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