HHsearch alignment for GI: 254780218 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=97.15 E-value=0.0019 Score=40.80 Aligned_cols=114 Identities=18% Similarity=0.308 Sum_probs=65.3
Q ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-CC--HH-------HHCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 8689986788879799999999999977981999877889844-10--01-------10012444541013456777889
Q gi|254780218|r 4 GLFISFEGIEGAGKTTHISLLKRFLQRKNYDVHVTREPGGTPA-AE--AA-------RHVLLSCGVDEFGAEAEAIVFAA 73 (225)
Q Consensus 4 g~~I~iEGiDGsGKsTq~~~L~~~L~~~g~~v~~~~eP~~t~~-ge--~i-------r~~l~~~~~~~~~~~~~~lLfaa 73 (225)
T Consensus 121 ~~ViMfVGLQGaGKTTtctKLA~YYk~rGfK~~lvC--ADTFRAGAFdQLkqNA~kA~iPFYG-sy~E~DPVkiA~---- 193 (453)
T TIGR01425 121 SSVIMFVGLQGAGKTTTCTKLAYYYKRRGFKPALVC--ADTFRAGAFDQLKQNATKAKIPFYG-SYLESDPVKIAS---- 193 (453)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCEEEEC--CCCCCCCHHHHHHHHHHHCCCCCCC-CCCCCCCEEEEC----
T ss_conf 215888621488715668787777632664325651--7754232489998747644897120-104898707800----
Q ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCCCEEHHCCCCCCCHHHHHHHHHHHCCCCCCCEEEE-EEECH
Q ss_conf 99997763565542345258723542431000100344424577654442038898411566-52034
Q gi|254780218|r 74 ARLDHVENVIRPALMEGKILLCDRFLDSSYAYQGERDSSQHLFLDSLQEISVQEVMPDCTII-LDLPV 140 (225)
Q Consensus 74 dr~~~~~~~I~p~L~~g~iVI~DRy~~S~lAYQ~~~~~~~~~~i~~l~~~~~~~~~PDl~i~-Ldv~~ 140 (225)
T Consensus 194 EGv~~Fk------~E~~diIivDT---------SGRHkQe~~LF~Em~qv-~~Ai~Pd~iifVMDGsI 245 (453)
T TIGR01425 194 EGVEKFK------KEKFDIIIVDT---------SGRHKQEEELFEEMVQV-AEAIKPDSIIFVMDGSI 245 (453)
T ss_pred CCHHHHH------CCCCCEEEEEC---------CCCCHHHHHHHHHHHHH-HHCCCCCCEEEEECCCH
T ss_conf 2011322------12784799837---------98732258888998768-63349983699806616