TABLE 2.
Highlighted direct PKA target candidate proteinsa
| Parameter | Value | Phosphopeptide sequence | Phosphorylation site(s) |
Localization probability(ies) (%) |
PKA target motif |
Phosphorylation fold change (WT vs ΔpkaC1) |
Adjusted phosphorylation fold change |
P value |
|---|---|---|---|---|---|---|---|---|
| Protein name | Atg24 | RRM(Sp)SVHEDPPQAGPLADAVDLAGIGDGVLEC | S47 | 82.6 | Yes | 25.3 | 31.67 | 0.0020 |
| GenBank accession no. | XP_751536.1 | RRM(Sp)SVHEDPPQAGPLADAVDLA | S47 | 97.5 | Yes | −1.16 | 1.08 | 0.3630 |
| Description | Vacuolar targeting protein | RM(Sp)SVHEDPPQAGPL | S47 | 100 | Yes | −1.53 | −1.22 | 0.0179 |
| No. of interactome spectra | 2 | RRM(Sp)SVHEDPPQAGPL | S47 | 99.8 | Yes | −1.88 | −1.50 | 0.0039 |
| No. of PKA motifs | 4 | RE(Sp)DLEADYNDL | S266 | 100 | Yes | −1.78 | −1.42 | 0.0285 |
| Expression ratio (WT/ΔpkaC1) | 0.80 | VARRE(Sp)DLEADYNDL | S266 | 100 | Yes | −2.94 | −2.35 | 0.0088 |
| RE(Sp)DLEADYNDL | S266 | 100 | Yes | −3.5 | −2.80 | 0.0011 | ||
| MEGDLDNDPEM(Sp)EHGR | S487 | 100 | No | −1.64 | −1.31 | 0.0103 | ||
| Protein name | HapB | RM(Sp)HVGSPHVQ | S181 | 100 | Yes | −1.13 | 1.67 | 0.4860 |
| GenBank accession no. | XP_755804.1 | RM(Sp)HVG(Sp)PHVQ | S181; S185 | 100; 100 | Yes; no | 1.3 | 2.46 | 0.3060 |
| Description | CCAAT-binding transcription factor subunit | MSHVG(Sp)PHVQ | S185 | 100 | No | 1.97 | 3.73 | 0.0033 |
| No. of interactome spectra | 0 | NVDSGKPAEENPSSAPKRK(Sp)SEVNDDNANSVKKS | S330 | 73.3 | Yes | 1.16 | 2.19 | 0.5290 |
| No. of PKA motifs | 3 | RKS(Sp)EVNDDNANSVK | S331 | 99.2 | Yes | 82.2 | 155.53 | 0.0081 |
| Expression ratio (WT/ΔpkaC1) | 0.53 | RKS(Sp)EVNDDNANSVK | S331 | 100 | Yes | 1.94 | 3.67 | 0.0345 |
| KS(Sp)EVNDDNANSVK | S331 | 99.8 | Yes | −1.71 | 1.11 | 0.0029 | ||
| Protein name | Not4 | RA(Sp)LAGSQASQSPRPVHAT | S311 | 100 | Yes | 102 | 108.84 | 0.0059 |
| GenBank accession no. | XP_750771.1 | RA(Sp)LAGSQAS | S311 | 100 | Yes | 20.3 | 21.66 | 0.0471 |
| Description | CCR4-NOT core complex subunit | RA(Sp)LAGSQASQSPR | S311 | 100 | Yes | 15.6 | 16.65 | 0.0364 |
| No. of interactome spectra | 2 | RA(Sp)LAGSQ | S311 | 100 | Yes | −2.38 | −2.23 | 0.0094 |
| No. of PKA motifs | 6 | TRRA(Sp)LAG(Sp)QASQSPRPVHAT | S311; S315 | 97.3; 99.5 | Yes; no | 1.07 | 1.14 | 0.8000 |
| Expression ratio (WT/ΔpkaC1) | 0.94 | TRRA(Sp)LAG(Sp)QA(Sp)QSPRPVHAT | S311; S315; S318 | 100; 100; 99.8 | Yes; no; no | 4.24 | 4.52 | 0.1370 |
| RA(Sp)LAGSQA(Sp)QSPRPVHAT | S311; S318 | 100; 86.3 | Yes; no | 2.12 | 2.26 | 0.0325 | ||
| TAG(Tp)PPISGGGMFAQ | T638 | 99.7 | No | 1.18 | 1.26 | 0.3500 | ||
| NISEISLG(Sp)PLPK | S919 | 100 | No | 1.32 | 1.41 | 0.0879 | ||
a
Lowercase “p” following parenthetically enclosed amino acid residue abbreviations within peptide sequences indicates phosphorylation of corresponding residues. Bold text indicates phosphorylated amino acid residues identified on peptide fragments with no additional phosphorylation and showing significant enrichment (P < 0.05) of at least 2-fold (unadjusted) in the WT strain compared to ΔpkaC1.