HHsearch alignment for GI: 254780787 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=96.53  E-value=0.025  Score=33.86  Aligned_cols=106  Identities=22%  Similarity=0.251  Sum_probs=62.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHCC-CCCCE---ECCCE---------------EEEE-----------------CC
Q ss_conf             3898623685044677788642221001-23100---01214---------------9995-----------------17
Q gi|254780787|r  385 VVTIMGHVDHGKTSLLDAIRKADVAKGE-IGGIT---QHIGA---------------YQVA-----------------YQ  428 (884)
Q Consensus       385 vv~v~ghvd~GKt~lld~~r~~~~~~~e-~ggit---q~iga---------------~~~~-----------------~~  428 (884)
T Consensus         2 Vi~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~   81 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHAREE   81 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             99998999998899999999999976992899974887577999999999974985992277558799999999998756


Q ss_pred             CCEEEEEECCCH--HHHHHH---HH-HHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCC--CC-EEEECCCCCCC
Q ss_conf             843888851661--578999---86-6642068059999836674023577789899709--94-15612331244
Q gi|254780787|r  429 GKNITFLDTPGH--AAFYEM---RA-RGARVTDIAVLVLAADEEIMPQAIESINHAKAAD--VS-IIVAINKIDKL  495 (884)
Q Consensus       429 ~~~~~~iDtPGh--~~f~~~---r~-rg~~~~d~~ilvv~~~~g~~~qt~e~~~~~~~~~--~p-~iva~nk~d~~  495 (884)
T Consensus        82 ~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~~~LVl~a~~~-----~~~~~~~~~f~~~~~~~~~I~TKlDet  152 (173)
T cd03115          82 NFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTG-----QDAVNQAKAFNEALGITGVILTKLDGD  152 (173)
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCCCH-----HHHHHHHHHHHHCCCCCEEEEEEECCC
T ss_conf             89989997888787999999999999864489721574246550-----658999999874279978999714389