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 ENOG4107RMC 5'-Nucleotidase domain protein 0.052295
2 ENOG4105GAC Sulfur oxidation protein 0.038209
3 ENOG4105QN4 diheme cytochrome 0.029971
4 ENOG4105CUC YeeE YedE family protein 0.024541
5 ENOG4107E84 Cytochrome c 0.023239
6 ENOG4108NPU thioredoxin SoxW 0.022961
7 ENOG4106001 sulfur oxidation protein SoxZ 0.021042
8 ENOG4105C61 Beta-lactamase domain protein 0.020441
9 ENOG4105XSY Regulatory protein SoxS 0.019215
10 ENOG4105N94 The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase (By similarity) 0.018766
11 ENOG4107S7U Sulfide dehydrogenase 0.018520
12 ENOG4105WWQ Sulfur oxidation 0.016902
13 ENOG4108ZBQ cytochrome C 0.016346
14 ENOG4105C5E polysaccharide biosynthesis protein -0.015953
15 ENOG41088H4 Diheme cytochrome SoxA (Sulfur oxidation) 0.015591
16 ENOG4107RWC DNA helicase -0.014291
17 ENOG4105TAT Sulfur oxidation protein 0.014080
18 ENOG410600T transposase -0.013757
19 ENOG4108W1J Virulence-associated protein e -0.013588
20 ENOG4105E9I Appr-1-p processing domain protein -0.013540
21 ENOG41090AH NA 0.013286
22 ENOG4107S4J Sulfur oxidation V protein 0.013155
23 ENOG4105CSG Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm. This transfer involves a cascade of disulfide bond formation and reduction steps (By similarity) 0.012855
24 ENOG4108KHX Diguanylate cyclase 0.012668
25 ENOG4106B22 Type 4 fimbrial biogenesis protein PilV -0.012623
26 ENOG4106HUX NA 0.011923
27 ENOG4107WEC Periplasmic Protein -0.011835
28 ENOG4105C6E dna polymerase iii 0.011779
29 ENOG4105CHC glucokinase (EC 2.7.1.2) -0.011777
30 ENOG4105J76 Periplasmic binding protein 0.011766
31 ENOG4108Q79 6-phosphogluconolactonase (EC 3.1.1.31) -0.011661
32 ENOG4108NMI NA -0.011623
33 ENOG4105YG2 Bifunctional DNA primase polymerase -0.011556
34 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit 0.011395
35 ENOG4105C30 Nad-dependent epimerase dehydratase -0.011374
36 ENOG4108V1U phospholipid-binding protein 0.011260
37 ENOG4105U2P bfd domain protein (2fe-2s)-binding domain protein -0.011189
38 ENOG4105Z8F Protein of unknown function (DUF433) -0.011057
39 ENOG4108FZZ NA 0.011030
40 ENOG4105F8F radical SAM domain protein -0.010839
41 ENOG4105CDA abc transporter atp-binding protein -0.010726
42 ENOG4105EKD Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism (By similarity) -0.010725
43 ENOG4108K28 Arsenite oxidase, large subunit -0.010623
44 ENOG4107WTS domain protein 0.010580
45 ENOG4107WUI DNA Methylase -0.010564
46 ENOG4108K71 fad dependent oxidoreductase 0.010538
47 ENOG4105CD2 stage iii sporulation protein aa -0.010520
48 ENOG41081YG arsenite oxidase, small subunit -0.010502
49 ENOG41064JB Uncharacterised protein family (UPF0150) -0.010367
50 ENOG4107SSH DNA mismatch repair protein MutS domain protein -0.010367
51 ENOG4105H1J Pfam:DUF820 -0.000691
51 ENOG4105X13 Protein of unknown function (DUF433) -0.000691
51 ENOG41063FR domain protein -0.000691
51 ENOG4106J5U NA -0.000691
51 ENOG4107BTQ Bacterial regulatory protein, Fis family -0.000691
51 ENOG4107G3U NA -0.000691
51 ENOG4107N8H Nucleotidyltransferase domain -0.000691
51 ENOG4107UWM molybdopterin oxidoreductase -0.000691
51 ENOG4107X1Y radical SAM domain protein -0.000691
51 ENOG4107YMZ methyltransferase, type 11 -0.000691
51 ENOG4108BJJ Pfam:Transposase_11 -0.000691
51 ENOG4108FXK NA -0.000691
51 ENOG4108FYF NA -0.000691
51 ENOG4108G0C NA -0.000691
51 ENOG41090MM NA -0.000691
52 ENOG4105SU0 efflux transporter, rnd family, mfp subunit 0.010354
53 ENOG4105CGN Glycosyl transferase (Group 1 -0.010303
54 ENOG4105M96 Disulfide interchange protein -0.010227
55 ENOG4105CZD Thiol oxidoreductase 0.010213
56 ENOG4107QVN Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) -0.010154
57 ENOG4105UA5 NA 0.001447
57 ENOG410759Y NA 0.001447
57 ENOG4107T91 Inherit from COG: Aldolase 0.001447
57 ENOG4108FX7 NA 0.001447
57 ENOG4108FZ8 NA 0.001447
57 ENOG4108G0T NA 0.001447
57 ENOG4108UT0 metallophosphoesterase 0.001447
58 ENOG4106CZ8 NA -0.010059
59 ENOG4107W96 NA -0.009982
60 ENOG4105EE5 Membrane protein terC -0.009950
61 ENOG4105DYN 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity) 0.009946
62 ENOG4107QIX Phosphoglucomutase (EC 5.4.2.2 -0.009901
63 ENOG4105WD1 Membrane -0.009874
64 ENOG4108SHC Integrase, catalytic region -0.009860
65 ENOG4108UQY Iron-storage protein -0.009850
66 ENOG4105SPF Tripartite ATP-independent periplasmic transporter dctq component 0.009744
67 ENOG4108Z47 Rhodanese domain protein 0.009663
68 ENOG4108RC8 Csm4 family CRISPR-associated ramp protein 0.009577
69 ENOG4108K5T symporter -0.009551
70 ENOG4105DG4 malate L-lactate dehydrogenase 0.009510
71 ENOG4105I5W Transporter 0.009474
72 ENOG41066S1 Toxic component of a toxin-antitoxin (TA) module. A -0.009365
73 ENOG4105D8W glucose-6-phosphate 1-dehydrogenase -0.009308
74 ENOG4105DSS Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.009302
75 ENOG4105IUK Pin domain protein -0.009298
76 ENOG4105CYX Short-chain dehydrogenase reductase Sdr -0.009289
77 ENOG4105CY0 Metallo-Beta-Lactamase 0.009208
78 ENOG4107RBX acriflavin resistance protein 0.009208
79 ENOG4105F3W Outer membrane efflux protein 0.009203
80 ENOG4105JIG Two component transcriptional regulator (Winged helix family 0.009162
81 ENOG4105EGG ABC transporter -0.009148
82 ENOG4105S0S Inherit from COG: transposase -0.000651
82 ENOG4105XTW NA -0.000651
82 ENOG410650G NA -0.000651
82 ENOG4106XF4 NA -0.000651
82 ENOG4107RH0 Type IV secretory pathway VirD4 -0.000651
82 ENOG4108FX2 NA -0.000651
82 ENOG4108FZF conjugal transfer protein Trbc -0.000651
82 ENOG4108FZT Zinc finger, swim domain protein -0.000651
82 ENOG4108FZW NA -0.000651
82 ENOG4108G0S NA -0.000651
82 ENOG4108G11 NA -0.000651
82 ENOG4108G12 NA -0.000651
82 ENOG4108G2F NA -0.000651
82 ENOG4108G40 NA -0.000651
83 ENOG41062IF Mitomycin resistance protein -0.009094
84 ENOG4107TI6 MotA TolQ exbB proton channel 0.009079
85 ENOG4106H9Y DNA binding domain protein, excisionase family -0.009074
86 ENOG4105HX6 NA -0.008987
87 ENOG4107R1D Lytic transglycosylase catalytic -0.008965
88 ENOG4105VF2 DNA Polymerase Beta Domain Protein Region 0.008961
89 ENOG4107A6K microcystin lr degradation protein -0.008952
90 ENOG41067RR Toxin-antitoxin system, toxin component, HicA family -0.008949
91 ENOG4105EUB pirin domain protein -0.008877
92 ENOG4107667 NA 0.001775
92 ENOG4107WPB Major Facilitator 0.001775
92 ENOG4107ZE0 biopolymer transport protein ExbD TolR 0.001775
92 ENOG4108G19 NA 0.001775
92 ENOG4108G1Y NA 0.001775
93 ENOG4105K91 EamA-like transporter family 0.008859
94 ENOG4105KZE Death-On-Curing Family -0.008838
95 ENOG4105C9Q fumarate hydratase class II -0.008826
96 ENOG4105ER5 DNA-binding protein -0.008818
97 ENOG41080HT Transcriptional regulator, arsr family 0.008813
98 ENOG4105X44 SMC domain protein 0.008782
99 ENOG4107WCB Multicopper oxidase 0.008774
100 ENOG4105PW4 Sugar fermentation stimulation protein homolog 0.008769
101 ENOG4105VGN Protein of unknown function (DUF1499) -0.008738
102 ENOG4107QIW Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism (By similarity) 0.008718
103 ENOG41068R5 CopG domain protein DNA-binding domain protein -0.008681
104 ENOG4105E36 cytochrome C 0.008681
105 ENOG4105MGE Rhodanese domain protein 0.008679
106 ENOG41076QQ Glycosyl transferase, family 2 0.008644
107 ENOG4107RDJ Sulfotransferase -0.008615
108 ENOG4108K9W NA 0.008610
109 ENOG4107EQT Protein of unknown function (DUF2283) -0.008593
110 ENOG4105INR host attachment protein 0.008575
111 ENOG4105TNC Membrane 0.008524
112 ENOG4108JQX Phosphoglucomutase (EC 5.4.2.2 0.008514
113 ENOG4105W1Y Transcriptional regulator 0.008512
114 ENOG4108PUY CRISPR-associated protein Crm2 family 0.008507
115 ENOG4107VZP Hemolysin-type calcium-binding repeat 2 copies family protein -0.008398
116 ENOG4105CEN a g-specific adenine glycosylase -0.008372
117 ENOG4105EME Glycosyl transferase (Group 1 0.008368
118 ENOG4105G6B ABC transporter -0.008345
119 ENOG4105VT3 DNA binding domain protein, excisionase family 0.008327
120 ENOG4108W5X Transcriptional Regulator, LuxR family 0.008316
121 ENOG4105CVP deoxyribo-dipyrimidine photolyase 0.008302
122 ENOG4105I4Y extracellular ligand-binding receptor 0.008271
123 ENOG4105CX0 fumarate reductase succinate dehydrogenase flavoprotein domain protein -0.008265
124 ENOG41072D2 NA -0.002752
124 ENOG4107VTG DNA methylase -0.002752
124 ENOG410820U Rhodanese domain protein -0.002752
125 ENOG41069GX Transcriptional regulator -0.008240
126 ENOG4108YYC ycei family -0.008215
127 ENOG4108FXH NA -0.008211
128 ENOG4105C6Y Udp-glucose 6-dehydrogenase -0.008116
129 ENOG4106D5Z Transcriptional regulator CopG family -0.008105
130 ENOG4108W8P Diguanylate cyclase with PAS PAC sensor 0.008075
131 ENOG4108XRS Monoheme cytochrome SoxX (Sulfur oxidation) 0.008053
132 ENOG4105V9J phenylacetic acid degradation operon negative regulatory protein 0.008049
133 ENOG4106329 NA -0.008041
134 ENOG4107WMV HTH domain -0.004020
134 ENOG4108FZK NA -0.004020
135 ENOG4105DG7 nitrate ABC transporter 0.008026
136 ENOG4107GFK fumarate 0.008025
137 ENOG4105PF0 Antitoxin component of a toxin-antitoxin (TA) module. Functions as an mRNA interferase antitoxin -0.007976
138 ENOG4107KBT 8-Amino-7-oxononanoate synthase -0.007956
139 ENOG4105DPN Oligoendopeptidase f -0.007949
140 ENOG4107T9R methyltransferase 0.007937
141 ENOG4105CIN aminoacyl-histidine dipeptidase -0.007932
142 ENOG4105DKC membrane protein involved in aromatic hydrocarbon degradation 0.007924
143 ENOG4105IYI Short-chain dehydrogenase reductase Sdr -0.007857
144 ENOG4107NJ0 Sodium calcium exchanger membrane region -0.007848
145 ENOG4108KMK Diguanylate cyclase -0.007839
146 ENOG41088YR Sulfide dehydrogenase 0.007827
147 ENOG4105IJ9 Glycosyl transferase, family 2 0.007819
148 ENOG4105YIA S-layer protein 0.003902
148 ENOG4108YC6 peptidase S8 and S53, subtilisin, kexin, sedolisin 0.003902
149 ENOG4107MRR Binding-protein-dependent transport system inner membrane 0.003901
149 ENOG4108CRW Prokaryotic N-terminal methylation motif 0.003901
150 ENOG4108PEB Histidine kinase -0.007801
151 ENOG4107R0M Integrase -0.007780
152 ENOG4107RBZ sulfate transporter 0.007724
153 ENOG4108ZFX Mannosyl-3-phosphoglycerate phosphatase 0.007723
154 ENOG4105CTD carboxy-peptidase -0.007708
155 ENOG4108S57 peptidase C14 caspase catalytic subunit p20 -0.007703
156 ENOG410626T hicA protein -0.007690
157 ENOG4108FZ1 Transcriptional regulator -0.007681
158 ENOG4108D1Y Polypeptide-transport-associated domain protein, ShlB-type 0.007671
159 ENOG4107XGM Glycosyl transferase (Group 1 -0.007667
160 ENOG4105DJQ tetratricopeptide tpr_2 repeat protein -0.007667
161 ENOG41089UC methyltransferase, type 11 -0.007664
162 ENOG4105YFU NA 0.007662
163 ENOG4105NCJ NA -0.007649
164 ENOG4105ECW sulfate abc transporter -0.003822
164 ENOG4108I5D sulfate abc transporter -0.003822
165 ENOG4105MDR response regulator -0.007622
166 ENOG4107RI5 (ABC) transporter 0.007616
167 ENOG4105ETT transcriptional Regulator, LysR family -0.007589
168 ENOG4105ZUB AbrB family transcriptional regulator -0.007563
169 ENOG41063PH NA -0.007556
170 ENOG4105E0A ABC, transporter -0.007535
171 ENOG4107SPR Family of unknown function (DUF490) -0.007511
172 ENOG4105CR6 AtP-binding protein 0.007508
173 ENOG4108Y02 Transcriptional regulator, arsr family -0.007473
174 ENOG4107RJ7 Glycosyl transferase (Group 1 -0.007471
175 ENOG4105CHH sulfate transporter 0.007465
176 ENOG4108UMI ABC transporter, permease -0.007459
177 ENOG4105D01 (LipO)protein -0.007459
178 ENOG4108T8T NA -0.007456
179 ENOG4105FT6 finger domain protein -0.007450
180 ENOG4105EE9 pfkb domain protein 0.007449
181 ENOG4105CE4 GlcNAc 6-P deacetylase -0.007446
182 ENOG4108NA5 Inherit from COG: DNA primase -0.007435
183 ENOG4105DWC glycoside hydrolase family protein 0.007421
184 ENOG4106867 Phosphate-starvation-inducible E 0.007420
185 ENOG4105CCA Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle (By similarity) -0.007414
186 ENOG4108NUC Major Facilitator -0.007411
187 ENOG4105JR2 flavin reductase domain protein, FMN-binding -0.007407
188 ENOG4105CIH Imidazole acetol-phosphate transaminase 0.007398
189 ENOG4105E26 Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and or degradation of damaged proteins (By similarity) -0.007352
190 ENOG4108WTJ EamA-like transporter family 0.007351
191 ENOG4106FIV Lipocalin-like domain -0.007327
192 ENOG4106IQC argininosuccinate lyase -0.007321
193 ENOG4105F14 permease -0.007313
194 ENOG4105EJQ L-serine dehydratase -0.007306
195 ENOG41085MA prevent-host-death family 0.007303
196 ENOG4105DA5 (ABC) transporter -0.007302
197 ENOG4108YZA Nitrogen regulatory protein pii 0.007301
198 ENOG4108WHA ompa motb domain protein -0.007295
199 ENOG4105HBC Transcriptional regulator -0.007293
200 ENOG4105CBG Sulfatase -0.007285
201 ENOG4108PDN Crispr-associated ramp protein, Cmr4 family 0.007251
202 ENOG4105F5W AtP-binding protein -0.007231
203 ENOG4105CUR 5'-nucleotidase, lipoprotein e(p4) family -0.007221
204 ENOG4106034 NA -0.007215
205 ENOG4105J0B DsrE/DsrF-like family 0.007207
206 ENOG4105E0F Histidine kinase -0.007201
207 ENOG4105F2W methyltransferase -0.007199