TABLE 1.
Sequence homologs of the A. tumefaciens vir box in vir promoter regions of R. etli/p42a
|
R. etli CFN42 |
A. tumefaciens |
No. of nucleotide hits/total no. of nucleotides | ||
|---|---|---|---|---|
| Operon | Sequence (position)a | Operon | Sequence (position)b | |
| virB | AAAAATCGAAAA (−102) | virB | AGCAATTGAAAA* (−110) | 9/12 |
| virG | TAAAATTGAAAT (−78) | 9/12 | ||
| virD | CGAATTCAAAAT (−415) | virC | CGAATTTGAAAT* (−116) | 10/12 |
| TTAATTTGCAAG (−188) | virD | TTAAATTGCAAT (−151) | 10/12 | |
| AGCAGTTCAATG (−178) | virB | AGCAATTGAAAA* (−110) | 9/12 | |
| AATGATTGCGAT (−143) | virG | AACGATTGAGAA (−99) | 9/12 | |
| TGCGATTGTAAT (−137) | virD | TTCAATTGTAAT (−141) | 10/12 | |
| ATAAACTGAAAT (−122) | virB | TTCAATTGAAAT* (−130) | 9/12 | |
| virB | TTCAAATGAAAT (−132) | 9/12 | ||
| ATAAACTGAAAT (−123) | virC | TA-AAATTGAAAT (−117) | 11/12 | |
| virE | TACATA-TGAAAC (−126) | 10/12 | ||
| TAAACTGAAATT (−125) | virC | TACAATAAAATT (−122) | 9/12 | |
| TATAATATTGAT (−102) | virD | TATAATTTCAAT (−147) | 9/12 | |
| virE | TTCAGATGAAGC (−436) | virB | TTCAAATGAAAT (−132) | 9/12 |
| TTCACTTCAATT (−376) | virA | TTCACTTGAAAC (−117) | 9/12 | |
| virD | TTCAATTTTATT (−163) | 10/12 | ||
| virB2 | TTCGCTTCAAAT (−537) | virA | TTCACTTGAAAC (−117) | 10/12 |
| virB | TTCAATTGAAAT* (−130) | 10/12 | ||
| TGAGATTGAAAT (−526) | virC | CGAATTTGAAAT* (−116) | 9/12 | |
| virC | TAAAATTGAAAT (−117) | 10/12 | ||
| AGAAATCGAAAA (−512) | virB | AGCAATTGAAAA* (−110) | 10/12 | |
| virF1 | TGTGATTGAAAG (−33) | virE | TTCAATTGAAAT* (−130) | 10/12 |
| virF2 | ACCATTTGAAAG (−210) | virB | AGCAATTGAAAA* (−110) | 9/12 |
| virA | TTCATTTGAAAC (−117) | 9/12 | ||
| virC | TTCAAAGGGATT (−742) | virB | TTCAAATGAAAT (−132) | 9/12 |
| AACAAGTGCTAC (−613) | virC | TATAATTGCTAC* (−147) | 10/12 | |
| CCATCTTGAAAT (−460) | virC | CGAATTTGAAAT* (−116) | 11/12 | |
| AAATATAAAATT (−109) | virC | TACAATAAAATT (−122) | 10/12 | |
| TTCGATTAATAG (−99) | virB | TTCAATTGAAAT* (−130) | 9/12 | |
| virG | TATGTTTGTAAC (−59) | virD | TTTTATTGTAAT (−158) | 10/12 |
| virE | TACATATGAAAC (−126) | 10/12 | ||
a
Consensus bases of the vir box sequences (19) are indicated by boldface. Position coordinates are relative to the position of the annotated translation initiation codons.
b
Sequences that have been validated experimentally are indicated by asterisks.