HHsearch alignment for GI: 254780487 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=98.01  E-value=0.00051  Score=44.60  Aligned_cols=160  Identities=17%  Similarity=0.193  Sum_probs=79.0

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCCCCE--ECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             29998358987479999999999840486120--1388738068999998557873114430014510347889998502
Q gi|254780487|r    4 RLVIVGTDTSVGKTIFASALVHALNAYYWKPI--QSGMYEETDSKTIHRIGRIPKSHIIPEKWKLRTPASPHLAAEIDGV   81 (217)
Q Consensus         4 ~i~I~GT~t~vGKT~vs~~L~~~l~~~~~KPv--~~G~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (217)
T Consensus         2 Vi~lvGp-tGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~----v~~~~~~~~~~~~~~~~~---   73 (173)
T cd03115           2 VILLVGL-QGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVG----VPVFEEGEGKDPVSIAKR---   73 (173)
T ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHCC----CEEEECCCCCCHHHHHHH---
T ss_conf             9999899-99988999999999999769928999748875779999999999749----859922775587999999---


Q ss_pred             CCHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHH---HC-CCEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             3507886422328879992276555667675308999997---47-9448970577650457999999998479907999
Q gi|254780487|r   82 IIDPATINPPDINDSIIIEGIGGLLVPLTTEYLFIDLIER---WQ-FPIILCARTSLGTINHSLLSLETLRNRNINIIGI  157 (217)
Q Consensus        82 ~i~~~~~~~~~~~D~viIEGagg~~~~~~~~~~~~dla~~---l~-~~vILV~~~~~g~i~~~~l~~~~~~~~g~~i~Gi  157 (217)
T Consensus        74 ---~~~~~~~~~~D~IlIDTaGr~~---~d~~~~~el~~l~~~~~p~~~~LVl~a~~~--~~~~~~~~~f~-~~~~~~~~  144 (173)
T cd03115          74 ---AIEHAREENFDVVIVDTAGRLQ---IDENLMEELKKIKRVVKPDEVLLVVDAMTG--QDAVNQAKAFN-EALGITGV  144 (173)
T ss_pred             ---HHHHHHHCCCCEEEEECCCCCC---CCHHHHHHHHHHHHHHCCCCCEEECCCCCH--HHHHHHHHHHH-HCCCCCEE
T ss_conf             ---9999875689989997888787---999999999999864489721574246550--65899999987-42799789


Q ss_pred             EECCCC-CCCHHH--HHHHHCCCCEE
Q ss_conf             976977-800599--99986199899
Q gi|254780487|r  158 AFIGDS-MPKVEE--TIVKIGRIPHL  180 (217)
Q Consensus       158 IlN~~~-~~~~~~--~le~~~~ipvL  180 (217)
T Consensus       145 I~TKlDet~~~G~~ls~~~~~~~Pi~  170 (173)
T cd03115         145 ILTKLDGDARGGAALSIRAVTGKPIK  170 (173)
T ss_pred             EEEEECCCCCCCHHHHHHHHHCCCEE
T ss_conf             99714389975799999999890908