HHsearch alignment for GI: 254780401 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=96.34  E-value=0.0086  Score=40.49  Aligned_cols=190  Identities=18%  Similarity=0.268  Sum_probs=104.7

Q ss_pred             CEE-EECCEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEECCCCCHHHHCCHHHH-HHHC--C-----
Q ss_conf             889-982300078887489999999985247315987604578777755871456788770421233-2205--7-----
Q gi|254780401|r   45 PVI-CVGGFVMGGTGKTPTALAIAKAVIDKNLKPGFLSRGYGRKSRISFRVDLEKHSAYDVGDEPLL-LARR--A-----  115 (338)
Q Consensus        45 pVI-~VGNitvGGtGKTP~v~~l~~~l~~~g~~~~ilsRGYg~~~~~~~~v~~~~~~~~~vGDEp~l-la~~--~-----  115 (338)
T Consensus       122 ~ViMfVG---LQGaGKTTtctKLA~YYk~rGfK~~lvCA------------DTFRAGAF----dQLkqNA~kA~iPFYGs  182 (453)
T TIGR01425       122 SVIMFVG---LQGAGKTTTCTKLAYYYKRRGFKPALVCA------------DTFRAGAF----DQLKQNATKAKIPFYGS  182 (453)
T ss_pred             EEEEEEE---CCCCCHHHHHHHHHHHHHCCCCCEEEECC------------CCCCCCHH----HHHHHHHHHCCCCCCCC
T ss_conf             1588862---14887156687877776326643256517------------75423248----99987476448971201


Q ss_pred             -----CCCCCCCHHHHHHHHCCCCCCEEEECCCCCCCC--------------CCCEEEEEEECCCCCCCCCCCCCCHHHH
Q ss_conf             -----634652012256641024574799718322344--------------1230699996184335665537613652
Q gi|254780401|r  116 -----VTIVTSDRKIGVQMLLQEGVDIIIMDDGFHSAD--------------LQADFSLIVVNSHRGLGNGLVFPAGPLR  176 (338)
Q Consensus       116 -----pv~V~~~R~~~~~~~~~~~~diiIlDDGfQh~~--------------l~rdl~Ivl~d~~~~~gn~~llPaGpLR  176 (338)
T Consensus       183 y~E~DPVkiA---~EGv~~Fk~E~~diIivDTSGRHkQe~~LF~Em~qv~~Ai~Pd~iifVMDGsIGQ--A--------A  249 (453)
T TIGR01425       183 YLESDPVKIA---SEGVEKFKKEKFDIIIVDTSGRHKQEEELFEEMVQVAEAIKPDSIIFVMDGSIGQ--A--------A  249 (453)
T ss_pred             CCCCCCEEEE---CCCHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHH--H--------H
T ss_conf             0489870780---0201132212784799837987322588889987686334998369980661667--8--------8


Q ss_pred             HCCHHHH---HHHHHHHHCCCCHH-----HHHHH--CCCCH-HHHHHHH-CCCCCCCCCEEEE-EECCCCHHHHHHHHHH
Q ss_conf             1002556---65145442044124-----57763--13501-1122220-1321116863898-7415535789998874
Q gi|254780401|r  177 VPLSRQL---SYVDAILYVGNKKN-----VISSI--KNKSV-YFAKLKP-RLTFDLSGKKVLA-FSGIADTEKFFTTVRQ  243 (338)
Q Consensus       177 Ep~~~~l---~rad~vi~~~~~~~-----~~~~~--~~~~i-~~~~~~~-~~~~~l~~k~v~a-fsGIa~P~~F~~~L~~  243 (338)
T Consensus       250 ~~QAkAFK~~~~vGSvIiTKLDGHAkGGGALSAVAATKsPiiFIGTGEhv~d~E~F~~~~FvskLLGmGDl~GL~~~v~~  329 (453)
T TIGR01425       250 FSQAKAFKDSVEVGSVIITKLDGHAKGGGALSAVAATKSPIIFIGTGEHVDDFEIFDAEPFVSKLLGMGDLKGLIDKVQD  329 (453)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHH
T ss_conf             99999863003500388751567767623788987535977981377502760578997147754020218899999975


Q ss_pred             HCCCCCC----CCCCCCCCCCCHHHHH
Q ss_conf             0100001----2214332348989999
Q gi|254780401|r  244 LGALIEQ----CYSFGDHAHLSDKKIA  266 (338)
Q Consensus       244 ~g~~i~~----~~~fpDHh~ys~~dl~  266 (338)
T Consensus       330 l~~~~~~~hk~li~~L~eG~fTlRd~~  356 (453)
T TIGR01425       330 LKLDDEEKHKELIEKLKEGTFTLRDLY  356 (453)
T ss_pred             HCHHCCCHHHHHHHHHHCCCCCHHHHH
T ss_conf             142103107999999835961068899