HHsearch alignment for GI: 254780810 and conserved domain: cd03115

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=95.81  E-value=0.15  Score=29.24  Aligned_cols=85  Identities=21%  Similarity=0.311  Sum_probs=48.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECC-CCHHHHHH---HHHHHCCEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             2220487787899999999998611886469999508-78789999---9984034278236678888999999999999
Q gi|254780810|r  177 SLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLID-ERPEEVTD---MQRSVQGEVISSTFDESAARHVQVAEMVIAK  252 (423)
Q Consensus       177 ~~i~~~~~~gkt~ll~~ia~~~~~~~~~v~~i~~lig-Er~~ev~e---~~~~~~~~vv~st~d~~~~~~~~~a~~a~~~  252 (423)
T Consensus         3 i~lvGptGvGKTTTiaKLA~~~~~~~~k--V~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~---~~~~~~---   74 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKK--VLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPV---SIAKRA---   74 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCE--EEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHH---HHHHHH---
T ss_conf             9998999998899999999999976992--89997488757799999999997498599227755879---999999---


Q ss_pred             HHHHHHCCCCEEEEEECH
Q ss_conf             999997799289998163
Q gi|254780810|r  253 AKCLVEYGLDVVILLDSI  270 (423)
Q Consensus       253 a~~~~e~G~dVll~~Dsl  270 (423)
T Consensus        75 ~~~~~~~~~D~-IlIDTa   91 (173)
T cd03115          75 IEHAREENFDV-VIVDTA   91 (173)
T ss_pred             HHHHHHCCCCE-EEEECC
T ss_conf             99987568998-999788