gi_545778205_gb_U000_487

cmsearch-Rfam

Family :

yybP-ykoY

Id:

RF00080

Type:

Cis-reg;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This RNA was originally discovered in E. coli during a large scale screen and was named
SraF [1]. The family was later found to exist upstream of related families of protein
genes in many bacteria, including the the yybP and ykoK genes in B. subtilis. The
specific functions of these proteins are unknown, but this structured RNA element may be involved
in their genetic regulation as a riboswitch [2].

Score:

41.3

E-value:

4e-09

From sequence:

1905456

To sequence:

1905557

Alignments:

                                                                                                                 NC
                               :::::::::::.:::::::::::::<<<_.____________>>>,<<<<<<<<<<-------<<<<<____>>>>>>>>> CS
               RF00080       1 ccaccgGUCAu.uGGGGAGUAGCcgccuU.UAuuuauuUugAaggGGcuugCgUCAACAUACUUGgcCcacaGgcCAUGGc 79     
                                   C  UCAU UGGGGAGUAGCCG :UU +A++U++   GAA:  G:::G:GUCAACAUACU G : +  A : C UGGC
  gi_545778205_gb_U000 1905456 UGCGCCCUCAUuUGGGGAGUAGCCGAUUUcCAGAUUCC-GGAAAU-GUACGUGUCAACAUACUCGUU-GCAA-AACGUGGC 1905532
                               **********637************5665587777644.455555.*******************99.8888.9******* PP

                                     v                                                                           NC
                               >>>>>><<<<<<<_______...__________________________________________________________ CS
               RF00080      80 GcaagCGguuccagccguuu...gggcauuccucucacguaCcgCCgucuggucGGCGggGgGgGguggggguuuugUuuu 157    
                               :C:::CGG::::A                                                                    
  gi_545778205_gb_U000 1905533 ACGUACGGACUGAAUA----cuu---------------------------------------------------------- 1905551
                               ******7777776443....353.......................................................... PP

                                                v NC
                               ___________>>>>>>> CS
               RF00080     158 gcccgcgccuauggaacU 175    
                                          U::::C 
  gi_545778205_gb_U000 1905552 -----------UCAGUC- 1905557
                               ...........677777. PP

RNAfold
>gi_545778205_gb_U000_487
CAACAGUUGUUUUAUAUUCUCAAAAUAUGUUAAGGUUGCGCCCUCAUUUG
GGGAGUAGCCGAUUUCCAGAUUCCGGAAAUGUACGUGUCAACAUACUCGU
UGCAAAACGUGGCACGUACGGACUGAAUACUUUCAGUCAGGCGAGACCAU
AUGCACAUCAAUCGCUAUGCCUGCA
...(((.((((((........))))))......((((((.((((.....)))).)))))).((((((.......))))))((((((((((.......((((....)))))))))))))).(((((((....))))))).(((((.................)))))....))).. (-51.50)

Length sequence

: 175

Length match:

100