HHsearch alignment for GI: 254780487 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=98.74 E-value=1.2e-06 Score=61.09 Aligned_cols=195 Identities=19% Similarity=0.188 Sum_probs=115.7
Q ss_pred EEEEECCCCCCCHHHHHHHHHHH--HHCCCCCCEECCCCCCCHHHHHHHHHCCCCCCCCCCCCC-CCCCHH---HHHHHH
Q ss_conf 29998358987479999999999--840486120138873806899999855787311443001-451034---788999
Q gi|254780487|r 4 RLVIVGTDTSVGKTIFASALVHA--LNAYYWKPIQSGMYEETDSKTIHRIGRIPKSHIIPEKWK-LRTPAS---PHLAAE 77 (217)
Q Consensus 4 ~i~I~GT~t~vGKT~vs~~L~~~--l~~~~~KPv~~G~~~~~D~~~~~~~~~~~~~~~~~~~~~-~~~~~~---~~~~~~ 77 (217)
T Consensus 104 vilmvGL-QGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~-Lg-~Q~gVpvf~h~~~~~~p~~Pv~ia~ 180 (439)
T TIGR00959 104 VILMVGL-QGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKV-LG-EQVGVPVFAHLGKGQSPDDPVEIAR 180 (439)
T ss_pred EEEEECC-CCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHH-HH-HHCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf 8997313-7885788999999999998638970340321034789999999-76-7528871100478889887789999
Q ss_pred HHHCCCHHHHHH-HHHHCCEEEEECCCCCCCCCCCCCCHHH---HHHHHC-CCEEEEECCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 850235078864-2232887999227655566767530899---999747-94489705776504579999999984799
Q gi|254780487|r 78 IDGVIIDPATIN-PPDINDSIIIEGIGGLLVPLTTEYLFID---LIERWQ-FPIILCARTSLGTINHSLLSLETLRNRNI 152 (217)
Q Consensus 78 ~~~~~i~~~~~~-~~~~~D~viIEGagg~~~~~~~~~~~~d---la~~l~-~~vILV~~~~~g~i~~~~l~~~~~~~~g~ 152 (217)
T Consensus 181 -------~Al~~Ak~~~~D~vI~DTAGRL~I---D~~LM~EL~~iK~~~nP~EiLlVvDaM~G--QdAvn~A~~F-~e~l 247 (439)
T TIGR00959 181 -------QALEEAKENGFDVVIVDTAGRLQI---DEELMEELAEIKEILNPDEILLVVDAMTG--QDAVNTAKTF-NERL 247 (439)
T ss_pred -------HHHHHHHHCCCCEEEEECCCCHHH---HHHHHHHHHHHHHHHCCCEEEECCHHCCH--HHHHHHHHHH-CCCC
T ss_conf -------999999974897899726751255---59999999999888688705412201021--6999999863-6600
Q ss_pred EEEEEEECC-CCCCCHHH--HHHHHCCCCEE--EEECC---CCCCCHHHHH-------------HHHHHHHHHHHHHHHH
Q ss_conf 079999769-77800599--99986199899--99478---8888887999-------------9999713399999999
Q gi|254780487|r 153 NIIGIAFIG-DSMPKVEE--TIVKIGRIPHL--GRLPK---IDPIDPDVLH-------------QKFQEHFTQSLLQKYF 211 (217)
Q Consensus 153 ~i~GiIlN~-~~~~~~~~--~le~~~~ipvL--G~iP~---~~~~~~~~l~-------------~~~~~~~~~~~l~~~~ 211 (217)
T Consensus 248 gltG~vltK~DGDaRGGAALS~~~~tg~PIKFiG~GEK~~dLe~FhP~R~A~RILGMGDv~SLvEKA~~~~D~~~a~~~~ 327 (439)
T TIGR00959 248 GLTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGVGEKIEDLEPFHPDRMASRILGMGDVLSLVEKAQEVVDEEEAKKLA 327 (439)
T ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf 13547885475660578999999996896188841777233124674789863236552236999999851889999999
Q ss_pred HHH
Q ss_conf 985
Q gi|254780487|r 212 YES 214 (217)
Q Consensus 212 ~~~ 214 (217)
T Consensus 328 ~K~ 330 (439)
T TIGR00959 328 EKM 330 (439)
T ss_pred HHH
T ss_conf 986