HHsearch alignment for GI: 254780831 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=97.60 E-value=6e-05 Score=52.97 Aligned_cols=209 Identities=13% Similarity=0.220 Sum_probs=110.0
Q ss_pred HHHHHHHHHHCCCCCCCCCEEECCCEEEEEEE-CCEE-EEEEEECCCCHHHHHHHHHHHHHHH-H-CCCCCCC-EEEECC
Q ss_conf 89999987203384797643635876556988-9989-9999966878478999999999998-6-0676342-355032
Q gi|254780831|r 6 KNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-HNTV-YLSITVPHTIAHQLQSLRSNAQQII-Q-NIPTVKN-AVVTLT 80 (341)
Q Consensus 6 ~~~I~e~L~~V~DPel~~dIv~lGlI~~I~I~-~~~V-~i~l~lt~~~cp~~~~l~~~i~~~l-~-~i~gv~~-v~V~lt 80 (341)
T Consensus 25 e~vl~~~Lkei~~ALL~~dv-n~klv~~l~~Nik~kid~~n~e~~~~g~nKRk~iq~~vF~EL~~LvDp~~~APkPkkls 103 (453)
T TIGR01425 25 EEVLNEMLKEICTALLESDV-NVKLVRQLRENIKKKIDKINLEELASGLNKRKLIQKAVFEELCNLVDPGVEAPKPKKLS 103 (453)
T ss_pred HHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 89999999999887511335-26778988887887405035133210324789999989999897608632346875333
Q ss_pred CCCCCCCC---CCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCEECCCCCCCCCCCCCC
Q ss_conf 22343332---223465420102446665425789999898723577506988224678765310002456311233445
Q gi|254780831|r 81 ENKNPPQQ---RNNLNVKKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISGKVEISDKKFL 157 (341)
Q Consensus 81 ~~~~~~~~---~~~~~~~~iiav~SgKGGVGKSt~s~nLa~ala~~G~~V~liDaDi~~ps~~~~lg~~~~~~~~~~~~i 157 (341)
T Consensus 104 tstktinGkk~~p~Kgk~~ViMfV-GLQGaGKTTtctKLA~YYk~rGfK~~lvCADTFRAGA------FdQLkqNA~kA~ 176 (453)
T TIGR01425 104 TSTKTINGKKFTPKKGKSSVIMFV-GLQGAGKTTTCTKLAYYYKRRGFKPALVCADTFRAGA------FDQLKQNATKAK 176 (453)
T ss_pred CCCEEECCCEEECCCCCCEEEEEE-ECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCH------HHHHHHHHHHCC
T ss_conf 211010350341156882158886-2148871566878777763266432565177542324------899987476448
Q ss_pred CCCCCCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCC--CC-----CCHHHHCCCCCCE
Q ss_conf 7663223032233343552210001342024789998675213777589974556444--21-----0000000223402
Q gi|254780831|r 158 KPKENYGIKIMSMASLVDENVAMIWRGPMVQSAIMHMLHNVVWGQLDFLLIDMPPGTG--DA-----HLTIAQKIPLSGV 230 (341)
Q Consensus 158 ~p~~~~gi~~~s~g~l~~~~~~~~~rg~~~~~~l~~~l~~~~w~~~D~liiD~ppG~g--d~-----~lsl~~~~~~~~~ 230 (341)
T Consensus 177 iP--FYGsy~-------E-~DPVk----iA~EGv~~Fk~----E~~diIivDTS-GRHkQe~~LF~Em~qv~~Ai~Pd~i 237 (453)
T TIGR01425 177 IP--FYGSYL-------E-SDPVK----IASEGVEKFKK----EKFDIIIVDTS-GRHKQEEELFEEMVQVAEAIKPDSI 237 (453)
T ss_pred CC--CCCCCC-------C-CCCEE----EECCCHHHHHC----CCCCEEEEECC-CCCHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 97--120104-------8-98707----80020113221----27847998379-8732258888998768633499836
Q ss_pred EEEECCCCCHHHHH
Q ss_conf 67421443113456
Q gi|254780831|r 231 VIVSTPQDLALIDV 244 (341)
Q Consensus 231 iiVttP~~~s~~da 244 (341)
T Consensus 238 ifVMD---GsIGQA 248 (453)
T TIGR01425 238 IFVMD---GSIGQA 248 (453)
T ss_pred EEEEC---CCHHHH
T ss_conf 99806---616678