Table II Summary of chloroplast-localized proteins analyzed using organelle targeting programs and BLAST algorithm

From a total of 895 chloroplast-localized proteins, 279 proteins were also localized to the chloroplast by PPDB. The 855 nucleus-encoded, chloroplast-localized proteins were processed by the localization prediction tools ChloroP and TargetP, yielding an overlap of 411 proteins for ChloroP and 166 proteins for TargetP. CP, chloroplast. Numbers in parentheses refer to the safe CP proteome.

DescriptionCandidate + safe CP proteomeSafe CP proteome
Total CP proteome size895606
    With a chloroplast/mitochondria ratio ≥5 (10)172113
    With no mitochondria identifications but at least 2 (5) chloroplast identifications723493
    Nucleus-encoded855570
    Chloroplast-encoded4036
PPDB chloroplast-localized proteins279219
Comparison with localization prediction tools (regarding the 855 (570) nucleus-encoded proteins)
    ChloroP chloroplast-localized proteins411308
    TargetP chloroplast-localized proteins166119
    TargetP mitochondria-localized proteins357263
    TargetP secretory pathway-localized proteins7240
        With signal peptide2619
BLAST results for the 855 (570) nucleus-encoded, chloroplast-localized proteins
    Best non-Chlamydomonas hit in V. carteri789534
    Results for best non-Chlamydomonas and non-Volvox best hit
        Photosynthesis
            Photosynthetic623432
            Not photosynthetic12276
            Unknown11062
        Kingdom
            Plantae553382
            unknown11062
            Bacteria8761
            Animalia4226
            Other6339
    Algae-specific proteins6842