HHsearch alignment for GI: 255764460 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=97.54 E-value=0.00036 Score=45.93 Aligned_cols=114 Identities=23% Similarity=0.387 Sum_probs=75.0
Q ss_pred CCCCCCCEEEEEECCCCHHHHHHHHHHHH--HHHCCCEEEEEECCCCCCHHHHHHH-------CCCHHHEEEEE-CCCHH
Q ss_conf 97268807999706872378999999875--2008987999973885566889981-------98833448972-58489
Q gi|255764460|r 62 GGFPKGRIVEIYGPESSGKTTLALHTIAQ--SQKTGGTCAFVDAEHALDSIYARKL-------GVDLKNLLISQ-PDTGE 131 (363)
Q Consensus 62 GG~p~Gri~ei~G~~~sGKTtlal~~~a~--~qk~g~~~~~iD~E~~~~~~~a~~~-------Gvd~~~l~~~~-~~~~E 131 (363)
T Consensus 99 ~~~P~--vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D-~yRPAA~~QL~~Lg~Q~gVpv-----f~h~~~~~ 170 (439)
T TIGR00959 99 EKRPT--VILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACD-LYRPAAIEQLKVLGEQVGVPV-----FAHLGKGQ 170 (439)
T ss_pred CCCCE--EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHH-CCCHHHHHHHHHHHHHCCCCC-----CCCCCCCC
T ss_conf 78683--89973137885788999999999998638970340321-034789999999767528871-----10047888
Q ss_pred H---HHHHHHH---HHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf 9---9999999---974489768998143332202655434555302247888767767777642017818999
Q gi|255764460|r 132 Q---ALEITDM---LVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVF 199 (363)
Q Consensus 132 ~---~~~i~~~---li~~~~~~liViDSi~al~p~~Eie~~~~d~~~g~~ar~ms~~lrkl~~~~~k~~~~~i~ 199 (363)
T Consensus 171 ~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAG----RL~ID~~-----------LM~-EL~~iK~~~nP~EiLlVv 228 (439)
T TIGR00959 171 SPDDPVEIARQALEEAKENGFDVVIVDTAG----RLQIDEE-----------LME-ELAEIKEILNPDEILLVV 228 (439)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCEEEEECCC----CHHHHHH-----------HHH-HHHHHHHHHCCCEEEECC
T ss_conf 988778999999999997489789972675----1255599-----------999-999998886887054122