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 ENOG4105DVW rieske (2Fe-2S) 0.039795
2 ENOG4105CIV prophage primase 0.023797
3 ENOG4105D13 transposase 0.023491
4 ENOG4108EMG Integral membrane protein TerC family -0.021610
5 ENOG4105M2N XRE family Transcriptional regulator -0.021241
6 ENOG4105M5J Cupin 2, conserved barrel domain protein -0.020100
7 ENOG4108MZ0 NA -0.019790
8 ENOG4105M5B (LipO)protein -0.019265
9 ENOG4105C30 Nad-dependent epimerase dehydratase -0.019216
10 ENOG4105XUP Phage derived protein Gp49-like (DUF891) 0.019152
11 ENOG4105X54 addiction module antidote protein 0.019053
12 ENOG4108JIX abc transporter atp-binding protein -0.018989
13 ENOG4108MBK is1 orf2 0.018619
14 ENOG4105Q7N Transcriptional regulator 0.018564
15 ENOG4105C0K Gdp-mannose 4,6-dehydratase -0.018508
16 ENOG4108MHR Repressor involved in choline regulation of the bet genes (By similarity) 0.018398
17 ENOG4105CYY Plasma membrane H -transporting two-sector ATPase -0.018308
18 ENOG4105CCT upf0313 protein -0.018267
19 ENOG4108N9Z Replicative dna helicase -0.018173
20 ENOG4105G79 NA -0.018171
21 ENOG41066PS insecticidal toxin 0.018147
22 ENOG4105K2Z endo-1,4-d-glucanase (EC 3.2.1.4) -0.017679
23 ENOG4108BUD transposase 0.017632
24 ENOG4105CNG UPF0061 protein -0.017559
25 ENOG4105M44 transposase, IS3 IS911 family protein 0.008779
25 ENOG4105EF9 Integrase catalytic subunit 0.008779
26 ENOG41081VN RHS Repeat -0.017465
27 ENOG4107RG3 methyl-accepting chemotaxis -0.017429
28 ENOG4105FKQ transcriptional regulator -0.017416
29 ENOG4105VJ2 Transcriptional regulator, TraR DksA family -0.017377
30 ENOG4106FQJ NA 0.017358
31 ENOG4107Y59 type iii secretion 0.017358
32 ENOG4106A57 NA -0.017304
33 ENOG4105CZ6 Can catalyze the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine (By similarity) 0.017265
34 ENOG4105E3G Phosphotransfer intermediate protein in two-component regulatory system with RcsBC -0.017210
35 ENOG4105JC6 Zonular occludens toxin 0.008582
35 ENOG4108R1Z Type II and III secretion system protein 0.008582
36 ENOG4107088 NA -0.002448
36 ENOG41075NE NA -0.002448
36 ENOG4108WT7 Histidine kinase -0.002448
36 ENOG4107NE1 NA -0.002448
36 ENOG4105VTA Addiction module antitoxin, RelB DinJ family -0.002448
36 ENOG4105FAW cDP-glucose 4,6-dehydratase -0.002448
36 ENOG41083M5 Transcriptional Regulator AraC Family -0.002448
37 ENOG41060AS Nicotinamide-nucleotide adenylyltransferase 0.008551
37 ENOG4105DKR Na( ) H( ) antiporter that extrudes sodium in exchange for external protons (By similarity) 0.008551
38 ENOG4108RF0 Cold-Shock Protein -0.017050
39 ENOG4105D7T ABC transporter -0.017050
40 ENOG4105ENR peptidase, M24 -0.017004
41 ENOG4108C33 Resolvase 0.016950
42 ENOG4105SEJ insertion element 0.016862
43 ENOG4105VBK rop protein 0.016815
44 ENOG41081UR RHS repeat-associated core domain protein -0.016803
45 ENOG4105IDF Transposase -0.016679
46 ENOG410729D NA -0.016665
47 ENOG4107SKS 5'-nucleotidase -0.004158
47 ENOG4105S8Q sugar efflux transporter -0.004158
47 ENOG4105CBT Fructose-1,6-bisphosphatase -0.004158
47 ENOG4108MXZ Esterase -0.004158
48 ENOG4105C4Z Metal Dependent Phosphohydrolase -0.016495
49 ENOG4105WD1 Membrane -0.016477
50 ENOG4108M21 NA -0.016427
51 ENOG4106AKC NA -0.016427
52 ENOG4105EAA nucleoside 0.016403
53 ENOG4108ARB NA -0.016343
54 ENOG4105TWF Transposase -0.016179
55 ENOG4105CHH sulfate transporter -0.015996
56 ENOG4105BZT Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA (By similarity) -0.007951
56 ENOG4105CQC Prephenate dehydratase -0.007951
57 ENOG4105S14 Pesticin domain protein 0.000723
57 ENOG4105VQ2 NA 0.000723
57 ENOG4106CG8 Inner membrane protein YjeO 0.000723
57 ENOG4108SD2 Ceramide Glucosyltransferase 0.000723
57 ENOG4107GD2 NA 0.000723
57 ENOG4108IC3 transposase 0.000723
57 ENOG4108NXD Membrane 0.000723
57 ENOG4108G83 NA 0.000723
57 ENOG4108K3T NA 0.000723
57 ENOG4107AB8 DNA gyrase (Topoisomerase II) B subunit 0.000723
57 ENOG41066W6 NA 0.000723
57 ENOG4106GV2 NA 0.000723
57 ENOG4106RYA NA 0.000723
57 ENOG4106569 phage-related membrane protein 0.000723
57 ENOG41085I6 NA 0.000723
57 ENOG4105QVE insertion element 0.000723
57 ENOG4108WJC Phage replication protein CRI 0.000723
57 ENOG410732N immunity protein 0.000723
57 ENOG4107YKR integral membrane protein 0.000723
57 ENOG41063R9 NA 0.000723
57 ENOG41077M9 NA 0.000723
57 ENOG41073E3 TlcR protein 0.000723
58 ENOG4105XZD Fe-S protein 0.015873
59 ENOG4105EUR Domain-Containing protein -0.015835
60 ENOG4107710 NA -0.015795
61 ENOG4105KXH PAAR repeat-containing protein -0.007881
61 ENOG41078JR NA -0.007881
62 ENOG4105NNM Transposase 0.015717
63 ENOG4107ET6 NA -0.015585
64 ENOG4105MGC IS630 family transposase 0.015572
65 ENOG4107F3C Hemin uptake protein -0.007739
65 ENOG4106G4A NA -0.007739
66 ENOG4107S2I Transposase 0.007686
66 ENOG4108KB1 transcriptional regulator, arac family 0.007686
67 ENOG4106JGA Chromosome (Plasmid) partitioning protein, ParB 0.015315
68 ENOG41085EM Integrase -0.015292
69 ENOG4105CXC rtn protein -0.015285
70 ENOG41083JZ Plasmid stabilisation system protein 0.007544
70 ENOG4106YYK type IIi 0.007544
71 ENOG4106SFG Pfam:Transposase_8 0.015084
72 ENOG4105CN8 Transcriptional regulator 0.015081
73 ENOG4105C60 DNA-binding protein -0.014999
74 ENOG4105D99 atp gtp-binding protein -0.004992
74 ENOG41069M3 Transcriptional regulator -0.004992
74 ENOG4105K33 Periplasmic Protein -0.004992
75 ENOG4107UB8 ABC transporter, permease -0.000348
75 ENOG4108SD4 Appr-1-p processing domain protein -0.000348
75 ENOG41081P7 )-transporter -0.000348
75 ENOG4106VBS NA -0.000348
75 ENOG4107WAS Zinc iron permease -0.000348
75 ENOG4108K4U Diguanylate cyclase -0.000348
75 ENOG4106PFQ NA -0.000348
75 ENOG4105S2I NA -0.000348
75 ENOG4105FF4 NA -0.000348
75 ENOG4107W32 5-nucleotidase -0.000348
75 ENOG4107KSK Protein of unknown function (DUF805) -0.000348
75 ENOG4106IFQ Peripheral inner membrane phage-shock protein -0.000348
75 ENOG4107CI4 NA -0.000348
75 ENOG4108H52 Oxidoreductase family, C-terminal alpha/beta domain -0.000348
75 ENOG4106J5W DNA polymerase III (alpha subunit) -0.000348
75 ENOG4105Y5U Protein of unknown function (DUF2778) -0.000348
75 ENOG41087JS group II -0.000348
75 ENOG4108QQA transposase is116 is110 is902 family -0.000348
75 ENOG4106TMK NA -0.000348
75 ENOG4106B3P NA -0.000348
75 ENOG4106THZ NA -0.000348
75 ENOG4108EG3 Type II and III secretion system protein -0.000348
75 ENOG4105ZTN Protein of unknown function (DUF497) -0.000348
75 ENOG41082AX Inherit from COG: filamentous hemagglutinin family outer membrane protein -0.000348
75 ENOG41084PM thiamine transporter -0.000348
75 ENOG4108E65 NA -0.000348
75 ENOG4105WTD ATP-dependent DNA ligase -0.000348
75 ENOG4108IBT Inherit from COG: transposase -0.000348
75 ENOG41066CY Protein of unknown function (DUF1003) -0.000348
75 ENOG41081Z7 deacetylase -0.000348
75 ENOG410883Z Septum formation initiator -0.000348
75 ENOG4106936 NA -0.000348
75 ENOG4109051 YadA domain protein -0.000348
75 ENOG4106GQ1 secreted protein -0.000348
75 ENOG4107A2G NA -0.000348
75 ENOG4105YHH Glycosyl Transferase -0.000348
75 ENOG41063RV NA -0.000348
75 ENOG4105PK8 NA -0.000348
75 ENOG4106WNG NA -0.000348
75 ENOG41075VJ NA -0.000348
75 ENOG41072ME NA -0.000348
75 ENOG41075RT NA -0.000348
75 ENOG4106MSC Histidine kinase -0.000348
76 ENOG4105KAF membrAne 0.014902
77 ENOG4106NZI LysR family Transcriptional regulator -0.014697
78 ENOG4106974 biofilm formation -0.014642
79 ENOG41090BT NA -0.014494
80 ENOG4107RBZ sulfate transporter -0.014488
81 ENOG4107HDS Transposase 0.014455
82 ENOG41081V1 type iii secretion 0.014423
83 ENOG4107U5R The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate (By similarity) 0.014373
84 ENOG41061DC General secretion pathway -0.014264
85 ENOG4108F15 penicillin-binding protein 1C -0.007120
85 ENOG4105WRP NA -0.007120
86 ENOG4105G3E Probably involved in ribonucleotide reductase function (By similarity) 0.007108
86 ENOG4107RGM aldo keto reductase 0.007108
87 ENOG4105F8P NA 0.014184
88 ENOG4105Y1Q Integrase -0.014104
89 ENOG4107RQA Aminotransferase -0.014044
90 ENOG41069KQ Phage regulatory protein -0.013978
91 ENOG4105F6H The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3- phosphate (By similarity) 0.006964
91 ENOG4105CIY formyltetrahydrofolate deformylase 0.006964
92 ENOG4107959 NA 0.006926
92 ENOG41066GD Flagellar biogenesis protein 0.006926
93 ENOG4107AQH NA -0.013728
94 ENOG4105J58 Secretion system effector C (SseC) like family 0.000442
94 ENOG4108WTQ Type III 0.000442
94 ENOG4106HJ6 Translocation protein in type III secretion 0.000442
94 ENOG4108FAC auxin efflux carrier 0.000442
94 ENOG41061J9 translocator protein PopD 0.000442
94 ENOG41070MY type iii secretion 0.000442
94 ENOG410650Y Yersinia/Haemophilus virulence surface antigen 0.000442
94 ENOG410641W Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein includes tyrosine phosphatase and GTPase activating protein (GAP) activities. After bacterial internalization, GAP mediates the reversal of the cytoskeletal changes induced by SopE. This function is independent of its tyrosine phosphatase activity, which remains unclear 0.000442
94 ENOG4108KQZ Serine Threonine protein kinase 0.000442
94 ENOG41078HP Tir chaperone protein (CesT) family 0.000442
94 ENOG4106YUX Type III secretion system YscX (type_III_YscX) 0.000442
94 ENOG410746A NA 0.000442
94 ENOG41071GJ TyeA 0.000442
94 ENOG4107AKS type iii secretion 0.000442
94 ENOG4106YBP NA 0.000442
94 ENOG41084IW type IIi 0.000442
94 ENOG41072JS exoenzyme T 0.000442
94 ENOG4105JTD outer membrane protein PopN 0.000442
94 ENOG4107CIX Type III export protein 0.000442
94 ENOG410660X type iii secretion 0.000442
94 ENOG4105YPA V antigen (LcrV) protein 0.000442
94 ENOG4106G51 effector protein 0.000442
94 ENOG4105VK8 type iii secretion 0.000442
94 ENOG4106V7F Type III secretion system regulator (LcrR) 0.000442
94 ENOG41066XE Type III export protein 0.000442
94 ENOG41077AN chaperone 0.000442
94 ENOG4107AR9 regulator in type III secretion 0.000442
94 ENOG4105IB0 filamentous hemagglutinin family outer membrane protein 0.000442
94 ENOG4105ZWX type iii secretion 0.000442
94 ENOG4106BKA Type III secretion chaperone, CesT family 0.000442
94 ENOG4106XTA Type III secretion component protein SctB 0.000442
95 ENOG410724Q NA -0.013708
96 ENOG4108WHT Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.003421
96 ENOG410804A Flagellar hook-associated 2 domain-containing protein 0.003421
96 ENOG410619D Flagellar hook-length control protein 0.003421
96 ENOG410834V flagellar protein FliS 0.003421
97 ENOG41075TJ NA -0.013685
98 ENOG4105DBM Siderophore biosynthesis protein -0.013617
99 ENOG4106TNF Periplasmic binding protein -0.013529
100 ENOG4105D05 Receptor -0.013528
101 ENOG4106CEK ImpA domain protein -0.013421
102 ENOG4108MA7 Inherit from COG: YD repeat protein -0.013421
103 ENOG41077KJ NA -0.006645
103 ENOG410694M NA -0.006645
104 ENOG41067UG Cyd operon protein YbgT -0.013132
105 ENOG4105CQT polysaccharide deacetylase -0.013082
106 ENOG4105EM7 Selenocysteine-specific translation elongation factor -0.013040
107 ENOG4105ENN converts alpha-aldose to the beta-anomer. It is active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose (By similarity) -0.012903
108 ENOG4105E2D ec 3.2.1.52 -0.012845
109 ENOG4105C9X ppx gppa phosphatase -0.012797
110 ENOG41070TU Inherit from COG: Retrotransposon protein 0.006399
110 ENOG4106T5Q NA 0.006399
111 ENOG4107U30 nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC 0.012758
112 ENOG4105ED5 insecticidal toxin complex protein -0.012702
113 ENOG4105E3J oxidoreductase 0.012648
114 ENOG4108MPS synthase III -0.012583
115 ENOG4107SQK Major Facilitator superfamily 0.012525
116 ENOG4107QJ7 formate dehydrogenase alpha subunit -0.012510
117 ENOG4108SYJ Type VI secretion system 0.012334
118 ENOG4105EA5 molybdopterin oxidoreductase fe4s4 region -0.012314
119 ENOG4105CWI transcriptional regulator -0.012037
120 ENOG4107AVE This protein is involved in the determination of copy number in gene replication. It binds to the repA promoter thus inhibiting the synthesis of the mRNA for the initiator protein repA (By similarity) 0.005981
120 ENOG4106CQM replication 0.005981
121 ENOG4105VAS Could be involved in insertion of integral membrane proteins into the membrane (By similarity) -0.011904
122 ENOG4108TUY outer membrane protein PgaA 0.011864
123 ENOG4105F6U Short-chain dehydrogenase reductase Sdr 0.011756
124 ENOG4105IPU prepilin peptidase dependent protein A -0.011750
125 ENOG4105CY2 Citrate transporter 0.011664
126 ENOG4107I69 Allophanate hydrolase subunit 1 -0.011426
127 ENOG4108KU3 Integrase -0.011372
128 ENOG4105F35 Catalyzes the NAD( )-dependent oxidation of L-carnitine to 3-dehydrocarnitine (By similarity) 0.011288