Genes Lost from S. cerevisiae: N. crassa Discontigs with Nonfungal Homologs that Lack Detectable S. cerevisiae Orthologs
| Discontig | Identification | NF E-value[i] | SC E-value[ii] | Global distribution[iii] | Fungal distribution[iv] |
| I. Cell division[v] | |||||
| 391 | Sir2p family homolog, human | 3 × 10−7 | —[vi] | An, Eu, A, B | En |
| II. Cell signaling/cell communication | |||||
| 39 | DdCAD-1 (Ca2+-binding protein) | 2 × 10−10 | — | Eu | |
| 563 | NPH1 (nonphototrophic hypocotyl) | 2 × 10−8 | — | Pl, B | |
| 861 | shaker K+channel | 2 × 10−48 | 3 × 10−21 g | An, Pl, A, B | Sp |
| III. Cell structure/cytoskeleton | |||||
| 223 | N-acetyl-β-d-glucosaminidase | 10−17 | — | An, Pl, Eu, B | Ca |
| 789 | α-actinin | 10−34 | 10−6 | An, Eu | Sp |
| V. Metabolism | |||||
| 70 | BPG-independent phosphoglycerate mutase | 8 × 10−26 | — | An, Pl, Eu, B | En |
| 71 | pyruvate decarboxylase | 10−28 | 7 × 10−15 | B | Sp |
| 97 | glycine amidinotransferase | 10−5 | — | An, B | |
| 125 | citrate lyase β-chain | 3 × 10−15 | — | An, B | |
| 209 | UDP-glucose dehydrogenase | 2 × 10−6 | — | An, Pl, B, A | |
| 220 | annexin XIV | 6 × 10−33 | — | An, Pl, Eu | |
| 225 | β-glucosidase | 2 × 10−47 | 0.07 | Pl, Eu, B | NA, Ca, En |
| 338 | peroxisomal copper amine oxidase | 4 × 10−27 | — | B | Ca |
| 362 | dioxygenase, C. elegans | 3 × 10−8 | — | An, B | Ca |
| 368 | nitrite reductase | 4 × 10−22 | — | B | NA, En |
| 396 | 4-hydroxyphenylpyruvate dioxygenase | 6 × 10−21 | — | An, B | En |
| 454 | α-glucosidase (maltase) | 3 × 10−37 | 3 × 10−7 | An, Pl, Eu, A, B | NA, Sp, Ca, En |
| 474 | fructosyl amino acid oxidase | 4 × 10−6 | — | An, B | Sp, En |
| 521 | methylmalonate-semialdehyde dehydrogenase | 9 × 10−15 | — | An, Pl, B | Ca, En |
| 522 | sterol carrier protein thiolase | 6 × 10−20 | 0.022 | An, A, B | |
| 526 | enoyl-CoA hydratase | 4 × 10−14 | — | An, Pl, A, B | |
| 536 | γ-glutamyl transpeptidase | 8 × 10−11 | — | B | Ca |
| 595 | NADP-dependent oxidoreductase | 10−13 | 0.019 | An, Pl, Eu, B | En |
| 604 | sorbitol utilization protein | 6 × 10−17 | 10−6 | An, Pl, B | Sp, Ca, En |
| 693 | uricase (urate oxidase), peroxisomal | 7 × 10−8 | — | An | Sp, Ca, En |
| 794 | monooxygenase | 2 × 10−24 | — | B | Ca |
| 826 | 3-hydroxyisobutyrate dehydrogenase | 2 × 10−8 | — | An, B | En |
| 876 | esterase | 2 × 10−8 | — | An, B | Sp |
| 880 | α-amylase | 10−5 | — | An, Eu, B | NA, Sp, En |
| 1016 | thioesterase II | 2 × 10−8 | — | An, Pl, B | |
| 1090 | glycerol kinase | 2 × 10−28 | 6 × 10−11 | An, A, B | |
| VI. Protein synthesis | |||||
| 128 | rabGTPase | 5 × 10−70 | 4 × 10−57 | An, Pl, Eu | Sp, Ca, En |
| 144 | Int-6 (eIF3 subunit) | 8 × 10−9 | — | An | |
| 253 | 40S ribosomal protein S15 | 3 × 10−44 | 2 × 10−32 | An, Pl, Eu, A, B | Sp, Ca |
| 276 | BRCA1 associated protein 1 | 5 × 10−17 | — | An, Pl | Sp, Ca |
| 621 | dolichol monophosphate transferase | 2 × 10−23 | 6 × 10−10 | An, Eu, A, B | Sp, Ca |
| 910 | ubiquitin-activating enzyme | 7 × 10−16 | — | An, Pl, Eu | Sp |
| 1079 | r-Vps33a | 10−15 | — | An | Sp |
| 1110 | eIF-3 p40 | 10−21 | 10−5 | An | Sp |
| Unclassified | |||||
| 133 | C. elegansC25D7.8 | 3 × 10−7 | — | An | |
| 467 | hypothetical protein, Streptomyces coelicolor | 4 × 10−7 | — | B | Sp |
| 577 | regucalcin (Ca2+-binding protein) | 10−5 | — | An, A, B | En |
| 606 | hypothetical protein similar to NO synthase | 9 × 10−8 | — | An | Sp |
| 1012 | C. elegans F18F11.1 (peroxisomal protein homolog) | 4 × 10−17 | — | An | |
| 1054 | 5′-nucleotidase precursor | 8 × 10−15 | — | An, B | |
[i] E-value of best BLAST hit against nonfungal data set.
[ii] E-value of best BLAST hit against S. cerevisiae data set.
[iii] Phylogenetic distribution of orthologs based upon BLAST searches. (An) = Animals; (Pl) = plants; (Eu) = Other Eukaryotes; (A) = Archaea; (B) = Bacteria.
[iv] Distribution of orthologs within the fungi based upon BLAST searches. (NA) = Nonascomycete fungi; (Sp) = S. pombe; (Ca) = C. albicans; (En) = A. nidulans). Presence of an ortholog to the N. crassa sequence in any of these fungi, except A. nidulans, was considered evidence for loss in theS. cerevisiae lineage.
[v] Functional categories are as described in Nelson et al. (1997), based on a modification of the system described by White and Kerlavage (1996).
[vi] No S. cerevisiae database sequence received anE-value < 0.1.
[vii] N. crassa sequences with S. cerevisiaehomologs that are listed in this table are likely to correspond to cases in which the orthologous S. cerevisiae gene has been lost but a paralogous gene retained.