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