HHsearch alignment for GI: 254780709 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=100.00  E-value=0  Score=733.13  Aligned_cols=289  Identities=33%  Similarity=0.531  Sum_probs=274.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCC-----CHHHHHHHHHHH
Q ss_conf             99999999999998605677899----999999999997388989999999999987512789-----989999999998
Q gi|254780709|r   21 FASTSLKLKEGITDIISSRRLDD----GVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDV-----SVQRVLYDVSEL   91 (321)
Q Consensus        21 L~kt~~~L~~~l~~l~~~~~lde----~~leeLee~LL~ADVg~~va~~Iie~ik~~~~~~~i-----~~~~i~~~l~~~   91 (321)
T Consensus         1 fe~Ls~~l~~~~~~L~~~~~itE~~i~~al~EiR~ALLeADVnl~VvK~Fi~~V~ekA~G~eV~~~~~P~Qq~iKIV~eE   80 (439)
T TIGR00959         1 FESLSERLQRIFKKLSGKGTITEKNIKEALREIRLALLEADVNLQVVKDFIKKVKEKALGQEVLKSLSPGQQFIKIVHEE   80 (439)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHEEHHHHHH
T ss_conf             90157899999985117777588999999999999887731576899999998888752254412678020120224689


Q ss_pred             HHHHCCCC---CCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHH--HHHCCCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             78520100---12100013667412311354444424789999999--85226742677434512456889999975303
Q gi|254780709|r   92 IHKMLMPL---SKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKK--MSDAGLKVMLAAGDTFRSAAIDQLKIWADRTS  166 (321)
Q Consensus        92 L~~~L~~~---~~~~~~~~~~~p~vil~vG~nG~GKTTT~aKLA~~--~~~~g~kV~lva~DtfR~aA~eQL~~~a~~~~  166 (321)
T Consensus        81 L~~~LG~~~~E~~~L~~~-~~~P~vilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~g  159 (439)
T TIGR00959        81 LVAILGGKGRESAELKLA-EKRPTVILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVLGEQVG  159 (439)
T ss_pred             HHHHCCCCCCCCCCCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHHHHHCC
T ss_conf             998516667325675556-7868389973137885788999999999998638970340321034789999999767528


Q ss_pred             CCCCC-CCCCCC---CHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             53212-235866---12454228999965148759986543332115778999989987630222343011231023352
Q gi|254780709|r  167 ADFVC-SEIGSD---AAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTG  242 (321)
Q Consensus       167 v~~~~-~~~~~d---p~~v~~~a~~~a~~~~~DvvliDTAGR~~~~~~lm~EL~ki~~v~~~~~~~~p~~~~lVlda~~g  242 (321)
T Consensus       160 Vpvf~h~~~~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~n------P~EiLlVvDaM~G  233 (439)
T TIGR00959       160 VPVFAHLGKGQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILN------PDEILLVVDAMTG  233 (439)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHC------CCEEEECCHHCCH
T ss_conf             8711004788898877899999999999748978997267512555999999999988868------8705412201021


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             25778999876435897699965457870699999999976988999758981325557789999987286564
Q gi|254780709|r  243 QNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVAKDFSAVITGCLDY  316 (321)
Q Consensus       243 q~~~~~a~~F~~~~~~~g~I~TKlD~ta~~G~~ls~~~~~~~Pi~fig~Ge~i~Dl~~f~~~~~~~~llG~gd~  316 (321)
T Consensus       234 QdAvn~A~~F~e~lgltG~vltK~DGDaRGGAALS~~~~tg~PIKFiG~GEK~~dLe~FhP~R~A~RILGMGDv  307 (439)
T TIGR00959       234 QDAVNTAKTFNERLGLTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGVGEKIEDLEPFHPDRMASRILGMGDV  307 (439)
T ss_pred             HHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHCCCCCH
T ss_conf             69999998636600135478854756605789999999968961888417772331246747898632365522