HHsearch alignment for GI: 255764460 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=96.91 E-value=0.0013 Score=42.38 Aligned_cols=135 Identities=18% Similarity=0.184 Sum_probs=87.4
Q ss_pred HHHHHHHHHHHHHH-HHHHHHHHCCCCEEEECCCCCCCC-CCCCCCCCCHHHHH---HHCCCCCCCCCEEEEEECCCCHH
Q ss_conf 54167699999999-999867618873797036655334-65501477278999---72389726880799970687237
Q gi|255764460|r 6 EMNIVDKSKALEAA-LSQIQRVYGKGAIMQLGSQGSIFE-GIEVVSSGSLGLDI---ALGIGGFPKGRIVEIYGPESSGK 80 (363)
Q Consensus 6 ~~~~~~k~~~l~~~-~~~i~k~~g~~~~~~lg~~~~~~~-~~~~i~TG~~~lD~---~Lg~GG~p~Gri~ei~G~~~sGK 80 (363)
T Consensus 68 ~~~g~nKRk~iq~~vF~EL~~---------L-vDp~~~APkPkklststktinGkk~~p-~Kg--k~~ViMfVGLQGaGK 134 (453)
T TIGR01425 68 LASGLNKRKLIQKAVFEELCN---------L-VDPGVEAPKPKKLSTSTKTINGKKFTP-KKG--KSSVIMFVGLQGAGK 134 (453)
T ss_pred HHHHHHHHHHHHHHHHHHHHH---------H-CCCCCCCCCCCCCCCCCEEECCCEEEC-CCC--CCEEEEEEECCCCCH
T ss_conf 210324789999989999897---------6-086323468753332110103503411-568--821588862148871
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHCCCHHH--EE----EEECCCHHHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf 89999998752008987999973885566889981988334--48----9725848999999999974489768998143
Q gi|255764460|r 81 TTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKN--LL----ISQPDTGEQALEITDMLVRSGAVDIIVIDSV 154 (363)
Q Consensus 81 Ttlal~~~a~~qk~g~~~~~iD~E~~~~~~~a~~~Gvd~~~--l~----~~~~~~~E~~~~i~~~li~~~~~~liViDSi 154 (363)
T Consensus 135 TTtctKLA~YYk~rGfK~~lvCAD-TFRAGAFdQLkqNA~kA~iPFYGsy~E~DPVkiA~EGv~~Fk-~E~~diIivDTS 212 (453)
T TIGR01425 135 TTTCTKLAYYYKRRGFKPALVCAD-TFRAGAFDQLKQNATKAKIPFYGSYLESDPVKIASEGVEKFK-KEKFDIIIVDTS 212 (453)
T ss_pred HHHHHHHHHHHHCCCCCEEEECCC-CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCHHHHH-CCCCCEEEEECC
T ss_conf 566878777763266432565177-542324899987476448971201048987078002011322-127847998379
Q ss_pred C
Q ss_conf 3
Q gi|255764460|r 155 A 155 (363)
Q Consensus 155 ~ 155 (363)
T Consensus 213 G 213 (453)
T TIGR01425 213 G 213 (453)
T ss_pred C
T ss_conf 8