53 lines
2.3 KiB
Plaintext
53 lines
2.3 KiB
Plaintext
prokaryotic wts for promoters
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-35 region:
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P -50-49-48-47-46-45-44-43-42-41-40-39-38-37-36-35-34-33-32-31-30-29-28-27-26
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107109109110110110110110110111111110111112112112112112112112112112112112112
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T 41 33 32 25 34 22 35 35 42 27 32 42 47 14 92 94 11 19 15 37 46 34 38 48 34
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C 22 27 18 29 20 14 20 12 22 23 16 25 10 43 7 6 11 18 60 8 25 23 23 17 20
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A 28 38 30 37 35 56 42 42 37 42 39 18 25 26 2 6 2 72 26 50 26 34 25 26 31
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G 16 11 29 19 21 18 13 21 9 19 24 26 29 29 11 6 88 3 11 17 15 21 26 21 27
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-10 region:
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P -23-22-21-20-19-18-17-16-15-14-13-12-11-10 -9 -8 -7 -6 -5
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112112112112112112112112112112112112112112112112112112112
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T 35 28 28 27 39 51 34 43 26 31 89 3 49 15 19108 31 29 21
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C 34 21 24 27 12 25 20 25 20 27 10 2 16 14 22 3 13 16 30
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A 20 39 33 33 39 23 29 16 23 19 2106 29 66 57 1 35 23 31
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G 23 24 27 25 22 13 29 28 43 35 11 1 18 17 14 0 33 24 30
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+ region:
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P -2 -1 1 2 3 4 5 6 7 8 9 10
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86 88 88 88 88 88 88 88 88 88 88 88
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T 16 22 2 42 27 23 20 25 27 15 16 29
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C 29 49 4 25 25 13 18 22 17 17 16 17
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A 20 9 45 16 24 25 28 24 24 32 35 26
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G 21 8 37 5 12 27 22 17 20 24 21 16
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Notes:
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D. K. and McClure, R., nar 11 2237-2255 (1983)
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E. coli promoters have been shown to contain 2 regions of conserved sequence
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located about 10 and 35 bases upstream of the transcription startsite. These
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are TATAAT and TTGACA with an allowed spacing of 15 to 21 bases between. The
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spacing with maximum efficiency was 17 bases and all but 12 of the 112
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sequences could be aligned with a separation of 17 +or-1 bases. The standard
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promoter has spacing 7 and 17 bases between the startsite and the -10 region,
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and the -10 and -35 regions, respectively. The spacing between the -10 region
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and the startsite is usually 6 or 7 bases but varies between 4 and 8 bases.
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There is an AT rich region of 8 to 10 bases upstream of the -35 region.
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Iniation with a purine is highly prefered with G being used if A is not
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present.
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Gap penalties:
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15 0.02 (only exists as mutant)
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16 0.2
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17 1.0
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18 0.2
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19 0.05 (guess)
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20 0.02 (guess)
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21 0.01 (guess)
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Two processes in volved: 1) recognition
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2) melting (needs recognition for initiation
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and then AT richness)
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factor of about 1 order of magnitude difference for all AT against all GC
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in terms of activity.
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Andrew Travers says there are upstream regions that resemble -35 and -10
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regions (on both strands).
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