HHsearch alignment for GI: 254780334 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=96.86  E-value=0.011  Score=39.04  Aligned_cols=160  Identities=23%  Similarity=0.277  Sum_probs=93.1

Q ss_pred             HHHHHHHCCC---CC-------CCCEEEEECCCCCCHHHHHHHHHHH--HHCCCCCEEEEECCC----CHHHHHHHHHHC
Q ss_conf             2488886598---57-------8708999549875188999999999--850398199998646----304788887520
Q gi|254780334|r   77 DELDRVTGGG---FV-------RGSVILVGGDPGIGKSTLLMQTAAS--LAYKKHRITYVSGEE----AIGQIRLRAQRL  140 (479)
Q Consensus        77 ~eLDrvLGGG---l~-------~Gs~~Li~G~PGvGKSTL~Lqia~~--~a~~g~~vlYvS~EE----s~~Qi~~Ra~Rl  140 (479)
T Consensus        79 eEL~~~LG~~~~E~~~L~~~~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~  158 (439)
T TIGR00959        79 EELVAILGGKGRESAELKLAEKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVLGEQV  158 (439)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHHHHHC
T ss_conf             89998516667325675556786838997313788578899999999999863897034032103478999999976752


Q ss_pred             CCCCCCHH-EECCCC---HHHHHHHH---HHCCCCCEEEECHHHHHHHHHHCCCCCCHHH---HHHHH------------
Q ss_conf             15775100-003478---89999999---7316982899721687665420445563679---99999------------
Q gi|254780334|r  141 NTINSSVY-IAIETN---VEDIIATL---ITNEKPDLVIIDSIQTLWSQTAESSPGTVIQ---VRTSV------------  198 (479)
Q Consensus       141 ~~~~~~i~-~~~e~~---l~~il~~~---i~~~~~~~vVIDSIQtl~~~~~~s~~GsvsQ---vre~~------------  198 (479)
T Consensus       159 gVpv--f~h~~~~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~-----LM~EL~~iK~~~nP~EiLlVvDaM  231 (439)
T TIGR00959       159 GVPV--FAHLGKGQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEE-----LMEELAEIKEILNPDEILLVVDAM  231 (439)
T ss_pred             CCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHH-----HHHHHHHHHHHHCCCEEEECCHHC
T ss_conf             8871--100478889887789999999999974897899726751255599-----999999998886887054122010


Q ss_pred             --HHHHHHHHHCCCEEEEEEEE-CC-CCCCCCHHHH--HHHHHEEEEEECC
Q ss_conf             --99999753079789998630-36-6543311457--8775302785155
Q gi|254780334|r  199 --QAMIQYAKKNGVAMVLVGHV-TK-EGQIAGPRVI--EHMVDAVLYFEGG  243 (479)
Q Consensus       199 --~~L~~~AK~~~i~vilighv-TK-~G~iAGp~~L--eH~VD~vl~~ege  243 (479)
T Consensus       232 ~GQdAvn~A~~F~e~lgltG~vltK~DGDaRGGAALS~~~~tg~PIKFiG~  282 (439)
T TIGR00959       232 TGQDAVNTAKTFNERLGLTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGV  282 (439)
T ss_pred             CHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEC
T ss_conf             216999999863660013547885475660578999999996896188841