HHsearch alignment for GI: 254780627 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=95.01  E-value=0.26  Score=29.31  Aligned_cols=98  Identities=17%  Similarity=0.233  Sum_probs=56.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEHHHHH-------HHHHHHHH-------C-CCHHH-HH-----HHH
Q ss_conf             8986278888579999999999863068816864698889-------99999986-------1-98899-99-----997
Q gi|254780627|r  199 LFIHASVGLGKTHLLQAIANASIKRQPNLRVVYLTAEYFM-------WRFASAIR-------D-NCALN-LK-----DSL  257 (502)
Q Consensus       199 Lfi~G~~GlGKTHLl~ai~~~~~~~~~~~~v~y~~~e~F~-------~~~~~a~~-------~-~~~~~-fr-----~~~  257 (502)
T Consensus         3 i~lvGptGvGKTTTiaKLA~~~~~~--~~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~~~~   80 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKK--GKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHARE   80 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             9998999998899999999999976--99289997488757799999999997498599227755879999999999875


Q ss_pred             HHCCHHHHHHHHHHCCCC-HHHHHHHHHHHHHHCCCEEEEEC
Q ss_conf             403102054444531750-69999999999885698799964
Q gi|254780627|r  258 RNIDLLLIDDMQFLQGKL-IQHEFCHLLNSLLDSAKQVVAAA  298 (502)
Q Consensus       258 r~~DvLliDDiqfl~gk~-tqee~f~~~n~l~~~gkqiv~ts  298 (502)
T Consensus        81 ~~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~~~LVl~a  122 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDA  122 (173)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCC
T ss_conf             689989997888787999999999999864489721574246