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 ENOG4108J4B Beta-lactamase 0.509128
2 ENOG4106I73 repressor 0.428525
3 ENOG4108HWY Beta-lactamase 0.412366
4 ENOG4108FPN Integrase 0.163012
5 ENOG410869V Inherit from COG: Resolvase 0.141049
6 ENOG4108KU9 integrase family 0.139430
7 ENOG4105EEH Integrase, catalytic region 0.119977
8 ENOG4107MUZ AtP-binding protein 0.090353
9 ENOG41081HJ Transcriptional regulator, MarR family 0.089186
10 ENOG4107A9Z NA -0.078336
11 ENOG41061ME transport protein -0.071274
12 ENOG4108TG4 cadmium resistance 0.064211
13 ENOG4105ZX1 Transposase C 0.063872
14 ENOG4105GNH type I restriction-modification system 0.063400
15 ENOG410683M YopX protein 0.063241
16 ENOG4105T7F Bacteriophage Mu Gam like protein 0.060725
17 ENOG4108VVK transcriptional Regulator, AsnC 0.059308
18 ENOG41078KA NA -0.057075
19 ENOG410755P NA -0.019007
19 ENOG4108J8C transporter major facilitator family protein -0.019007
19 ENOG41060VH transcription activator, effector binding -0.019007
20 ENOG4105VTR Integrase 0.056826
21 ENOG4108SK8 Reverse transcriptase (RNA-dependent DNA polymerase) 0.054917
22 ENOG4108FPF anti-repressor 0.053929
23 ENOG4106DI1 Metallothionein family 14 -0.053854
24 ENOG41063K0 cell wall associated fibronectin-binding protein 0.053720
25 ENOG4106XZ4 NA 0.053189
26 ENOG4107H9P ArsR family transcriptional regulator -0.052975
27 ENOG41065X2 NA 0.051387
28 ENOG4105ZU7 Transcriptional regulator 0.050829
29 ENOG4108YM7 Gcn5-related n-acetyltransferase -0.050295
30 ENOG4105WUM NA -0.049836
31 ENOG4105WKT Replication Protein -0.049187
32 ENOG4105EYG tyrosine recombinase. Not involved in the cutting and rejoining of the recombining DNA molecules on dif(SL) site (By similarity) 0.048862
33 ENOG41061NS Spore coat protein 0.047603
34 ENOG41084V8 Transcriptional regulator -0.047356
35 ENOG41060I3 NA -0.047356
36 ENOG4106QP4 HTH_ARSR 0.047213
37 ENOG410649Q NA -0.047066
38 ENOG4105FQS NA 0.046603
39 ENOG4105NA7 transcriptional regulator 0.045616
40 ENOG4108BHT HTH_XRE -0.045565
41 ENOG4108MSW NA 0.045552
42 ENOG4105JGP host cell surface-exposed lipoprotein -0.045453
43 ENOG4106C6B NA 0.045186
44 ENOG4105PFV Transposase -0.045041
45 ENOG41072DS NA -0.045041
46 ENOG41063CS Replication Protein 0.044663
47 ENOG4105W1Y Transcriptional regulator -0.044073
48 ENOG4106CTQ NA 0.043063
49 ENOG4105GXC methyltransferase -0.042757
50 ENOG4107YW6 Integrase core domain -0.042232
51 ENOG4105ENU Cupin 2, conserved barrel domain protein 0.042002
52 ENOG4108BJX Pfam:Transposase_17 0.041238
53 ENOG41081FA mutator MutT protein -0.040894
54 ENOG4108759 YopX protein -0.040775
55 ENOG4106B51 transposase -0.040381
56 ENOG4108SSE Transposase -0.040072
57 ENOG4107B6F Flagellar export protein flij 0.039741
58 ENOG4106YPY NA -0.039527
59 ENOG41071BU NA -0.039527
60 ENOG41083KF Resolvase, N terminal domain 0.039440
61 ENOG4105YIR NA 0.038448
62 ENOG4105WP0 NA 0.038322
63 ENOG410843U RNA polymerase -0.038201
64 ENOG4106IMF NA 0.037853
65 ENOG4108PI2 O-Methyltransferase 0.037619
66 ENOG4108BUD transposase -0.037245
67 ENOG4106FTB Protein of unknwon function (DUF3310) -0.037121
68 ENOG4108X80 Transposase 0.037113
69 ENOG4105YJE holin, phage phi LC3 family 0.036653
70 ENOG41067YF Family Transcriptional Regulator 0.036537
71 ENOG41074T7 Inherit from COG: Transcriptional regulator 0.036280
72 ENOG4105FTQ Dna gyrase -0.036078
73 ENOG4107EF9 amino acid adenylation domain protein -0.035895
74 ENOG41074WZ NA -0.035827
75 ENOG4107M22 Hsp20/alpha crystallin family -0.035719
76 ENOG4107DZW NA 0.035161
77 ENOG4108M4B domain protein -0.035061
78 ENOG4105HYF Transcriptional regulator 0.034798
79 ENOG41085FG BON domain 0.034752
80 ENOG4106Z91 NA 0.034664
81 ENOG4105KY0 addiction module toxin, Txe YoeB family -0.033990
82 ENOG4106H2A Pfam:PhdYeFM -0.033990
83 ENOG4106CU9 Pathogenesis-related transcriptional factor and ERF 0.033939
84 ENOG41090CA NA 0.033739
85 ENOG4108C9U prophage protein 0.033723
86 ENOG41082AV single-stranded DNA-binding protein -0.033463
87 ENOG4105EUN Transposase -0.033431
88 ENOG4108FWE Phage antirepressor protein KilAC domain -0.033421
89 ENOG4107CDB HIRAN domain 0.033402
90 ENOG41066RB phage protein 0.033287
91 ENOG4107JCS PriCT_1 -0.033243
92 ENOG4106CB5 single-stranded DNA-binding protein 0.033112
93 ENOG4107STQ Multicopper oxidase -0.032973
94 ENOG41074TU Inherit from COG: type iii restriction protein res subunit -0.032967
95 ENOG4107YP1 SCCmec staphylococcal cassette region, isolate CMFT106 0.032395
96 ENOG4105MM3 Protein of unknown function (DUF1643) 0.032395
97 ENOG41065WX Staphylococcal protein of unknown function (DUF960) 0.032395
98 ENOG4107B0R HTH_XRE 0.032293
99 ENOG4105F6H The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3- phosphate (By similarity) 0.031681
100 ENOG410779U NA -0.031681
101 ENOG4107666 Excalibur 0.031319
102 ENOG4106JKS LuxR family Transcriptional regulator 0.015565
102 ENOG4105CI5 domain protein 0.015565
103 ENOG4108YXY alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen 0.030491
104 ENOG4108C9S Inherit from NOG: domain protein 0.030366
105 ENOG4105T6C Cell surface-associated protein implicated in virulence by promoting bacterial attachment to both alpha- and beta-chains of human fibrinogen and inducing the formation of bacterial clumps 0.030359
106 ENOG4106EBY NA -0.029948
107 ENOG4105DUM transcriptional regulator, lysR family 0.029933
108 ENOG4107FQI NA 0.029895
109 ENOG4107WKS Macrolide 2'-phosphotransferase 0.029827
110 ENOG4105EEN pathogenesis -0.029621
111 ENOG41068Z8 NA -0.029595
112 ENOG4107W2Q Inherit from COG: transposase 0.029484
113 ENOG4108ZJE Fibronectin-binding protein -0.029481
114 ENOG4105EN2 IstB domain-containing protein ATP-binding protein 0.029261
115 ENOG4108M1Z surface protein -0.029188
116 ENOG41085NQ NA 0.029124
117 ENOG41086DV NA 0.028759
118 ENOG4105WXW Antirepressor 0.028703
119 ENOG4107HKV NA -0.028666
120 ENOG4107YID Cadmium efflux system accessory protein -0.028584
121 ENOG4105PXR Erf family 0.028420
122 ENOG4108XC1 Bifunctional DNA primase polymerase 0.028340
123 ENOG4105GRP Gcn5-related n-acetyltransferase -0.028246
124 ENOG4107FRG HTH_XRE 0.028106
125 ENOG4108VCE Phage Portal Protein 0.028047
126 ENOG4108U1G type I restriction modification DNA specificity domain protein 0.027777
127 ENOG4107HNI N-acetylmuramoyl-L-alanine amidase -0.027455
128 ENOG4106STF NA -0.027309
129 ENOG4107BVE Domain of unknown function (DUF2479) 0.027274
130 ENOG41067SI Uncharacterised protein family (UPF0154) -0.027034
131 ENOG4105PXK NA -0.026936
132 ENOG4105QJV Domain of unknown function (DUF771) -0.026852
133 ENOG41078NF NA 0.026707
134 ENOG410785C NA 0.026323
135 ENOG4106PJW NA -0.008761
135 ENOG4105C67 Transketolase -0.008761
135 ENOG4108KB0 deacetylase -0.008761
136 ENOG4105CIV prophage primase -0.026066
137 ENOG4107RJ1 sodium solute -0.026048
138 ENOG4105KUM terminase (Small subunit) -0.025936
139 ENOG4108G8K HTH_XRE -0.025895
140 ENOG4108RM5 Nad-dependent epimerase dehydratase -0.025893
141 ENOG4106JUT Streptomycin 3''-adenylyltransferase -0.025889
142 ENOG4105PBZ NA -0.012889
142 ENOG4105UQW NA -0.012889
143 ENOG4107PQ2 Replication Protein 0.025666
144 ENOG4107JRA Terminase small subunit 0.025606
145 ENOG4108AFA type I restriction-modification system -0.025562
146 ENOG4107EH6 transposase 0.025486
147 ENOG4107DWF Bacteriocin (Lactococcin_972) 0.025466
148 ENOG4107BHU NA -0.025407
149 ENOG4107BUF HTH_XRE -0.025070
150 ENOG4108PCX Major Facilitator -0.024764
151 ENOG410745K NA 0.024749
152 ENOG4106A5I NA -0.024507
153 ENOG410726H mobilization protein 0.024286
154 ENOG4105MU5 relaxase mobilization nuclease domain protein 0.024286
155 ENOG4108RY9 This enzyme is an effector of chloramphenicol resistance in bacteria (By similarity) 0.024286
156 ENOG4106HRD Inherit from COG: Retrotransposon protein 0.023981
157 ENOG4105CCN Peptidase M56 0.023840
158 ENOG4106FMB NA -0.023617
159 ENOG4105VW6 gCN5-related N-acetyltransferase 0.023581
160 ENOG41086TG Septum formation initiator -0.023581
161 ENOG4105X1K Prokaryotic N-terminal methylation motif -0.002620
161 ENOG4107EIA ecf subfamily rna polymerase -0.002620
161 ENOG41076V9 NA -0.002620
161 ENOG4105WWX n-acetylmuramoyl-l-alanine amidase -0.002620
161 ENOG4107MEV NA -0.002620
161 ENOG410607N Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatE shares overlapping functions with TatA (By similarity) -0.002620
161 ENOG4108HI5 response regulator -0.002620
161 ENOG41068Z9 Bacterial protein of unknown function (DUF910) -0.002620
161 ENOG4108HE0 ABC transporter, substrate-binding protein, family 5 -0.002620
162 ENOG4106VMY NA -0.023581
163 ENOG41081DF restriction modification system DNA specificity domain -0.023581
164 ENOG4108FKG Phage-related minor tail protein 0.023434
165 ENOG41089BK Glutamine amido-transferase -0.023334
166 ENOG41072K8 domain protein -0.023127
167 ENOG4105C6I Resolvase 0.023052
168 ENOG41069E5 NA 0.022967
169 ENOG4106EYG NA 0.022967
170 ENOG4107C2J NA -0.022791
171 ENOG4107PFR AP2 domain 0.022758
172 ENOG4107BVM NA -0.007506
172 ENOG41087X0 septum formation initiator -0.007506
172 ENOG4107PEE NA -0.007506
173 ENOG4107QM2 Aldo Keto reductase 0.011164
173 ENOG4108RAI NA 0.011164
174 ENOG41077QD NA 0.022328
175 ENOG4108KK1 membrane protein AbrB duplication -0.022328
176 ENOG4108QYW Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Beta-hemolysin is a phospholipase C with specific activity toward sphingomyelins. Has a high specificity for sphingomyelin, hydrolyzes lysophosphatidylcholine at a much lower rate, but has no activity towards phosphatidylcholine, phosphatidylethanolamine, or phosphatidylserine (By similarity) -0.022328
177 ENOG4108R3E Dna-3-methyladenine glycosylase i -0.022227
178 ENOG4105CQM Urea amidohydrolase subunit alpha 0.007397
178 ENOG4105KI2 Urea amidohydrolase subunit beta 0.007397
178 ENOG4108YZ9 Urea amidohydrolase subunit gamma 0.007397
179 ENOG4107A43 NA -0.022190
180 ENOG4107A2J NA -0.022190
181 ENOG4107NHU NA -0.022078
182 ENOG4105NSX NA 0.022011
183 ENOG4105XIX Protein of unknown function (DUF1064) 0.021970
184 ENOG4105ZAZ Hypothetical protein (DUF2513) -0.021636
185 ENOG41069HQ D-Ala-teichoic acid biosynthesis protein -0.021632
186 ENOG4106ABJ NA -0.021618
187 ENOG41085SA peptidase 0.010709
187 ENOG4107EIZ UspA domain protein 0.010709
188 ENOG4106FXD Glyoxalase Bleomycin resistance protein (Dioxygenase -0.021386
189 ENOG4105EH1 NA -0.021385
190 ENOG4105MDI NA -0.021259
191 ENOG4106AM8 polysaccharide lyase family 8 0.021253
192 ENOG4108FNH Uncharacterised protein family (UPF0104) -0.021103
193 ENOG4107HIQ Cassette chromosome recombinase A 0.020968
194 ENOG4108424 Inherit from COG: Helicase -0.020966
195 ENOG41075ZN orf cn004 -0.020960
196 ENOG4108PY0 Peptidase S24-like protein -0.020894
197 ENOG4105DKS phage plasmid primase, p4 family -0.020835
198 ENOG4105Y0C transposase, IS3 IS911 family protein 0.020807
199 ENOG4107NQ5 HTH_XRE -0.020782
200 ENOG4108JB9 formate dehydrogenase 0.020780
201 ENOG4108IEG Formate dehydrogenase Alpha subunit -0.020780
202 ENOG4108FN8 Involved in the biosynthesis of D-alanyl-lipoteichoic acid (LTA). Catalyzes an ATP-dependent two-step reaction where it forms a high energy D-alanyl AMP intermediate and transfers the alanyl residues from AMP to Dcp (By similarity) -0.020722
203 ENOG4107ZZJ Major Facilitator superfamily -0.020706
204 ENOG4105ISA NA 0.020632
205 ENOG4105FP3 KAP P-loop domain-containing protein 0.020632
206 ENOG4106V96 NA -0.020580
207 ENOG4105N9C Transposase -0.020453
208 ENOG41069WJ NA 0.020448
209 ENOG4106850 NA 0.020375
210 ENOG41068TG NA 0.020374
211 ENOG4105PXC MarR family Transcriptional regulator -0.020362
212 ENOG410799G NA 0.020335
213 ENOG4105SAY Replication initiator protein 0.020282
214 ENOG4106I62 holin, SPP1 family 0.020261
215 ENOG4108HF1 Inherit from COG: peptidase (S8 and S53, subtilisin, kexin, sedolisin 0.005044
215 ENOG4108FSN HTH_ARSR 0.005044
215 ENOG4105EKX Restriction modification system DNA (Specificity 0.005044
215 ENOG4106HET NA 0.005044
216 ENOG4107S8Q Peptide synthetase 0.020176
217 ENOG4105CGH 5'-nucleotidase -0.020176
218 ENOG4106F5C transposase 0.006720
218 ENOG4108IKS HTH_XRE 0.006720
218 ENOG4107FQV NA 0.006720
219 ENOG41081PB XRE family Transcriptional regulator 0.019918
220 ENOG4105EH2 Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr) (By similarity) 0.009946
220 ENOG410624H Pfam:TRF2 0.009946
221 ENOG4107WTH Galactitol-1-phosphate dehydrogenase -0.019893
222 ENOG4108CVG LysM 0.019745
223 ENOG4108Q46 Protein of unknown function (DUF3644) -0.019721
224 ENOG41067YN Transcriptional regulator 0.019696