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 ENOG4107S8B Cys/Met metabolism PLP-dependent enzyme 0.035991
2 ENOG4107U7Y Peptidase M48, Ste24p 0.024341
3 ENOG4105C5E polysaccharide biosynthesis protein 0.023219
4 ENOG4108UI1 Probably functions as a manganese efflux pump (By similarity) 0.021487
5 ENOG4105DFE Dna adenine methylase -0.020866
6 ENOG41086BM amino acid AbC transporter 0.002298
6 ENOG4105CM4 permease protein 0.002298
6 ENOG4107JGA PP2Cc 0.002298
6 ENOG4105V49 Opioid growth factor receptor (OGFr) conserved region 0.002298
6 ENOG4105D9M gamma-glutamylcysteine synthetase 0.002298
6 ENOG4106APZ NA 0.002298
6 ENOG41060VH transcription activator, effector binding 0.002298
6 ENOG4105SBV Inherit from COG: serine acetyltransferase 0.002298
6 ENOG4106HYS NA 0.002298
7 ENOG4108EM1 reductase -0.010183
7 ENOG4105PE1 Receptor -0.010183
8 ENOG4107UJA Pfam:DUF2081 0.020346
9 ENOG4108ZT8 Pyrimidine dimer DNA glycosylase 0.020074
10 ENOG4105CHI Involved in the active translocation of vitamin B12 (cyanocobalamin) across the outer membrane to the periplasmic space. It derives its energy for transport by interacting with the trans-periplasmic membrane protein TonB (By similarity) 0.019805
11 ENOG4107KGK dmso reductase anchor subunit -0.009806
11 ENOG4107J0A lipopolysaccharide biosynthetic process -0.009806
12 ENOG4105FEE aaa atpase central domain protein 0.019408
13 ENOG4105EBY tonB-dependent Receptor 0.019060
14 ENOG4108RVA ribokinase -0.018944
15 ENOG4108VB5 Sel1 domain protein repeat-containing protein 0.018808
16 ENOG4105QNH glycosyl transferase 0.018768
17 ENOG4107RAN Peptidase, M16 -0.018757
18 ENOG4105HA6 Glycosyl transferase, family 2 0.018756
19 ENOG4108YZA Nitrogen regulatory protein pii -0.018410
20 ENOG4105DZR Type I site-specific deoxyribonuclease 0.018305
21 ENOG410696E Membrane 0.018283
22 ENOG4107RAZ it plays a direct role in the translocation of protons across the membrane (By similarity) 0.018014
23 ENOG4105E6X Zn-dependent Hydrolase of the beta-lactamase 0.018002
24 ENOG4108JUK Inherit from COG: 4fe-4S ferredoxin iron-sulfur binding domain protein -0.008850
24 ENOG4108NEM leader-binding protein dmsD -0.008850
25 ENOG4105S10 periplasmic binding protein 0.005867
25 ENOG4105PF3 O-Antigen polymerase 0.005867
25 ENOG4108PQF modD protein 0.005867
26 ENOG4108ERS NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol (By similarity) -0.017444
27 ENOG4105C3R Methionine synthase 0.017294
28 ENOG4108W15 Protein of unknown function (DUF1456) 0.016637
29 ENOG4105C5C n-acetylmuramoyl-l-alanine amidase 0.016574
30 ENOG4108ST3 glycosyltransferase -0.016532
31 ENOG4108R3F Nudix family 0.016205
32 ENOG4105C5B carbamate kinase -0.016142
33 ENOG4105DPX Hydrogenase, large subunit 0.016134
34 ENOG4105EV4 Multidrug resistance protein mdtH 0.008050
34 ENOG4105W49 UPF0434 protein 0.008050
35 ENOG4105E4P ATPase (AAA -0.016011
36 ENOG410681U heavy metal transport detoxification protein -0.015970
37 ENOG41086EX HhH1 0.001219
37 ENOG4105XIV Mercuric transport protein, periplasmic component 0.001219
37 ENOG4105CJ5 hydrogenase 2 b cytochrome subunit 0.001219
37 ENOG4106CJF NA 0.001219
37 ENOG4105D16 lipopolysaccharide heptosyltransferase i 0.001219
37 ENOG4105FBX amino acid AbC transporter 0.001219
37 ENOG4108IPW abc transporter atp-binding protein 0.001219
37 ENOG4108VTX Hhh-gpd family 0.001219
37 ENOG4105DHS permease protein 0.001219
37 ENOG4105KVJ Periplasmic binding protein 0.001219
37 ENOG4105YTA Protein of unknown function (DUF541) 0.001219
37 ENOG4105D1A Methyltransferase 0.001219
37 ENOG4107RA5 ABC transporter substrate-binding protein 0.001219
38 ENOG4108C33 Resolvase 0.015785
39 ENOG4105CBA glutamine phosphoribosylpyrophosphate amidotransferase 0.015687
40 ENOG4105X58 receptor -0.007765
40 ENOG41067DM NA -0.007765
41 ENOG4105TEC Pfam:Hep_Hag 0.015411
42 ENOG4105F5D NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol (By similarity) 0.015393
43 ENOG4106986 thioredoxin domain-containing protein 0.015382
44 ENOG4108IQK o-acetylhomoserine 0.015357
45 ENOG4108K36 ATPase aaa-2 domain protein 0.015325
46 ENOG41069B0 Membrane-bound lysozyme-inhibitor of c-type lysozyme -0.015234
47 ENOG4107RKE D5 N terminal like 0.015196
48 ENOG4108PY3 NA 0.015102
49 ENOG41075TA NA 0.015033
50 ENOG4105EE4 it plays a direct role in the translocation of protons across the membrane (By similarity) -0.004926
50 ENOG4105DR6 Trap dicarboxylate transporter, dctp subunit -0.004926
50 ENOG4105N1P Ferredoxin-type protein -0.004926
51 ENOG4105R3P Inner membrane protein yagU -0.002924
51 ENOG410783I NA -0.002924
51 ENOG4108X8N Protein of unknown function (DUF2827) -0.002924
51 ENOG4105EQ2 LysR family Transcriptional regulator -0.002924
51 ENOG4108IEF Nitrate reductase -0.002924
52 ENOG4105NB5 NA 0.002896
52 ENOG4108PMA NA 0.002896
52 ENOG4107UEQ rhs element vgr protein 0.002896
52 ENOG4108QGN NA 0.002896
52 ENOG4105KN5 NA 0.002896
53 ENOG4105C3U ABC transporter -0.004805
53 ENOG4107Y66 Could be a nuclease that resolves Holliday junction intermediates in genetic recombination (By similarity) -0.004805
53 ENOG4107104 thymidine kinase -0.004805
54 ENOG4105NDF NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. May also have NAD-dependent lysine demalonylase and desuccinylase activity (By similarity) 0.014324
55 ENOG41074R3 NA 0.014301
56 ENOG410676N NA 0.014299
57 ENOG4107X4X cell filamentation protein -0.014175
58 ENOG4108I61 cytidylyl-transferase -0.014121
59 ENOG4105DWK Membrane 0.014087
60 ENOG4108VGH Abortive infection bacteriophage resistance protein -0.014087
61 ENOG4107S6X Glycosyl transferase, family 2 0.013983
62 ENOG4105DVU site-specific recombinase 0.013830
63 ENOG4107QPK )-transporter -0.013809
64 ENOG410608X Caudovirus prohead protease 0.013783
65 ENOG41071S1 NA 0.013754
66 ENOG4105KR2 Chorismate binding enzyme -0.006857
66 ENOG4107V3Y chorismate binding enzyme -0.006857
67 ENOG4105CQM Urea amidohydrolase subunit alpha 0.003410
67 ENOG4108XNJ Required for maturation of urease via the functional incorporation of the urease nickel metallocenter (By similarity) 0.003410
67 ENOG4105KI2 Urea amidohydrolase subunit beta 0.003410
67 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.003410
68 ENOG4105D3Q Sugar transferase 0.013633
69 ENOG4107UNG Ser Thr phosphatase family protein -0.013609
70 ENOG4105VVS Pfam:DUF3532 0.013604
71 ENOG41060J8 NA 0.013593
72 ENOG4108HMR Key enzyme in the regulation of glycerol uptake and metabolism (By similarity) 0.013583
73 ENOG4105DJY efflux transporter, rnd family, mfp subunit 0.013539
74 ENOG4105C60 DNA-binding protein -0.013410
75 ENOG4105NIV Esterase 0.013307
76 ENOG4105F8N transfer protein 0.013260
77 ENOG4105EUB pirin domain protein 0.013186
78 ENOG4106YJS accessory processing protein 0.006589
78 ENOG4108EE5 Part of the ABC transporter complex MacAB involved in macrolide export. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation (By similarity) 0.006589
79 ENOG4105DAA L-lactate -0.013161
80 ENOG4108V4B ThiJ pfpI 0.013160
81 ENOG4108VCS NA 0.013104
82 ENOG4105FB9 CRISPR-associated protein 0.013095
83 ENOG4107QVS Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC). Interaction with SRP-RNC leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components (By similarity) 0.006510
83 ENOG4106SMU thiamine transporter membrane protein 0.006510
84 ENOG4108S77 Transposase -0.012971
85 ENOG4106T7D NA 0.012948
86 ENOG4105I2P choline ethanolamine kinase -0.001608
86 ENOG41081XE plasmid maintenance system antidote protein, xre family -0.001608
86 ENOG4105K41 Toxin-antitoxin system, toxin component, RelE family -0.001608
86 ENOG4106MCE EamA-like transporter family -0.001608
86 ENOG4105KDP XRE family -0.001608
86 ENOG4106N74 Inherit from COG: domain protein -0.001608
86 ENOG4107SS6 2-dehydro-3-deoxygluconokinase -0.001608
86 ENOG41080ET plasmid maintenance system killer protein -0.001608
87 ENOG4105ZB5 hicB family -0.012846
88 ENOG4107CWK NA 0.000210
88 ENOG41073X6 NA 0.000210
88 ENOG4107RY9 Pfam:GSPII_E 0.000210
88 ENOG410767C Sel1 repeat 0.000210
88 ENOG4108WX4 Type IV secretion system protein VirB8 0.000210
88 ENOG41086JC Heavy-metal-associated domain 0.000210
88 ENOG4108NR3 Integrase 0.000210
88 ENOG4105PJV Fimbrial protein 0.000210
88 ENOG41073UF NA 0.000210
88 ENOG4106XMD NA 0.000210
88 ENOG4106C71 NA 0.000210
88 ENOG4105XMR NA 0.000210
88 ENOG4107J0C type IIi 0.000210
88 ENOG410699A Bacterial mobilisation protein (MobC) 0.000210
88 ENOG41065W5 NA 0.000210
88 ENOG4108EQA pts system 0.000210
88 ENOG4107C2N NA 0.000210
88 ENOG4108XAK NA 0.000210
88 ENOG4106CF3 NA 0.000210
88 ENOG41077WJ NA 0.000210
88 ENOG4105Y4R Capsular polysaccharide synthesis protein 0.000210
88 ENOG4108XRA Radical SAM 0.000210
88 ENOG4107FJR NA 0.000210
88 ENOG4106A6K transfer protein 0.000210
88 ENOG4105C9D Ferric reductase domain protein 0.000210
88 ENOG4106XG7 NA 0.000210
88 ENOG4105E30 Receptor 0.000210
88 ENOG4105NIR TrbM protein 0.000210
88 ENOG4107YZ2 ErfK YbiS YcfS YnhG 0.000210
88 ENOG410716U NA 0.000210
88 ENOG41081JF Glycosyl transferase (Group 1 0.000210
88 ENOG4106KBA Pfam:HIM 0.000210
88 ENOG4105MM1 Type IV secretion system protein VirB9 0.000210
88 ENOG41075RW NA 0.000210
88 ENOG4107DRZ Type IV secretion system protein VirB3 0.000210
88 ENOG4108Y05 relaxase Mobilization nuclease 0.000210
88 ENOG4105NT4 type IV secretion system protein VirB1 0.000210
88 ENOG4108MGN ATP-binding component of a transport system 0.000210
88 ENOG4106Z53 NA 0.000210
88 ENOG4105HEI LysR family (Transcriptional regulator 0.000210
88 ENOG4106PHI plasmid recombination enzyme 0.000210
88 ENOG4105KZA Thiol-disulfide oxidoreductase dcc 0.000210
88 ENOG4107F64 Prophage CP4-57 regulatory protein (AlpA) 0.000210
88 ENOG4107X1A hemagglutinin 0.000210
88 ENOG4107CN9 NA 0.000210
88 ENOG4106BNU NA 0.000210
88 ENOG41067WK Transcriptional regulator 0.000210
88 ENOG4108W54 Periplasmic binding protein 0.000210
88 ENOG4105S8B NA 0.000210
88 ENOG41090KJ transfer origin protein, TraL 0.000210
88 ENOG4105E80 TraG TraD family protein 0.000210
88 ENOG4106T4F NA 0.000210
88 ENOG4108WQU molybdopterin oxidoreductase Fe4S4 0.000210
88 ENOG4106A9D General secretion pathway protein I 0.000210
88 ENOG4108UIP NA 0.000210
88 ENOG4108VYD Bacterial mobilisation protein (MobC) 0.000210
88 ENOG4108H3A HTH_XRE 0.000210
88 ENOG4107YCB isochorismatase 0.000210
88 ENOG4108RZC NA 0.000210
88 ENOG4105EJX conjugal transfer ATPase 0.000210
88 ENOG4107142 NA 0.000210
89 ENOG4105CSF NADPH-dependent glycerol-3-phosphate dehydrogenase -0.006408
89 ENOG4105CCW damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity) -0.006408
90 ENOG4108BSC Methyltransferase 0.004255
90 ENOG4105WMJ Positive regulator of sigma E, RseC MucC 0.004255
90 ENOG4105CK7 Sodium proline symporter 0.004255
91 ENOG4105D7A ATP-binding protein 0.012725
92 ENOG4105CHH sulfate transporter 0.012699
93 ENOG4108UHU Aldolase -0.012683
94 ENOG4105CGZ zinc metallopeptidase 0.012679
95 ENOG4107XM3 UPF0442 protein 0.012591
96 ENOG4105CE7 Amidase, hydantoinase carbamoylase family -0.012574
97 ENOG410740Q transfer protein 0.012544
98 ENOG4108UM2 RNA polymerase 0.012544
99 ENOG4105FJH Di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions (By similarity) 0.012500
100 ENOG4108Z6H mu-like prophage Flumu protein gp27 -0.002083
100 ENOG4107XVI synthase -0.002083
100 ENOG4106IJH Protein of unknown function (DUF2730) -0.002083
100 ENOG4105QIB mu-like prophage Flumu protein gp29 -0.002083
100 ENOG4105Y97 NA -0.002083
100 ENOG4105IKI host-nuclease inhibitor protein -0.002083
101 ENOG4105J8I CRISPR-associated protein Csd1 family 0.006219
101 ENOG4105KCF 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) 0.006219
102 ENOG4105KVH Transcriptional regulator 0.012352
103 ENOG410834Z tol-pal system protein YbgF 0.012270
104 ENOG4105YV5 NA 0.012190
105 ENOG4105CVX Polysaccharide Biosynthesis Protein 0.012097
106 ENOG4107S5F Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG (By similarity) 0.006041
106 ENOG4105HFU Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly (By similarity) 0.006041
107 ENOG4108XPC ResB-like family -0.012078
108 ENOG4107QQG Dehydrogenase 0.012067
109 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) 0.012038
110 ENOG4107QR9 Iron-sulfur cluster binding protein -0.012036
111 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) 0.011969
112 ENOG4105U3S NA 0.011838
113 ENOG41082MP copper ion binding protein -0.011790
114 ENOG4106A3J Protein of unknown function (DUF3298) 0.011781
115 ENOG4105YNP NA -0.001671
115 ENOG4105CW0 outer membrane usher protein -0.001671
115 ENOG41061SD Biogenesis protein -0.001671
115 ENOG4106BYK NA -0.001671
115 ENOG4105GQR Chaperone -0.001671
115 ENOG4105PCE PemK-like protein -0.001671
115 ENOG4105DU0 nucleoside hydrolase -0.001671
116 ENOG4105D2T synthase 0.011534
117 ENOG4105KPE licD family -0.011497
118 ENOG4105DMW Dehydrogenase reductase -0.011487
119 ENOG4106TFU NA -0.011399
120 ENOG4105VMV gpw gp25 family protein 0.011371
121 ENOG4105Q58 NA -0.011367
122 ENOG4105EIZ Catalyzes the conversion of 6-carboxy-5,6,7,8- tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG) (By similarity) -0.011337