HHsearch alignment for GI: 254780401 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=95.54 E-value=0.029 Score=36.75 Aligned_cols=209 Identities=19% Similarity=0.241 Sum_probs=110.1
Q ss_pred CCCCCCEEEECCEEECCCCCCHHHHHHHHH--HHHCCCCEEEEEECCCCCCCCCEEEECCCCCHHHHCCHHH-HHHHC--
Q ss_conf 338898899823000788874899999999--8524731598760457877775587145678877042123-32205--
Q gi|254780401|r 40 LHAPIPVICVGGFVMGGTGKTPTALAIAKA--VIDKNLKPGFLSRGYGRKSRISFRVDLEKHSAYDVGDEPL-LLARR-- 114 (338)
Q Consensus 40 ~~~~~pVI~VGNitvGGtGKTP~v~~l~~~--l~~~g~~~~ilsRGYg~~~~~~~~v~~~~~~~~~vGDEp~-lla~~-- 114 (338)
T Consensus 99 ~~~P~vilmvG---LQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yR------------PAA----~~QL~~Lg~Q~g 159 (439)
T TIGR00959 99 EKRPTVILMVG---LQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYR------------PAA----IEQLKVLGEQVG 159 (439)
T ss_pred CCCCEEEEEEC---CCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCC------------HHH----HHHHHHHHHHCC
T ss_conf 78683899731---37885788999999999998638970340321034------------789----999999767528
Q ss_pred CCCCC-C---CC---H----HHHHHHHCCCCCCEEEECCC---------CC-----CCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf 76346-5---20---1----22566410245747997183---------22-----344123069999618433566553
Q gi|254780401|r 115 AVTIV-T---SD---R----KIGVQMLLQEGVDIIIMDDG---------FH-----SADLQADFSLIVVNSHRGLGNGLV 169 (338)
Q Consensus 115 ~pv~V-~---~~---R----~~~~~~~~~~~~diiIlDDG---------fQ-----h~~l~rdl~Ivl~d~~~~~gn~~l 169 (338)
T Consensus 160 Vpvf~h~~~~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~EiLlVvDaM~GQd--Av 237 (439)
T TIGR00959 160 VPVFAHLGKGQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPDEILLVVDAMTGQD--AV 237 (439)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHCCHHH--HH
T ss_conf 8711004788898877899999999999748978997267512555999999999988868870541220102169--99
Q ss_pred CCCHHHHHCCHHHHHHHHHHHHCCCCHHH-------HHHHCCCCHHHHHH--HHCCCCCCCCCEEE-EEECCCCHHHHHH
Q ss_conf 76136521002556651454420441245-------77631350111222--20132111686389-8741553578999
Q gi|254780401|r 170 FPAGPLRVPLSRQLSYVDAILYVGNKKNV-------ISSIKNKSVYFAKL--KPRLTFDLSGKKVL-AFSGIADTEKFFT 239 (338)
Q Consensus 170 lPaGpLREp~~~~l~rad~vi~~~~~~~~-------~~~~~~~~i~~~~~--~~~~~~~l~~k~v~-afsGIa~P~~F~~ 239 (338)
T Consensus 238 n~A---~-~F~e~lg-ltG~vltK~DGDaRGGAALS~~~~tg~PIKFiG~GEK~~dLe~FhP~R~A~RILGMGDv~SLvE 312 (439)
T TIGR00959 238 NTA---K-TFNERLG-LTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGVGEKIEDLEPFHPDRMASRILGMGDVLSLVE 312 (439)
T ss_pred HHH---H-HHCCCCC-CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 999---8-6366001-3547885475660578999999996896188841777233124674789863236552236999
Q ss_pred HHHH----HCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf 8874----010000122143323489899999999756479
Q gi|254780401|r 240 TVRQ----LGALIEQCYSFGDHAHLSDKKIAYLLDQAQQKG 276 (338)
Q Consensus 240 ~L~~----~g~~i~~~~~fpDHh~ys~~dl~~i~~~a~~~~ 276 (338)
T Consensus 313 KA~~~~D~~~a~~~-~~K~~-~~~FdleDfl~Ql~~~~KMG 351 (439)
T TIGR00959 313 KAQEVVDEEEAKKL-AEKML-KGQFDLEDFLEQLRQIKKMG 351 (439)
T ss_pred HHHHHCCHHHHHHH-HHHHH-CCCCCHHHHHHHHHHHHHCC
T ss_conf 99985188999999-99863-05889899999999997227