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. 2006 Sep 22;5(12):2079–2091. doi: 10.1128/EC.00222-06

TABLE 1.

EST clusters

Cluster IDa Annotation Organism with top BLASTp hit BLASTp score Presequence length (aa) TP length (aa)b TMH1 positionc TMH2 positionc Id
Class IA proteins
    0726 Ferredoxin Arabidopsis thaliana 3e−06 148 60 7-29 89-111 2
    0899 50S ribosomal protein L3 Cyanophora paradoxa 3e−12 168 52 13-35 87-109 2
    1043 Putative ferredoxin Arabidopsis thaliana 4e−09 144 65 7-29 94-113 1
    1116 30S ribosomal protein S20 Synechococcus elongatus 4e−08 170 64 13-35 99-121 2
    1127 Zeta-carotene desaturase Oryza sativa 1e−22 182 55 21-43 98-121 2
    1204 Uroporphyrinogen decarboxylase Anopheles gambiae 2e−31 149 60 21-38 98-120 2
    1312 Putative ferredoxin Arabidopsis thaliana 3e−09 143 58 11-33 91-110 1
    1428 RubisCO small subunit Euglena gracilis e−118 120 56 4-26 82-104 2
    1495 Glutaredoxin 2 Actinobacillus actinomycetem- comitans 6e−10 130 55 7-24 79-101 2
    1503 Membrane-associated 30-kDa protein Pisum sativum 2e−10 168 75 7-29 104-126 1
    1573 Putative ferredoxin Arabidopsis thaliana 6e−09 147 61 13-35 96-118 1
    1674 Sugar nucleotide phosphorylase Arabidopsis thaliana 7e−12 168 66 21-43 109-131 1
    1706 50S ribosomal protein L34 Arabidopsis thaliana 7e−06 190 63 13-35 98-117 1
    2042 Peptidyl-prolyl cis-trans isomerase Oryza sativa 6e−07 178 67 7-26 93-117 1
    2448 Ferredoxin-like protein Rhizobium loti 8e−05 120 58 15-37 95-117 1
    2566 Ribose-5-phosphate isomerase Spinacia oleracea 2e−24 144 61 20-42 103-125 1
    2596 Ycf53 (tetrapyrrole-binding protein) Synechococcus elongatus 2e−12 182 58 12-34 92-114 1
    2669 50S ribosomal protein L11 Odontella sinensis 3e−12 186 55 19-41 96-118 2
    2795 d-Ribulose-5-phosphate 3-epimerase Arabidopsis thaliana 1e−24 150 58 21-40 98-120 2
    2990 Albino 3 Bigelowiella natans 5e−37 211 77 29-51 128-150 1
    3121 Chaperonin PSII quinone-binding protein Arabidopsis thaliana 8e−30 189 94 3-25 119-136 1
    3164 Rhodanese domain-containing protein Oryza sativa 6e−08 133 58 5-24 82-104 1
    3171 Photosystem II 22-kDa protein Arabidopsis thaliana 3e−17 152 67 21-40 107-126 1
    3330 Coproporphyrinogen III oxidase Chlamydomonas reinhardtii e−108 156 53 22-44 97-119 2
    3362 ATP synthase delta chain Nicotiana tabacum 7e−22 147 57 15-37 94-116 2
    3372 50S ribosomal protein L15 Bigelowiella natans 1e−14 191 54 24-46 100-119 1
    3375 Light-regulated Chlp-localized protein Solanum tuberosum 4e−20 120 60 12-31 91-110 1
    3383 ATP synthase gamma chain Odontella sinensis 7e−78 137 60 13-35 95-113 3
    3449 Cytochrome f Euglena gracilis 4e−91 147 60 7-26 86-108 2
    3469 Porphobilinogen deaminase Euglena gracilis 0 151 56 17-39 95-112 2
    3474 Probable membrane-associated 30-kDa protein Synechocystis sp. 7e−49 151 63 7-26 89-111 1
    3482 Fructose-1,6-bisphosphatase Bigelowiella natans 2e−71 188 56 20-37 93-115 1
    3500 Glu 1-semialdehyde 2,1-aminomutase Chlorarachnion sp. e−148 138 53 7-29 82-99 2
    3504 Carbonic anhydrase Deinococcus radiodurans 7e−28 102 52 5-24 76-98 3
    3558 Carbonic anhydrase Deinococcus radiodurans 1e−10 140 62 13-35 97-119 1
    3594 50S ribosomal protein L28 Toxoplasma gondii 4e−18 160 55 13-35 90-112 2
    3603 Peroxiredoxin precursor Chlamydomonas reinhardtii 8e−85 134 57 5-27 84-106 2
    3619 50S ribosomal protein L21 Thermoanaerobacter tengcongensis 3e−11 168 52 13-35 87-109 1
    3635 Coproporphyrinogen III oxidase Chlamydomonas reinhardtii 1e−78 169 60 29-51 111-133 3
    3653 Delta 12 fatty acid desaturase Phaeodactylum tricornutum 2e−98 162 77 13-30 107-129 2
    3673 Carbonic anhydrase Deinococcus radiodurans 8e−30 179 68 13-32 100-122 4
    3676 30S ribosomal protein S1 Chlamydomonas reinhardtii 7e−32 233 66 4-26 92-114 1
    3817 Acyl carrier protein Synechocystis sp. 6e−13 122 49 15-34 83-105 1
    3830 Ferredoxin Euglena viridis 1e−41 138 56 17-39 95-117 3
    3881 ATP/ADP transporter Galdieria sulfuraria 0 148 52 12-34 86-105 1
    3900 PsbM Zea mays 0.017 154 63 13-35 98-120 3
    3911 LHCI Euglena gracilis 5e−86 179 50 13-35 85-107 1
    3934 Ferredoxin-NADP+ reductase Chlamydomonas reinhardtii e−144 114 51 5-27 78-100 1
    3943 NADPH protochlorophyllide reductase Chlorarachnion sp. 5e−69 155 53 12-34 87-109 1
    3946 RuBisCO activase Chlorococcum littorale e−145 95 59 13-35 72-101 2
    3996 LHCI Euglena gracilis e−116 158 55 13-35 90-109 2
    4008 LHCI Euglena gracilis 0 141 51 13-35 86-108 1
    4056 CP29 Oryza sativa 7e−57 136 50 12-34 84-106 1
    7084 Chl. synthase 33-kDa subunit Anabaena sp. 9e−10 141 45 15-34 79-101 1
    7147 SOUL-heme-binding protein Arabidopsis thaliana 7e−20 136 68 5-22 90-112 1
    7392 ATP-dependent Clp protease Vibrio cholerae 1e−44 143 58 15-37 95-117 1
    7739 Ycf3 (PSI assembly) Physcomitrella patens 3e−27 162 64 20-42 106-128 1
    7766 RuBisCO 60-kDa chaperonin Arabidopsis thaliana 5e−37 122 67 7-29 96-118 1
    8108 YebC-related protein Arabidopsis thaliana 7e−17 108 57 7-29 86-108 1
    8254 Chlorophyll b synthase Dunaliella salina 8e−18 114 70 6-22 92-111 1
    8643 Uroporphyrinogen decarboxylase Ashbya gossypii 1e−17 164 63 17-39 102-124 1
    8888 3-Isopropylmalate dehydrogenase Bifidobacterium longum 7e−13 150 71 13-35 106-128 1
    9366 Photosystem II family protein Arabidopsis thaliana 4e−11 137 61 13-35 96-118 1
Class IB proteins
    3955 Oxygen evolving enhancer (OEE1) Euglena gracilis e−116 142 53 5-27 80-99 3
    4026 Oxygen evolving enhancer (OEE2) Lycopersicon esculentum 6e−17 153 49 20-42 91-113 2
    3381 HCF136 (PSII stability factor) Arabidopsis thaliana 5e−07 142 52 7-29 81-103 1
    3249 Putative ascorbate peroxidase Lycopersicon esculentum 2e−04 184 70 13-35 105-127 1
    3902 Cytochrome c6 Euglena gracilis 4e−69 123 60 29-51 111-133 2
    3752 PSI subunit III (PsaF) Chlamydomonas reinhardtii 6e−53 144 60 13-35 95-114 2
    2674 Thylakoid luminal 17.4-kDa protein Arabidopsis thaliana 5e−22 171 71 15-37 108-127 1
Class II proteins
    3630 Photosystem II (PsbW) Chlorarachnion sp. 4e−15 82 52 20-37 3
    3294 ABC transporter (cytochrome c biogenesis) Nostoc punctiforme 5e−33 175 135 34-53 1
    0923 PEP/phosphate translocator Phaeodactylum tricornutum 4e−10 166 132 13-35 1
    4012 Oxygen evolving enhancer (OEE3) Chlamydomonas reinhardtii 3e−22 61 36 13-35 2
    2060 Mg-protoporphyrin IX methyltransferase Synechococcus elongatus 4e−17 66 40 5-27 1
    2416 Peptide chain release factor (RF) 2 Synechocystis sp. 3e−42 99 70 13-35 1
    3797 PSI subunit IV (PsaE) Chlamydomonas reinhardtii 6e−17 95 61 15-37 3
    4932 50S ribosomal protein L9 Bigelowiella natans 6e−05 62 39 15-33 1
    8550 Short-chain (SC) dehydrogenase Prochlorococcus marinus 8e−07 120 82 29-51 2
    3784 Phosphoribulokinase Vaucheria litorea 1e−76 100 75 20-42 1
    9282 MECP synthase Arabidopsis thaliana 2e−36 121 80 28-50 1
    6808 Squalene and phytoene synthases Prochlorococcus marinus 1e−27 98 47 35-52 1
    2660 ClpB Phaseolus lunatus 8e−48 123 76 37-52 1
a

Original cluster IDs had “EEL0000” preceding the 4-digit numbers shown.

b

For class I proteins, this is the region between the signal sequence and the stop-transfer region.

c

TMH1 and TMH2 are the hydrophobic domains (range of amino acids is given from the start Met) of the signal sequence and stop-transfer sequence, respectively, as predicted by the TMHMM program. Underlined regions indicate that the TMHMM program did not predict a TMH (TMHMM value, 0.1 < P < 0.9) but that a hydrophobic patch is apparent from a Kyte-Doolittle analysis.

d

Number of nearly identical isoforms detected.