HHsearch alignment for GI: 254780824 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=94.56  E-value=0.039  Score=33.61  Aligned_cols=77  Identities=23%  Similarity=0.336  Sum_probs=52.9

Q ss_pred             EEECCCHHHHHHHHHH---HHHHC---CCCCEEEEECCCCCCHHHHHHHHHHH-HCCCCCCCCCCCHHHHHHHCCCCCCE
Q ss_conf             9982998999999999---99845---89969999878786889999999976-07888530245202011003788608
Q gi|254780824|r   10 VIPIPNEKNTICLGRH---LASIL---RLGDCLTLSGDLGSGKSFLARSIIRF-LMHDDALEVLSPTFTLVQLYDASIPV   82 (162)
Q Consensus        10 ~i~l~~~~~t~~la~~---la~~l---~~g~ii~L~GdLGaGKTtfvr~i~~~-lg~~~~~~V~SPTF~l~~~Y~~~~~i   82 (162)
T Consensus        73 ~iKIV~eEL~~~LG~~~~E~~~L~~~~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~---------------~kvLL  137 (439)
T TIGR00959        73 FIKIVHEELVAILGGKGRESAELKLAEKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEG---------------KKVLL  137 (439)
T ss_pred             EEHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCC---------------CCEEE
T ss_conf             202246899985166673256755567868389973137885788999999999998638---------------97034


Q ss_pred             EEEEEECCCCHHHHHCCCH
Q ss_conf             9998651789777530583
Q gi|254780824|r   83 AHFDFYRLSSHQEVVELGF  101 (162)
Q Consensus        83 ~H~DlYRL~~~~E~~~lg~  101 (162)
T Consensus       138 va~D~yRPAA~~QL~~Lg~  156 (439)
T TIGR00959       138 VACDLYRPAAIEQLKVLGE  156 (439)
T ss_pred             EEHHCCCHHHHHHHHHHHH
T ss_conf             0321034789999999767