Additional file 1 of Substrate specificity mapping of fungal CAZy AA3_2 oxidoreductases
Notice bibliographique
Résumé
Additional file 1: Table S1. List of the previously biochemically characterized proteins with the information of the database source, source organism, strain, protein activity, name, and the related publication. Table S2. Statistics of the major SSN clusters. Table S3. The AA3_2 sequences that were selected in this study with the database source, organism, and the production status and the biochemical information. Table S4. The list of substrates that were tested for the activity assays. Table S5. UPLC PDA retention time for each compound and the spectrum of each compound. Table S6. Substrate depletion by KiOdhA followed by HPAEC-PAD after 24 h incubation. Table S7. The extinction coefficient and wavelength to be used for the activity assay on aryl alcohols under different pH. Fig S1. SSN at the cut-off of 470 for the further division of cluster II. Fig S2. Absorption spectra of the concentrated AA3_2s. The oxidized FAD should have two absorbance maxima at 375-380 nm and at 440-444 nm. Fig S3. SDS page gel of the successfully produced AA3_2 proteins. Fig S4. UPLC-PDA Chromatogram (290 nm) of a) Standards of coniferyl alcohol, coniferaldehyde, ferulic acid, benzoquinone and hydroquinone b) Coniferyl alcohol after 8 h incubation with boiled PsAaoA at 30 °C (C) Coniferyl alcohol after PsAaoA oxidation for 8 h at 30 °C, showing the formation of coniferaldehyde. Fig S5. Mass spectra collected in negative ion mode showing a) Glucose b) Glucose after oxidation by ApGoxA and c) Glucose after oxidation by TaGdhA. Fig S6. Mass spectra collected in negative ion mode showing a) Gentiobiose b) Gentiobiose after oxidation by KiOdhA. Fig S7. Mass spectra collected in negative ion mode showing a) Glucose; b) Glucose after incubation with ApAA3_2B; c) Glucose after incubation with PcAA3_2A; and d) Glucose after incubation with McGdhA. Fig S8. Multiple Sequence Alignment (MSA) of characterized AA3_2 members in this study and previously. Red boxes show the primary sequence differences between the different enzymes. Fig S9. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of PsAaoA. The FAD and catalytic residues colored in green, hydrophobic residues to form the tunnel to block free access to active site are shown in orange, and the unique motifs identified from MSA are shown in Cyan. c) Alignment for the active site of PsAaoA (Red) and PeAAOx (white, PDB: 3FIM). Fig S10. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of TaGdhA. The FAD and catalytic residues colored in green, residues for substrate binding are shown in orange, and the unique motifs identified from MSA are shown in cyan. c) Alignment for the active site of TaGdhA (blue), AfGDH (white, PDB: 4YNT), and AfGDH in complex with D-glucono-1,5-lactone (pink, PDB: 4YNU). Fig S11. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of ApGoxA. The FAD and catalytic residues colored in green, residues for substrate binding are shown in orange, and the unique motifs identified from MSA are shown in cyan. c) Alignment for the active site of ApGoxA (blue), TcODH (white, PDB: 6XUT), and TcODH in complex with glucose (pink, PDB: 6XUU). Fig S12. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of AsAadhA. The FAD and catalytic residues colored in green and the unique motifs identified from MSA are shown in cyan. c) Alignment for the active site of AsAadhA (Red) and PeAAO (white, PDB: 3FIM). Fig S13. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of AsAadhB. The FAD and catalytic residues colored in green and the unique motifs identified from MSA are shown in cyan. c) Alignment for the active site of AsAadhB (Red) and PeAAO (white, PDB: 3FIM). Fig S14. a) Surface and b) ribbon and sticks (active site and FAD) of the AlphaFold homology model of KiOdhA. The FAD and catalytic residues colored in green, residues for substrate binding are shown in orange, and the unique motifs identified from MSA are shown in cyan. c) Alignment for the active site of KiOdhA (blue), TcODH (white, PDB: 6XUT), and TcODH in complex with glucose (pink, PDB: 6XUU). Fig S15. Amino acids and positions within the characterized AA3_2 sequences that are implicated in catalysis and substrate preference. Fig S16. Sequence logos of the active site residues from clades IIa, IIb, IV, VI, XI, XII, and XXX. The amino acid numbering of the sequences is based on PsAaoA for cluster IIa, AmPDH1 for cluster IIb, AsAadhA for cluster IV, TaGdhA for cluster VI, ApGoxA for cluster XI, AnGOx for cluster XII, and KiOdhA for cluster XXX.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,938 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».