HHsearch alignment for GI: 254781149 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=96.45 E-value=0.034 Score=35.53 Aligned_cols=88 Identities=22% Similarity=0.206 Sum_probs=53.1
Q ss_pred EEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHH--HHHHHHHCCCCCCCCHHHCCCCCCCHHHHHHHH-
Q ss_conf 68870687414889999999996302232364116753489999--999963022323478555017889989999999-
Q gi|254781149|r 144 LILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGA--RALSNLLYPSSSRIPYLNLIRGEINQEQYRISQ- 220 (266)
Q Consensus 144 LiviaaRP~mGKTa~alnia~~~a~~g~~Vl~fSlEMs~~ql~~--R~ls~~t~~~~s~I~~~~l~~g~l~~~e~~~i~- 220 (266)
T Consensus 2 Vi~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~-----l~v~~~~~~~----~~~~~~~~~ 72 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQ-----VGVPVFEEGE----GKDPVSIAK 72 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHH-----CCCEEEECCC----CCCHHHHHH
T ss_conf 9999899999889999999999997699289997488757799999999997-----4985992277----558799999
Q ss_pred HHHHH--HHHCCCEEECCCCCC
Q ss_conf 99999--972995474799889
Q gi|254781149|r 221 GICEK--LQDFPLIIDDRPSPG 240 (266)
Q Consensus 221 ~a~~~--l~~~pl~IdD~~~~t 240 (266)
T Consensus 73 ~~~~~~~~~~~D~IlIDTaGr~ 94 (173)
T cd03115 73 RAIEHAREENFDVVIVDTAGRL 94 (173)
T ss_pred HHHHHHHHCCCCEEEEECCCCC
T ss_conf 9999987568998999788878