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 ENOG41082SJ Transcriptional regulator 0.007831
2 ENOG4107QIQ HAD-superfamily subfamily IB hydrolase 0.006251
3 ENOG4105C9A Phoh family -0.006251
4 ENOG4105D7N magnesium and cobalt transport protein CorA 0.006115
5 ENOG4107TB6 phosphoglycerate mutase 0.006051
6 ENOG4105D6N CoA-transferase, subunit a 0.005932
7 ENOG4107QRR aspartate 0.005845
8 ENOG4105VFF UPF0102 protein 0.005701
9 ENOG4107WCV Phenazine biosynthesis protein 0.005532
10 ENOG4105MKH Cupin 2 Conserved Barrel Domain Protein 0.005393
11 ENOG4105DEF Extracellular solute-binding protein, family 5 0.005360
12 ENOG4108IIH CoA-transferase subunit B 0.005296
13 ENOG4105CBT Fructose-1,6-bisphosphatase 0.005276
14 ENOG41067SR s4 domain protein 0.005225
15 ENOG4107QM1 Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine (By similarity) -0.005194
16 ENOG4105KEM Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation (By similarity) -0.005139
17 ENOG4107YDG Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization (By similarity) 0.005095
18 ENOG4107VJZ DNA modification (methyltransferase 0.005072
19 ENOG4105EQ8 radical SAM domain protein 0.005022
20 ENOG4105E59 Participates in a DNA-damage check-point. DisA forms globular foci that rapidly scan along the chromosomes searching for lesions (By similarity) 0.004987
21 ENOG4105DY9 regulatoR 0.004947
22 ENOG4107UA6 flavin reductase domain protein 0.004939
23 ENOG4107YHQ hydrolase 0.004936
24 ENOG4108YZT Adenosylcobinamide kinase 0.004933
25 ENOG41083CN Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell (By similarity) 0.004905
26 ENOG4105CZF Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism (By similarity) 0.004880
27 ENOG4105CR1 Thiamine biosynthesis protein 0.004860
28 ENOG4105FDK ABC transporter 0.004846
29 ENOG41082XB radical SAM domain protein 0.004836
30 ENOG4107RD6 cobalamin synthesis protein, P47K 0.004810
31 ENOG4107S0U radical SAM domain protein 0.004755
32 ENOG4105DER m42 family 0.004753
33 ENOG4105FEU K -dependent Na -Ca exchanger -0.004723
34 ENOG41080WF Electron transport complex, RnfABCDGE type, G subunit 0.004701
35 ENOG4107R0B ComEC rec2-like protein 0.004694
36 ENOG4105K4W Could be involved in septation (By similarity) 0.004669
37 ENOG4108GCZ Septum formation initiator 0.004649
38 ENOG4108ZIA glycerol-3-phosphate responsive antiterminator 0.004642
39 ENOG4105F6S Spore photoproduct lyase 0.004591
40 ENOG4107UE1 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) 0.004581
41 ENOG41068MT Positive regulator of 0.004581
42 ENOG41083Q8 Sodium:dicarboxylate symporter family 0.004532
43 ENOG4105CMH dehydratase 0.004519
44 ENOG4108J7D Nitroreductase 0.004504
45 ENOG4106KBT YibE F family protein 0.004480
46 ENOG4108XI2 Domain of unknown function (DUF1963) 0.004462
47 ENOG4105KUR CAAX amino terminal protease family protein 0.004450
48 ENOG4105C87 Aminotransferase class I and II 0.004450
49 ENOG4105CYW agmatinase -0.004400
50 ENOG4105VYW UPF0251 protein 0.004400
51 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) 0.004399
52 ENOG4108ZDX Binds together with S18 to 16S ribosomal RNA (By similarity) -0.004396
53 ENOG4107QR5 DNA helicase 0.004390
54 ENOG4107YU2 histidine triad (hIT) protein 0.004385
55 ENOG4107QWG 2-Nitropropane dioxygenase 0.004380
56 ENOG41082I2 s4 domain protein 0.004346
57 ENOG4105HSH RelA SpoT domain protein 0.004337
58 ENOG4107R0D fad dependent oxidoreductase 0.004319
59 ENOG4105CJR Integral membrane protein (MviN 0.004310
60 ENOG4105D7Q type ii secretion system 0.004307
61 ENOG4105KGH Transcriptional regulator, MarR family 0.004288
62 ENOG4105WPN DNA integration recombination invertion protein 0.004265
63 ENOG4108ZMD Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity) -0.004252
64 ENOG4107SGK Adenylosuccinate lyase 0.004240
65 ENOG4107WIA FMN-dependent alpha-hydroxy acid dehydrogenase 0.004237
66 ENOG4105CU1 amidohydrolase 0.004214
67 ENOG4108P62 biosynthesis protein (CbiG) 0.004198
68 ENOG4105DVK Precorrin-2 c20-methyltransferase 0.004177
69 ENOG41081F0 Precorrin-8x methylmutase 0.004177
70 ENOG4105D2T synthase 0.004173
71 ENOG41090I5 UPF0735 ACT domain-containing protein 0.004144
72 ENOG4108BMA 50S ribosomal protein L36 0.004144
73 ENOG4108DFG Nitrite and sulphite reductase 4Fe-4S domain 0.004129
74 ENOG41086WW Heavy-metal-associated domain 0.004125
75 ENOG4107PPM cobalt chelatase 0.004098
76 ENOG4106PT6 cdpdiacylglycerol-serine O-phosphatidyltransferase 0.004033
77 ENOG4107TGU Thiamine biosynthesis protein ThiF 0.004018
78 ENOG4107QW9 peptidase, M24 0.004011
79 ENOG4105X5S Methyl-accepting chemotaxis 0.004004
80 ENOG4105E3C Inherit from COG: coA-substrate-specific enzyme activase 0.000154
80 ENOG4105GAX Motility accessory factor 0.000154
80 ENOG4105M2I NA 0.000154
80 ENOG4105MEI membrane 0.000154
80 ENOG4105SSV Had-superfamily hydrolase, subfamily ia, variant 1 0.000154
80 ENOG4105UKX (CBS) domain 0.000154
80 ENOG4105WAG Metal Dependent Phosphohydrolase 0.000154
80 ENOG41060V4 small acid-soluble spore protein, alpha beta type 0.000154
80 ENOG41063JZ PilZ domain 0.000154
80 ENOG41068HB NA 0.000154
80 ENOG4106A44 NA 0.000154
80 ENOG4106BKG Domain of Unknown Function (DUF1599) 0.000154
80 ENOG4106XVS NA 0.000154
80 ENOG41070QT NA 0.000154
80 ENOG4107KFS Domain of Unknown Function (DUF1540) 0.000154
80 ENOG4107U4H Methyl-accepting chemotaxis 0.000154
80 ENOG4107V2J NA 0.000154
80 ENOG4107YSI ErfK YbiS YcfS YnhG family protein 0.000154
80 ENOG4108BAA Inherit from COG: Transcriptional regulator 0.000154
80 ENOG4108FUH Magnesium chelatase, subunit ChlI 0.000154
80 ENOG4108HWP PAP2 family 0.000154
80 ENOG4108J53 cell adhesion domain-containing protein 0.000154
80 ENOG4108JGH Tetr family transcriptional regulator 0.000154
80 ENOG4108PC7 NA 0.000154
80 ENOG4108R3C Nitroreductase 0.000154
80 ENOG410908H NA 0.000154
81 ENOG4108R6P synthase III 0.004004
82 ENOG4107R37 Glutamate dehydrogenase -0.003987
83 ENOG41082BM Transcriptional regulator, arsr family -0.003980
84 ENOG4106DP4 NA 0.003977
85 ENOG41079MB NA 0.003969
86 ENOG4105CEN a g-specific adenine glycosylase -0.003964
87 ENOG4105C3K feS assembly ATPase SufC -0.003958
88 ENOG4106PMH Extracellular solute-binding protein family 3 0.003946
89 ENOG4105CEV competence damage-inducible protein 0.003945
90 ENOG4105F2N NA 0.003919
91 ENOG4105D8I Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity) -0.003891
92 ENOG4107T4M dehydratase 0.003867
93 ENOG4105VXR cytoplasmic protein -0.003856
94 ENOG4108YYD acetyltransferase -0.003842
95 ENOG4105KRI phosphocarrier protein (HPr 0.003833
96 ENOG41060R6 Efflux transporter rnd family, mfp subunit 0.001914
96 ENOG4108BMI recombinase 0.001914
97 ENOG4108G8Z NA 0.003828
98 ENOG4107QZ1 phosphate acetyltransferase 0.003828
99 ENOG4105C0H protease -0.001914
99 ENOG4105K5M 30s ribosomal protein S16 -0.001914
100 ENOG4107TZI 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis 0.003828
101 ENOG4108G9W tetratricopeptide repeat family protein 0.003828
102 ENOG4105E69 ABC transporter integral membrane protein 0.000040
102 ENOG4105FZJ Ribosomal Large Subunit Pseudouridine Synthase D 0.000040
102 ENOG4105GAI short-chain dehydrogenase 0.000040
102 ENOG4105GN3 RNA Polymerase 0.000040
102 ENOG4105K95 (LipO)protein 0.000040
102 ENOG4105PHC abc transporter integral membrane protein 0.000040
102 ENOG4105QFH outer membrane protein (ompH) 0.000040
102 ENOG4105SXT Inherit from COG: Alpha beta hydrolase 0.000040
102 ENOG4105U8S nitrogen regulatory IIA protein 0.000040
102 ENOG410615F Integral membrane protein (intg_mem_TP0381) 0.000040
102 ENOG41061RH Esterase 0.000040
102 ENOG41062UG NA 0.000040
102 ENOG410643Y Smr domain 0.000040
102 ENOG41064F0 NfeD-like C-terminal, partner-binding 0.000040
102 ENOG41064HV Endonuclease Exonuclease phosphatase 0.000040
102 ENOG4106838 polypeptide-transport-associated domain protein, FtsQ-type 0.000040
102 ENOG410696V biopolymer transport EXBD protein 0.000040
102 ENOG410698M Cell division protein that is part of the divisome complex and is recruited early to the Z-ring. Probably stimulates Z-ring formation, perhaps through the cross-linking of FtsZ protofilaments. Its function overlaps with FtsA (By similarity) 0.000040
102 ENOG4106AJD Tetratricopeptide repeat protein 0.000040
102 ENOG4106F02 NA 0.000040
102 ENOG4106F8S Protein of unknown function (DUF552) 0.000040
102 ENOG4106IP8 NA 0.000040
102 ENOG4106Z5N NA 0.000040
102 ENOG41073SW NA 0.000040
102 ENOG410744R NA 0.000040
102 ENOG410747I NA 0.000040
102 ENOG41077F3 NA 0.000040
102 ENOG41078PG integral membrane protein 0.000040
102 ENOG41079XJ Major outer membrane protein 0.000040
102 ENOG4107D1V Zinc finger protein 0.000040
102 ENOG4107I7J s-layer protein 0.000040
102 ENOG4107Q6D Cell division protein FtsX 0.000040
102 ENOG4107QFF Ribosomal-protein-alanine acetyltransferase 0.000040
102 ENOG4107RIU May be involved in the formation or repair of Fe-S clusters present in iron-sulfur proteins (By similarity) 0.000040
102 ENOG4107RJW Involved in formation and maintenance of cell shape (By similarity) 0.000040
102 ENOG4107RSD Multi-copper polyphenol oxidoreductase laccase 0.000040
102 ENOG4107RVD Membrane 0.000040
102 ENOG4107S62 Radical SAM Protein 0.000040
102 ENOG4107S9C Permease, YjgP YjgQ family 0.000040
102 ENOG4107SDV permease 0.000040
102 ENOG4107TER DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP- independent) along duplex DNA (By similarity) 0.000040
102 ENOG4107U6Q lipid A biosynthesis 0.000040
102 ENOG4107UNE Phosphohydrolase 0.000040
102 ENOG4107VB9 Precorrin-6y C5,15-methyltransferase 0.000040
102 ENOG4107VRC Na H -antiporter 0.000040
102 ENOG4107VT8 extracellular solute-binding protein family 1 0.000040
102 ENOG4107VYE precorrin-6x reductase 0.000040
102 ENOG4107XHB Transcriptional regulator, BadM Rrf2 family 0.000040
102 ENOG4107XK9 50S ribosomal protein L10 0.000040
102 ENOG41080GA heptaprenyl diphosphate synthase component I 0.000040
102 ENOG41081RY An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes (By similarity) 0.000040
102 ENOG41082B1 30S ribosomal protein S16 0.000040
102 ENOG41083F0 translocase subunit YajC 0.000040
102 ENOG410842Z 50S ribosomal protein L32 0.000040
102 ENOG410849Z 50s ribosomal protein L35 0.000040
102 ENOG41084GR hemin receptor 0.000040
102 ENOG4108527 (ribosomal) protein 0.000040
102 ENOG41085C7 Domain of unknown function (DUF1858) 0.000040
102 ENOG41085P3 50S ribosomal protein L30 0.000040
102 ENOG41085ZV 50S ribosomal protein l28 0.000040
102 ENOG410860H Protein of unknown function (DUF1312) 0.000040
102 ENOG41087CR biopolymer transport EXBD protein 0.000040
102 ENOG41088BS DNA polymerase 0.000040
102 ENOG41089FY Peptidyl-prolyl cis-trans isomerase 0.000040
102 ENOG4108B8F Bacterial protein of unknown function (DUF896) 0.000040
102 ENOG4108BW8 UPF0109 protein 0.000040
102 ENOG4108CMW NA 0.000040
102 ENOG4108CZ8 Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides (By similarity) 0.000040
102 ENOG4108G6I NA 0.000040
102 ENOG4108G77 anti-sigma B factor 0.000040
102 ENOG4108G7P protein translocase subunit secE 0.000040
102 ENOG4108G85 NA 0.000040
102 ENOG4108G8E NA 0.000040
102 ENOG4108G8S NA 0.000040
102 ENOG4108G93 NA 0.000040
102 ENOG4108G97 NA 0.000040
102 ENOG4108GA9 Morn variant repeat protein 0.000040
102 ENOG4108GBS NA 0.000040
102 ENOG4108GBV Preprotein translocase SecG subunit 0.000040
102 ENOG4108GBW NA 0.000040
102 ENOG4108GC2 NA 0.000040
102 ENOG4108GE5 NA 0.000040
102 ENOG4108GE6 NA 0.000040
102 ENOG4108GEC NA 0.000040
102 ENOG4108GEP NA 0.000040
102 ENOG4108GEU HD domain 0.000040
102 ENOG4108GGF Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity) 0.000040
102 ENOG4108GGH tetratricopeptide repeat family protein 0.000040
102 ENOG4108GGM NA 0.000040
102 ENOG4108GHM NA 0.000040
102 ENOG4108GI8 general secretion pathway protein G 0.000040
102 ENOG4108GIR NA 0.000040
102 ENOG4108IQJ site-determining protein 0.000040
102 ENOG4108JJW Aminotransferase class i 0.000040
102 ENOG4108NZ1 NA 0.000040
102 ENOG4108WTY tRNA (Guanine-N(1)-)-methyltransferase 0.000040
103 ENOG4107XH4 PPIases accelerate the folding of proteins (By similarity) 0.001276
103 ENOG41080FR Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity) 0.001276
103 ENOG41080G3 Could be a nuclease that resolves Holliday junction intermediates in genetic recombination (By similarity) 0.001276
104 ENOG4105HVR Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. Cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step (By similarity) 0.003825
105 ENOG4108VJJ Nitroreductase 0.003816
106 ENOG4105UDU tonb protein 0.000950
106 ENOG4108GBD NA 0.000950
106 ENOG4108GEQ NA 0.000950
106 ENOG4108PDR lipopolysaccharide core biosynthesis protein 0.000950
107 ENOG4108Z3G 3H domain protein 0.003795
108 ENOG4107XPA Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin) (By similarity) 0.003794
109 ENOG4105K4S protein with conserved CXXC pairs 0.003792
110 ENOG4105DFM M18 family aminopeptidase 0.003792
111 ENOG4105D2K citrate carrier protein 0.003786
112 ENOG4105Q9P Inherit from COG: UPF0754 membrane protein 0.003785
113 ENOG4105W44 ompa motb domain protein 0.003785
114 ENOG4107Y92 Single-stranded nucleic acid binding R3H domain-containing protein 0.001891
114 ENOG4108GB3 NA 0.001891
115 ENOG4108GFI NA 0.003783
116 ENOG4105VJX repeat protein 0.003781
117 ENOG41081BD CRP FNR family transcriptional regulator 0.003774
118 ENOG4108Z29 Flavodoxin 0.003766
119 ENOG4105W28 NA 0.000937
119 ENOG4105W8G NA 0.000937
119 ENOG4105WE8 NA 0.000937
119 ENOG4106DQC NA 0.000937