Table 1.
Fold assignment by clear sequence–structure compatibility but not by sequence comparison alone
| Z-score | Code | TIGR Characterization | ID% | PDB | Name |
|---|---|---|---|---|---|
| 33.0 | MG053 | Phosphomannomutase (cpsG) | 22 | 3pmga | Phosphoglucomutase |
| 29.2 | MG324 | Aminopeptidase P (pepP) | 17 | 1chma | Creatine amidinohydrolase |
| 20.8 | MG004 | DNA gyrase subunit A (gyrA) | 23 | 1bgw | Topoisomerase |
| 18.3 | MG204 | Topoisomerase IV subunit A (parC) | 23 | 1bgw | Topoisomerase |
| 17.7 | MG310 | Proline iminopeptidase (pip) | 18 | 1broa | Bromoperoxidase A2 |
| 16.5 | MG327 | Magnesium-chelatase 30 kDa subunit | 15 | 1broa | Bromoperoxidase A2 |
| 14.6 | MG365 | Methionyl-tRNA formyltransferase | 18 | 1cde | P. ribosylglycinamide formyltransferase |
| 14.4 | MG375 | Threonyl-tRNA synthetase (thrSv) | 17 | 1htta | Histidyl-trna synthetase |
| 14.0 | MG020 | Proline iminopeptidase (pip) | 22 | 1broa | Bromoperoxidase A2 |
| 13.7 | MG344 | Lipase–esterase (lip1) | 21 | 1broa | Bromoperoxidase A2 |
| 13.2 | MG274 | Pyruvate dehydrogenase E1-alpha | 24 | 1trka | Transketolase |
| 11.4 | MG006 | Thymidylate kinase (CDC8) | 20 | 1uky | Uridylate kinase |
| 10.8 | MG412 | 19 | 1pbp | Phosphate-binding protein | |
| 9.7 | MG353 | 21 | 1huea | HU protein | |
| 9.1 | MG470 | SpoOJ regulator | 14 | 1nipb | Nitrogenase iron protein |
| 8.9 | MG030 | Uracil phosphoribosyltransferase | 20 | 1hgxa | Hypoxanthine-guanine-xanthine phosphoribosyltransferase |
| 8.8 | MG335 | Hypothetical protein | 23 | 1gky | Guanylate kinase |
| 8.8 | MG367 | Ribonuclease III (rnc) | 16 | 1finb | Cyclin A |
| 8.7 | MG287 | Nodulation protein F (nodF) | 26 | 1acp | Acyl carrier protein |
| 8.6 | MG001 | DNA polymerase III beta subunit | 19 | 2pola | Pol III |
| 8.4 | MG394 | Serine hydroxymethyltransferase | 19 | 1tpla | Tyrosine phenol-lyase |
| 8.4 | MG194 | Phenylalanyl-tRNA synthetase beta | 23 | 1asya | Aspartyl trna synthetase |
| 8.4 | MG383 | Sporulation protein (outB) | 23 | 1gpma | Gmp synthetase |
| 8.2 | MG283 | Prolyl-tRNA synthetase (proS) | 13 | 1htta | Histidyl-trna synthetase |
| 8.2 | MG330 | Cytidylate kinase (cmk) | 18 | 3adk | Adenylate kinase |
| 7.9 | MG323 | Hypothetical protein | 22 | 1hyha | L-2-Hydroxyisocaproate dehydrogenase |
| 7.9 | MG149 | 31 | 1hcd | Hisactophilin | |
| 7.8 | MG088 | Ribosomal protein S7 (rpS7) | 20 | 1guha | Glutathione S-transferase |
The table lists the 28 fold assignments automatically detected by the fold-recognition server (scores above the threshold Zth = 7). These assignments do not fulfill our criteria of assignability by sequence–sequence methods (see Materials and Methods). Z-score, confidence score (Z) attached to the assignment; code, identification code of a sequence in the genome of Mycoplasma genitalium assigned by TIGR (10); TIGR characterization, name (if any) of a homologous sequence from another organism found in the sequence database, as annotated by TIGR; ID %, sequence identity percentage between the MG sequence and the assigned fold; PDB, PDB (13) code of the assigned fold; name, name of the protein as given in the PDB entry. Note: Our server identified one MG sequence >500 residues with Z > Zth, which is not shown in the table. Because large sequences may contain more than one domain and are prone to be high-scoring false positives, we applied the following additional filter for all large sequences (>500 residues) scoring above Zth. First, we cut the large sequence into shorter pieces of various lengths, and then we execute separate sequence–structure searches for each of the shorter pieces. If the Z of the fold assignment of each of the shorter pieces is below Zth, then we reject the assignment.