HHsearch alignment for GI: 254780806 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=97.98 E-value=1.8e-05 Score=51.42 Aligned_cols=146 Identities=21% Similarity=0.282 Sum_probs=76.1
Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCC
Q ss_conf 76874999980889888899999999999987995999987877680112124633345411676302577121024444
Q gi|254780806|r 3 EKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTA 82 (265)
Q Consensus 3 ~~~~kvI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~ 82 (265)
T Consensus 118 Kgk~~ViMfV-GLQGaGKTTtctKLA~YYk~rGfK~~lvCADTFR--------------AGAFdQLkq--NA~kA~iP-- 178 (453)
T TIGR01425 118 KGKSSVIMFV-GLQGAGKTTTCTKLAYYYKRRGFKPALVCADTFR--------------AGAFDQLKQ--NATKAKIP-- 178 (453)
T ss_pred CCCCEEEEEE-ECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCC--------------CCHHHHHHH--HHHHCCCC--
T ss_conf 6882158886-2148871566878777763266432565177542--------------324899987--47644897--
Q ss_pred CCCEEECCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC---CCCCCCHHHH-----HHHCCCCC
Q ss_conf 44200014887457750-001232222102333224765102782033101333---2222101123-----31001111
Q gi|254780806|r 83 IPNLSIIPSTMDLLGIE-MILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF---NLLTMNAMAA-----ADSILVPL 153 (265)
Q Consensus 83 ~~~l~iipa~~~~~~~~-~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~---~~~~~~al~a-----ad~viip~ 153 (265)
T Consensus 179 FYGsy--------~E~DPVkiA~E--Gv~~Fk-------~E~~diIivDTSGRHkQe~~LF~Em~qv~~Ai~Pd~iifVM 241 (453)
T TIGR01425 179 FYGSY--------LESDPVKIASE--GVEKFK-------KEKFDIIIVDTSGRHKQEEELFEEMVQVAEAIKPDSIIFVM 241 (453)
T ss_pred CCCCC--------CCCCCEEEECC--CHHHHH-------CCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE
T ss_conf 12010--------48987078002--011322-------12784799837987322588889987686334998369980
Q ss_pred CCCC--HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCC
Q ss_conf 1231--13788875335777655432026774310020231253
Q gi|254780806|r 154 QCEF--FALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRN 195 (265)
Q Consensus 154 ~p~~--~s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~ 195 (265)
T Consensus 242 DGsIGQAA~~QA-----------kAFK~~~~vGSvIiTKLDGHA 274 (453)
T TIGR01425 242 DGSIGQAAFSQA-----------KAFKDSVEVGSVIITKLDGHA 274 (453)
T ss_pred CCCHHHHHHHHH-----------HHHHHCCCCEEEEEECCCCCC
T ss_conf 661667889999-----------986300350038875156776