gi_545778205_gb_U000_219

cmsearch-Rfam

Family :

RtT

Id:

RF00391

Type:

Cis-reg;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family represents a bacterial cis-regulatory element known as RtT RNA. The exact function of RtT
is unknown although it is thought that it may be involved in changing the cellular
response in relation to amino acid starvation [1].

Score:

58.0

E-value:

5.7e-11

From sequence:

781154

To sequence:

781320

Alignments:

                                             v    v                           v     vv         vv                 NC
                              ::::::::::::::(((((((-(---....-----.-((-((.----((((,,,<<___~~~~~~>>,,,,,,<<<<<<____ CS
               RF00391      1 uuauuuugcauaugGgGgaGGAUGAg....AAcCu.UCGacc.aAGGUuCGAgucgAGC*[ 4]*cgAGAaAaCGucGCgucA 75    
                              U+  U++G++ +U+G G:AG  UGA     AA+C+ U:G+:C  AGGU CGA UC  GC         GA AACGU:GCG CA
  gi_545778205_gb_U000 781154 UAGCUCAGUUGGUAGAGCAGU-UGACuuuuAAUCAaUUGGUCgCAGGUUCGAAUCCUGC*[44]*--GGAUAACGUUGCGCCA 781271
                              *********************.***999999999989999999***********76655...*....456777********** PP

                                         v                           v    v           NC
                              >>>>>>,,,))))-))))-------------------)-)))))))::::::::: CS
               RF00391     76 GCgaCGgCCCGaAGggCGAGGcgCgaAGcGaCGAgUaAUCCucCcCccaCCACCA 130   
                              GC:ACGGCCCG AGG:C:AG  +        CGAGU+AU CU:C C ++CCACCA
  gi_545778205_gb_U000 781272 GCAACGGCCCGUAGGGCGAGCGA------AGCGAGUCAUCCUGCACGACCCACCA 781320
                              *****************985433......6678********************** PP

>>

RNAfold
>gi_545778205_gb_U000_219
AGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGUCGCAGGUUCGA
AUCCUGCACGACCCACCAGUUUUAACAUCAAACUCAGAUGUUAAGCGUGA
AGGAUAACGUUGCGCCAGCAACGGCCCGUAGGGCGAGCGAAGCGAGUCAU
CCUGCACGACCCACCA
......((.(((...((((.((((((..........(((((((((.......)))))..))))...((..(((((((((.......)))))))))..))........((((((....))))))((((...))))..((...))))))))..))))...))).)).. (-53.70)

Length sequence

: 166

Length match:

165