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. 2022 Mar 31;20(3):e3001590. doi: 10.1371/journal.pbio.3001590

Table 2. Medium-confidence validated PPT1 substrates.

Protein name (UniProt ID) Gene name Description Palmitome ratio Palmitome p-value Proteome ratio Proteome p-value CRAPome (%) Kang and colleagues Swiss Palm (%) CSS Palm
1433B_MOUSE Ywhab 14-3-3 protein beta/alpha 6.1651 0.0345 0.9858 0.5572 0 X
ACON_MOUSE Aco2 Aconitate hydratase, mitochondrial 2.376 0.027 1.026 0.810 6.569 0 X
ACSF2_MOUSE Acsf2 Medium-chain acyl-CoA ligase ACSF2, mitochondrial 6.8591 0.0431 1.1975 0.0262 0.4866 0 X
ACTN1_MOUSE Actn1 Alpha-actinin-1 2.9415 0.0091 1.0425 0.5896 0
ADDG_MOUSE Add3 Gamma-adducin 2.0263 0.0064 0.9829 0.5518 7.2993 0
AIFM1_MOUSE Aifm1 Apoptosis-inducing factor 1, mitochondrial 2.8165 0.0430 0.9702 0.4086 0 X
AL1L1_MOUSE Aldh1l1 Cytosolic 10-formyltetrahydrofolate dehydrogenase 3.1219 0.0122 1.0338 0.5529 0.9732 0 X
ANK3_MOUSE Ank3 Ankyrin-3 2.4417 0.0253 1.0168 0.8537 3.6496 0.487
AP2A1_MOUSE Ap2a1 AP-2 complex subunit alpha-1 1.6594 0.0299 0.9960 0.7766 5.8394 1.217 X
AP2B1_MOUSE Ap2b1 AP-2 complex subunit beta 2.3904 0.0227 0.9999 0.8375 2.433
AP2M1_MOUSE Ap2m1 AP-2 complex subunit mu 2.5018 0.0466 0.9800 0.5819 5.1095 X 2.433 X
ASTN1_MOUSE Astn1 Astrotactin-1 1.6647 0.0160 0.9877 0.7745 0.2433 X 5.353 X
AT2B4_MOUSE Atp2b4 Plasma membrane calcium-transporting ATPase 4 1.7388 0.0114 0.9954 0.7361 3.1630 5.882
ATAD3_MOUSE Atad3 ATPase family AAA domain-containing protein 3 1.7738 0.0372 0.9826 0.4550 5.882 X
ATPG_MOUSE Atp5f1c ATP synthase subunit gamma, mitochondrial 3.3911 0.0316 1.0012 0.7784 5.882 X
BAIP2_MOUSE Baiap2 Brain-specific angiogenesis inhibitor 1-associated protein 2 2.5954 0.0460 0.9172 0.0518 0.9732 5.882
CA2D1_MOUSE Cacna2d1 Voltage-dependent calcium channel subunit alpha-2/delta-1 3.1679 0.0182 0.9515 0.2687 0.7299 11.76 X
CAPS1_MOUSE Cadps Calcium-dependent secretion activator 1 2.4798 0.0483 0.9837 0.5833 0.4866 17.65 X
CBPE_MOUSE Cpe Carboxypeptidase E 3.1240 0.0467 1.0509 0.2354 0.0000 17.65 X
CCG8_MOUSE Cacng8 Voltage-dependent calcium channel gamma-8 subunit 3.1719 0.0204 0.9912 0.6364 0.0000 X 22.14 X
CD47_MOUSE Cd47 Leukocyte surface antigen CD47 2.9829 0.0084 0.9688 0.3699 0.0000 X 29.41
CISY_MOUSE Cs Citrate synthase, mitochondrial 2.9715 0.0258 1.0134 0.8591 47.06
CLH1_MOUSE Cltc Clathrin heavy chain 1 2.8044 0.0232 0.9978 0.8026 52.94
CLUS_MOUSE Clu Clusterin 7.8734 0.0278 1.0804 0.3769 1.7032 58.82 X
COTL1_MOUSE Cotl1 Coactosin-like protein 2.2434 0.0267 1.0294 0.0758 0.2433 X 0 X
COX2_MOUSE Mtco2 Cytochrome c oxidase subunit 2 1.6676 0.0472 1.0305 0.5074 0
COX41_MOUSE Cox4i1 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial 8.0469 0.0285 0.9785 0.4664 4.3796 X 0
CRIP2_MOUSE Crip2 Cysteine-rich protein 2 6.8277 0.0496 0.9438 0.1959 0.4866 0 X
CTNA2_MOUSE Ctnna2 Catenin alpha-2 1.8749 0.0463 1.0109 0.8808 3.1630 0 X
CYFP1_MOUSE Cyfip1 Cytoplasmic FMR1-interacting protein 1 11.9841 0.0440 1.0567 0.3692 0 X
DCE1_MOUSE Gad1 Glutamate decarboxylase 1 2.8429 0.0430 1.0195 0.8945 0.0000 0
DCE2_MOUSE Gad2 Glutamate decarboxylase 2 1.877 0.050 1.052 0.246 0.000 0 X
DCLK1_MOUSE Dclk1 Serine/threonine-protein kinase DCLK1 2.6248 0.0212 1.0263 0.7258 0.4866 0 X
DCTN1_MOUSE Dctn1 Dynactin subunit 1 1.5601 0.0173 0.9741 0.3428 0 X
DEST_MOUSE Dstn Destrin 4.3473 0.0220 0.9684 0.4662 0 X
DMXL2_MOUSE Dmxl2 DmX-like protein 2 1.6352 0.0331 0.9837 0.5503 0.2433 0 X
DNJC5_MOUSE Dnajc5 DnaJ homolog subfamily C member 5 5.1200 0.0109 0.8396 0.0177 0.0000 X 0 X
DPP6_MOUSE Dpp6 Dipeptidyl aminopeptidase-like protein 6 1.5302 0.0185 0.9976 0.7721 0.2433 0
DYN1_MOUSE Dnm1 Dynamin-1 2.3159 0.0428 0.9753 0.4249 4.6229 0.243 X
EFTU_MOUSE Tufm Elongation factor Tu, mitochondrial 1.5273 0.0058 0.9989 0.7913 0.487 X
EP15R_MOUSE Eps15l1 Epidermal growth factor receptor substrate 15-like 1 1.8051 0.0421 0.9319 0.1354 6.5693 0.487
ERP29_MOUSE Erp29 Endoplasmic reticulum resident protein 29 17.3706 0.0265 1.0100 0.9527 6.5693 0.73 X
F10A1_MOUSE St13 Hsc70-interacting protein 2.0988 0.0335 0.9517 0.2199 0.973 X
FA49B_MOUSE Fam49b Protein FAM49B 2.0721 0.0411 0.9483 0.2902 0.9732 0.973
FAS_MOUSE Fasn Fatty acid synthase 2.0774 0.0122 1.0023 0.9295 1.217 X
FUMH_MOUSE Fh Fumarate hydratase, mitochondrial 2.4212 0.0422 1.0295 0.6925 5.8394 2.433
GNAI1_MOUSE Gnai1 Guanine nucleotide-binding protein G(i) subunit alpha-1 3.3180 0.0287 0.9355 0.2010 X 3.406 X
GNAI2_MOUSE Gnai2 Guanine nucleotide-binding protein G(i) subunit alpha-2 4.6764 0.0374 0.9933 0.6470 X 3.406 X
GNAO_MOUSE Gnao1 Guanine nucleotide-binding protein G(o) subunit alpha 4.8055 0.0254 1.0334 0.7333 X 3.893 X
GNAQ_MOUSE Gnaq Guanine nucleotide-binding protein G(q) subunit alpha 3.9366 0.0329 1.0152 0.9241 2.9197 X 4.136
GNAZ_MOUSE Gnaz Guanine nucleotide-binding protein G(z) subunit alpha 2.8957 0.0265 0.9815 0.5618 1.4599 X 4.38 X
GPDA_MOUSE Gpd1 Glycerol-3-phosphate dehydrogenase 2.0714 0.0477 0.9542 0.2820 0.0000 5.109 X
GRIA2_MOUSE Gria2 Glutamate receptor 2 (GluR-2) 2.0033 0.0397 0.9980 0.8023 0.0000 X 5.882
HEXB_MOUSE Hexb Beta-hexosaminidase subunit beta 2.2503 0.0402 1.2536 0.0001 1.7032 5.882
HXK1_MOUSE Hk1 Hexokinase-1 1.864 0.032 1.041 0.483 9.002 8.516 X
HS12A_MOUSE Hspa12a Heat shock 70 kDa protein 12A 2.0260 0.0458 1.0011 0.8019 0.2433 5.882 X
HSP74_MOUSE Hspa4 Heat shock 70 kDa protein 4 2.0908 0.0249 0.9931 0.7273 7.299 X
IMPA1_MOUSE Impa1 Inositol monophosphatase 1 3.8661 0.0392 0.9405 0.0634 2.1898 X 8.516 X
IVD_MOUSE Ivd Isovaleryl-CoA dehydrogenase, mitochondrial 1.6243 0.0289 1.0186 0.5851 2.4331 11.76 X
KCC2D_MOUSE Camk2d Calcium/calmodulin-dependent protein kinase type II subunit delta 1.5646 0.0170 0.9913 0.7451 3.6496 11.76 X
KIF5C_MOUSE Kif5c Kinesin heavy chain isoform 5C 1.6691 0.0351 0.9917 0.6342 11.76 X
LETM1_MOUSE Letm1 Mitochondrial proton/calcium exchanger protein 1.8560 0.0428 0.9614 0.2821 4.3796 11.76 X
LIPA3_MOUSE Ppfia3 Liprin-alpha-3 1.6859 0.0239 0.9300 0.1882 0.2433 11.76 X
LIS1_MOUSE Pafah1b1 Platelet-activating factor acetylhydrolase IB subunit alpha 2.0802 0.0263 0.9655 0.3596 4.3796 16.55
M2OM_MOUSE Slc25a11 Mitochondrial 2-oxoglutarate/malate carrier 3.1066 0.0359 1.0222 0.8429 17.65
MPP2_MOUSE Mpp2 MAGUK p55 subfamily member 2 2.3788 0.0249 1.1196 0.0430 0.0000 X 17.65
NAC1_MOUSE Slc8a1 Sodium/calcium exchanger 1 1.6078 0.0206 1.0694 0.2621 0.2433 X 23.53 X
NCALD_MOUSE Ncald Neurocalcin-delta 45.0986 0.0333 0.8888 0.0594 0.0000 23.53 X
NCKP1_MOUSE Nckap1 Nck-associated protein 1 1.7610 0.0369 1.0207 0.6890 8.5158 25.06
NRX3A_MOUSE Nrxn3 Neurexin-3 2.8629 0.0254 1.0057 0.9531 0.0000 41.18 X
NSF_MOUSE Nsf Vesicle-fusing ATPase 1.7968 0.0111 0.9932 0.6500 7.5426 41.18 X
OAT_MOUSE Oat Ornithine aminotransferase, mitochondrial 2.3834 0.0408 1.1231 0.2428 47.06
ODO1_MOUSE Ogdh 2-oxoglutarate dehydrogenase, mitochondrial 2.7338 0.0474 1.0213 0.8685 7.7859 47.06 X
ODPX_MOUSE Pdhx Pyruvate dehydrogenase protein X component, mitochondrial 1.5552 0.0191 0.9543 0.0361 2.9197 52.94
OPA1_MOUSE Opa1 Dynamin-like 120 kDa protein, mitochondrial 1.9052 0.0425 0.9759 0.3227 3.1630 X 64.71 X
OXR1_MOUSE Oxr1 Oxidation resistance protein 1 1.6551 0.0027 0.9682 0.3713 0.0000 0
PCCA_MOUSE Pcca Propionyl-CoA carboxylase alpha chain, mitochondrial 1.5242 0.0322 0.9542 0.2035 0 X
PDE2A_MOUSE Pde2a cGMP-dependent 3’,5’-cyclic phosphodiesterase 1.7097 0.0100 1.0481 0.3392 0.7299 X 0.243 X
PGM1_MOUSE Pgm1 Phosphoglucomutase-1 1.9775 0.0013 1.0370 0.6444 3.8929 2.433
PLCB1_MOUSE Plcb1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 1.9949 0.0198 1.0061 0.7702 0.0000 5.882 X
PP2BA_MOUSE Ppp3ca Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 1.7693 0.0242 0.9565 0.1996 1.7032 X 11.76
PRDX6_MOUSE Prdx6 Peroxiredoxin-6 1.6130 0.0299 1.0689 0.0748 X 17.65
PRRT3_MOUSE Prrt3 Proline-rich transmembrane protein 3 2.2877 0.0290 0.9837 0.5961 0.2433 17.65 X
PTPRD_MOUSE Ptprd Receptor-type tyrosine-protein phosphatase delta 2.8642 0.0307 1.0097 0.9828 0.0000 X 17.65 X
PTPRS_MOUSE Ptprs Receptor-type tyrosine-protein phosphatase S 2.2591 0.0261 0.9756 0.4610 0.0000 29.41
PYGB_MOUSE Pygb Glycogen phosphorylase, brain form 3.9945 0.0321 1.0839 0.0150 4.6229 35.29
RAB1A_MOUSE Rab1a Ras-related protein Rab-1A 3.9014 0.0486 0.9073 0.0628 37.96 X
RAB7A_MOUSE Rab7a Ras-related protein Rab-7a 1.8488 0.0354 1.0068 0.8316 X 41.18 X
RAP2B_MOUSE Rap2b Ras-related protein Rap-2b 8.6218 0.0214 0.9733 0.4554 1.7032 X 0 X
S12A2_MOUSE Slc12a2 Solute carrier family 12 member 2 2.5952 0.0396 0.9641 0.3628 1.2165 0 X
SAHH2_MOUSE Ahcyl1 S-adenosylhomocysteine hydrolase-like protein 1 2.7124 0.0136 1.0495 0.2339 3.8929 0 X
SATT_MOUSE Slc1a4 Neutral amino acid transporter A 8.4285 0.0440 1.2718 0.0002 0.0000 X 0.243 X
SC6A1_MOUSE Slc6a1 Sodium- and chloride-dependent GABA transporter 1 3.4145 0.0466 1.0470 0.4440 0.0000 X 0.973 X
SCAM1_MOUSE Scamp1 Secretory carrier-associated membrane protein 1 3.2759 0.0336 0.9115 0.0531 0.7299 X 1.46 X
SDHB_MOUSE Sdhb Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial 2.8442 0.0205 1.0124 0.8729 4.3796 2.676 X
SEPT8_MOUSE Septin8 Septin-8 1.7848 0.0199 1.0574 0.3595 X 5.109
SFXN1_MOUSE Sfxn1 Sideroflexin-1 7.9333 0.0425 1.0657 0.3687 6.5693 X 5.882 X
SFXN3_MOUSE Sfxn3 Sideroflexin-3 2.3725 0.0162 0.9884 0.6007 0.9732 X 5.882 X
SSDH_MOUSE Aldh5a1 Succinate-semialdehyde dehydrogenase, mitochondrial 1.6663 0.0050 1.0534 0.4846 4.3796 5.882 X
SYIM_MOUSE Iars2 Isoleucine—tRNA ligase, mitochondrial 1.8534 0.0348 1.0386 0.5893 4.3796 8.516 X
SYNJ1_MOUSE Synj1 Synaptojanin-1 2.1789 0.0289 1.0211 0.8514 2.9197 9.489 X
SYNPR_MOUSE Synpr Synaptoporin 6.445 0.018 0.963 0.365 0.000 11.76 X
SYT2_MOUSE Syt2 Synaptotagmin-2 2.4842 0.0494 0.9862 0.7697 0.0000 X 11.76 X
SYT7_MOUSE Syt7 Synaptotagmin-7 2.7289 0.0129 1.0495 0.6112 0.0000 X 11.76 X
TERA_MOUSE Vcp Transitional endoplasmic reticulum ATPase) 2.1826 0.0257 1.0105 0.9593 0.4063 14.36
UBA1_MOUSE Uba1 Ubiquitin-like modifier-activating enzyme 1 2.3035 0.0188 0.9517 0.2816 0.2603 23.53 X
UCRI_MOUSE Uqcrfs1 Cytochrome b-c1 complex subunit Rieske, mitochondrial 4.8396 0.0492 1.1149 0.0848 2.4331 X 28.71
VA0D1_MOUSE Atp6v0d1 V-type proton ATPase subunit d 4.6384 0.0334 1.0246 0.7738 1.2165 29.41 X
VAMP1_MOUSE Vamp1 Vesicle-associated membrane protein 1 6.0833 0.0172 0.8937 0.0789 0.0000 X 29.41
VATE1_MOUSE Atp6v1e1 V-type proton ATPase subunit E 2.8166 0.0390 0.9533 0.1839 3.8929 29.41
VPS35_MOUSE Vps35 Vacuolar protein sorting-associated protein 35 2.2835 0.0102 0.9934 0.6715 8.5158 47.06
VTA1_MOUSE Vta1 Vacuolar protein sorting-associated protein VTA1 homolog 39.3736 0.0420 0.9281 0.0333 2.1898 0

X = validation of given dataset; blank cells or a score of zero indicate lack of identification in that dataset [12,31,39,97]. SwissPalm score indicates percentage of palmitoylation experiments in which the protein has been identified.