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 ENOG4108QKB Methyl-accepting chemotaxis 0.028136
2 ENOG4105EXW epimerase dehydratase 0.026760
3 ENOG4108XPF NA -0.025043
4 ENOG4107QSV RmuC domain protein 0.024806
5 ENOG4107R8B 5'-nucleotidase -0.024611
6 ENOG41069QB NA -0.024430
7 ENOG4108JPC ATP-binding protein 0.024225
8 ENOG4106SMX NA -0.024069
9 ENOG4107DCE Haemolysin XhlA -0.024050
10 ENOG4105KDA Transcriptional regulator, GntR family -0.023965
11 ENOG4105HB2 NA 0.011917
11 ENOG4106BMY NA 0.011917
12 ENOG4106G3M NA 0.023833
13 ENOG4108S4N thiJ PfpI domain-containing protein 0.023786
14 ENOG41073SP NA 0.023677
15 ENOG4108IY0 amino acid ABC transporter substrate-binding protein, PAAT family -0.023580
16 ENOG4107YAG Inherit from COG: sulfurtransferase activity -0.023442
17 ENOG4108NNA glycosyl transferase group 1 0.023441
18 ENOG41079U7 NA 0.023438
19 ENOG4105G6R Stage v sporulation protein ae -0.023354
20 ENOG4106NDE Ammonium Transporter Family -0.023285
21 ENOG4106X7S NA 0.011642
21 ENOG41078RD helix-turn-helix type 11 domain-containing protein 0.011642
22 ENOG4107Y98 NmrA family -0.023278
23 ENOG4107Y8T tetratricopeptide tpr_2 repeat protein 0.023050
24 ENOG4105KUR CAAX amino terminal protease family protein 0.023050
25 ENOG41061KH NA 0.011521
25 ENOG4106CKA Bacteriocin transport accessory protein 0.011521
26 ENOG410840R Mg2 transporter protein cora family protein -0.022966
27 ENOG4107FFF Protein of unknown function (DUF2970) -0.022935
28 ENOG4107QJT sodium dicarboxylate symporter -0.022912
29 ENOG4105CIS alcohol dehydrogenase -0.022827
30 ENOG4105U7I Bacterial ABC transporter protein EcsB 0.022803
31 ENOG4108SEW NA -0.022792
32 ENOG4107R9Y phosphoglycerol transferase alkaline phosphatase superfamily protein 0.022750
33 ENOG4105CGQ conserved protein UCP033563 0.022629
34 ENOG4105XJR Branched-chain amino acid -0.022547
35 ENOG4107UCE ferrous iron transport protein -0.011244
35 ENOG4107UW2 Ferrous iron transport protein B C terminus -0.011244
36 ENOG4108S3Y transcriptional regulator 0.022482
37 ENOG410797K NA 0.022445
38 ENOG4105CPK Glycosyl transferase (Group 1 -0.022399
39 ENOG4105ERT s-layer domain protein 0.022355
40 ENOG4105E92 Erythromycin esterase 0.022343
41 ENOG41085K1 gtp-binding protein -0.022334
42 ENOG4106HJE NA 0.022296
43 ENOG410692Z NA 0.022230
44 ENOG41090PH Protease synthase and sporulation negative regulatory protein pai 1 -0.022175
45 ENOG4105DCD NA 0.000354
45 ENOG4105EZ3 site-specific recombinase 0.000354
45 ENOG4105N17 NA 0.000354
45 ENOG4105P13 Inherit from COG: Serine Threonine protein kinase 0.000354
45 ENOG4105S7R DNA Polymerase Beta Domain Protein Region 0.000354
45 ENOG4105VDG NA 0.000354
45 ENOG4105YFY Tic20-like protein 0.000354
45 ENOG4105Z0K NA 0.000354
45 ENOG410600H Phage-related XpaF1 protein, involved in cell lysis 0.000354
45 ENOG41060B9 NA 0.000354
45 ENOG41063VB Conserved Protein 0.000354
45 ENOG41066M5 NA 0.000354
45 ENOG410687E Flagellar basal body-associated protein FliL 0.000354
45 ENOG41069JC NA 0.000354
45 ENOG41069V1 NA 0.000354
45 ENOG4106CB4 NA 0.000354
45 ENOG4106CT7 NA 0.000354
45 ENOG4106DAP NA 0.000354
45 ENOG4106GWE NA 0.000354
45 ENOG4106HIM NA 0.000354
45 ENOG4106I7V NA 0.000354
45 ENOG4106NKK NA 0.000354
45 ENOG4106NUX Sodium solute symporter family 0.000354
45 ENOG4106WSA NA 0.000354
45 ENOG41072X6 NA 0.000354
45 ENOG4107343 NA 0.000354
45 ENOG41073ZG NA 0.000354
45 ENOG41074GR NA 0.000354
45 ENOG41074I7 NA 0.000354
45 ENOG41076U4 NA 0.000354
45 ENOG41079HZ NA 0.000354
45 ENOG4107A0Y NA 0.000354
45 ENOG4107A28 NA 0.000354
45 ENOG4107B4U NA 0.000354
45 ENOG4107BD0 NA 0.000354
45 ENOG4107BQ5 NA 0.000354
45 ENOG4107C9S Inherit from COG: YD repeat protein 0.000354
45 ENOG4107CQ5 Flagellar hook-length control protein FliK 0.000354
45 ENOG4107CVH NA 0.000354
45 ENOG4107D1H NA 0.000354
45 ENOG4107DCA NA 0.000354
45 ENOG4107DIU NA 0.000354
45 ENOG4107FE7 Multiple resistance and ph regulation protein f 0.000354
45 ENOG4107GK3 NA 0.000354
45 ENOG4107HIR Inherit from NOG: filamentous hemagglutinin 0.000354
45 ENOG4107MR9 Pfam:DUF2078 0.000354
45 ENOG4107RAF solute symporter 0.000354
45 ENOG4107TN8 Peptidase dimerisation domain 0.000354
45 ENOG4107YJ4 chain length determinant protein 0.000354
45 ENOG41085E3 NA 0.000354
45 ENOG41085EY HTH_XRE 0.000354
45 ENOG41087UR O-Antigen ligase 0.000354
45 ENOG4108FJR Domain of unknown function (DUF202) 0.000354
45 ENOG4108KJY Inherit from NOG: Family with sequence similarity 115, member 0.000354
45 ENOG4108S7W membrAne 0.000354
45 ENOG4108SMS transposase 0.000354
45 ENOG4108T3X Phosphotransferase enzyme family 0.000354
45 ENOG4108VKD Histidine kinase 0.000354
45 ENOG4108YU6 Domain-Containing protein 0.000354
45 ENOG4108Z5G NA 0.000354
45 ENOG41090QX NA 0.000354
45 ENOG41090TM glycosyl transferase family 0.000354
46 ENOG4108V5C ABC transporter -0.021878
47 ENOG4105HJ0 transposase -0.000810
47 ENOG4105MJN Transcriptional regulator, TetR family -0.000810
47 ENOG4105N09 integral membrane protein -0.000810
47 ENOG4105TD6 Protein of unknown function (DUF2812) -0.000810
47 ENOG41066K9 Inherit from COG: filamentous hemagglutinin family outer membrane protein -0.000810
47 ENOG41069NG NA -0.000810
47 ENOG41069YH Transposase -0.000810
47 ENOG4106AWE NA -0.000810
47 ENOG4106MJ4 NA -0.000810
47 ENOG4106WUS NA -0.000810
47 ENOG4107F5N Uncharacterized protein conserved in bacteria (DUF2065) -0.000810
47 ENOG4107FK9 PbH1 -0.000810
47 ENOG4107H8E Flagellar M-ring protein fliF -0.000810
47 ENOG4107HPM Transposase -0.000810
47 ENOG4107JH8 NA -0.000810
47 ENOG4107U4Y signal transduction Histidine kinase -0.000810
47 ENOG4107V1P abc transporter atp-binding protein -0.000810
47 ENOG4107W03 Inherit from COG: cell filamentation protein -0.000810
47 ENOG4107WF7 NA -0.000810
47 ENOG410811X Methylamine utilization protein mauE -0.000810
47 ENOG4108BUS alpha/beta hydrolase fold -0.000810
47 ENOG4108C8K HTH_ARAC -0.000810
47 ENOG4108C9F Poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit -0.000810
47 ENOG4108HR5 polar amino acid ABC transporter, inner membrane subunit -0.000810
47 ENOG4108IQV Domain of unknown function DUF11 -0.000810
47 ENOG4108JSF K07001 NTE family protein -0.000810
47 ENOG4108T0D glyoxalase -0.000810
48 ENOG4105U9X Bacterial regulatory proteins, tetR family 0.021832
49 ENOG410693T Transcriptional regulator -0.021709
50 ENOG4108ZXY Glycosyl transferase, family 2 0.021678
51 ENOG4105ZMF Domain of Unknown Function (DUF1540) 0.021650
52 ENOG41079VA NA 0.021642
53 ENOG4106959 NA 0.021616
54 ENOG41086DA Protein of unknown function (DUF1272) 0.021604
55 ENOG41077C5 NA 0.021586
56 ENOG4107AUG NA -0.021570
57 ENOG4108BWS Protein of unknown function (DUF466) 0.021564
58 ENOG4108D8A Periplasmic binding protein -0.021479
59 ENOG41085GI NA 0.021467
60 ENOG4108GYP domain protein -0.021423
61 ENOG4105EP0 Glycosyl transferase (Group 1 0.021423
62 ENOG41080I8 transcriptional regulator), MarR family 0.021247
63 ENOG4108DJJ Cache domain 0.021232
64 ENOG41073DR NA 0.021110
65 ENOG4105VCD cytoplasmic protein -0.021062
66 ENOG4106Z2Q NA 0.021032
67 ENOG4107QJZ Glycosyl transferase, family 2 0.021025
68 ENOG4105XXU Phage terminase small subunit 0.010512
68 ENOG4106BGB Uncharacterized small protein (DUF2292) 0.010512
69 ENOG4108NQ1 repeat-containing protein 0.020980
70 ENOG41069U5 Protein of unknown function (DUF2602) 0.020851
71 ENOG4105PV6 Rhodanese domain protein -0.020841
72 ENOG4107B5U Transposase -0.020767
73 ENOG4106H2G NA 0.006901
73 ENOG4106HNU NA 0.006901
73 ENOG4107D3H Probable sporulation protein (Bac_small_yrzI) 0.006901
74 ENOG4108VF8 ABC transporter 0.020695
75 ENOG4106IDA glycerophosphoryl diester phosphodiesterase 0.020610
76 ENOG4106UIA NA -0.020544
77 ENOG41062BC Acetyltransferase (GNAT) family 0.020471
78 ENOG4105VX4 NA -0.020379
79 ENOG4106BBM NA 0.020260
80 ENOG4106MFW NA 0.010119
80 ENOG4106VCP S4 0.010119
81 ENOG4105P5G pyridine nucleotide-disulfide oxidoreductase -0.020237
82 ENOG4106AXD NA 0.006721
82 ENOG410732S Sporulation inhibitor A 0.006721
82 ENOG41077X5 conserved protein, contains two CXXC motifs 0.006721
83 ENOG41066FG Protein of unknown function (DUF2759) 0.004942
83 ENOG4106BBT NA 0.004942
83 ENOG41077IC NA 0.004942
83 ENOG4107BZP NA 0.004942
84 ENOG4108WIN Transcriptional regulator -0.019741
85 ENOG4108AEB Calcineurin-like phosphoesterase 0.019519
86 ENOG4105YHT Collagen triple helix -0.019337
87 ENOG4108PG8 lipolytic protein G-D-S-L family 0.019079
88 ENOG4105DYV ABC transporter -0.018135
89 ENOG4108YX8 Lysophospholipase 0.018046
90 ENOG4105DST XRE family Transcriptional regulator -0.017374
91 ENOG4105XNK sarcosine oxidase (alpha subunit) -0.015409
92 ENOG4105CNA YD repeat protein 0.013570
93 ENOG4105ENR peptidase, M24 0.012968
94 ENOG4107GIM Short-chain dehydrogenase reductase Sdr 0.011908
95 ENOG4105UCJ NA 0.011225
96 ENOG4105TFN Glutathione-dependent formaldehyde-activating Gfa 0.010388
97 ENOG4107WGV tail tape measure protein 0.010266
98 ENOG41082DT Glutamine amido-transferase 0.010118
99 ENOG4105EKQ RNA-directed DNA polymerase 0.010117
100 ENOG4105E5N succinylglutamate desuccinylase aspartoacylase 0.009927
101 ENOG4105C8X 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 (By similarity) 0.009601
102 ENOG4108K43 mandelate racemase muconate lactonizing -0.009495
103 ENOG4105CIF Ornithine Cyclodeaminase 0.009493
104 ENOG4106C2P NA 0.009492
105 ENOG4105QPS Monooxygenase 0.009276
106 ENOG4105D8E domain protein 0.009203
107 ENOG4108I67 Catalyzes the synthesis of activated sulfate (By similarity) -0.009082
108 ENOG4108M4W Major Facilitator -0.009068
109 ENOG4105PZ7 Baseplate assembly protein 0.008990
110 ENOG4105ZI1 response regulator 0.008942
111 ENOG4108KT4 Ectoine hydroxyectoine ABC transporter solute-binding protein 0.008903
112 ENOG4105KM0 Protein of unknown function (DUF1810) 0.008893
113 ENOG4105YYQ prevent-host-death family 0.008879
114 ENOG4107RGR short-chain dehydrogenase reductase 0.008812
115 ENOG4105C4V Extracellular solute-binding protein, family 5 -0.008759
116 ENOG4105E2K Glycosyl transferase (Group 1 0.008750
117 ENOG4105DMH Transposase 0.008677
118 ENOG4108VHC Short-chain dehydrogenase reductase Sdr 0.008647
119 ENOG4108DNH Rubredoxin 0.008563
120 ENOG4105JSC dimethylmenaquinone methyltransferase 0.008559
121 ENOG4105QTI tail protein 0.008432
122 ENOG4108JQ4 (ABC) transporter -0.008304
123 ENOG4106GCW LysR family (Transcriptional regulator 0.008281
124 ENOG4107QZX amino acid adenylation 0.008268
125 ENOG4105DNH Major Facilitator -0.008260
126 ENOG4105CQH Protein of unknown function (DUF1254) -0.008210
127 ENOG4107SH4 Major Facilitator superfamily 0.008200
128 ENOG4105E4F Isochorismate synthase -0.008179
129 ENOG4105EX2 Binding-protein-dependent transport systems, inner membrane component 0.008138
130 ENOG4108T86 baseplate J family protein 0.008126
131 ENOG4108RPI (ABC) transporter 0.008051
132 ENOG4107FKI transcriptional regulator antitoxin, MazE 0.004003
132 ENOG4108020 transcriptional modulator of maze toxin, mazf 0.004003
133 ENOG4106831 Protein of unknown function (DUF2971) 0.007998
134 ENOG4105WR6 Phage protein, GP46 0.007975
135 ENOG410604Q amidohydrolase 0.007971
136 ENOG4105IKQ hydratase -0.007950
137 ENOG4108QJS PBS lyase HEAT domain protein repeat-containing protein 0.007932
138 ENOG4108EWY citrate synthase 0.007915
139 ENOG4108DKR ABC transporter, permease 0.007911
140 ENOG410900D Inherit from NOG: repeat-containing protein 0.007873
141 ENOG4105P12 pyruvate phosphate dikinase 0.007869
142 ENOG4105CMG Carbohydrate kinase -0.007857
143 ENOG4105KUW Hnh endonuclease -0.007764
144 ENOG4108Y06 Alpha Beta Hydrolase Fold protein 0.007689
145 ENOG4108TJN glycosyl transferase group 1 0.007664
146 ENOG4107IEK Inherit from COG: Hemolysin-type calcium-binding 0.003826
146 ENOG41087Y0 Glycosyl transferase, family 2 0.003826
147 ENOG4105EXU Membrane 0.007637
148 ENOG4105M0P NA -0.007628