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The proteome of the apicoplast |
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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: |
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Comparison was made with list of nuclear genes with apicoplast signal sequences taken from PlasmoDB |
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Functional class |
Reference |
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Annotation |
Pf Essentiality |
Present in gene list |
Transcript |
EC# |
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35048 |
DNA metabolism |
PF3D7_0103600 |
 |
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ATP-dependent DNA/RNA helicase psh1 |
Mutable in CDS |
NO |
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3.6.4.13 |
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35194 |
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PF3D7_1223300 |
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DNA gyrase subunit A |
Non - Mutable in CDS |
YES |
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5.99.1.3 |
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35200 |
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PF3D7_1239500 |
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DNA gyrase subunit B |
Non - Mutable in CDS |
YES |
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5.99.1.3 |
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35211 |
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PF3D7_1313400 |
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DEAD box helicase, putative |
Mutable in CDS |
YES |
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3.6.1.3 |
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35233 |
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PF3D7_1405400 |
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DNA mismatch repair protein, putative |
Mutable in CDS |
NO |
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35055 |
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PF3D7_0204600 |
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5'-3' exonuclease, putative |
Mutable in CDS |
NO |
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3.1.11.- |
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35170 |
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PF3D7_1106300 |
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5'-3' exoribonuclease 1, putative |
Non - Mutable in CDS |
YES |
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3.1.4.1 |
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35091 |
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PF3D7_0508800 |
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single-stranded DNA-binding protein |
Non - Mutable in CDS |
YES |
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35206 |
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PF3D7_1304100 |
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DNA ligase I |
Non - Mutable in CDS |
YES |
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6.5.1.1 |
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35237 |
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PF3D7_1411400 |
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plastid replication-repair enzyme |
Non - Mutable in CDS |
YES |
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2.7.7.7 |
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35053 |
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PF3D7_0112000 |
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TatD-like deoxyribonuclease |
Non - Mutable in CDS |
YES |
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3.1.21.- |
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35087 |
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PF3D7_0504400 |
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ATP-dependent helicase, putative |
Non - Mutable in CDS |
YES |
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3.6.1.3 |
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35207 |
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PF3D7_1307600 |
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DNA-directed RNA polymerase subunit alpha, putative |
Non - Mutable in CDS |
YES |
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2.7.7.6 |
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35054 |
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PF3D7_0203900 |
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5'-3' exonuclease, putative |
Non - Mutable in CDS |
YES |
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3.1.16.1 |
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35265 |
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PF3D7_1472700 |
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DNA-directed RNA polymerase, alpha subunit, putative |
Non - Mutable in CDS |
YES |
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2.7.7.6 |
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35217 |
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PF3D7_1332600 |
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DNA-(apurinic or apyrimidinic site) lyase 1 |
Mutable in CDS |
YES |
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4.2.99.18 |
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38907 |
RNA metabolism |
PF3D7_0319200 |
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ccr4 domain-containing protein 4, putative |
Mutable in CDS |
YES |
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35076 |
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PF3D7_0408900 |
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tRNA N6-adenosine threonylcarbamoyltransferase |
Non - Mutable in CDS |
YES |
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2.6.99.4 |
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35115 |
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PF3D7_0707800 |
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RAP protein, putative |
Non - Mutable in CDS |
NO |
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35120 |
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PF3D7_0727500 |
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mterf domain-containing protein, putative |
Non - Mutable in CDS |
NO |
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35202 |
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PF3D7_1244000 |
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glucose inhibited division protein a homologue, putative |
Non - Mutable in CDS |
YES |
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35203 |
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PF3D7_1244400 |
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RNA-binding protein, putative |
Non - Mutable in CDS |
NO |
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35144 |
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PF3D7_0914300 |
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met-10+ like protein, putative |
Mutable in CDS |
YES |
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2.1.1.- |
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35161 |
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PF3D7_1018000 |
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tRNA pseudouridine synthase, putative |
Mutable in CDS |
YES |
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5.4.99.12 |
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35193 |
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PF3D7_1221700 |
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FbpA domain protein, putative |
Non - Mutable in CDS |
NO |
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35074 |
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PF3D7_0405400 |
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pre-mRNA-processing-splicing factor 8, putative |
Non - Mutable in CDS |
NO |
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35112 |
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PF3D7_0627700 |
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transportin |
Non - Mutable in CDS |
NO |
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35119 |
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PF3D7_0723700 |
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metallo-hydrolase/oxidoreductase, putative |
Non - Mutable in CDS |
NO |
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3.1.26.11 |
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35094 |
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PF3D7_0516300 |
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tRNA pseudouridine synthase, putative |
Mutable in CDS |
NO |
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4.2.1.70 |
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35225 |
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PF3D7_1350700 |
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N6-adenine-specific methylase, putative |
Non - Mutable in CDS |
YES |
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2.1.1.62 |
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35096 |
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PF3D7_0518100 |
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protein amr2 |
Mutable in CDS |
NO |
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35125 |
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PF3D7_0811900 |
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RNA-binding protein, putative |
Non - Mutable in CDS |
NO |
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35174 |
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PF3D7_1120500 |
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tRNA nucleotidyltransferase, putative |
Non - Mutable in CDS |
YES |
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2.7.7.72 |
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35086 |
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PF3D7_0504200 |
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ATP-dependent RNA helicase ddx27, putative |
Non - Mutable in CDS |
YES |
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3.6.4.13 |
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35061 |
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PF3D7_0218300 |
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rRNA methyltransferase, putative |
Mutable in CDS |
YES |
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2.1.1.- |
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35062 |
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PF3D7_0219500 |
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pseudouridine synthase, putative |
Mutable in CDS |
YES |
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4.2.1.70 |
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35201 |
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PF3D7_1242200 |
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queuine tRNA-ribosyltransferase, putative |
Non - Mutable in CDS |
YES |
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2.4.2.29 |
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35131 |
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PF3D7_0817100 |
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tRNA modification GTPase, putative |
Non - Mutable in CDS |
NO |
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35199 |
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PF3D7_1236700 |
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S-adenosyl-methyltransferase, putative |
Non - Mutable in CDS |
YES |
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2.1.1.12 |
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35147 |
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PF3D7_0918800 |
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dihydrouridine synthase, putative |
Mutable in CDS |
YES |
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1.3.1.42 |
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35183 |
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PF3D7_1207500 |
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RNA-binding protein, putative |
Non - Mutable in CDS |
NO |
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35075 |
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PF3D7_0407200 |
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peptidyl-tRNA hydrolase 2, putative |
Non - Mutable in CDS |
YES |
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3.1.1.29 |
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35143 |
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PF3D7_0914000 |
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pseudouridylate synthase, putative |
Mutable in CDS |
YES |
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4.2.1.70 |
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35177 |
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PF3D7_1133800 |
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RNA (uracil-5-)methyltransferase, putative |
Non - Mutable in CDS |
NO |
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2.1.1.35 |
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35149 |
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PF3D7_0920200 |
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CS domain protein, putative |
Non - Mutable in CDS |
NO |
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35058 |
Translation |
PF3D7_0208600 |
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ribosome-recycling factor |
Non - Mutable in CDS |
YES |
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35079 |
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PF3D7_0410700 |
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ribosome biogenesis GTPase A, putative |
Non - Mutable in CDS |
YES |
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3.6.5.1 |
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35081 |
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PF3D7_0414700 |
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GTP-binding protein, putative |
Mutable in CDS |
YES |
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35092 |
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PF3D7_0509600 |
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asparagine--tRNA ligase |
Non - Mutable in CDS |
YES |
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6.1.1.22 |
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35093 |
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PF3D7_0514300 |
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aspartate--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
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6.1.1.12 |
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35103 |
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PF3D7_0602400 |
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elongation factor G |
Non - Mutable in CDS |
YES |
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35133 |
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PF3D7_0827500 |
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ribosomal protein l21, apicoplast, putative |
Non - Mutable in CDS |
YES |
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35134 |
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PF3D7_0828200 |
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leucine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
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6.1.1.4 |
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35139 |
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PF3D7_0911700 |
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GTP-binding protein, putative |
Mutable in CDS |
YES |
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35142 |
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PF3D7_0913900 |
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arginine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
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6.1.1.19 |
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35156 |
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PF3D7_0934000 |
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histidine--tRNA ligase, putative |
Mutable in CDS |
YES |
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6.1.1.21 |
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35067 |
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PF3D7_0311200 |
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valine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
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6.1.1.9 |
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35164 |
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PF3D7_1032000 |
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ribosome maturation factor RimM, putative |
Non - Mutable in CDS |
NO |
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35192 |
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PF3D7_1217300 |
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GTP-binding protein ENGA |
Non - Mutable in CDS |
YES |
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35195 |
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PF3D7_1225100 |
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isoleucine--tRNA ligase, putative |
Mutable in CDS |
YES |
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6.1.1.5 |
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35196 |
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PF3D7_1232000 |
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phenylalanine--tRNA ligase |
Non - Mutable in CDS |
YES |
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6.1.1.20 |
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35239 |
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PF3D7_1413400 |
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30S ribosomal protein S9, putative |
Non - Mutable in CDS |
YES |
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35064 |
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PF3D7_0305000 |
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elongation factor Ts |
Non - Mutable in CDS |
YES |
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35095 |
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PF3D7_0516600 |
 |
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translation initiation factor IF-2 sporozoite surface antigen MB2 |
Non - Mutable in CDS |
YES |
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35099 |
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PF3D7_0524600 |
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50S ribosomal protein L12, apicoplast, putative |
Non - Mutable in CDS |
YES |
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35114 |
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PF3D7_0704900 |
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peptide chain release factor 2 |
Non - Mutable in CDS |
YES |
 |
3.1.1.29 |
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35238 |
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PF3D7_1411600 |
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GTP-binding protein protein obg1 |
Non - Mutable in CDS |
YES |
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35245 |
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PF3D7_1428600 |
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peptide chain release factor 1 |
Non - Mutable in CDS |
YES |
|
3.1.1.29 |
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35246 |
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PF3D7_1429100 |
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ribosomal protein l15, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
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35241 |
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PF3D7_1416800 |
 |
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lysine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
 |
6.1.1.6 |
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35137 |
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PF3D7_0907900 |
 |
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peptide deformylase |
Non - Mutable in CDS |
YES |
 |
3.5.1.88 |
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35158 |
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PF3D7_1005000 |
 |
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methionine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
 |
6.1.1.10 |
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35210 |
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PF3D7_1313200 |
|
 |
methionyl-tRNA formyltransferase, putative |
Mutable in CDS |
YES |
 |
2.1.2.9 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35153 |
|
PF3D7_0925300 |
 |
 |
proline--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
 |
6.1.1.15 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35231 |
|
PF3D7_1367700 |
 |
|
alanine--tRNA ligase |
Non - Mutable in CDS |
YES |
 |
6.1.1.7 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35146 |
|
PF3D7_0918200 |
|
|
50S ribosomal protein L3, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35244 |
|
PF3D7_1420400 |
 |
|
glycine--tRNA ligase |
Non - Mutable in CDS |
YES |
 |
6.1.1.14 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35172 |
|
PF3D7_1117500 |
 |
 |
tyrosine--tRNA ligase |
Non - Mutable in CDS |
YES |
 |
6.1.1.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35191 |
|
PF3D7_1216000 |
|
|
serine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
 |
6.1.1.11 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35176 |
|
PF3D7_1126000 |
 |
 |
threonine--tRNA ligase |
Non - Mutable in CDS |
YES |
 |
6.1.1.3 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35205 |
|
PF3D7_1251700 |
 |
 |
tryptophanyl-tRNA synthetase, putative tryptophan--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
|
6.1.1.2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35160 |
|
PF3D7_1015200 |
 |
|
cysteine--tRNA ligase, putative |
Non - Mutable in CDS |
YES |
 |
6.1.1.16 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35260 |
|
PF3D7_1460900 |
|
|
ribosomal protein S10, apicoplast, putative |
Non - Mutable in CDS |
YES |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35260 |
|
PF3D7_1460900 |
|
|
ribosomal protein S10, apicoplast, putative |
Non - Mutable in CDS |
YES |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35169 |
|
PF3D7_1106100 |
|
|
ribosomal protein s15, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35155 |
|
PF3D7_0932600 |
|
|
apicoplast ribosomal protein S6, putative |
Mutable in CDS |
YES |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35157 |
|
PF3D7_1003200 |
|
|
ribosome-binding factor A, putative |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35204 |
|
PF3D7_1249900 |
|
|
ribosomal RNA small subunit methyltransferase a2, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35078 |
|
PF3D7_0409700 |
|
|
peptide chain release factor 2, putative |
Non - Mutable in CDS |
NO |
 |
3.1.1.29 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35185 |
|
PF3D7_1208000 |
|
|
ribosomal protein L29, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35165 |
|
PF3D7_1034200 |
|
|
ribosomal protein l27, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35124 |
|
PF3D7_0810100 |
|
|
ribosomal protein l33, apicoplast, putative |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35066 |
|
PF3D7_0310000 |
|
|
50S ribosomal protein L9, apicoplast, putative |
Non - Mutable in CDS |
NO |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35097 |
|
PF3D7_0522500 |
|
|
50S ribosomal protein L17, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35080 |
|
PF3D7_0413800 |
|
|
50S ribosomal protein L10, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35188 |
|
PF3D7_1210000 |
|
|
50S ribosomal protein L1, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35136 |
|
PF3D7_0907800 |
|
|
ribosomal protein L35, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35106 |
|
PF3D7_0613400 |
|
|
50s ribosomal protein l18, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35262 |
|
PF3D7_1467400 |
|
 |
50S ribosomal protein L22, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35179 |
|
PF3D7_1137500 |
|
 |
ribosomal protein s14, apicoplast, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35226 |
|
PF3D7_1357200 |
|
 |
glutamate--tRNA ligase |
Non - Mutable in CDS |
YES |
 |
6.1.1.17 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35263 |
|
PF3D7_1469000 |
 |
 |
translation initiation factor IF-1 |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35166 |
|
PF3D7_1034600 |
 |
 |
translation initiation factor IF-3, putative |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35116 |
|
PF3D7_0711000 |
 |
 |
AAA family ATPase, CDC48 subfamily |
Non - Mutable in CDS |
YES |
 |
3.6.4.6 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35180 |
|
PF3D7_1144700 |
|
 |
apicoplast import protein Tic20, putative |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35198 |
|
PF3D7_1234600 |
|
|
protein TOC75, putative |
Non - Mutable in CDS |
NO |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35228 |
Post-translational modifications |
PF3D7_1358300 |
 |
|
rhomboid protease ROM7 |
Mutable in CDS |
NO |
 |
3.4.21.105 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35234 |
PF3D7_1406400 |
 |
|
pentatricopeptide repeat domain-containing protein 1 |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35126 |
PF3D7_0812220 |
 |
|
GTP-binding protein YihA3 |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35128 |
|
PF3D7_0815700 |
 |
|
apicoplast ubiquitin-like protein aubl |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35130 |
|
PF3D7_0816600 |
 |
 |
chaperone protein ClpB1 |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35251 |
|
PF3D7_1440200 |
|
 |
stromal-processing peptidase, putative |
Non - Mutable in CDS |
YES |
 |
3.4.24.56 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35208 |
|
PF3D7_1308800 |
|
|
tyrosine recombinase |
Non - Mutable in CDS |
NO |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35197 |
|
PF3D7_1232100 |
 |
|
60 kDa chaperonin |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35254 |
|
PF3D7_1446200 |
 |
 |
M17 leucyl aminopeptidase |
Non - Mutable in CDS |
YES |
 |
3.4.11.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35218 |
|
PF3D7_1333000 |
 |
|
20 kDa chaperonin |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35253 |
|
PF3D7_1443900 |
|
 |
heat shock protein 90, putative |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35219 |
|
PF3D7_1333200 |
 |
|
ubiquitin-activating enzyme |
Non - Mutable in CDS |
YES |
 |
6.2.1.45 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35235 |
|
PF3D7_1406600 |
 |
 |
ATP-dependent Clp protease regulatory subunit Clpc, putative |
Non - Mutable in CDS |
YES |
 |
3.4.21.92 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35221 |
|
PF3D7_1338900 |
|
|
serine/threonine protein kinase, putative |
Non - Mutable in CDS |
YES |
 |
2.7.11.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35141 |
|
PF3D7_0913500 |
 |
|
apicoplast-minus ipp-rescued 4 |
Non - Mutable in CDS |
YES |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35140 |
|
PF3D7_0912400 |
 |
|
alkaline phosphatase, putative |
Mutable in CDS |
NO |
 |
3.1.3.1 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35159 |
|
PF3D7_1009600 |
|
|
protein phosphatase ppm10, putative |
Non - Mutable in CDS |
NO |
 |
3.1.3.16 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35088 |
|
PF3D7_0507200 |
 |
|
subtilisin-like protease 3 |
Mutable in CDS |
NO |
 |
3.4.21.62 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35065 |
|
PF3D7_0307400 |
 |
 |
ATP-dependent Clp protease proteolytic subunit |
Non - Mutable in CDS |
YES |
 |
3.4.21.92 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35248 |
|
PF3D7_1436800 |
|
|
ATP-dependent Clp protease proteolytic subunit |
Non - Mutable in CDS |
YES |
 |
3.4.21.92 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
35077 |
|
PF3D7_0409400 |
|