KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and Virus Strains | ||
| E coli BL21(DE3) | Lucigen | Cat# 60401–1 |
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Golden Gate Assembly Kit | New England Biolabs | Cat#: E1601 |
| LB Broth | Fisher Scientific | Cat#: BP9723 |
| LB Agar | Fisher Scientific | Cat#: BP1425 |
| QIAprep Spin Miniprep Kit | Qiagen | Cat#: 27104 |
| MagicMedia E. coli Expression Medium | ThermoFisher Scientific | Cat#: K6803 |
| BugBuster® 10X Protein Extraction Reagent | Millipore | Cat#: 70921 |
| rLysozyme Solution | Millipore | Cat#: 71110 |
| DNase I | New England Biolabs | Cat#: M0303 |
| Potassium phosphate | Sigma Aldrich | Cat#: P5655 |
| 4-Methylumbelliferyl β-D-glucopyranoside | Sigma Aldrich | Cat#: M3633 |
| Critical Commercial Assays | ||
| Deposited Data | ||
| Protein G domain B1 data set | Olson et al. 2014 | SRR2054943,SRR2054944 |
| Pyrrolidine Ketide Synthase data set | Wrenbeck et al. 2019 | SRR8238223,SRR8238221,SRR8238219,SRR8238217,SRR8238222,S RR8238220,SRR8238218,SRR8238216 |
| Levoglucosan kinase data set | Wrenbeck et al. 2019 | SRR8238225,SRR8238229,SRR8238231,SRR8238227,SRR8238224,S RR8238228,SRR8238230,SRR8238226 |
| Small ubiquitin-related modifier 1 data set | Weile et al. 2017 | SRR5680627,SRR5680629,SRR5680640,SRR5680625,SRR5680634,S RR5680638 |
| SUMO-conjugating enzyme UBC9 data set | Weile et al. 2017 | SRR5680697,SRR5680703,SRR5680713,SRR5680715,SRR5680731,S RR5680699,SRR5680705,SRR5680707,SRR5680727,SRR5680733 |
| Thiamin pyrophosphokinase 1 data set | Weile et al. 2017 | SRR5680677,SRR5680635,SRR5680674,SRR5680718,SRR5680717,S RR5680693,SRR5680694,SRR5680669,SRR5680632,SRR5680722,SR R5680719,SRR5680689,SRR5680692,SRR5680670 |
| Hemagglutinin data set | Doud & Bloom 2016 | SRR3113656,SRR3113660 |
| Beta-glucosidase data set | Romero et al. 2015 | SRR11472224, SRR11472223, SRR11472221, SRR11472220, SRR11472219, SRR11472215, SRR11472218, SRR11472216, SRR11472214, SRR11472217, SRR11472222 |
| 1-deoxy-D-xylulose-5-phosphate synthase data set | Romero Lab, UW-Madison | SRR11467347,SRR11467346 |
| Rocker data set | Romero Lab, UW-Madison | SRR12767727,SRR12767726 |
| Protein G domain B1 protein structure | Protein Data Bank | PDB ID: 1FCC |
| Beta-glucosidase protein structure | Protein Data Bank | PDB ID: 1GNX |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| Beta-glucosidase gene (bgl3) from Streptomyces sp. strain QM-B814 | GenBank | GenBank: CAA82733.1 |
| Software and Algorithms | ||
| Bowtie2 | Langmead & Salzberg 2012 | http://bowtie-bio.sourceforge.net/bowtie2 |
| Rosetta | Alford et al. 2017 | https://www.rosettacommons.org/software/ |
| EVmutation | Hopf et al. 2017 | https://marks.hms.harvard.edu/evmutation/ |
| DeepSequence | Riesselman et al. 2018 | https://github.com/debbiemarkslab/DeepSequence |
| HMMER | Wheeler & Eddy 2013 | http://hmmer.org/ |
| PU learning code | This Paper | https://github.com/RomeroLab/pudms |
| scripts used to analyze the data sets and generate the figures | This Paper | https://github.com/RomeroLab/PU-learning-paper-analysis |
| Other | ||