HHsearch alignment for GI: peg_409 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=90.87 E-value=0.26 Score=28.94 Aligned_cols=78 Identities=22% Similarity=0.178 Sum_probs=51.5
Q ss_pred HHHHHHHHHCC---CHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHH-HH-CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88897323509---48999982768887998488899679999999999-82-478988956677687899999999999
Q 537021.9.peg.4 10 HSETIDLISQT---KSEQLLASDPTRSAWVSANAGSGKTHILVQRVLRL-LL-ANAHPSTLLCLTHTKAAAAEMSHRVLE 84 (242)
Q Consensus 10 ~~~~~~~~~~~---~~qq~~a~~~~~~~lV~A~aGSGKT~tL~~rv~~l-l~-~g~~P~~IL~lTFT~kAA~El~~RI~~ 84 (242)
T Consensus 78 ~eEL~~~LG~~~~E~~~L~~~~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvL-Lva~D~yRPAA~~QL~~Lg~ 156 (439)
T TIGR00959 78 HEELVAILGGKGRESAELKLAEKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKVL-LVACDLYRPAAIEQLKVLGE 156 (439)
T ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEE-EEEHHCCCHHHHHHHHHHHH
T ss_conf 68999851666732567555678683899731378857889999999999986389703-40321034789999999767
Q ss_pred HHHH
Q ss_conf 9677
Q 537021.9.peg.4 85 IITA 88 (242)
Q Consensus 85 ~l~~ 88 (242)
T Consensus 157 Q~gV 160 (439)
T TIGR00959 157 QVGV 160 (439)
T ss_pred HCCC
T ss_conf 5288