HHsearch alignment for GI: 254780240 and conserved domain: TIGR00959
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=95.20 E-value=0.037 Score=34.23 Aligned_cols=80 Identities=26% Similarity=0.267 Sum_probs=48.1
Q ss_pred EEEECCCCCCHHHHHHHHHHH--HC-C---CEECHHHHHHHHHH-HHHHHHHHHHH-HHH-C--CCCC--CCHHHHHHHH
Q ss_conf 999878899967899999997--18-9---48957899999996-00145666677-641-3--4455--4103566555
Q gi|254780240|r 3 IIFLGPPGSGKGTQACRLSQK--LN-V---PQLSTGDMLRAEVD-RNTLLGKQVKG-SME-S--GSLI--SDAIVNQVVC 69 (201)
Q Consensus 3 I~i~G~PGsGK~T~a~~la~~--~~-~---~~is~gdllR~~~~-~~s~~g~~i~~-~l~-~--G~lv--pd~ii~~li~ 69 (201)
T Consensus 105 ilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~gVpvf~h~~~~~~p~~Pv~ia~~Al~ 184 (439)
T TIGR00959 105 ILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVLGEQVGVPVFAHLGKGQSPDDPVEIARQALE 184 (439)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 99731378857889999999999986389703403210347899999997675288711004788898877899999999
Q ss_pred HHHCCCCCCCEEEEC
Q ss_conf 420232225317863
Q gi|254780240|r 70 DRIRLPDCDSGFILD 84 (201)
Q Consensus 70 ~~l~~~~~~~g~ilD 84 (201)
T Consensus 185 ~A--k~~~~D~vI~D 197 (439)
T TIGR00959 185 EA--KENGFDVVIVD 197 (439)
T ss_pred HH--HHCCCCEEEEE
T ss_conf 99--97489789972