HHsearch alignment for GI: 254780332 and conserved domain: TIGR00959
>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=97.37 E-value=0.012 Score=39.57 Aligned_cols=148 Identities=20% Similarity=0.295 Sum_probs=103.3
Q ss_pred CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCC--CHHHHHHHHHHHHHHHCCCC-CCC
Q ss_conf 726776213100276999999999985101112333332124797589995852--17999878999987410110-001
Q gi|254780332|r 219 SDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEM--SSEQLATRIISEQTEVPSSK-IRR 295 (504)
Q Consensus 219 G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEM--s~~el~~R~is~~s~I~~~~-i~~ 295 (504)
T Consensus 102 P~vilmvGLQGsGKTTt~gKLA~~ll~-------------kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~gVpvf~h~~~ 168 (439)
T TIGR00959 102 PTVILMVGLQGSGKTTTAGKLALYLLK-------------KKEGKKVLLVACDLYRPAAIEQLKVLGEQVGVPVFAHLGK 168 (439)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHH-------------HHCCCCEEEEEHHCCCHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 838997313788578899999999999-------------8638970340321034789999999767528871100478
Q ss_pred CCCCHHHHHHHHHHHHHHHHC--CEEEECCC-CCCHHH-HHHHHHHHCCCCCCC--EEEECCHHHCCCCCCCCCHHHHHH
Q ss_conf 213768899899999998627--80782589-988999-999886402244474--677671353256644321137889
Q gi|254780332|r 296 GELTRPDYEKIVACSQVMQKL--PLYIDQTG-GISMSQ-LATRARRLKRQRGLD--LLIVDYIQLMTTSKKIEENRVLEI 369 (504)
Q Consensus 296 g~l~~~e~~~i~~a~~~l~~~--~l~I~d~~-~~ti~~-I~~~~r~~~~~~gi~--~vvIDYLqli~~~~~~~~~r~~~i 369 (504)
T Consensus 169 ~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~EiLlVvDaM~--------G----QdA 236 (439)
T TIGR00959 169 GQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPDEILLVVDAMT--------G----QDA 236 (439)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHCC--------H----HHH
T ss_conf 8898877899999999999748978997267512555999999999988868870541220102--------1----699
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECC
Q ss_conf 9999999999988279199977138
Q gi|254780332|r 370 TGITMALKALAKELNIPIIALSQLS 394 (504)
Q Consensus 370 ~~is~~lK~lA~e~~ipvi~lsQLn 394 (504)
T Consensus 237 vn---~A~~F~e~lgltG~vltK~D 258 (439)
T TIGR00959 237 VN---TAKTFNERLGLTGVVLTKLD 258 (439)
T ss_pred HH---HHHHHCCCCCCCEEEEECCC
T ss_conf 99---99863660013547885475