Supplementary Table 2. Consensus protein identifications from BUDAPEST pipeline.
Inferred Proteina / NZEHb / 1516b / 371b2-oxogluterate dehydrogenase E1 component / - / 29a (2) / -
3R-hydroxyacyl-ACP dehydratase / - / 36a (2) / 26a (4)
40S ribosomal protein S16 / - / - / 36a (2)
40S ribosomal protein S19 / - / - / 33a (3)
50S ribosomal protein L4 / - / - / 20a (4)
60S ribosomal protein L10 / - / - / 32a (3)
60S ribosomal protein L18 / - / - / 28a (3)
60S ribosomal protein L23A / - / - / 34a (3)
60S ribosomal protein L6 / - / - / 29a (2)
Acetyl-CoA carboxylase * / 06a (21) / 07a|07b|07c|07d|07e|07f (55); 19a|19b (6) * / 08a|08b|08c|08d (48)
Actin * / 16a|16b|16c (8) * / 13a|13b|13c|13d|13e|13f (6) * / -
ADP-ribosylation factor * / 36a (2) * / - / 23a|23b (9)
ATP synthase subunit alpha / 04c (8) / - / -
ATP synthase, vacuolar, subunit a * / 04b (15) * / 14a|14b (11) * / -
ATP synthase subunit beta * / 04a (6) * / - / -
ATP synthase, vacuolar, subunit e / 32a (6) / - / 24a (4)
ATP synthase, subunit gamma / 14a (4) / - / -
ATP synthase, subunit gamma (chloroplastic) / 14b (5) / - / -
Beta adaptin / - / 28a (3) / -
Carbamoyl phosphate synthetase / - / - / 14a (2) |16a (2)
Carbonic anhydrase / 29a (5) / - / -
Inferred Proteina / NZEHb / 1516b / 371b
Cell division cycle protein 48 * / - / 02a|02b (14) * / 06a (4)
Chloroplast light harvesting protein / 23a|23b|23c|23d|23e|23f|23g|23h|23i|23j|23k|23l (27) / - / 12a|12b|12c|12d|12e|12f|12g|12h|12i|12j (21)
Chloroplast O-acetyl-serine lyase * / 19a|19b|19c (8) * / - / -
Clathrin heavy chain * / 20a (2) / 12a (7); 17a (5); 20a (16) / 11a|11b (9)
; 13a (12) *
Elongation factor 1 alpha like protein * / 02a (6) * / 03a|03b (6) * / -
Elongation factor 2 / - / 03c (2); 16b|16c (2) / 04a (4)
Elongation factor 3-related protein / - / 18a (2); 30a (3) / 05c|05d|05e (7)
Elongation factor G / - / 16a (8) / -
Enolase / - / 31a (3) / -
Enoyl-acyl carrier reductase / 25a (3) / - / -
Enoyl-CoA hydratase / - / - / 18a (2)
Ferredoxin NADP+ reductase / 10a|10b (6) / - / -
Fructose-bisphosphate aldolase / 21a (3); 24a (3) / - / -
GDP-mannose 3,5-epimerase / 22a|22b (3) / - / -
Gelosin/severin like / - / - / 17a (2)
Glucose-6-phosphate isomerase * / - / 09a|09b (4)* / -
Glutamate 1-semialdehyde aminomutase / 28a (2) / - / -
Glutamine synthase / 26a (7) / 11a (16) / 09a (5)
Glyceraldehyde-3-phosphate dehydrogenase (chloroplastic) *
Glyceraldehyde-3-phosphate dehydrogenase / 12a (6)*
12b (4) / - / -
Heat shock protein 60 * / 27a (3) / 32a (3)* / -
Heat shock protein 70 * / 01a|01b|01c (11) * / 01a|01b|01c (15); 10a|10b|10c|10d (8) * / 01a|01b (16) *
Inferred Proteina / NZEHb / 1516b / 371b
Heat shock protein 90 * / 03a (2); 08a|08b|08c (12) * / 04a|04b|04c|04d|04e (18)* / 03a|03b|03c (19) *
High mobility group protein / - / 21a (2) / -
Histone H2A * / 39a|39b|39c (8) * / - / 35a|35b|35c (6) *
Histone H2B / 35a|35b (4) / - / 31a (4)
Histone H4 * / 38a (8) * / - / 30a|30b|30c (11) *
Inorganic pyrophosphatase / 37a (2) / - / -
Isocitrate dehydrogenase / - / 34a (3) / -
Long-chain fatty acid CoA synthetase / - / 33a (3) / -
Malonyl-CoA:ACP transacylase / - / 35a (3) / -
MC family transporter / 07a|07b (5) / - / -
Methionine synthase / - / 15a|15b (7); 37a (3) / -
Peptidyl-prolyl cis-trans isomerase * / - / - / 25a|25b (5) *
Phosphoglycerate kinase * / 05a|05b|05c|05d (13) * / - / -
Phopshoribulokinase, Chloroplast / 13a (8) / - / -
Phosphoribosylamine-glycine ligase / - / 23a (2) / -
Photosystem II stability/assembly factor HCF135 / 40a (3) / - / -
Polyketide synthase / - / 27a (2) / -
Precursor of pyruvate dehydrogenase E1 alpha / - / 25a (4) / 22a (2)
Protein translocase subunit secA / - / 26a (2) / -
Pyruvate carboxylase * / - / 19c (2) / 02a (17) *
Ribose 5-phosphate isomerase / 34a (3) / - / -
Inferred Proteina / NZEHb / 1516b / 371b
S-adenosylmethionine synthetase / 17a|17b (4); 30a|30b (2) / - / -
Serine hydroxylmethyltransferase / 18a|18b (4) / - / -
Splicing factor 3B / - / - / 19a (3)
Transkelotase / 15a|15b|15c|15d|15e (18) / 22a|22b|22c (15) / 15a (5)
Translational activator / - / - / 05a|05b (7)
Translocator of the inner chloroplast envelope membrane 110k / - / 05a (2) / 10a (7)
Uncharacterised protein 1 / - / - / 07a (2)
Uncharacterised protein 2 / - / 08a|08b (3) / -
Uncharacterised protein 3a / 31a (2) / - / -
Uncharacterised protein 3b / 31b (2) / - / -
Unknown protein (No BLAST hit) 1 / 11a|11b|11c|11d (8) / - / -
Unknown protein (No BLAST hit) 2 / 33a (2) / - / -
Unknown protein (No BLAST hit) 3 / 09a (3) / - / -
Unknown protein (No BLAST hit) 4 / - / 06a (2) / -
Unknown protein (No BLAST hit) 5 / - / 24a (3) / -
Unknown protein (No BLAST hit) 6 / - / - / 21a (2)
Unknown protein (No BLAST hit) 7 / - / - / 27a (3)
TOTALc: 81(19*) / 41 / 83d (12*) / 33 / 68d (9*) / 35 / 63d (7*)
a. Inferred from UniProtKB annotation and/or HAQESAC trees with BUDAPEST consensus sequences.
b. Numbers in brackets indicate numbers of unique peptides identifying each cluster. NB: Analysis was carried out for each strain separately so identical consensus sequence numbers should not be interpreted as identical sequences
c. Total counts, grouping similar consensus sequences by broad function.
d. The second number for each strain refers to numbers of consensus sequences.
* Protein also identified from taxonomically-restricted protein search.