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 ENOG4108TN6 type iii secretion 0.028729
2 ENOG4108HR8 type iii secretion 0.027240
3 ENOG4107Y59 type iii secretion 0.025687
4 ENOG4105K44 type iii secretion 0.021432
5 ENOG4108HHI Type III secretion system protein 0.021422
6 ENOG41083GP type iii secretion 0.017313
7 ENOG4108IUF type iii secretion 0.016273
8 ENOG41076UM multiple antibiotic resistance (MarC)-related protein 0.011047
9 ENOG4105C1F The M ring may be actively involved in energy transduction (By similarity) 0.010964
10 ENOG4108QHK Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. This protein is an E3 ubiquitin ligase that interferes with host's ubiquitination pathway 0.010495
11 ENOG4105JGF anti-sigma regulatory factor serine threonine protein kinase 0.010124
12 ENOG4107B2H carbonic anhydrase 0.009932
13 ENOG4105EQ0 Major Facilitator superfamily 0.009800
14 ENOG41069RK type iii secretion 0.009729
15 ENOG4107SGM protein serine threonine phosphatase 0.009431
16 ENOG4105JJ8 Cytochrome c nitrite reductase, pentaheme subunit 0.009407
17 ENOG41081V1 type iii secretion 0.009366
18 ENOG4105FTC Lytic transglycosylase catalytic 0.009131
19 ENOG4105U07 type iii secretion 0.009099
20 ENOG41075IY surface presentation of antigens protein SpaP 0.004462
20 ENOG4108M6W surface presentation of antigens protein SpaS 0.004462
21 ENOG4108V77 5-carboxymethyl-2-hydroxymuconate 0.008889
22 ENOG4105DTA methyltransferase -0.008849
23 ENOG4107R91 Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position (By similarity) 0.008740
24 ENOG4105SFT Fimbrial protein -0.008489
25 ENOG4105E5D amino acid 0.008274
26 ENOG4108RBT type iii secretion 0.008165
27 ENOG4105DYT 3-hydroxyacyl-CoA dehydrogenase -0.008071
28 ENOG4105T85 surface presentation of antigens protein 0.007883
29 ENOG4106I8F Excisionase 0.007861
30 ENOG4105CK2 sodium dicarboxylate symporter 0.007794
31 ENOG4108HH7 Receptor -0.007786
32 ENOG4105W16 bluf domain protein -0.007755
33 ENOG4108AG4 Bacteriophage lambda integrase, N-terminal domain 0.007742
34 ENOG4105CT0 Protein of unknown function, DUF484 0.007728
35 ENOG4108IJ7 Glycine betaine 0.007590
36 ENOG41085PU Protein of unknown function (DUF2384) 0.007527
37 ENOG4108XS3 type III secretion apparatus protein 0.007516
38 ENOG4105CHH sulfate transporter 0.007483
39 ENOG4105EB3 Histidine kinase -0.007477
40 ENOG4105E54 alpha-amylase 0.007475
41 ENOG4108T6W phage minor tail protein L 0.007468
42 ENOG4105DQ6 Transposase 0.007450
43 ENOG4108Z58 rRNA Methylase 0.007397
44 ENOG4105E7T carrier protein 0.007387
45 ENOG41083UI stage II sporulation protein 0.007383
46 ENOG410833S tail length tape measure 0.007351
47 ENOG4106HU5 NA -0.007337
48 ENOG4105EUP HipA domain protein -0.007333
49 ENOG4105ZWX type iii secretion 0.007331
50 ENOG4105CNA YD repeat protein 0.007326
51 ENOG4108RC9 Type III secretion system protein 0.007308
52 ENOG4105CGF Aromatic amino acid aminotransferase 0.007302
53 ENOG41061TN Secretion system effector C (SseC) like family 0.007283
54 ENOG4108XNZ glycosyl transferase -0.007268
55 ENOG4105C3U ABC transporter 0.007257
56 ENOG4106F2U NA 0.007197
57 ENOG4105E2X shikimate dehydrogenase -0.007165
58 ENOG410804A Flagellar hook-associated 2 domain-containing protein 0.007148
59 ENOG410834V flagellar protein FliS 0.007148
60 ENOG4105CFY cytochrome d ubiquinol oxidase, subunit ii 0.007110
61 ENOG410617M Transcriptional regulator 0.007099
62 ENOG4105CGK Exodeoxyribonuclease III -0.007083
63 ENOG41062HK Pathogenesis-related transcriptional factor and ERF protein 0.007063
64 ENOG4108KQ5 Integrase catalytic subunit -0.007040
65 ENOG41090TI Catalyzes the excretion of spermidine (By similarity) 0.007040
66 ENOG4107581 Glycosyl transferase (Group 1 0.007028
67 ENOG4105C09 Bile acid -0.007002
68 ENOG4108ZBZ Catalyzes the excretion of spermidine (By similarity) 0.006994
69 ENOG4107T5D Carbon starvation protein CstA 0.006994
70 ENOG4106GBJ type iii secretion 0.006988
71 ENOG4105FYS replication protein O -0.006977
72 ENOG4105IKQ hydratase 0.006972
73 ENOG4106J9S Prophage -0.006970
74 ENOG4106III tail fiber protein 0.006955
75 ENOG4107QPE cytochrome c biogenesis protein, transmembrane region 0.006951
76 ENOG4107QJP DTDP-glucose 4-6-dehydratase -0.006941
77 ENOG4105FYV Amp nucleosidase 0.006934
78 ENOG4105H5P transposase -0.006910
79 ENOG4105E5Q amino acid AbC transporter 0.006906
80 ENOG41083G8 Multidrug resistance protein MdtM 0.006837
81 ENOG4105Y84 type iii secretion 0.006827
82 ENOG4106CZA Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC (By similarity) -0.006798
83 ENOG4105Y7Q type iii secretion 0.006781
84 ENOG4108Z7T Destroys radicals which are normally produced within the cells and which are toxic to biological systems (By similarity) 0.006756
85 ENOG41078HP Tir chaperone protein (CesT) family 0.006745
86 ENOG4107RCU alcohol dehydrogenase -0.006715
87 ENOG4105CWM branched-chain amino acid transport system II carrier protein 0.006709
88 ENOG4105D6A Electron transport complex -0.006698
89 ENOG4105C0R drug resistance transporter emrb qaca subfamily 0.006679
90 ENOG4106CIA Functions in complex with FlhD as a master transcriptional regulator that regulates transcription of several flagellar and non-flagellar operons by binding to their promoter region 0.006667
91 ENOG4105UFD tol-pal system protein YbgF 0.006664
92 ENOG4105KNR Activates the small RNA gene sgrS under glucose- phosphate stress conditions as well as yfdZ. Represses its own transcription under both stress and non-stress conditions. Might act as a sensor of the intracellular accumulation of phosphoglucose by binding these molecules in its C-terminal solute-binding domain (By similarity) 0.006648
93 ENOG4105F1N DNA alkylation repair -0.006622
94 ENOG41074AG NA -0.006613
95 ENOG4108PZQ Inner membrane protein YeeR -0.006612
96 ENOG4105D07 Signal peptide peptidase, SppA -0.006604
97 ENOG4105VXA transcriptional activator, Ogr delta 0.006603
98 ENOG4105SYG Fimbrial protein -0.006588
99 ENOG4105JXR Protein of unknown function (DUF3296) -0.006578
100 ENOG4105ECX polysaccharide export -0.006564
101 ENOG41062WK cellular response to acidity -0.006552
102 ENOG4105C4M (Ubiquinol oxidase) subunit I 0.006540
103 ENOG4108FRR sodium solute -0.006536
104 ENOG4105FEU K -dependent Na -Ca exchanger -0.006525
105 ENOG4105CHZ Catalyzes the dehydration of D-mannonate (By similarity) 0.006507
106 ENOG4108EP2 Dehydrogenase 0.006481
107 ENOG4108V5Y Flagellar motor switch protein 0.006481
108 ENOG4108R7K Metal Dependent Phosphohydrolase -0.006470
109 ENOG4108V8F Transcriptional regulator, MarR family 0.006467
110 ENOG4107U91 Rhomboid family 0.006402
111 ENOG4106AJS Involved in induction of the so-called NTR enzymes in response to nitrogen deprivation, as well as in glutamate biosynthesis. May mediate the glutamate-dependent repression of the GLT operon -0.006389
112 ENOG4105CS6 Rhs element vgr protein 0.006369
113 ENOG4107ZKY Acetolactate synthase small subunit 0.006354
114 ENOG4105FU2 Flagellar basal-body rod protein FlgC 0.006351
115 ENOG4105DG1 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.006343
116 ENOG4105VF7 tolerance protein 0.006342
117 ENOG41068IX NA 0.006336
118 ENOG4105XA0 heptosyltransferase ii 0.006330
119 ENOG4105F6U Short-chain dehydrogenase reductase Sdr 0.006325
120 ENOG4105GRN Iso-IS1 ORF2 0.006319
121 ENOG4105C7H Helicase, RecD TraA family 0.006305
122 ENOG410679B prophage CP4-57 regulatory protein alpA -0.006280
123 ENOG4105XPI Polarity suppression 0.006276
124 ENOG4105CHD Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1- P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity) 0.006255
125 ENOG4105K6D phospholipase d 0.006250
126 ENOG4105TKZ Tail Sheath 0.006231
127 ENOG4105DAA L-lactate -0.006214
128 ENOG4105KRQ Addiction module toxin, Txe YoeB family -0.006204
129 ENOG410619D Flagellar hook-length control protein 0.006183
130 ENOG41084RR Preprotein translocase subunit YajC 0.006178
131 ENOG41067CV Integrase -0.006175
132 ENOG4108Z67 carbohydrate kinase, thermoresistant glucokinase family 0.006174
133 ENOG4105X6K flagellar hook-basal body complex protein fliE 0.001027
133 ENOG4105Y8N Flagellar biosynthesis protein FliP 0.001027
133 ENOG4105YPB Flagellar motor switch protein 0.001027
133 ENOG41080VP Role in flagellar biosynthesis (By similarity) 0.001027
133 ENOG41080ZM flagellar hook-associated protein 0.001027
133 ENOG410833P Structural component of flagellum, the bacterial motility apparatus. Part of the rod structure of flagellar basal body (By similarity) 0.001027
134 ENOG4108UN4 phage SPO1 DNA polymerase-related protein -0.006152
135 ENOG4108I5G Major Facilitator superfamily 0.006143
136 ENOG4107AKS type iii secretion 0.006128
137 ENOG4105TSF type iii secretion 0.006117
138 ENOG4105H40 NA -0.006091
139 ENOG4105CAQ asparagine synthetase 0.006089
140 ENOG41062UC NA -0.006086
141 ENOG4105WG9 Conserved Protein 0.006085
142 ENOG4105CZ6 Can catalyze the oxidation of choline to betaine aldehyde and betaine aldehyde to glycine betaine (By similarity) -0.006084
143 ENOG410715K NA -0.006072
144 ENOG4105E1T DNA ligase -0.006055
145 ENOG4107THI 3,4-dihydroxyphenylacetate 2,3-dioxygenase 0.006048
146 ENOG4105DYS nad(p)h dehydrogenase (quinone) -0.006043
147 ENOG4105TS0 gtp-binding protein -0.002013
147 ENOG4106EG6 NA -0.002013
147 ENOG4106ZN7 UPF0401 protein YkfF -0.002013
148 ENOG41090SZ ABC-2 type transporter -0.005978
149 ENOG4107N3Y integral membrane protein 0.005974
150 ENOG4105CGY Dna recombination protein 0.005973
151 ENOG4105D13 transposase -0.005964
152 ENOG41064AS NA -0.005955
153 ENOG4108M7N phopq-activated pathogenicity-related protein pqaa type 0.005945
154 ENOG4108S80 Tail assembly protein 0.005934
155 ENOG4106P9E tail protein 0.005933
156 ENOG4108UKF 4-hydroxyphenylacetate degradation bifunctional isomerase decarboxylase 0.005915
157 ENOG4105C72 UPF0176 protein 0.005910
158 ENOG4105K2J Transcriptional regulator -0.005907
159 ENOG4108NVI NA 0.005897
160 ENOG4106S9G NA 0.005894
161 ENOG4105EAU Plays a role in nitrite reduction (By similarity) 0.005887
162 ENOG41081YP Inherit from COG: Outer membrane autotransporter 0.005886
163 ENOG4105DTZ bifunctional PTS system fructose-specific transporter subunit IIA HPr protein 0.005886
164 ENOG4105E0U tyrosine-specific transport protein 0.005884
165 ENOG4105F4I Transcriptional regulator 0.005878
166 ENOG41074DU domain protein 0.005873
167 ENOG4105DJ4 phosphatidylserine decarboxylase 0.005863
168 ENOG4105D5S Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity) 0.005862
169 ENOG4105K8R UPF0145 protein -0.005854
170 ENOG4105CDM Glutamate-1-semialdehyde aminotransferase 0.005853
171 ENOG4105P0Q fimbrial-like protein YadC -0.005847
172 ENOG4105SN2 fimbrial-like adhesin protein -0.002922
172 ENOG4108XEY fimbrial-like adhesin protein -0.002922
173 ENOG41079V8 NA 0.005839
174 ENOG4108X7Q Baseplate Assembly protein 0.005818
175 ENOG410832Q Flagellar biosynthetic protein FliQ 0.005816
176 ENOG4105QU8 transcriptional regulator 0.005811
177 ENOG4107VAM peptidase, m28 -0.005807
178 ENOG4107QW3 Sucrose phosphorylase -0.005805
179 ENOG4105KXI murein peptide amidase A 0.005799
180 ENOG4108RTD type II secretion system protein K 0.005795
181 ENOG4105C6F GntR Family Transcriptional Regulator 0.005788
182 ENOG4108HJ1 Uncharacterized conserved protein (DUF2303) -0.005786
183 ENOG4105CN7 Flagellar biosynthetic protein FliP 0.005775
184 ENOG4108Z75 Tir chaperone protein (CesT) family 0.005771
185 ENOG4108Z38 Catalyzes a trans-dehydration via an enolate intermediate (By similarity) -0.005770
186 ENOG4107S68 Flagellar motor switch protein 0.005769
187 ENOG4105DN4 Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity) 0.005767
188 ENOG41064N6 NA 0.005765
189 ENOG4106NZI LysR family Transcriptional regulator 0.005759
190 ENOG4105EZN Cobyrinic acid ac-diamide synthase 0.005759
191 ENOG4108UJT Fimbrial-like protein -0.005758
192 ENOG4108W1G NA 0.005752
193 ENOG4105CEA Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) (By similarity) 0.005744
194 ENOG4107UYV decarboxylase 0.005739
195 ENOG4105DEG Vwa containing coxe family protein -0.005737
196 ENOG4105VGJ Virulence-associated protein 0.005732
197 ENOG410634K single-stranded DNA-binding protein 0.005714
198 ENOG4105JDP Binds together with S18 to 16S ribosomal RNA (By similarity) 0.002857
198 ENOG4108MBZ Inherit from COG: repeat-containing protein 0.002857
199 ENOG41066DD Involved in DNA repair and RecF pathway recombination (By similarity) 0.002857
199 ENOG4108MBB NA 0.002857
200 ENOG4105NA2 Pfam:DUF322 0.005714
201 ENOG410801I Peptidyl-prolyl cis-trans isomerase 0.005714
202 ENOG410664T MutT NUDIX family protein 0.005714
203 ENOG41082SS Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions (By similarity) 0.005714
204 ENOG4105EIW domain protein 0.000060
204 ENOG4105EP7 Acyl-transferase 0.000060
204 ENOG4105H1K NA 0.000060
204 ENOG4105IFU YjgP YjgQ family 0.000060
204 ENOG4105IMQ NA 0.000060
204 ENOG4105JBW NA 0.000060
204 ENOG4105NGJ Skp-like protein 0.000060
204 ENOG4105NU1 BAF60b domain protein 0.000060
204 ENOG4105QGZ NA 0.000060
204 ENOG4105QK5 NA 0.000060
204 ENOG4105SAI NA 0.000060
204 ENOG4105SCY DNAK suppressor 0.000060
204 ENOG4105SKM NA 0.000060
204 ENOG4105UFR NA 0.000060
204 ENOG4105Z49 NA 0.000060
204 ENOG41060DB Type III secretion chaperone 0.000060
204 ENOG41063ZQ 30S ribosomal protein S21 0.000060
204 ENOG41064P5 NA 0.000060
204 ENOG410656K NA 0.000060
204 ENOG41065WR NA 0.000060
204 ENOG41065YW Preprotein translocase subunit SecG 0.000060
204 ENOG410666P Inherit from COG: Catalyzes the hydroxylation of the N(6)-(4-aminobutyl)- L-lysine intermediate to form hypusine, an essential post- translational modification only found in mature eIF-5A factor (By similarity) 0.000060
204 ENOG4106ABR general secretion pathway protein G 0.000060
204 ENOG4106AP9 histone H1-like protein 0.000060
204 ENOG4106C95 NA 0.000060
204 ENOG4106DIS phosphatidyltransferase 0.000060
204 ENOG4106E8M polymerase 0.000060
204 ENOG4106E9S 50S ribosomal protein L36 0.000060
204 ENOG4106G4J NA 0.000060
204 ENOG4106MFV virulence plasmid 0.000060
204 ENOG4106SXF NA 0.000060
204 ENOG4106TY7 NA 0.000060
204 ENOG4106V5C NA 0.000060
204 ENOG41075VU NA 0.000060
204 ENOG410777W NA 0.000060
204 ENOG41077E8 NA 0.000060