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