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