Nuclear genes with apicoplast signal sequences
Compiled with assistance from Stuart Ralph and checked against apicoplast proteomics  
Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E. Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites. PLoS Biol. 2018 Sep 13;16(9):e2005895.PMID: 30212465;
Function PfID Formal annotation with curator's notes Exists in proteome Transcript EC#
Replication and transcription 5'-3' exonuclease, N-terminal resolvase-like domain, putative X
35297 PF3D7_0203900
5'-3' exonuclease, putative X
35448 PF3D7_1106300 5'-3' exoribonuclease 1, putative
35460 PF3D7_1129500 A/G-specific adenine glycosylase, putative
35320 PF3D7_0305600
AP endonuclease (DNA-[apurinic or apyrimidinic site] lyase), putative X
35346 PF3D7_0504200 ATP-dependent RNA helicase ddx27, putative X
35347 PF3D7_0504400
ATP-dependent helicase, putative X
35504 PF3D7_1313400 DEAD box helicase, putative X
35478 PF3D7_1223300
DNA gyrase subunit A X
35485 PF3D7_1239500
DNA gyrase subunit B X
35498 PF3D7_1304100
DNA ligase I
35555 PF3D7_1449400 crossover junction endonuclease MUS81, putative X
35499 PF3D7_1307600
DNA-directed RNA polymerase subunit alpha, putative X
35566 PF3D7_1472700 DNA-directed RNA polymerase, alpha subunit, putative
35569 PFC10_API0016 RNA polymerase beta' subunit, putative (rpoC)
35437 PF3D7_1037600 TFIIH basal transcription factor complex helicase XBP subunit, putative
35383 PF3D7_0727300
DNA (cytosine-5)-methyltransferase X
35310 PF3D7_0219500
pseudouridine synthase, putative X
35407 PF3D7_0914000 pseudouridylate synthase, putative
35480 PF3D7_1228500 RNA pseudouridylate synthase, putative X
35412 PF3D7_0918800 dihydrouridine synthase, putative X
35350 PF3D7_0508800
single-stranded DNA-binding protein X
35491 PF3D7_1249900 ribosomal RNA small subunit methyltransferase a2, putative X
35290 PF3D7_0112000 TatD-like deoxyribonuclease
35349 PF3D7_0508500 nd6 protein, putative X
35409 PF3D7_0914300 met-10+ like protein, putative X
35487 PF3D7_1242200
queuine tRNA-ribosyltransferase, putative
35508 PF3D7_1319300 tRNA (guanine(26)-n(2))-dimethyltransferase, putative X
35309 PF3D7_0218300 rRNA methyltransferase, putative X
35455 PF3D7_1120500 tRNA nucleotidyltransferase, putative X
35513 PF3D7_1332600
DNA-(apurinic or apyrimidinic site) lyase 1 X
35534 PF3D7_1411400
plastid replication-repair enzyme X
35400 PF3D7_0904700
bacterial histone-like protein
35490 PF3D7_1247000 F-box only protein 9 homolog, putative X
35512 PF3D7_1329700
apicoplast calcium binding protein 1
Translation ribosomal protein S4, putative
35446 PF3D7_1105400 40S ribosomal protein S4, putative X
35420 PF3D7_0932600 apicoplast ribosomal protein S6, putative X
35536 PF3D7_1413400 30S ribosomal protein S9, putative X
35559 PF3D7_1460900 ribosomal protein S10, apicoplast, putative X
35462 PF3D7_1137500
ribosomal protein s14, apicoplast, putative X
35447 PF3D7_1106100 ribosomal protein s15, apicoplast, putative
35541 PF3D7_1421200 40S ribosomal protein S25 X
35472 PF3D7_1210000 50S ribosomal protein L1, apicoplast, putative
35461 PF3D7_1132700 50s ribosomal protein l2, putative X
35411 PF3D7_0918200 50S ribosomal protein L3, apicoplast, putative
35306 PF3D7_0212200 ribosomal protein l12, mitochondrial, putative X
35336 PF3D7_0413800 50S ribosomal protein L10, putative X
35358 PF3D7_0524600 50S ribosomal protein L12, apicoplast, putative
35545 PF3D7_1431700 60S ribosomal protein L14, putative X
35543 PF3D7_1429100 ribosomal protein l15, apicoplast, putative X
35357 PF3D7_0522500 50S ribosomal protein L17, apicoplast, putative X
35366 PF3D7_0613400 50s ribosomal protein l18, apicoplast, putative X
35397 PF3D7_0827500 ribosomal protein l21, apicoplast, putative X
35561 PF3D7_1467400
50S ribosomal protein L22, apicoplast, putative X
35434 PF3D7_1034200 ribosomal protein l27, putative
35343 PF3D7_0503000
50S ribosomal protein L28, apicoplast, putative X
35470 PF3D7_1208000 ribosomal protein L29, apicoplast, putative X
35401 PF3D7_0907800 ribosomal protein L35, apicoplast, putative X
35562 PF3D7_1469000
translation initiation factor IF-1 X
35319 PF3D7_0305000
elongation factor Ts X
35363 PF3D7_0602400
elongation factor G X
35376 PF3D7_0704900 peptide chain release factor 2 X
35542 PF3D7_1428600
peptide chain release factor 1 X
35376 PF3D7_0704900 peptide chain release factor 2 X
35542 PF3D7_1428600
peptide chain release factor 1 X
35302 PF3D7_0208600
ribosome-recycling factor X
35402 PF3D7_0907900
peptide deformylase X
35530 PF3D7_1367700
alanine--tRNA ligase
35477 PF3D7_1218600
arginine-tRNA ligase; arginyl-tRNA synthetase X
35406 PF3D7_0913900
arginine--tRNA ligase, putative X
35351 PF3D7_0509600
asparagine--tRNA ligase X
35353 PF3D7_0514300 aspartate--tRNA ligase, putative X
35426 PF3D7_1015200
cysteine--tRNA ligase, putative X
35525 PF3D7_1357200
glutamate--tRNA ligase X
35338 PF3D7_0416100
glutamyl-tRNA(Gln) amidotransferase subunit A X
35540 PF3D7_1420400
glycine--tRNA ligase X
35479 PF3D7_1225100
isoleucine--tRNA ligase, putative X
35421 PF3D7_0934000 histidine--tRNA ligase, putative X
35398 PF3D7_0828200 leucine--tRNA ligase, putative X
35539 PF3D7_1416800
lysine--tRNA ligase, putative X
35503 PF3D7_1313200
methionyl-tRNA formyltransferase, putative X
35481 PF3D7_1232000
phenylalanine--tRNA ligase X
35417 PF3D7_0925300
proline--tRNA ligase, putative
35379 PF3D7_0717700
serine--tRNA ligase, putative X
35474 PF3D7_1216000 serine--tRNA ligase, putative X
35458 PF3D7_1126000
threonine--tRNA ligase X
35469 PF3D7_1207600 tRNA dimethylallyltransferase, putative X
35425 PF3D7_1005000
methionine--tRNA ligase, putative X
35427 PF3D7_1018000 tRNA pseudouridine synthase, putative
35517 PF3D7_1336900
tryptophanyl-tRNA synthetase tryptophan--tRNA ligase X
35493 PF3D7_1251700
tryptophanyl-tRNA synthetase, putative tryptophan--tRNA ligase, putative X
35454 PF3D7_1117500
tyrosine--tRNA ligase X
35324 PF3D7_0311200 valine--tRNA ligase, putative
35396 PF3D7_0825200
translation initiation factor IF-3 X
35331 PF3D7_0407200 peptidyl-tRNA hydrolase 2, putative
35428 PF3D7_1020700 histone acetyltransferase, putative
Isoprenoid biosynthesis 1-deoxy-D-xylulose 5-phosphate reductoisomerase X
35560 PF3D7_1467300
1-deoxy-D-xylulose 5-phosphate reductoisomerase X
35518 PF3D7_1337200
1-deoxy-D-xylulose 5-phosphate synthase X
35304 PF3D7_0209300
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase X
35344 PF3D7_0503100
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative X
35430 PF3D7_1022800
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), putative X
35288 PF3D7_0104400
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Fatty acid and phospholipid metabolism 3-oxoacyl-(acyl-carrier protein) reductase, putative X
35415 PF3D7_0922900
3-oxoacyl-[acyl-carrier-protein] reductase X
35372 PF3D7_0626300
3-oxoacyl-acyl-carrier protein synthase I/II X
35301 PF3D7_0208500
acyl carrier protein
35307 PF3D7_0215000 acyl-CoA synthetase
35308 PF3D7_0215300
acyl-CoA synthetase
35467 PF3D7_1200700 acyl-CoA synthetase X
35510 PF3D7_1323000
beta-hydroxyacyl-ACP dehydratase X
35305 PF3D7_0211400
beta-ketoacyl-ACP synthase III oxoacyl-ACP synthase FABH X
35564 PF3D7_1469600
acetyl-coa carboxylase X
35551 PF3D7_1443700
dephospho-CoA kinase
35418 PF3D7_0930500 diacylglycerol kinase, putative X
35429 PF3D7_1020800
dihydrolipoamide acyltransferase component E2 X
35367 PF3D7_0615100
enoyl-acyl carrier reductase X
35507 PF3D7_1318200
glycerol-3-phosphate 1-O-acyltransferase, putative X
35339 PF3D7_0420200 holo-[acyl-carrier-protein] synthase, putative
35529 PF3D7_1366800
phosphatidylserine synthase, putative X
35394 PF3D7_0815900