HHsearch alignment for GI: 254780709 and conserved domain: TIGR01425
>TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325 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 the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=100.00 E-value=0 Score=594.14 Aligned_cols=292 Identities=29% Similarity=0.461 Sum_probs=267.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCC-HHH----HHHHHHHHHHCCCCHHHHHHHHHHHHH---HHHCCCCCH-----HHHHHH
Q ss_conf 9999999999999860567789-999----999999999738898999999999998---751278998-----999999
Q gi|254780709|r 21 FASTSLKLKEGITDIISSRRLD-DGV----REELEDLLIRSDIGVAVAQKIVEELLT---KRYAKDVSV-----QRVLYD 87 (321)
Q Consensus 21 L~kt~~~L~~~l~~l~~~~~ld-e~~----leeLee~LL~ADVg~~va~~Iie~ik~---~~~~~~i~~-----~~i~~~ 87 (321)
T Consensus 2 LA~LG~~l~~AL~~~~saTv~dse~vl~~~Lkei~~ALL~~dvn~klv~~l~~Nik~kid~~n~e~~~~g~nKRk~iq~~ 81 (453)
T TIGR01425 2 LADLGSSLVSALRSMSSATVIDSEEVLNEMLKEICTALLESDVNVKLVRQLRENIKKKIDKINLEELASGLNKRKLIQKA 81 (453)
T ss_pred CHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 10101489999860123611044899999999998875113352677898888788740503513321032478999998
Q ss_pred HHHHHHHHCCCCCCC-----C-----------CCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 999878520100121-----0-----------001366741231135444442478999999985226742677434512
Q gi|254780709|r 88 VSELIHKMLMPLSKP-----F-----------NWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151 (321)
Q Consensus 88 l~~~L~~~L~~~~~~-----~-----------~~~~~~~p~vil~vG~nG~GKTTT~aKLA~~~~~~g~kV~lva~DtfR 151 (321)
T Consensus 82 vF~EL~~LvDp~~~APkPkklststktinGkk~~p~Kgk~~ViMfVGLQGaGKTTtctKLA~YYk~rGfK~~lvCADTFR 161 (453)
T TIGR01425 82 VFEELCNLVDPGVEAPKPKKLSTSTKTINGKKFTPKKGKSSVIMFVGLQGAGKTTTCTKLAYYYKRRGFKPALVCADTFR 161 (453)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCEEECCCEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCC
T ss_conf 99998976086323468753332110103503411568821588862148871566878777763266432565177542
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 45688999997530353212235866124542289999651487599865433321157789999899876302223430
Q gi|254780709|r 152 SAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPH 231 (321)
Q Consensus 152 ~aA~eQL~~~a~~~~v~~~~~~~~~dp~~v~~~a~~~a~~~~~DvvliDTAGR~~~~~~lm~EL~ki~~v~~~~~~~~p~ 231 (321)
T Consensus 162 AGAFdQLkqNA~kA~iPFYGsy~E~DPVkiA~EGv~~Fk~E~~diIivDTSGRHkQe~~LF~Em~qv~~Ai~------Pd 235 (453)
T TIGR01425 162 AGAFDQLKQNATKAKIPFYGSYLESDPVKIASEGVEKFKKEKFDIIIVDTSGRHKQEEELFEEMVQVAEAIK------PD 235 (453)
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCC------CC
T ss_conf 324899987476448971201048987078002011322127847998379873225888899876863349------98
Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHC
Q ss_conf 11231023352257789998764358976999654578706999999999769889997589813255577899999872
Q gi|254780709|r 232 SVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVAKDFSAVIT 311 (321)
Q Consensus 232 ~~~lVlda~~gq~~~~~a~~F~~~~~~~g~I~TKlD~ta~~G~~ls~~~~~~~Pi~fig~Ge~i~Dl~~f~~~~~~~~ll 311 (321)
T Consensus 236 ~iifVMDGsIGQAA~~QAkAFK~~~~vGSvIiTKLDGHAkGGGALSAVAATKsPiiFIGTGEhv~d~E~F~~~~FvskLL 315 (453)
T TIGR01425 236 SIIFVMDGSIGQAAFSQAKAFKDSVEVGSVIITKLDGHAKGGGALSAVAATKSPIIFIGTGEHVDDFEIFDAEPFVSKLL 315 (453)
T ss_pred CEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCHHHHHC
T ss_conf 36998066166788999998630035003887515677676237889875359779813775027605789971477540
Q ss_pred CCCCCCC
Q ss_conf 8656463
Q gi|254780709|r 312 GCLDYGE 318 (321)
Q Consensus 312 G~gd~~~ 318 (321)
T Consensus 316 GmGDl~G 322 (453)
T TIGR01425 316 GMGDLKG 322 (453)
T ss_pred CCCCHHH
T ss_conf 2021889