Table 2.
MODBASE Model Data Sets Using the PDB Structures of the First 63 Released and Unique NYSGXRC Targets as Templates
| No. of Sequences
|
|||||||
|---|---|---|---|---|---|---|---|
| PDB code | Target Id | Database Accession | Annotation | Total | FM | M | F |
| 1b54 | P007 | P38197 | Hypothetical UPF0001 protein YBL036C | 151 | 132 | 17 | 2 |
| 1ci0 | P008 | P38075 | Pyridoxamine 5′-phosphate oxidase (EC 1.4.3.5) | 99 | 93 | 0 | 6 |
| 1dfc | P119 | 11513471 | Fascin (Singed-like protein) (p55) | 81 | 27 | 32 | 22 |
| 1f89 | P018 | P49954 | Hypothetical 32.5 kDa protein YLR351C | 547 | 488 | 10 | 55 |
| 1fi4 | P100 | P32377 | Diphosphomevalonate decarboxylase (EC 4.1.1.33) | 154 | 64 | 88 | 5 |
| 1g61 | P111a | Q60357 | Translation initiation factor 6 (alF-6) | 49 | 46 | 2 | 1 |
| 1g62 | P111 | Q12522 | Eukaryotic translation initiation factor 6 (elF-6) | 51 | 50 | 1 | 0 |
| 1hqz | T138 | 113000 | ABP1_YEAST actin binding protein | 175 | 50 | 124 | 2 |
| 1i9a | P109a | 6225535 | IDI_ECOLI isopentenyl-diphosphate delta-isomerase | 1140 | 510 | 11 | 619 |
| 1jd1 | P003 | P40037 | HMF1 protein (High dosage growth inhibitor) | 382 | 354 | 3 | 26 |
| 1jf9 | T129 | P77444 | Selenocysteine lyase (EC 4.4.1.16) | 1669 | 1616 | 0 | 54 |
| 1jfi | P048a | 7513394 | S70618 transcription regulator NC2 alpha chain | 86 | 15 | 0 | 71 |
| 1jg8 | P044a | 4982322 | L-allo-threonine aldolase | 1611 | 1461 | 69 | 123 |
| 1jr7 | T130 | P76621 | Hypothetical protein ygaT | 11 | 10 | 1 | 0 |
| 1jss | T526 | 13542895 | Similar to RIKEN cDNA 2310058G22 gene | 254 | 176 | 2 | 76 |
| 1jsx | T35 | 121191 | GIDB_ECOLI glucose inhibited division protein B | 1583 | 1064 | 27 | 496 |
| 1jyh | T473 | 465566 | GYRI_ECOLI DNA gyrase inhibitory protein Hypothetical 27.5 kDa protein in SPX19-GCR2 | 144 | 97 | 0 | 47 |
| 1jzt | P097 | P40165 | intergenic region | 1058 | 39 | 13 | 1006 |
| 1k47 | T27 | 9937409 | phosphomevalonate kinase | 539 | 385 | 33 | 124 |
| 1k4z | T139 | 399184 | CAP1_HUMAN adenylyl cyclase associated protein | 44 | 34 | 8 | 2 |
| 1k8f | T140 | 134897 | CAP_YEAST adenylyl cyclase associated protein | 48 | 36 | 10 | 2 |
| 1kag | T535 | P24167 | Shikimate kinase I (EC 2.7.1.71) (SKI) | 1005 | 250 | 51 | 706 |
| 1kcx | T45 | 2342488 | dihydropyrimidinase related protein 1 | 701 | 378 | 20 | 312 |
| 1ku9 | T136 | 3025177 | YF63_METJA HYPOTHETICAL PROTEIN MJ1563 | 572 | 131 | 253 | 214 |
| 1l9g | T299 | Q9WYY1 | Hypothetical protein TM0511 | 170 | 152 | 3 | 15 |
| 1la2 | T23 | P11986 | Inositol-3-phosphate synthase (EC 5.5.1.4) (IPS) | 102 | 86 | 0 | 16 |
| 1lnz | T131 | P20964 | Spo0B-associated GTP-binding protein | 1620 | 960 | 40 | 678 |
| 1lx7 | T24 | P12758 | Uridine phosphorylase (EC 2.4.2.3) (UDRPase) | 506 | 384 | 1 | 121 |
| 1m0t | P102 | Q08220 | Glutathione synthetase (EC 6.3.2.3) (GSH-S) | 38 | 37 | 1 | 1 |
| 1m0w | P102a | Q08220 | Glutathione synthetase (EC 6.3.2.3) (GSH-S) | 39 | 38 | 0 | 1 |
| 1n10 | T467 | 28373838 | Phl P 1, A Major Timothy Grass Pollen Allergen | 358 | 336 | 9 | 13 |
| 1ne8 | T503 | P96622 | YDCE protein | 111 | 84 | 21 | 6 |
| 1ni3 | T9 | O13998 | Similar to putative GTP-binding protein | 1058 | 103 | 1 | 955 |
| 1ni5 | T132 | P52097 | Putative cell cycle protein mesj Hypothetical 32.1 kDa protein in ADH3-RCA1 | 920 | 204 | 40 | 689 |
| 1njr | P089 | Q04299 | intergenic region Hypothetical 28.8 kDa protein in PSD1-SKO1 | 4 | 1 | 3 | 0 |
| 1nkq | P096 | P53889 | intergenic region | 379 | 207 | 0 | 172 |
| 1nlx | T746 | P43215 | Pollen allergen Phl p 6 precursor (Phl p VI) | 12 | 12 | 0 | 1 |
| 1nr0 | T745 | Q11176 | Actin interacting protein 1 (AIP1) | 752 | 633 | 33 | 142 |
| 1nvt | T576 | Q58484 | Shikimate 5-dehydrogenase (EC 1.1.1.25) | 543 | 189 | 348 | 7 |
| 1omi | T143 | P22262 | Listeriolysin regulatory protein | 1094 | 301 | 7 | 798 |
| 1p1l | T835 | O28301 | Periplasmic divalent cation tolerance protein (CUTA) | 68 | 63 | 0 | 5 |
| 1p1m | T834 | Q9X034 | Hypothetical protein TM0936 | 780 | 354 | 24 | 404 |
| 1pb6 | T803 | P75899 | Hypothetical transcriptional regulator ycdC | 1364 | 1152 | 74 | 155 |
| 1pqw | T109 | 7448840 | A70984 probable polyketide synthase | 1496 | 1426 | 39 | 35 |
| 1pqy | T783 | P77407 | Hypothetical protein yfdW | 607 | 579 | 11 | 23 |
| 1psq | T817 | P72500 | Probable thiol peroxidase | 950 | 664 | 23 | 263 |
| 1psu | T820 | O28020 | Hypothetical protein AF2264 | 662 | 244 | 26 | 393 |
| 1psw | T832 | Q51063 | ADP-heptose:LPS heptosyltransferase II | 642 | 258 | 229 | 194 |
| 1pug | T5 | P17577 | Hypothetical UPF0133 protein ybaB | 118 | 112 | 6 | 0 |
| 1pui | T16 | P24253 | Probable GTP-binding protein engB | 1380 | 925 | 52 | 438 |
| 1puj | T18 | O31743 | YLQF protein Hypothetical 33.9 kDa esterase in SMC3-MRPL8 | 1128 | 96 | 20 | 1012 |
| 1pv1 | P068 | P40363 | intergenic regionDE (EC 3.1.1.-) | 143 | 36 | 14 | 93 |
| 1q2y | T804 | O31628 | YJCF protein | 1676 | 1123 | 121 | 479 |
| 1q6w | T805 | O28346 | Monoamine oxidase regulatory protein, putative | 566 | 279 | 14 | 285 |
| 1q98 | T1429 | Q57549 | Probable thiol peroxidase (EC 1.11.1.-) | 1218 | 763 | 19 | 436 |
| 1q9j | T760 | P96208 | Hypothetical protein papA5 | 694 | 32 | 3 | 671 |
| 1r3d | T920 | Q9KQM4 | Hypothetical protein VC1974 | 1602 | 563 | 20 | 1030 |
| 1rc6 | T1521 | 16128499 | Hypothetical protein ylbA | 474 | 50 | 46 | 382 |
| 1ri6 | T1479 | 16128735 | Hypothetical protein ybhE | 1458 | 350 | 1126 | 77 |
| 1rvk | T1522 | 17937161 | isomerase/lactonizing enzyme | 1115 | 864 | 139 | 124 |
| 1s7j | T1581 | 29374770 | Phenazine biosynthesis protein PhzF family | 361 | 236 | 124 | 1 |
| 1ub4C | T1468 | 126777 | Peml-like protein 1 (MazE protein) | 40 | 9 | 8 | 23 |
| 1ub4A | T1469 | 464357 | PemK-like protein 1 (MazF protein) | 112 | 99 | 8 | 5 |
The PDB code, Database Accession, and Annotation columns define the template structure. (No. Sequences) The number of sequences in SWISS-PROT/TrEMBL that could be modeled reliably using the NYSGXRC structure as a template. (Total) The total number or sequences, (F) the number of sequences that have a reliable PSI-BLAST E-value of ≤ 10−4 but a low model reliability score (<0.7), (M) the number of sequences with a model score ≥ 0.7 (reliable model), but with insignificant PSI-BLAST E-value (>10−4), (FM) the number of sequences that have both a reliable model score and a significant PSI-BLAST E-value. The most reliable models have both a reliable PSI-BLAST E-value and a reliable model score (FM). For the models classified as F, the fold assignment is considered reliable, even though the model score is bad. Models classified as M have only a remote relationship to the template, but the good model score suggests that the modeled sequences indeed have the same fold as the template structure. The full table can be viewed at http://salilab.org/modbase/models_nysgxrc.html.