Exercise 3
- Given the following bacterial 5' UTRs find if they contain any cis-regulatory elements using the Rfam database.
- Are the predicted elements riboswitches?
- If so, you can use the ARNold terminator to predict whether or not the expression platforms are Rho-independent terminators or Shine-Dalgarno sequence.
- Are your riboswitches turning the corresponding gene on or off?
>Dhaf_2550 Len=729 extracellular solute-binding protein family 5; Desulfitobacterium hafniense DCB-2; CP001336.1/2753615-2754343;
ACUUCGCCAUCACCAAUACUAUUUUGAAGAAGCGUUUGAAUCUCGAGUGA
UCUUUGGGUUGUUAAUUGUCAUAAUAUAUGUUAUAAACAAUAUAAGUGAA
UUAAAUAUUCAGUUUUUAGGUGCCUCUGAUUUAUCGGAGGAUAAUAGGGA
ACCAGGUGAAAUUCCUGGACGGUCGCGCCACUGUAUGCGGAGAGCUUCUU
UUAUAACCACUGGUUUUAUCCGGGAAGGAGAAAGAAAGCAAAGACCCGCA
AGUCAGGAAACCUGCCUAAUACUGGUUGUCUACGCCUUUCGCGGAAAAAG
GGAUAUGACGGUUGCACUUGUGCUUUAACCCAUUUUCUUAGCGAAAAUGG
GUUUUGUUUGCUUUAAAACCGAAUACAUAGCUUAAGGUGCCCAUAGGGAG
AAUAGGGAAACCGGUAUAAGUCCGGUGCGGAUCCGCCGCUGUAAUCGGAG
ACGAAUCCCCAGAAUGUCACUGUCUUUUUUAGAGAUGGGAAGGCGUGGGA
GGAGGAUGACACGAGAGCCAGAAGACCUGCCUUUUAGAAAGCUGAUUAAG
UACACUAGUAAGGCUUUUUUAGGCUUGUUCAAGGUAAGUUCUCCCUGCAU
CAUUGCAGGGAGAUUUAUUAUUGGGGAGACUCUUUCGCCAUAAGGAGGUG
AAAAUGGAUAGCGAAAUAUCCAUAUUCCAGUUGAUAUAACAUGCUAUUAA
AAUCAAGAAUAAAAGGAGAAGGCCAUAUG
>gcvT Len=422 putative glycine cleavage system protein T; Saccharopolyspora erythraea; AM420293/6403499-6403920
GAACGUUCACGGCGCCGAGAUCACUCCGGCGUCCUGUUGACUGGGCAACC
CCGUCUACGUAGCGUCCUCGGCCAGAACGACAACCGAACACCGCAGCCGA
AGACGUCGUGCGGGAGAGUCCUCACCAGCGGAUGAGGCGCCGAAGGAGCA
AUACUCCCCGCCAAACUCUCAGGCCCAGUCACCGCACGGCACCAGGCUGA
ACACGGAGAAAAGCAGGGGCGCGCGAGCGCCUCUCGCCCAAGGUGCAAGC
CGCGCGUUCCGGCGUGGUGAAACUCUCAGGCCAAUGACUCCGGGGAGACC
GCCGACCAGCGCAUGCCCGCGCGGGUCGCAGUCGAGCUGGCCCGGAUAAG
GUAAGGCCGAAGUGAGCGGCCCGGCUCUGGACUGCCGACCGGCGCCCCCA
CCAGGAGGAGUUCCGCACCAUG
>Bsph_2042 Len=486 hypothetical protein; Lysinibacillus sphaericus C3-41; CP000817/2101124-2101609
UGUGGAGCUAUAGUAAGGGGUGGCACCUUUUUUAAAAAAUACAGACAGAA
GUAUAGAUAAUAUAAUUAAAUAGUGUUAUCGUAAGAACUAGCUAAAUAAA
AUGAUCCUUCGGGGUAGGGUGAAAUUCCCAAUCGGCGGUGAUGAAGUCAU
UCAAAGUCCGUGAGCGCAAGCUGAUUUGGUGCAAAUCCAAAACCGACAGU
AACAGUCUGGAUGGGAGAAGGGUAUAAGUGCGAGCUUUUUAAAUUCAAUG
UAAUUUAAAAGGUCUAUUUGAUUAUGCAUUUAUUACACUACUUCCCGCAA
ACUUGUAGGGAAGUUUUUUAUUUAGCCAAUCAAUUGAAUAGAAGAUGUUC
UUCGGGGUAGGGUGAAAUUCCCAAUCGGCGGUGAUGAAGUUAUUCAAAGU
CCGUGAGCGCAAGCUGAUUUGGUGCAAAUCCAAAACCGACAGUGAUAGUC
UGGAUGGGAGAAGAACAAAUAAGAUACUAGUCUAUG
>tenA Len=464 transcriptional regulator of extracellular enzymes; Bacillus cereus E33L; CP000001/741960-742423;
AAUAUAAGUAUUAUAUGGCUUAGUAAUUUUGUUGACAAUUGAGAAAAUUA
AAACAGUUGAUGAUGUCUUAUUACGGUGUUAUACUGACAGUGAUAAUUUU
AUAGUUUGCUAGGAGAGCUGGUGUUGCCAGCUGAGAGUAAGACCUUAAGU
CUUUGAUCCUUUUUAUUACCUGAUCUAGAUUAUGCUAGCGUAGGGAAGCA
AUUCGGACACUAAUAAUGAGUCCCCGUUUCUUUGCGUAUAGAAACGGGGC
UUUUUUAUUUGAAAAUUUCAUAUUGAAACCACUAGGGGUGCUUGUUGUGC
UGAGAGAGGAAUAAUCCUUAACCCUUAUAACACCUGAUCUAGGUAAUACU
AGCGAAGGGAAGUGGAACAACGAAUAAAUUAUAAUUUUAUUUGCUGUAAC
CACUUCUUAUAUAAAGAAGUGGUUUUUUAUUUAUAUACACAUACCGGAAG
GGGAUAGAGAAAUG
>Dhaf_4884 Len=449 amino acid carrier protein; Desulfitobacterium hafniense DCB-2; CP001336.1/5206919-5207367
AUUCUUGAAUAAAAUGGGAGCGGUAAUUAUAAUUAUAGAUACAAUUCCAG
AAAAUGCGGUGGCAAUCUGGAAUUUACGAAAAACUGCAUAGGAAUGCUGG
AUGAGAUUUACGGGAGAAGGGCACGGCCCGCCGAAGAAGUUGAAACUUUC
AGGUGACUGGAAUAAGUCAGGGACCGUAAAUUGACAGCACUCUGGAGAGA
CUCGAUUAGAGCGCCGAAGGGGCAAUACAAUGACGUGUUGUUAAAUCUCU
CAGGCAAAAGGACAGAGAAGGAACAGGGACUGCUACAGAGCAAUCUCUUA
CUUUUGUACCUAUCGUCCGAAUAUUCAGAGUCAAUCGCUAAGGAUUGACU
CUUUUUAUAUAUAAAUUGCCAUCCUUUUUGCGGGAGGCUGCCGCAACGGA
GAUGUGCAGAGAGAUGCGAAAAGAGAGAUUAAAGGAGGAACACUCAAUG