gi_545778205_gb_U000_220

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:

64.0

E-value:

1.6e-12

From sequence:

781376

To sequence:

781543

Alignments:

                                             v    v                                 vv        vv                  NC
                              ::::::::::::::(((((((-(---....-----.-((-((.----((((,,,<<__~~~~~~>>,,,,,,<<<<<<____> CS
               RF00391      1 uuauuuugcauaugGgGgaGGAUGAg....AAcCu.UCGacc.aAGGUuCGAgucgAG*[ 5]*cgAGAaAaCGucGCgucAG 76    
                              U+  U++G++ +U+G G:AG  UGA     AA+C+ U:G+:C  AGGUUCGA UC  G         GA AACGU:GCGU AG
  gi_545778205_gb_U000 781376 UAGCUCAGUUGGUAGAGCAGU-UGACuuuuAAUCAaUUGGUCgCAGGUUCGAAUCCUG*[44]*--GGAUAACGUUGCGUUAG 781493
                              *********************.***9999999999899*9999***********7665...9....456777*********** PP

                                                                    v    v           NC
                              >>>>>,,,))))-))))-------------------)-)))))))::::::::: CS
               RF00391     77 CgaCGgCCCGaAGggCGAGGcgCgaAGcGaCGAgUaAUCCucCcCccaCCACCA 130   
                              C:ACGGCCCGAAGG:C:AG CG +    G CGAGU+AU CU:C C ++CCACCA
  gi_545778205_gb_U000 781494 CAACGGCCCGAAGGGCGAGACGAA----GUCGAGUCAUCCUGCACGACCCACCA 781543
                              ******************998887....9************************* PP

>>

RNAfold
>gi_545778205_gb_U000_220
AGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGUCGCAGGUUCGA
AUCCUGCACGACCCACCAAUUUAAAGGUGGUUACUGGUAGAGAACGUGAA
GGAUAACGUUGCGUUAGCAACGGCCCGAAGGGCGAGACGAAGUCGAGUCA
UCCUGCACGACCCACCA
..(((..((((((((.(((((((.......))))))).))(((((.......))))).....(((((........))))).))))))..)))..((((.(((((..((((((....))))))((((...))))..(((........)))))))).))))........ (-55.80)

Length sequence

: 167

Length match:

166