HHsearch alignment for GI: 254780150 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=97.46 E-value=0.00014 Score=47.38 Aligned_cols=120 Identities=23% Similarity=0.286 Sum_probs=77.4
Q ss_pred CCEEEEEEEECCCCCHHHHHHHHHHH-HHH-HHHC----CCC------------------CCCCH-HHHHCCC--EEEEE
Q ss_conf 88279999904689887899999987-644-4200----131------------------26868-6986292--06378
Q gi|254780150|r 10 KESLGLSTIGHVDHGKTTLTAAITKY-YSE-EKKE----YGD------------------IDSAP-EEKLRGI--TIATA 62 (392)
Q Consensus 10 k~~~ni~~iGhvd~GKSTL~~~L~~~-~~~-~~~~----~~~------------------~D~~~-~E~~rGi--Ti~~~ 62 (392)
T Consensus 100 ~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~gVpvf~h~~~~~~p~~Pv~ia 179 (439)
T TIGR00959 100 KRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVLGEQVGVPVFAHLGKGQSPDDPVEIA 179 (439)
T ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 86838997313788578899999999999863897034032103478999999976752887110047888988778999
Q ss_pred ---EEEEECCCEEEEEEECCC--CHH--HHHHH--HHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHC----CCCCEEE
Q ss_conf ---999821990899984787--302--46779--8774002331452012344332106778888631----8760233
Q gi|254780150|r 63 ---HVSYETDKRFYSHIDCPG--HAD--YVKNM--ITGATQADGAILVCAAEDGPKPQTREHILLARQI----GISSIVV 129 (392)
Q Consensus 63 ---~~~~~~~~~~i~iiD~PG--H~~--f~~~m--i~g~~~~D~ailvVda~~G~~~QT~eh~~l~~~l----gi~~iIv 129 (392)
T Consensus 180 ~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~EiLlVvDaM~G---Qd--Avn~A~~F~e~lglt-G~v 253 (439)
T TIGR00959 180 RQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPDEILLVVDAMTG---QD--AVNTAKTFNERLGLT-GVV 253 (439)
T ss_pred HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHCCH---HH--HHHHHHHHCCCCCCC-EEE
T ss_conf 999999997489789972675125559999999999888688705412201021---69--999998636600135-478
Q ss_pred EECCCCC
Q ss_conf 1002333
Q gi|254780150|r 130 YMNKVDA 136 (392)
Q Consensus 130 ~iNKmD~ 136 (392)
T Consensus 254 -ltK~DG 259 (439)
T TIGR00959 254 -LTKLDG 259 (439)
T ss_pred -EECCCC
T ss_conf -854756