TABLE 3.
Short DRs in H. volcanii genes
| No. of DRs of indicated lengthb
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Genea | Putative functiona | 8 | 9 | 10 | 11 | 12 | >12 | Total | % in frame |
| trpC | Indole-3-glycerol-phosphate synthase | 16 | 5 | 3 | 2 | 0 | 0 | 26 | 65 |
| smc1 | Chromosome segregation protein | 7 | 5 | 0 | 0 | 0 | 0 | 12 | 67 |
| dnaK | Heat-shock protein | 4 | 5 | 1 | 0 | 0 | 0 | 10 | 70 |
| aspB1 | Aspartate aminotransferase | 12 | 4 | 2 | 0 | 0 | 0 | 18 | 78 |
| eif2a | Translation initiation factor eIF-2 subunit | 4 | 4 | 1 | 0 | 0 | 0 | 9 | 100 |
| udp2 | Uridine phosphorylase | 2 | 0 | 1 | 1 | 0 | 0 | 4 | 100 |
| flaB1 | Flagellin B1 precursor | 8 | 2 | 1 | 0 | 0 | 4 | 13 | 92 |
| argB | Ornithine carbamoyltransferase | 15 | 3 | 2 | 3 | 0 | 0 | 23 | 78 |
| glyA | Glycine hydroxymethyltransferase | 20 | 4 | 1 | 2 | 1 | 0 | 28 | 71 |
| hisD | Histidinol dehydrogenase | 24 | 6 | 4 | 2 | 0 | 0 | 36 | 78 |
| thrS | Threonyl-tRNA synthetase | 21 | 3 | 2 | 1 | 0 | 1 | 28 | 89 |
| ftsZ3 | Cell division protein | 5 | 2 | 0 | 0 | 0 | 0 | 7 | 100 |
| pyrD | Dihydroorotate dehydrogenase | 10 | 3 | 2 | 2 | 1 | 0 | 18 | 56 |
| rpoB | DNA-directed RNA pol subunit B | 9 | 3 | 2 | 0 | 0 | 0 | 14 | 86 |
| csg | Cell surface glycoprotein | 9 | 3 | 0 | 0 | 0 | 1 | 13 | 100 |
| (5′) | Region before pyE2 | 16 | 3 | 6 | 4 | 0 | 0 | 29 | 83 |
| (3′) | Region after pyrE2 | 10 | 2 | 0 | 1 | 0 | 0 | 13 | 77 |
| Column statistics: | Mean | 11.3 | 3.4 | 1.7 | 1.06 | 0.12 | 0.24 | 17.7 | 81.8 |
| Sample SD | 6.5 | 1.5 | 1.6 | 1.3 | 0.33 | 0.56 | 9.1 | 13.7 | |
| Median | 10 | 3 | 1 | 1 | 0 | 0 | 14 | 78.3 | |
| pyrE2 | Orotate phosphoribosyl transferase | 14 | 4 | 1 | 2 | 0 | 0 | 21 | 95.2 |
a
The indicated gene of Halobacterium sp. NRC-1 (Ng et al. 2000) was used to query unpublished H. volcanii sequence via the TIGR BLAST server (http://www.tigr.org) and the first 540 nt of H. volcanii sequence matching the Halobacterium gene were analyzed.
b
All DRs ≥8 nt were located in the 540-nt window using the RePuter program via the Bielefeld University Bioinformatics server (http://bibiserv.techfak.uni-bielefeld.de/reputer/).