HHsearch alignment for GI: 254780217 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=95.59 E-value=0.016 Score=40.00 Aligned_cols=105 Identities=15% Similarity=0.109 Sum_probs=66.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHH-CCCCCCCCCHHHCCCCCCCHHHH--HHHCCCCCCEEEEC-CCCHHHCCCC
Q ss_conf 88981663117989888999999999981-77998864312101267886799--99678987545300-1000101342
Q gi|254780217|r 31 GRMHHALLFEGEQGIGKATLGFRYAGHVL-QNPDFSKAPVRMCNPDPCSPFVK--QMASHALHDFLYLS-YSLNPKTGKW 106 (347)
Q Consensus 31 ~~l~ha~Lf~Gp~GiGK~~~A~~~A~~ll-c~~~~~~~~~~~~~~~~~~~~~~--~i~~~~hpd~~~i~-~~~~~k~~~~ 106 (347)
T Consensus 99 ~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kv---LLva~D~yRPAA~~QL~~Lg~Q~gVpvf~h~~----~~~~ 171 (439)
T TIGR00959 99 EKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKV---LLVACDLYRPAAIEQLKVLGEQVGVPVFAHLG----KGQS 171 (439)
T ss_pred CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCE---EEEEHHCCCHHHHHHHHHHHHHCCCCCCCCCC----CCCC
T ss_conf 7868389973137885788999999999998638970---34032103478999999976752887110047----8889
Q ss_pred CCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCHHHH
Q ss_conf 12323788755443102221111210353220554240001
Q gi|254780217|r 107 RTVITVDEIRRIRYFLSLTANTGYWRVIMIDPVDGMNRNAA 147 (347)
Q Consensus 107 ~~~I~vd~IR~l~~~~~~~~~~~~~Ki~IId~ad~ln~~Aa 147 (347)
T Consensus 172 p-~~Pv~ia~~Al~~Ak~~~----~D~vI~DTAGRL~ID~~ 207 (439)
T TIGR00959 172 P-DDPVEIARQALEEAKENG----FDVVIVDTAGRLQIDEE 207 (439)
T ss_pred C-CCHHHHHHHHHHHHHHCC----CCEEEEECCCCHHHHHH
T ss_conf 8-877899999999999748----97899726751255599