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