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