -0.000791
155 ENOG4108VF8 ABC transporter -0.000791
155 ENOG4108VKD Histidine kinase -0.000791
155 ENOG4108Z5G NA -0.000791
156 ENOG4107BD0 NA -0.011862
157 ENOG4108D8A Periplasmic binding protein 0.011852
158 ENOG4105KUR CAAX amino terminal protease family protein -0.011843
159 ENOG4106AXD NA -0.011796
160 ENOG41090QX NA -0.005897
160 ENOG41090TM glycosyl transferase family -0.005897
161 ENOG4105Y51 Glycosyl transferase family 2 -0.011791
162 ENOG4108YX8 Lysophospholipase -0.011780
163 ENOG4105Y9K phage protein -0.011732
164 ENOG4107TN8 Peptidase dimerisation domain -0.011711
165 ENOG41085K1 gtp-binding protein 0.011689
166 ENOG4108IQV Domain of unknown function DUF11 0.011653
167 ENOG4107H8E Flagellar M-ring protein fliF 0.011641
168 ENOG4106CD9 glycosyl transferase group 1 -0.011630
169 ENOG4107B4U NA -0.011622
170 ENOG4107TAW peptidase, M20 0.011618
171 ENOG4105C0Z ABC transporter 0.011614
172 ENOG4108SEK ompa motb domain protein -0.011604
173 ENOG4105FKQ transcriptional regulator -0.011580
174 ENOG4105DSQ Nitric oxide reductase 0.011576
175 ENOG4107AUG NA 0.011551
176 ENOG4108JQ0 Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) 0.011540
177 ENOG4107UCE ferrous iron transport protein 0.011511
178 ENOG4108HR5 polar amino acid ABC transporter, inner membrane subunit 0.011495
179 ENOG410600H Phage-related XpaF1 protein, involved in cell lysis -0.011485
180 ENOG4105ECI YeeC-like protein 0.011450
181 ENOG4107SVJ Dehydrogenase 0.011447
182 ENOG4107RAF solute symporter -0.011440
183 ENOG4108NQ1 repeat-containing protein -0.011421
184 ENOG4105NI6 heptaprenyl diphosphate synthase component I -0.011406
185 ENOG41085E3 NA -0.005702
185 ENOG4108DJJ Cache domain -0.005702
186 ENOG4107FSS Endonuclease that specifically degrades the RNA of RNA- DNA hybrids (By similarity) -0.011400
187 ENOG4105DC8 reductase 0.011379
188 ENOG4105T1S Transposase -0.011377
189 ENOG4105CGQ conserved protein UCP033563 -0.011367
190 ENOG41090UD (LipO)protein 0.011364
191 ENOG4108YH3 Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) -0.011334
192 ENOG41060F7 Phage envelope protein -0.011315
193 ENOG4107TJ0 Transporter protein -0.011297
194 ENOG4105DQW permease for cytosine purines, uracil, thiamine, allantoin 0.011294
195 ENOG4106BBT NA -0.011239
196 ENOG41079U7 NA -0.011228
197 ENOG4105V8I NA 0.011215
198 ENOG41062EA NA 0.011211
199 ENOG4105ES7 radical SAM domain protein 0.011178
200 ENOG4107QMH DNA methylase -0.011151
201 ENOG41068Z6 Predicted metal-binding protein (DUF2103) 0.011130
202 ENOG41081H5 TETR family transcriptional 0.011121
203 ENOG410800S response regulator -0.011092
204 ENOG4105F7Z ABC transporter 0.011090
205 ENOG4105KYB Mazg nucleotide pyrophosphohydrolase 0.011080
206 ENOG41066K9 Inherit from COG: filamentous hemagglutinin family outer membrane protein 0.011025
207 ENOG4105ED2 Beta-lactamase 0.011024
208 ENOG4108Z9I -acetyltransferase -0.011009
209 ENOG41085D9 Inherit from COG: transglutaminase domain-containing protein -0.011001
210 ENOG4108VSE mercuric transport protein 0.010990
211 ENOG4108ME1 Peptidase M55 D-aminopeptidase -0.010961
212 ENOG4105E15 Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate 0.010960
213 ENOG410908W Diguanylate cyclase -0.010957
214 ENOG4108PEI Trap dicarboxylate transporter, dctp subunit 0.010949
215 ENOG4106SMX NA 0.010930
216 ENOG4105ETW Luciferase-like -0.010907
217 ENOG4105DJN thiJ pfpI 0.010902
218 ENOG41073MC NA 0.010892
219 ENOG4105CIY formyltetrahydrofolate deformylase -0.010864
220 ENOG4105K6D phospholipase d 0.010857
221 ENOG4105C1F The M ring may be actively involved in energy transduction (By similarity) -0.010838
222 ENOG4108MTA extracellular solute-binding protein family 1 -0.010834