Table 3.
Examples of homologous proteins of known function containing promoter motifs with conserved nucleotides at degenerate positions. Bold nucleotides represent non-degenerate positions. A (-) denotes either a homolog does not exist or a homologous protein does not contain the motif. Degenerate positions are as follows: N = A/C/G/T, R = A/G, and Y = C/T
| 100% similar promoter motifs in at least two genomes | |||
|---|---|---|---|
| PBCV-1 | NY-2A | MT-325 | |
| Ribo. Reductase (large) | GTCGATACA | GTCGATACA | - |
| 6-phosphofructokinase | AACTTAAGA | AACTTAAGA | - |
| GDP-D-mannose dehydrogenase | AACTTAACA | AACTTAACA | - |
| Glycosyltransferase | AACTTAAGA | AACTTAAGA | - |
| PCNA | AACTTAAGA | AACTTAAGA | - |
| RNA triphosphatase | AACTTAACA | AACTTAACA | AGCTTAACA |
| Rnase III | AATTTAAGA | AATTTAAGA | AACTTAATA |
| TFIID | AATTTAAAA | AATTTAAAA | - |
| VLTF2-type transcription factor | AATTTAAGA | AATTTAAGA | AACTTAACA |
| Only one difference in a degenerate position in at least two genomes | |||
| PBCV-1 | NY-2A | MT-325 | |
| Replication factor C | GTCGATACG | GTCGATATG | - |
| dUTP pyrophosphatase | GTTGATACG | GTTGATATA | GTCGATATA |
| Coat protein-like | AACTTAAAA | AAATTAATA | AACTTAAGA |
| Fructose -2,6 bisphosphatase | AATTTAAAA | - | AACTTAAAA |
| Fucose synthase | AATTTAAGA | AACTTAAGA | - |
| Ubiquitin C-terminal hydrolase | AGCTTAACA | AGTTTAACA | - |
| UDP-glucose dehydrogenase | AGATTAACA | AATTTAACA | - |
| Two or more differences in degenerate positions | |||
| PBCV-1 | NY-2A | MT-325 | |
| Adenine DNA methylase | AAGTTAATA | AATTTAAAA | - |
| ATPase (AAA+ Class) | AAATTAATA | AATTTAAGA | - |
| ATPase (DNA repair) | AAATTAATA | - | AATTTAACA |
| Histidine decarboxylase | AAATTAATA | AATTTAAGA | - |
| Transposase | AACTTAAGA | AATTTAATA | AATTTAACA |