HHsearch alignment for GI: 254780724 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=97.03 E-value=0.0018 Score=42.85 Aligned_cols=116 Identities=16% Similarity=0.204 Sum_probs=57.8
Q ss_pred CEEEECCCCCCHHHHHHHHHHH-CCCCCCEEEE-ECCHHH----CCC---CCCEEEEEEECCCCCCCCCCHHHHHHHHHH
Q ss_conf 4899818888888999999830-3876767999-642131----256---787567787416666530001899998752
Q gi|254780724|r 252 NVLISGGTGSGKTTLLNCLTRY-IDKDERIVTC-EDTAEL----QLQ---QPHVVRLETRPPNIEGEGEITMRDLVKNCL 322 (483)
Q Consensus 252 nilVsG~TGSGKTT~L~al~~~-i~~~~rivtI-ED~~El----~l~---~~~~v~~~~~~~~~e~~~~~t~~~ll~~aL 322 (483)
T Consensus 2 Vi~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~--~~~~~~~~~~~~~~~~~ 79 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEG--EGKDPVSIAKRAIEHAR 79 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECC--CCCCHHHHHHHHHHHHH
T ss_conf 9999899999889999999999997699289997488757799999999997498599227--75587999999999987
Q ss_pred HCCCCEEEECCC----CCHHHHHHHHHH---HCCCCEEEHHHCCCCHHHHHHHHH
Q ss_conf 059988996575----879999999998---739701020004788888999999
Q gi|254780724|r 323 RMRPERIILGEV----RGPEVLDLLQAM---NTGHDGSMGTIHANNARESFGRME 370 (483)
Q Consensus 323 R~~PD~IiVGEi----Rg~Ea~~~l~A~---~TGH~G~ltTlHa~s~~~ai~RL~ 370 (483)
T Consensus 80 ~~~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~-~~LVl~a~~~~~~~~~~~ 133 (173)
T cd03115 80 EENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDE-VLLVVDAMTGQDAVNQAK 133 (173)
T ss_pred HCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCC-CEEECCCCCHHHHHHHHH
T ss_conf 568998999788878799999999999986448972-157424655065899999