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 ENOG4106A5H cytochrome c554 0.007447
2 ENOG4105E7Z methane monooxygenase ammonia monooxygenase subunit A 0.001862
2 ENOG4105HCI NA 0.001862
2 ENOG41064HC NA 0.001862
2 ENOG4108P7H monooxygenase, subunit B 0.001862
3 ENOG410719V NA 0.006451
4 ENOG4108UKM mov34 mpn pad-1 family protein 0.006282
5 ENOG4105CUW cytochrome C-TYPE protein 0.006239
6 ENOG4108XW3 Esterase lipase thioesterase family 0.006168
7 ENOG4105PCB ammonia monooxygenase methane monooxygenase subunit C 0.001989
7 ENOG4108X4B NA 0.001989
7 ENOG4108ZXY Glycosyl transferase, family 2 0.001989
8 ENOG4108PNC copper resistance 0.005938
9 ENOG4106ACQ amino acid 0.005928
10 ENOG410902D cobalamin (vitamin b12) biosynthesis cbix protein 0.005648
11 ENOG410690C hydroxylamine oxidase 0.005567
12 ENOG4108S0G Protein of unknown function (DUF2959) 0.005551
13 ENOG41075VY Squalene phytoene synthase 0.005325
14 ENOG4107UNM Coenzyme F390 synthetase-like protein 0.005286
15 ENOG4105MER NA 0.002635
15 ENOG4105YMV Domain of unknown function (DUF2024) 0.002635
16 ENOG4105CA5 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes (By similarity) 0.000752
16 ENOG4105DA4 cytochrome c-type biogenesis protein 0.000752
16 ENOG4105KWW Biogenesis protein 0.000752
16 ENOG41060IM Heme exporter protein 0.000752
16 ENOG4107EV4 once thought to export heme, this seems not to be the case, but its exact role is uncertain. Responsible for energy coupling to the transport system (By similarity) 0.000752
16 ENOG4107QX9 Thiol disulfide interChange protein 0.000752
16 ENOG4108ZKK Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH (By similarity) 0.000752
17 ENOG4105UHE Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits (By similarity) 0.002627
17 ENOG41082JU C subunit 0.002627
18 ENOG4105EWU Squalene--hopene cyclase 0.002625
18 ENOG4105F9Q Hopanoid biosynthesis associated radical SAM protein HpnH 0.002625
19 ENOG4108PNF NA 0.005239
20 ENOG4108THN cytochrome C 0.005171
21 ENOG4105F67 signal transduction Histidine kinase 0.005136
22 ENOG4105K78 MarR family Transcriptional regulator 0.005001
23 ENOG4107SPW HsdM N-terminal domain 0.004981
24 ENOG41090GT NA 0.004968
25 ENOG4105M08 Membrane 0.004927
26 ENOG4105DN2 repeat protein 0.004927
27 ENOG4108TSW Protoglobin 0.004889
28 ENOG4105DPZ Two component transcriptional regulator (Winged helix family -0.004847
29 ENOG4108QJ1 Multicopper oxidase, type 1 0.004805
30 ENOG4105HA8 hopanoid biosynthesis associated membrane protein HpnM 0.002388
30 ENOG41076NN NA 0.002388
31 ENOG4105C15 The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity) 0.004772
32 ENOG4105CI7 Hopanoid biosynthesis associated RND transporter like protein HpnN 0.004756
33 ENOG4105NSI phosphorylase 0.004756
34 ENOG4107T8V it plays a direct role in the translocation of protons across the membrane (By similarity) 0.004719
35 ENOG4108Q71 Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) (By similarity) 0.004719
36 ENOG4105W8H transhydrogenase (subunit alpha 0.004689
37 ENOG4109030 Protein of unknown function (DUF1318) 0.004643
38 ENOG4105VSV Copper resistance protein CopC 0.004627
39 ENOG4105VZQ Helix-turn-helix protein CopG family 0.004611
40 ENOG4107QRI Phosphoketolase 0.004577
41 ENOG4108U7K Intradiol ring-cleavage dioxygenase 0.004538
42 ENOG4105C0Y Responsible for the amidation of carboxylic groups at position A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) -0.004514
43 ENOG4105HT4 NA -0.004505
44 ENOG4108H18 Polysaccharide biosynthesis protein 0.004497
45 ENOG410666Z NA 0.004490
46 ENOG4108SII ferroxidase (EC 1.16.3.1) 0.004460
47 ENOG4105WD1 Membrane 0.004441
48 ENOG4105C47 NADH ubiquinone oxidoreductase 20 kda subunit -0.004437
49 ENOG4107QWE )-transporter 0.004430
50 ENOG4105CKK Glycosyl transferase, family 2 -0.004427
51 ENOG41087Y0 Glycosyl transferase, family 2 0.004415
52 ENOG4105D20 Nad-dependent epimerase dehydratase 0.004411
53 ENOG4108HM5 NADH-ubiquinone oxidoreductase chain 49kDa -0.004374
54 ENOG410633V NA 0.004357
55 ENOG4106RI3 Cytochrome C oxidase subunit II, periplasmic domain 0.004354
56 ENOG4107R30 NADH dehydrogenase -0.002174
56 ENOG4107RAG Respiratory-chain NADH dehydrogenase, subunit 1 -0.002174
57 ENOG4108E5V Phosphate-Selective Porin O and P 0.004335
58 ENOG4107QQX Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway (By similarity) 0.004331
59 ENOG4107REJ bifunctional glutamate synthase subunit beta 2-polyprenylphenol hydroxylase 0.004316
60 ENOG4109083 pas pac sensor-containing diguanylate cyclase 0.004312
61 ENOG4108VPQ HhH-GPD domain protein 0.004309
62 ENOG4107XTC May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins -0.004304
63 ENOG4105DAP Nicotinate phosphoribosyltransferase 0.004291
64 ENOG410902H NADH dehydrogenase (Ubiquinone), 24 kDa subunit -0.004279
65 ENOG4108SNX Mammalian cell entry related domain protein 0.004273
66 ENOG4105FHW DSBA oxidoreductase 0.004236
67 ENOG4105K89 arsenate reductase 0.004219
68 ENOG4105D6J arsenicaL-resistance protein -0.004219
69 ENOG4105CUZ uba thif-type nad fad binding protein -0.004219
70 ENOG4105M2B PEP-CTERM motif 0.004218
71 ENOG4107GKG Sulfate transporter family 0.004212
72 ENOG4108UHE carbonic anhydrase 0.004211
73 ENOG410830V Protein of unknown function (DUF497) 0.004202
74 ENOG4105KUA histidine triad (HIT) protein -0.004182
75 ENOG4105D1S lipid A biosynthesis -0.004164
76 ENOG4107ENK receptor 0.004164
77 ENOG4105VN1 Heat shock protein 0.004163
78 ENOG4105EBH Required during biogenesis of c-type cytochromes (cytochrome c6 and cytochrome f) at the step of heme attachment (By similarity) -0.004156
79 ENOG41067VP Protein of unknown function (DUF1049) 0.004151
80 ENOG4105KJJ Uncharacterized ACR, COG1993 0.002076
80 ENOG4107BMI NA 0.002076
81 ENOG4105CHF Glutathione S-transferase 0.004137
82 ENOG4107QQA kelch repeat-containing protein 0.004135
83 ENOG4105NKG ankyrin repeat-containing protein 0.004125
84 ENOG4105CEI nitrite reductase 0.004112
85 ENOG4105VGT s23 ribosomal protein -0.004093
86 ENOG4107EQG BFD domain protein (2Fe-2S)-binding domain protein 0.004090
87 ENOG4105XUX domain protein 0.004088
88 ENOG4105CCC Dihydrolipoamide dehydrogenase 0.004087
89 ENOG4105F7J membrane-bound serine protease 0.004081
90 ENOG41090HT Inherit from COG: transposase 0.004059
91 ENOG4105KEU Polysaccharide deacetylase 0.004051
92 ENOG4108I67 Catalyzes the synthesis of activated sulfate (By similarity) 0.004044
93 ENOG41082JX Excinuclease ABC C subunit domain protein 0.004033
94 ENOG4105EDC Efflux transporter rnd family, mfp subunit 0.004023
95 ENOG4105EYA deoxyribonuclease -0.003997
96 ENOG4107QN5 Band 7 protein 0.003995
97 ENOG4105Y4Z Outer Membrane Lipoprotein 0.003993
98 ENOG4105D45 K07001 NTE family protein 0.003988
99 ENOG4105KYB Mazg nucleotide pyrophosphohydrolase -0.003987
100 ENOG4107QPN acyl-Coa dehydrogenase 0.003982
101 ENOG4105DVC DnaJ domain protein 0.003970
102 ENOG4105DRC Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.003966
103 ENOG4107S9W DNA methylase N-4 N-6 0.003948
104 ENOG4105C58 cytochrome c oxidase accessory protein ccog -0.003945
105 ENOG4105D6P C-type cytochrome. Part of the cbb3-type cytochrome c oxidase complex (By similarity) -0.003945
106 ENOG4107QQC pyridine nucleotide-disulfide oxidoreductase 0.003942
107 ENOG4105RYU Thiol-disulfide oxidoreductase dcc 0.003939
108 ENOG4105D4I Uncharacterized protein conserved in bacteria (DUF2130) 0.003910
109 ENOG4108UNV SUF system FeS assembly protein, NifU family 0.003906
110 ENOG41081KP Iron-regulated protein 0.003896
111 ENOG4108AAZ Bile acid sodium symporter 0.003896
112 ENOG4108KXP Outer membrane efflux protein 0.003878
113 ENOG4105CAA catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation (By similarity) -0.003872
114 ENOG4105H8Y Protein of unknown function (DUF1614) 0.003857
115 ENOG4107EP0 Heme exporter protein 0.003855
116 ENOG4107IY0 NA 0.003855
117 ENOG4105CD8 aminopeptidase N -0.003848
118 ENOG4105BZJ Electron transfer flavoprotein -0.001920
118 ENOG4105C10 Electron transfer flavoprotein -0.001920
119 ENOG41090BR NA 0.003831
120 ENOG4105CBX hi0933 family 0.003828
121 ENOG4106G2I secreted hydrolase-like protein 0.003826
122 ENOG4105KZC NA 0.003818
123 ENOG4107IQ5 Carrier of the growing fatty acid chain in fatty acid biosynthesis (By similarity) 0.003809
124 ENOG41090M2 Protein of unknown function (DUF1207) 0.003789
125 ENOG4105DZR Type I site-specific deoxyribonuclease 0.003787
126 ENOG4106FRQ PEP-CTERM motif 0.003785
127 ENOG4108ZIT Ferredoxin, 2FE-2S -0.003782
128 ENOG4105ZKX NA 0.003780
129 ENOG4105E1P Modifies, by uridylylation or deuridylylation the PII (GlnB) regulatory protein (By similarity) -0.003774
130 ENOG4105EVB acetyltransferase 0.003770
131 ENOG4105YBU NA 0.001253
131 ENOG4106BYH NA 0.001253
131 ENOG4107Y9E nuclease 0.001253
132 ENOG4105E4M (twin-arginine translocation) pathway signal 0.003758
133 ENOG4105ZJM Archease protein family (MTH1598/TM1083) 0.003757
134 ENOG4105XHE NA 0.001871
134 ENOG410665V Protein of unknown function (DUF2283) 0.001871
135 ENOG4105ETP RND efflux system, outer membrane lipoprotein -0.003742
136 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) 0.003727
137 ENOG4106PA4 NA 0.003725
138 ENOG4107T1N adenine specific DNA methylase 0.003719
139 ENOG4105BZK Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity) 0.003718
140 ENOG4107EP5 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). Functions as a ssRNA-specific endoribonuclease (By similarity) 0.003717
141 ENOG4105GWV ATPase with chaperone activity ATP-binding subunit 0.003714
142 ENOG4106A2A (LipO)protein 0.003714
143 ENOG4105KC0 Glyoxalase Bleomycin resistance protein (Dioxygenase 0.003703
144 ENOG4106F5G NA 0.003693
145 ENOG4108ZZP Transcriptional regulator, TetR family 0.003689
146 ENOG4108TA9 Response regulator receiver 0.003688
147 ENOG4107GFK fumarate -0.003686
148 ENOG4105YGM Outer membrane efflux protein 0.003686
149 ENOG4108DND heavy metal efflux pump, CzcA family 0.003686
150 ENOG4107R16 Multicopper oxidase 0.003666
151 ENOG4107S4N sulfate transporter 0.003659
152 ENOG4108J1P NA 0.003658
153 ENOG4108UNF response regulator 0.003652
154 ENOG4105MUC DoxX Family 0.003650
155 ENOG4108SK6 type III restriction system methylase 0.003629
156 ENOG4107WI0 lipid A biosynthesis -0.003606
157 ENOG4105UV2 general secretion pathway protein K 0.003606
158 ENOG4105C9Q fumarate hydratase class II 0.003606
159 ENOG4108C33 Resolvase 0.003603
160 ENOG4108UQY Iron-storage protein 0.003582
161 ENOG4105MY1 NA 0.001788
161 ENOG4108KMA NA 0.001788
162 ENOG4105C6V Glycerol-3-phosphate dehydrogenase 0.003575
163 ENOG41080IJ Diacylglycerol kinase -0.003560
164 ENOG4105VXS exported protein -0.003558
165 ENOG4105I81 cmp dcmp deaminase, zinc-binding 0.003556
166 ENOG410650F NA 0.003548
167 ENOG4105C5R Aminotransferase 0.003545
168 ENOG41064AB Electron transport protein 0.001768
168 ENOG4106TT8 NA 0.001768
169 ENOG4107QPT Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis (By similarity) 0.003526
170 ENOG4105WYU NA 0.003519
171 ENOG41066RF FAD linked oxidase domain protein -0.003512
172 ENOG4108RAR dienelactone hydrolase 0.003500
173 ENOG41060UM Phosphopantetheine attachment site 0.003497
174 ENOG4105DSS Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity) 0.003494
175 ENOG4105Q84 sucrose synthase 0.003493
176 ENOG4105FD1 Membrane 0.003487
177 ENOG4105P9R UspA domain-containing protein 0.003484
178 ENOG41080I3 integral membrane protein CcmA involved in cell shape determination 0.003475
179 ENOG4108S6J ABC transporter, periplasmic molybdate-binding protein -0.003473
180 ENOG4107RGG Peroxiredoxin 0.003464
181 ENOG4105SZT Methyltransferase, type 11 0.003461
182 ENOG4105EIN peptidylprolyl cis-trans isomerase 0.003450
183 ENOG4106BY3 NA 0.003439
184 ENOG4105EPH radical SAM domain protein -0.003430
185 ENOG4108HNQ peptidase 0.003430
186 ENOG4105W3H MtN3 and saliva related transmembrane protein -0.003424
187 ENOG4105EXM tonB-dependent Receptor 0.003421
188 ENOG4108JI8 Folate biopterin transporter 0.003420
189 ENOG4108R5Q alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.003420
190 ENOG41089BK Glutamine amido-transferase 0.003416
191 ENOG4108YY7 Invasion gene expression up-regulator SirB 0.003415
192 ENOG4108W0M calcium-binding 0.003409
193 ENOG4105EUH cytochrome C oxidase, cbb3-type, subunit i -0.003408
194 ENOG4106H3A restriction 0.003407
195 ENOG41083ED Esterase lipase thioesterase family 0.003407
196 ENOG4105E80 TraG TraD family protein 0.003405
197 ENOG4107RU8 SPFH domain, Band 7 family protein -0.003405
198 ENOG4108NWC CRISPR-associated protein, NE0113 family 0.003404
199 ENOG41082VH Transcriptional regulator 0.003401
200 ENOG4105EF8 ABC transporter, permease 0.001133
200 ENOG4105F9I RND Family Efflux Transporter MFP Subunit 0.001133
200 ENOG4107QZH ABC transporter, permease 0.001133
201 ENOG4105CUB amino acid 0.003395
202 ENOG4106H6N NA 0.003394
203 ENOG4107UA2 methyl-accepting chemotaxis 0.003388
204 ENOG4105G1G alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.003387
205 ENOG4108IQE Amp-dependent synthetase and ligase 0.003386
206 ENOG4108KYK Efflux transporter rnd family, mfp subunit 0.003384
207 ENOG4105XCP PRC-barrel domain protein 0.003380
208 ENOG4106FW7 NA 0.003375
209 ENOG41080UK Membrane-bound metal-dependent hydrolase 0.003370
210 ENOG4108VX5 3-methyladenine DNA glycosylase 0.003358
211 ENOG4105DEM Methyltransferase -0.003354
212 ENOG410681N tpr repeat protein 0.003354
213 ENOG4107QS5 ATP-dependent DNA helicase RecQ -0.003354
214 ENOG4105CBC glutamate synthase 0.003349
215 ENOG4105UGU tonB-dependent Receptor 0.003348
216 ENOG4108WB2 Phosphatase 0.003343
217 ENOG4105HSZ Cytoskeletal protein that is involved in cell-shape control through regulation of the length of the long axis (By similarity) 0.003341
218 ENOG41068H8 transposase 0.003338
219 ENOG4105CIA precorrin-4 C(11)-methyltransferase -0.001669
219 ENOG4105E4R Precorrin-3B C17-methyltransferase -0.001669
220 ENOG41081F0 Precorrin-8x methylmutase -0.003337
221 ENOG4105MWN Alpha beta hydrolase -0.003337
222 ENOG4105DUJ cytochrome C oxidase -0.003327
223 ENOG4105M5D Putative trans-membrane protein 0.003323
224 ENOG41063ZP 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). Functions as a ssRNA-specific endoribonuclease (By similarity) 0.003323