gi_545778205_gb_U000_134

cmsearch-Rfam

Family :

Lysine

Id:

RF00168

Type:

Cis-reg; riboswitch;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

Riboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their
corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results
in modulation of gene expression. This family includes riboswitches that sense lysine [1] in a
number of genes involved in lysine metabolism, including lysC [3].

Score:

126.5

E-value:

6e-34

From sequence:

4233521

To sequence:

4233325

Alignments:

                                                 v   v         v                                  v       v   v  NC
                               :::::((((((,,,,<<<<<<<<<-------.<<<<<<<<____________________>>>>>>>>------>>>>>>> CS
               RF00168       1 aaugacgguAGAGGUGCgucccucAugAGUA.acuuuucuGAggggaugaaaucCgaUGAagaaaaguGAAAGGgagggac 80     
                                A G C:G:AGAGG+GCG ::C CA+  GUA  ::U:U::GA  GGA   A+UCC  UGA::A:A:: GA++GGG G:: C
  gi_545778205_gb_U000 4233521 CAGGCCAGAAGAGGCGCGUUGCCCAA--GUAaCGGUGUUGGA--GGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUC 4233445
                               *************************8..**************..99*********************************** PP

                                         v                    v         v                  v           v         NC
                               >>,,,<<<<<<<<<<<<__._____>>>>>>>>>>>><<<<<<<<<<<_.____>>>>>>>>>>>,<<<<<<<________ CS
               RF00168      81 GCCGAagugaguggaccuc.guuaagguccacucgcuGGccccguggcC.GAAugccacggggCUGuCAccguauuugUuc 159    
                               GCCGA:::GA+UG:AC: C G+++A:GU:CA UC:::G:C:+C::GG:C GAAU:CC::G :G:UGUCACC: A+  GUUC
  gi_545778205_gb_U000 4233444 GCCGAGGUGAUUGAACGGCuGGCCACGUUCA-UCAUCGGCUACAGGGGCuGAAUCCCCUG-GGUUGUCACCAGAAGCGUUC 4233366
                               ********************9**********.****************************.******************** PP

                                                  v                      NC
                               .................__>>>>>>>,,,,))))))::::: CS
               RF00168     160 .................acacggUGgAGcGCUaccggguga 183    
                                                A+ :GGUGGAGC CU:C:GGGUGA
  gi_545778205_gb_U000 4233365 gcagucgggcguuucgcAAGUGGUGGAGCACUUCUGGGUGA 4233325
                               ***************************************** PP

RNAfold
>gi_545778205_gb_U000_134
CACCCAGAAGUGCUCCACCACUUGCGAAACGCCCGACUGCGAACGCUUCU
GGUGACAACCCAGGGGAUUCAGCCCCUGUAGCCGAUGAUGAACGUGGCCA
GCCGUUCAAUCACCUCGGCGAUGCACCCCCUCAGGUGUUAUCACAGGACU
GGCUCCUCCAACACCGUUACUUGGGCAACGCGCCUCUUCUGGCCUG
...(((((((.....(((((...(((...(((......)))..)))...)))))......((((((......))))))..((((((((((((((.(.....)))))).))))..)))))((((((((......)))).))))..((((.....))))...............((((.....))))))))))).... (-67.70)

Length sequence

: 196

Length match:

195