Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Haemophilus
influenzae) |
UxuA | This paper, pNYCOMPSC-tagless HiUxuA vector |
Uniprot:P44488 | See Supplementary file 7. cloned into the C-terminal TEV cleavable 10x-Histag containing vector pNYCOMPS-LIC-TH10- ccdB (C-term) such that the tag is out of frame |
| Gene (H.
influenzae) |
GulD | This paper, pNYCOMPSC-tagless HiGulD vector |
Uniprot:Q57517 | See Supplementary file 7. cloned into the C-terminal TEV cleavable 10x-Histag containing vector pNYCOMPS-LIC-TH10- ccdB (C-term) such that the tag is out of frame |
| Gene (H.
influenzae) |
KdgK | This paper, HiKdgK-pSGC-His vector |
Uniprot:P44482 | See Supplementary file 7. cloned into the N-terminal TEV cleavable 6x-Histag containing vector pNIC28-Bsa4 |
| Gene (H.
influenzae) |
UxuB | This paper, HiUxuB-pSGC-His vector |
Uniprot:P44481 | See Supplementary file 7. cloned into the N-terminal TEV cleavable 6x-Histag containing vector pNIC28-Bsa4 |
| Gene (H.
influenzae) |
KdgA | This paper, HiKdgA-pSGC-His vector |
Uniprot:P44480 | See Supplementary file 7. cloned into the N-terminal TEV cleavable 6x-Histag containing vector pNIC28-Bsa4 |
| Gene (H.
influenzae) |
GulP | This paper | Uniprot:P71336 | See Supplementary files 8 and 9 |
| Gene (H.
influenzae) |
GulQ | This paper | Uniprot:P44484 | See Supplementary files 8 and 9 |
| Gene (H.
influenzae) |
GulM | This paper | Uniprot:P44483 | See Supplementary files 8 and 9 |
| Gene (H.
influenzae) |
UxuR | This paper | Uniprot:P44487 | See Supplementary files 8 and 9 |
| Oligonucleotide (H. influenzae) |
UxuA, UxuR, GulD, GulP, GulQ, GulM, KdgK, UxuB, KdgA, Hflu |
This paper | See Supplementary file 8. qRT-PCR oligonucleotide sequences used for gene expression profiling |
|
| Strain, strain background (H. influenzae Rd KW20) |
H. flu | https://www.atcc.org | ATCC 51907 |
Supplementary file 9. Genetic deletion mutants of the putative L-gulonate catabolism pathway in H. influenzae Rd KW20 |
| Genetic reagent (H. influenzae) |
∆GulP | This paper |
Supplementary file 8. Genetic deletion mutants of the putative L-gulonate catabolism pathway in H. influenzae Rd KW20 |
|
| Genetic reagent (H. influenzae) |
∆GulD | This paper |
Supplementary file 8. Genetic deletion mutants of the putative L-gulonate catabolism pathway in H. influenzae Rd KW20 |
|
| Transfected construct (E. coli BL21 (DE3) |
BL21 (DE3) E. coli
containing the pRIL plasmid |
Stratagene | Growth media contain 25 μg/mL Kanamycin or 100 μg/mL Carbomycin and 34 μg/mL Chloramphenicol |
|
| Commercial assay or kit |
RNAprotect Bacteria Reagent |
Qiagen | Cat No./ID: 76506 | |
| Commercial assay or kit |
RNeasy Mini Kit | Qiagen | Cat No./ID: 74104 | |
| Commercial assay or kit |
ProtoScript First Strand cDNA Synthesis Kit |
New England BioLabs | Cat No./ID: E6300S | |
| Chemical compound, drug |
2-keto-3-deoxy-D- gluconate |
Enzymatically synthesized | CAS: 17510-99-5 | Enzymatic synthesis by D-mannonate dehydratase (Uniprot ID B0T0B1). Verified via 1H-NMR |
| Chemical compound, drug |
2-keto-3-deoxy-D- gluconate-6- phosphate |
Enzymatically synthesized | CAS: 884312-23-6 | Enzymatic synthesis by D-mannonate dehydratase (Uniprot ID B0T0B1) and 1 μM 2-keto-3-deoxy-D-gluconate kinase (Uniprot ID A4XF21). Verified via 1H-NMR |
| Software, algorithm | Integrative Pathway Mapping |
This paper | https://github.com/salilab/pathway_mapping | The source code for the IMP program, benchmark, input scripts files, and output files for the benchmark and the gulonate pathway calculations are available here(50) |
| Software, algorithm | IMP program | Russel D, et al, Putting the pieces together: integrative structure determination of macromolecular assemblies. PLoS Biology. 10(1):e1001244, 2012 |
http://integrativemodeling.org | Integrative modeling |
| Software, algorithm | MODELLER | B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., 5.6.1- 5.6.32, 2014. |
https://salilab.org/modeller/ | Comparative modeling |
| Software, algorithm | DOCK3.6 | Mysinger MM, Shoichet BK. Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model. 50(9):1561-73, 2010. |
http://dock.compbio.ucsf.edu/ | Docking |
| Software, algorithm | Automated version DOCK3.6 |
Irwin JJ, et al. Automated Docking Screens: A Feasibility Study. J. Med. Chem. 52(18)5712–5720, 2009. |
http://blaster.docking.org/ | Docking |
| Software, algorithm | Similarity Ensemble Approach (SEA) |
Keiser MJ, et al. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 25(2): 197-206, 2007. |
http://sea.bkslab.org/ | SEA chemo-informatic calculations |
| Software, algorithm | OpenEye Scientific Software |
OpenEye Scientific Software I. OEChem. 2.0.2 ed2014. |
https://www.eyesopen.com/ | In silico chemical transformations |
| Software, algorithm | RDKit | Landrum G. RDKit: Open-source cheminformatics. Release_2016.03.1 ed2016 |
http://www.rdkit.org/ | Chemical similarity calculations |
| Software, algorithm | EFI-EST | Gerlt JA, et al. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochim. Biophys. Acta. 1854(8):1019- 1037, 2015. |
http://efi.igb.illinois.edu/efi-est/index.php | Genome neighborhood networks |
| Software, algorithm | Pythoscape v1.0 | Barber AE, Babbitt PC. Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics. 28(21):2845- 2846, 2012. |
http://www.rbvi.ucsf.edu/trac/Pythoscape | Sequence similarity networks |
| Software, algorithm | Cytoscape v3.4 | Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498-504, 2003. |
http://www.cytoscape.org/ | Network visualization |