HHsearch alignment for GI: 254780827 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=97.58  E-value=0.00036  Score=48.06  Aligned_cols=79  Identities=30%  Similarity=0.414  Sum_probs=58.0

Q ss_pred             HHHHHHHHCCC---C-----CCCCCEEEEEECCCCCCHHHHHHHHHHH-HHHCCCCCEEEEEECCCCCCHHHHHHHCHHH
Q ss_conf             99999871677---6-----6787679995278666733799999999-9733898689995088758826887600020
Q gi|254780827|r   67 CHQYNKFLNLK---E-----ESKIPFVVGITGSVAVGKSTFARILCIL-LQQISNFKVSLITTDGFLFPNAVLTANNLMQ  137 (311)
Q Consensus        67 ~~~~~~fl~~~---~-----~~k~PfIIGIAG~~asGKST~Ar~L~~l-L~~~~~~~V~lis~DgF~~~n~~l~~~~l~~  137 (311)
T Consensus        78 ~eEL~~~LG~~~~E~~~L~~~~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~y-RPAA~--------  148 (439)
T TIGR00959        78 HEELVAILGGKGRESAELKLAEKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLY-RPAAI--------  148 (439)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCC-CHHHH--------
T ss_conf             689998516667325675556786838997313788578899999999999863897034032103-47899--------


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             1898133128999999997412664058740443
Q gi|254780827|r  138 RKGFPESYDSNKLLTFLSDVKSGKKKVAVPRYSH  171 (311)
Q Consensus       138 rkGfPeS~D~~~L~~~L~~lK~G~~~V~~PvYsh  171 (311)
T Consensus       149 --------------~QL~~L--g~-Q~gVpvf~h  165 (439)
T TIGR00959       149 --------------EQLKVL--GE-QVGVPVFAH  165 (439)
T ss_pred             --------------HHHHHH--HH-HCCCCCCCC
T ss_conf             --------------999997--67-528871100