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 ENOG4107ZQV short-chain dehydrogenase reductase 0.031728
2 ENOG4105FEU K -dependent Na -Ca exchanger 0.013977
3 ENOG4105MG1 Diguanylate cyclase phosphodiesterase -0.013959
4 ENOG4107V4H DNA methylase 0.013589
5 ENOG4105KVJ Periplasmic binding protein 0.013031
6 ENOG4105CM4 permease protein 0.006246
6 ENOG4108IPW abc transporter atp-binding protein 0.006246
7 ENOG4105DQ4 alcohol dehydrogenase 0.011988
8 ENOG41061X9 NA -0.002372
8 ENOG41066CJ NA -0.002372
8 ENOG4106VWA XisI protein -0.002372
8 ENOG4108TEY Pfam:DUF820 -0.002372
8 ENOG4108VSR Pfam:DUF820 -0.002372
9 ENOG410801S Inherit from COG: Glycosyl transferase, family 2 0.011637
10 ENOG4105F38 ABC transporter, permease 0.011463
11 ENOG4105E6K 4-Hydroxyphenylpyruvate dioxygenase 0.011395
12 ENOG410613J NA 0.002224
12 ENOG41062YC NA 0.002224
12 ENOG4106VCZ Domain of unknown function DUF29 0.002224
12 ENOG410780I phosphoprotein phosphatase activity 0.002224
12 ENOG4108RIH NA 0.002224
13 ENOG4105HA9 of methanol dehydrogenase type 0.010978
14 ENOG41080DC ankyrin-like protein -0.010956
15 ENOG4105VTW prevent-host-death family 0.010941
16 ENOG4105DHS permease protein 0.010800
17 ENOG4108NRN NA 0.010612
18 ENOG4108TEB UPF0114 protein 0.010516
19 ENOG4105ZQ1 NA -0.010486
20 ENOG4105C2S Catalyzes the NADPH dependent reduction of L-gamma- glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate (By similarity) 0.005202
20 ENOG4105CGT Catalyzes the transfer of a phosphate group to glutamate to form glutamate 5-phosphate which rapidly cyclizes to 5- oxoproline (By similarity) 0.005202
21 ENOG4108UY6 tripartite ATP-independent periplasmic transporter, DctQ component 0.010386
22 ENOG4105CBH Hydroxymethylglutaryl-CoA lyase 0.010308
23 ENOG4107R0A malonate decarboxylase subunit beta -0.010269
24 ENOG4105KK4 UPF0060 membrane protein -0.010209
25 ENOG4107R73 Mate efflux family protein 0.010199
26 ENOG4105DUX Transporter 0.010146
27 ENOG4108ZFX Mannosyl-3-phosphoglycerate phosphatase 0.010138
28 ENOG4106JRM HPT 0.010126
29 ENOG4105CQ3 Poorly processive error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by polIV. Exhibits no 3-5 exonuclease (proofreading) activity. May be involved in translesional synthesis in conjunction with the beta clamp from polIII (By similarity) 0.010060
30 ENOG4105DUN Mediates zinc uptake. May also transport other divalent cations (By similarity) 0.010040
31 ENOG4108UEQ NA 0.009930
32 ENOG4106A3M Cytochrome p-450 0.009913
33 ENOG4108RVA ribokinase 0.009911
34 ENOG4105PGM cation diffusion facilitator family transporter 0.009816
35 ENOG4105DFD Na H antiporter 0.009784
36 ENOG4107RGH Aldehyde dehydrogenase 0.009758
37 ENOG4107SEQ Methyltransferase Type 0.009735
38 ENOG4108ZHX TM2 domain containing protein 0.009717
39 ENOG4105RT3 Hnh endonuclease -0.000808
39 ENOG41062XI NA -0.000808
39 ENOG41063I8 NA -0.000808
39 ENOG4106DCB NA -0.000808
39 ENOG4106DYE NA -0.000808
39 ENOG4106S3G Domain of unknown function DUF29 -0.000808
39 ENOG4106S57 Domain of Unknown Function (DUF928) -0.000808
39 ENOG4106WY9 NA -0.000808
39 ENOG4106X8C Inherit from COG: Addiction module toxin, RelE StbE family -0.000808
39 ENOG4107HTC NA -0.000808
39 ENOG41082M9 Protein of unknown function DUF262 -0.000808
39 ENOG41084Z5 Protein of unknown function (DUF497) -0.000808
40 ENOG4106NQW sterol desaturase 0.009623
41 ENOG4108YSG O-Antigen polymerase -0.009553
42 ENOG4105CV8 reductase 0.009545
43 ENOG4105M1N CHP02436-containing protein 0.009446
44 ENOG4105EKD Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism (By similarity) 0.009426
45 ENOG4105D2R type I restriction-modification system -0.001343
45 ENOG4105GHP NA -0.001343
45 ENOG4106IF1 NA -0.001343
45 ENOG4107FWQ NA -0.001343
45 ENOG4107SVZ Adenylate -0.001343
45 ENOG4107VE9 Aldo Keto reductase -0.001343
45 ENOG4108NXA Inherit from COG: transposase -0.001343
46 ENOG4107X0W catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR (By similarity) -0.009366
47 ENOG4108P45 Sulfotransferase -0.009364
48 ENOG4105CNA YD repeat protein -0.009327
49 ENOG4105MIR Phenylalanine 4-monooxygenase 0.009293
50 ENOG4105EWI Short-chain dehydrogenase reductase Sdr -0.009293
51 ENOG4105D82 Glutamate dehydrogenase -0.009288
52 ENOG4108JZJ Phosphoadenosine phosphosulfate reductase 0.009272
53 ENOG4105DIE 6-aminohexanoate-dimer hydrolase 0.009241
54 ENOG4105CE1 Ferrous iron transport protein b 0.009190
55 ENOG4105VJY transcriptional regulator -0.009166
56 ENOG4105PWP Protein of unknown function (DUF1211) -0.009153
57 ENOG4108UUM single-stranded DNA-binding protein 0.009146
58 ENOG41082NM hemolysin-type calcium-binding region 0.009084
59 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) 0.009053
60 ENOG4108NJZ Sensory box GGDEF EAL domain protein 0.009044
61 ENOG4105E9V Periplasmic binding protein LacI transcriptional regulator 0.009040
62 ENOG4105CEY Amp-dependent synthetase and ligase -0.009038
63 ENOG4105C18 Uncharacterized protein conserved in bacteria (DUF2252) -0.009027
64 ENOG4105ENV phosphonate C-P lyase system protein PhnK -0.004513
64 ENOG4105FT8 Phosphonate metabolism -0.004513
65 ENOG4108ZXC Two component transcriptional regulator, luxr family -0.009024
66 ENOG4105DV0 amidase (EC 3.5.1.4 0.008913
67 ENOG4105C7W Xanthine dehydrogenase 0.008896
68 ENOG4105E0N fumarylacetoacetase EC 3.7.1.2 0.008865
69 ENOG4105CC4 NA -0.002213
69 ENOG4105GF3 Pfam:DUF820 -0.002213
69 ENOG41072DJ NA -0.002213
69 ENOG4108PMG periplasmic binding protein -0.002213
70 ENOG4105Z8H single-stranded DNA-binding protein -0.008830
71 ENOG4108V0P LemA family 0.008813
72 ENOG41070Y4 NA 0.008795
73 ENOG41065ZE NA -0.008733
74 ENOG4105KT7 mgtC SapB transporter 0.008707
75 ENOG4107CH6 NA 0.004332
75 ENOG4107VKG repeat protein 0.004332
76 ENOG4105D33 fg-gap repeat protein 0.000360
76 ENOG4105GBP NA 0.000360
76 ENOG4105JCT NA 0.000360
76 ENOG4105MKE Protein of unknown function (DUF497) 0.000360
76 ENOG4105P45 NA 0.000360
76 ENOG4105P9Z NA 0.000360
76 ENOG4105PTD NA 0.000360
76 ENOG41061TA NA 0.000360
76 ENOG41062VX 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) 0.000360
76 ENOG4106EMC NA 0.000360
76 ENOG4106Z5Y NA 0.000360
76 ENOG410706A NA 0.000360
76 ENOG41072Q6 NA 0.000360
76 ENOG410795Z NA 0.000360
76 ENOG4107DID NA 0.000360
76 ENOG4107DSD NA 0.000360
76 ENOG4107F70 feoA family 0.000360
76 ENOG4107IMX Inherit from NOG: transposase 0.000360
76 ENOG4107S3I DNA methylase N-4 N-6 0.000360
76 ENOG4107UED Aminotransferase 0.000360
76 ENOG410849Q Protein of unknown function (DUF559) 0.000360
76 ENOG41085FP dual specificity protein phosphatase 0.000360
76 ENOG4108JVA Ferredoxin 0.000360
76 ENOG4108NAW Type II site-specific deoxyribonuclease 0.000360
77 ENOG4108Z7T Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) 0.008597
78 ENOG4105ZF6 NA -0.008531
79 ENOG4105MJ7 glutathione-dependent formaldehyde-activating Gfa 0.008517
80 ENOG4105CI0 Citrate lyase 0.008512
81 ENOG4107U81 Protein of unknown function (DUF1524) 0.008494
82 ENOG4105DEU major facilitator superfamily 0.008479
83 ENOG4108Q73 NA 0.008460
84 ENOG4105CQ0 ABC transporter 0.008442
85 ENOG4105E7W lamb ycsf family protein -0.008418
86 ENOG4108IRD NA -0.008407
87 ENOG4107S83 Endonuclease Exonuclease phosphatase -0.008388
88 ENOG4107VS1 KR domain -0.008383
89 ENOG4107R7A Allophanate hydrolase subunit 2 -0.008355
90 ENOG4105C87 Aminotransferase class I and II 0.008344
91 ENOG4108RAV Conserved protein -0.008315
92 ENOG4107RAN Peptidase, M16 0.008290
93 ENOG4107RSU Glycosyl transferase, family 2 0.008274
94 ENOG4105DRD mechanosensitive ion channel 0.008236
95 ENOG4106TC3 peptidase 0.008224
96 ENOG4107RGK Monooxygenase 0.008207
97 ENOG4108S33 NA -0.008205
98 ENOG4105VNT transposase (IS4 family) protein -0.008193
99 ENOG4108R5P Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery (By similarity) 0.008163
100 ENOG4107J5X Diguanylate cyclase with PAS PAC sensor 0.008138
101 ENOG4105NXF Protein of unknown function (DUF3124) 0.008138
102 ENOG4105D13 transposase 0.008123
103 ENOG4105CHH sulfate transporter 0.008118
104 ENOG4105I99 Inherit from NOG: molybdenum cofactor biosynthesis protein 0.000812
104 ENOG4105PYX NA 0.000812
104 ENOG41061I6 NA 0.000812
104 ENOG410621P NA 0.000812
104 ENOG410677V NA 0.000812
104 ENOG41067PX Signal transduction protein with Nacht domain 0.000812
104 ENOG4106BY3 NA 0.000812
104 ENOG41078YF NA 0.000812
104 ENOG4107U3N Response regulator receiver modulated diguanylate phosphodiesterase 0.000812
104 ENOG41081WP NA 0.000812
105 ENOG4105M12 Membrane 0.008096
106 ENOG4105CYW agmatinase 0.008070
107 ENOG4105E2Z phosphate ABC transporter (Permease 0.008070
108 ENOG4105UBP i restriction-modification system -0.008068
109 ENOG4108Z0Z intracellular protease Pfpi family 0.008038
110 ENOG4107T6Y 6-O-methylguanine DNA methyltransferase, DNA binding domain -0.008032
111 ENOG4108HEW Response regulator receiver domain 0.008016
112 ENOG4105CAQ asparagine synthetase 0.008014
113 ENOG4105E9Q Acyl-transferase 0.008011
114 ENOG4105NAE bifunctional deaminase-reductase domain protein -0.008010
115 ENOG4105UKP Protein of unknown function (DUF1778) -0.008002
116 ENOG4105GT0 NA -0.000995
116 ENOG4105JU0 Pfam:DUF820 -0.000995
116 ENOG4105PXB Tetr family transcriptional regulator -0.000995
116 ENOG4105Z6C NA -0.000995
116 ENOG41063D5 DNA polymerase beta domain-containing protein -0.000995
116 ENOG4106EDH sensor with hamp domain -0.000995
116 ENOG4107UVF Integrase catalytic subunit -0.000995
116 ENOG4108VP2 aaa ATPase -0.000995
117 ENOG4108QJS PBS lyase HEAT domain protein repeat-containing protein -0.007955
118 ENOG4105CU5 Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine (By similarity) 0.007946
119 ENOG4108Z0R Transferase 0.007944
120 ENOG4105MZG transcriptional modulator of maze toxin, mazf -0.007941
121 ENOG4105DR1 Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration (By similarity) 0.007939
122 ENOG4105EKV Phosphonate metabolism protein -0.003968
122 ENOG4105HRV phosphonate c-p lyase system protein phnl -0.003968
123 ENOG4105ETT transcriptional Regulator, LysR family 0.007926
124 ENOG4105EKQ RNA-directed DNA polymerase 0.007862
125 ENOG4107UNG Ser Thr phosphatase family protein 0.007845
126 ENOG4107S47 Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC) (By similarity) 0.007829
127 ENOG4105N77 NA 0.007824
128 ENOG41080D9 Swarming motility protein YbiA -0.007813
129 ENOG4105C4N this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis (By similarity) 0.007792
130 ENOG4105CK7 Sodium proline symporter -0.007786
131 ENOG41060S4 immunity protein -0.007774
132 ENOG4105DF3 Catalyzes the retro-aldol cleavage of 4-hydroxy-2- oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds (By similarity) 0.007750
133 ENOG4108S6J ABC transporter, periplasmic molybdate-binding protein -0.007748
134 ENOG4105KHT Tetr family transcriptional regulator -0.007746
135 ENOG41090AW NA -0.007733
136 ENOG4105C5A transporter -0.007722
137 ENOG4108RXX maleylacetoacetate isomerase 0.007717
138 ENOG4105SRG K07001 NTE family protein 0.007696
139 ENOG41072A1 esterase 0.007687
140 ENOG4105K6U NA -0.007665
141 ENOG4107ZI0 Inherit from NOG: 4fe-4S ferredoxin iroN-sulfur binding 0.007647
142 ENOG4108Z5K methylglyoxal synthase 0.007643
143 ENOG4105E53 ec 3.2.1.28 -0.007643
144 ENOG4105CUP Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6- dimethylbenzimidazole (DMB) (By similarity) 0.007641
145 ENOG4105MVG cadmium resistance -0.000635
145 ENOG4105QB8 NA -0.000635
145 ENOG4105RF4 NA -0.000635
145 ENOG41062P0 Pfam:DUF3532 -0.000635
145 ENOG4106KIJ Cadmium resistance transporter -0.000635
145 ENOG4106NS8 sensor with HAMP domain protein -0.000635
145 ENOG41073MR NA -0.000635
145 ENOG4107R9R Rhodanese domain-containing protein -0.000635
145 ENOG4107X3Q Band 7 protein -0.000635
145 ENOG4107ZXG Methyltransferase domain -0.000635
145 ENOG4108HSI sensor with HAMP domain protein -0.000635
145 ENOG4108Q14 O-Antigen polymerase -0.000635
146 ENOG4108ABK Inherit from COG: acetyltransferase 0.007623
147 ENOG4105CH5 extracellular solute-binding protein, family 7 0.007622
148 ENOG4105P1F NA 0.007620
149 ENOG4105CNU cell division protein FtsK 0.007603
150 ENOG4105KUS lysozyme -0.007596
151 ENOG4105C6Y Udp-glucose 6-dehydrogenase 0.007578
152 ENOG4108JCZ Dehydrogenase 0.007571
153 ENOG4105D0M Protease HtpX homolog 0.007571
154 ENOG4105CSU acyl-Coa dehydrogenase 0.007569
155 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) 0.007561
156 ENOG4105FD8 phosphonate metabolism protein PhnM -0.007528
157 ENOG4105N1E membrAne 0.007522
158 ENOG4105CD8 aminopeptidase N 0.007519
159 ENOG4105DDI hemolysin-type calcium-binding region 0.007515
160 ENOG4105R9B Major Facilitator 0.007501
161 ENOG4105G4N Gcn5-related n-acetyltransferase -0.007487
162 ENOG4105TRH NA 0.007469
163 ENOG4105ER6 polysaccharide biosynthesis protein 0.007449
164 ENOG41061H0 Monooxygenase -0.007439
165 ENOG4105MYR cina domain protein 0.007433
166 ENOG4107V2T HTH_GNTR 0.007415
167 ENOG4105DTW Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.007411