Table 2.
Results of the building block assignment algorithm
| Target protein | Matching sequences | |||||
| Protein name (class) | PDB code | Matched sequence positions | Protein name (class) | PDB code | Matched sequence positions | Percent sequence similarity (identity) |
| Squid glutathione S-transferase (α/β) | ||||||
| Human glutathione S-transferase, class pi, chain A (α/β) | 13gs | 1-32 | S. japonicum glutathione S-transferase (all-α) | 1gsq | 1-32 | 58 (40) |
| 38-72 | Methane monooxygenase hydrolase, β subunit (all-α) | 1gne | 154-184 | 53 (31) | ||
| 77-122 | Pyruvate phosphate dikinase (α/β) | 1mtyB | 345-384 | 57 (34) | ||
| 124-149 | S. japonicum glutathione S-transferase (all-α) | 1dik | 472-497 | 53 (42) | ||
| 153-185 | 1gne | 155-184 | 60 (42) | |||
| Pseudoazurin from Alcaligenes faecalis (all-β) | 1paz | 1-33 | Phosphoglycerate kinase (α/β) | 3pgk 1mn2 2cjn 1plb 1epaB | 118-147 | 45 (27) |
| 34-49 | Manganese peroxidase (all-α) | 1mn2 | 91-106 | 55 (37) | ||
| 50-70 | 2Fe-2S ferredoxin (α + β) | 2cjn | 10-30 | 51 (28) | ||
| 68-92 | Plastocyanin from parsley (all-β) | 1plb | 72-96 | 48 (36) | ||
| 93-112 | Retinoic acid-binding protein (all-β) | 1epaB | 70-90 | 52 (38) | ||
| Human immunoglobulin (all-β) | 2imm | 3-20 | Immunoglobulin Bence-Jones VL (λ) dimer RHE (all-β) | 2rhe | 3-20 | 78 (52) |
| 21-48 | 20-43 | 53 (39) | ||||
| 50-66 | Immunoglobulin Fab NC10 (all-β) | 1nmaH | 5-21 | 52 (35) | ||
| 67-84 | β2-Microglobulin from cow (all-β) | 1bmg | 85-112 | 46 (21) | ||
| 95-109 | Azurin from N. aeruginosa (all-β) | 1iluH | 81-101 | 60 (38) | ||
| Fumarase from E. coli (all-α) | 1fupA | |||||
| Barstar from B. amyloliquefaciens, chain D (α/β) | 1brs | 4-23 | Adenylate kinase from pig (α + β) | 3adk | 133-150 | 53 (33) |
| 23-37 | IU-NH from C. fasciculata (α/β) | 2masB | 294-308 | 66 (40) | ||
| 40-66 | Leu aminopeptidase from cow (α/β) | 1lap | 123-149 | 55 (33) | ||
| 66-83 | Parvalbumin from pike (all-α) | 1pvaA | 61-78 | 55 (33) | ||
| Anti-ψ factor antagonist SpoIIaa from B. sphaericus, chain A (α/β) | 1h4x | 5-21 | DNA polymerase β (α and β) | 1bpe | 154-170 | 58 (29) |
| 17-36 | Annexin XII from hydra (all-α) | 1aeiD | 249-271 | 50 (35) | ||
| 38-63 | Pepsin (ogen) from pig (all-β) | 5pep | 143-168 | 57 (34) | ||
| 65-89 | Human myeloperoxidase (all-β) | 1mhlC | 253-278 | 48 (28) | ||
| 91-108 | Histidine-binding protein (α/β) | 1hslB | 195-213 | 54 (27) | ||
| Clp protease, ClpP subunit from E. coli, chain A (α/β) | 1tyf | 6-35 | Restriction endonuclease Cfr10I (α/β) | 1cfr | 99-131 | 48 (33) |
| 41-70 | Glycogen phosphorylase (α/β) | 1noiA | 121-147 | 77 (55) | ||
| 67-94 | Leu-Ile-Val-binding protein (α/β) | 2liv | 252-279 | 45 (35) | ||
| 96-123 | Trp synthase, β-subunit (α/β) | 1ttpB | 135-165 | 57 (24) | ||
| 125-152 | Annexin IV from cow (all-α) | 1ann | 109-136 | 53 (39) | ||
| 154-171 | Chorismate mutase (α + β) | 2chtL | 12-29 | 55 (33) | ||
| Cytochrome c6 from D. vulgaris (all-α) | 1dvh | 3-39 | 3-Isopropylmalate dehydrogenase (α/β) | 1osiC | 255-291 | 40 (27) |
| 37-54 | Socitrate dehydrogenase (α/β) | 1iso | 45-62 | 55 (33) | ||
| 52-70 | Interleukin-5 from human (all-α) | 1hulB | 66-84 | 51 (36) | ||
| Phycocyanin from red alga, chain A (all-α) | 1phn | 5-26 | GreA transcript cleavage protein (all-α) | 1grj | 29-50 | 40 (40) |
| 27-53 | α-Trichosanthin (α + β) | 1tcs | 216-242 | 36 (25) | ||
| 52-88 | Phycoerythrin (all-α) | 1liaK | 52-86 | 54 (32) | ||
| 89-107 | Thioredoxin reductase (α/β) | 1vdc | 130-148 | 57 (31) | ||
| 110-128 | Adenovirus hexon (all-β) | 1dhx | 728-746 | 57 (42) | ||
| 129-145 | Plasmepsin ii (all-β) | 1smeB | 178-194 | 47 (47) | ||
| E. coli Rck domain from putative potassium channel Kch, chain B (α/β) | 1idl | 12-33 | Troponin C from chicken (all-α) | 1top | 76-97 | 58 (31) |
| 33-78 | CheY-binding domain of CheA (α + β) | 1fwp | 5-41 | 45 (28) | ||
| 80-102 | Lysozyme from chicken (α + β) | 1mlcF | 99-121 | 56 (30) | ||
| 101-132 | Lipase from B. cepacia (α/β) | 1oilA | 69-112 | 42 (27) | ||
| 130-151 | Phosducin from rat (α/β) | 2trcP | 181-205 | 60 (36) | ||
| C-terminal part of pyridoxine 5′-phosphate synthase from E. coli, chain A (α/β) | 1hol | 43-101 | Triacylglycerol lipase (α/β) | 1lgyC | 199-256 | 41 (23) |
| 106-127 | 6PGD from sheep (α/β) | 1pgq | 106-123 | 59 (50) | ||
| 124-148 | Methylamine dehydrogenase (all-β) | 2bbkJ | 322-346 | 48 (28) | ||
| 148-236 | Pyruvate phosphate dikinase (α/β) | 1dik | 664-733 | 38 (21) | ||
| Cytochrome c552 from Thermus thermophilus (all-α) | 1c52 | 6-28 | Adenovirus hexon from human adenovirus type 2 (all-β) | 1dhx | 827-849 | 39 (39) |
| 31-45 | 4dfrB | 86-100 | 53 (59) | |||
| 45-64 | DHFR from E. coli (α/β) | 1hiwA | 79-98 | 35 (60) | ||
| 73-99 | HIV-1 matrix protein (all-α) | 1pgn | 290-305 | 37 (48) | ||
| 97-112 | 6PGD from sheep (all-α) Cyclin H (mcs2) from human (all-α) | 1jkw | 259-274 | 43 (68) | ||
| YopH Tyr phosphatase N-terminal domain from Y. pestis (α + β) | 1huf | 6-20 | Staphylococcal nuclease (all-β) | 1syf | 7-21 | 33 (66) |
| 19-35 | Tyrosyl-tRNA synthetase (α/β) | 1tyaE | 77-93 | 41 (46) | ||
| 37-53 | p-Hydroxybenzoate hydroxylase (α/β) | 2phh | 161-177 | 41 (52) | ||
| 57-78 | 7-α-Hydroxysteroid dehydrogenase (α/β) | 1ahhA | 192-213 | 36 (54) | ||
| 78-94 | Methane monooxygenase hydrolase (all-α) | 1mhyD | 234-250 | 58 (35) | ||
| 94-114 | T4 endonuclease V from bacteriophage T4 (all-α) | 1enj | 4-23 | 35 (55) | ||