HHsearch alignment for GI: 254780332 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=97.69 E-value=0.002 Score=45.51 Aligned_cols=90 Identities=24% Similarity=0.399 Sum_probs=57.2
Q ss_pred EEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCH
Q ss_conf 67762131002769999999999851011123333321247975899958521799987899998741011000121376
Q gi|254780332|r 221 LIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTR 300 (504)
Q Consensus 221 l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEMs~~el~~R~is~~s~I~~~~i~~g~l~~ 300 (504)
T Consensus 2 Vi~lvGptGvGKTTTiaKLA~~~~~---------------~~~kV~lit~Dt------~R~gA----------------- 43 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLKK---------------KGKKVLLVAADT------YRPAA----------------- 43 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHH---------------CCCEEEEEECCC------CCHHH-----------------
T ss_conf 9999899999889999999999997---------------699289997488------75779-----------------
Q ss_pred HHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEECCH
Q ss_conf 8899899999998627807825899889999998864022444746776713
Q gi|254780332|r 301 PDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYI 352 (504)
Q Consensus 301 ~e~~~i~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~~~gi~~vvIDYL 352 (504)
T Consensus 44 --~eQL~~~a~~-l~v~~~~~~~~~-~~~~~~~~~~~~~~~~~~D~IlIDTa 91 (173)
T cd03115 44 --IEQLRVLGEQ-VGVPVFEEGEGK-DPVSIAKRAIEHAREENFDVVIVDTA 91 (173)
T ss_pred --HHHHHHHHHH-CCCEEEECCCCC-CHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf --9999999997-498599227755-87999999999987568998999788