HHsearch alignment for GI: 254780453 and conserved domain: TIGR00959

>TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 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 various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=92.07  E-value=1.1  Score=24.93  Aligned_cols=119  Identities=20%  Similarity=0.209  Sum_probs=65.0

Q ss_pred             HHHHHHHHHH----CHHHHH-HHHHCC---HHHHHHHHHHHHCCCCCEEEEEECCC------HHHHHHHHHHCCCCC--C
Q ss_conf             8999999851----546678-776404---24678987765215675089972460------467777653023553--1
Q gi|254780453|r   53 LELARDLISD----GKSVFL-DMKLFD---IGSSVTAAIEHIANMGVAMLTVHAYP------QTMRSAVSVVRDTGI--C  116 (238)
Q Consensus        53 ~~~i~~l~k~----~~~If~-D~K~~D---IpnTv~~~v~~~~~~g~d~iTvH~~~------~~l~~~~~~~~~~~~--~  116 (238)
T Consensus       145 PAA~~QL~~Lg~Q~gVpvf~h~~~~~~p~~Pv~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~Ei  224 (439)
T TIGR00959       145 PAAIEQLKVLGEQVGVPVFAHLGKGQSPDDPVEIARQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPDEI  224 (439)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEE
T ss_conf             78999999976752887110047888988778999999999997489789972675125559999999999888688705


Q ss_pred             EEEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHH-HHHCCCCCCCCCCHH-------HHHHHHHHCCCCEEEEECCCCC
Q ss_conf             0466641477768876520121048876544542-110244311134103-------4455442024403551011357
Q gi|254780453|r  117 LLAVTVLTSMDDFDLRESGYEKDISDMVRMRAVQ-ARDIGMGGIVCSPQE-------VRMVREIVGHNMVIVTPGIRML  187 (238)
Q Consensus       117 il~Vt~LTS~~~~~l~~~g~~~~~~~~v~~~a~~-a~~~g~~GvV~s~~e-------i~~ir~~~~~~~~~itPGI~~~  187 (238)
T Consensus       225 LlVvDaM~---G------------QdAv-n~A~~F~e~lgltG~vltK~DGDaRGGAALS~~~~tg~PIKFiG~GEK~~  287 (439)
T TIGR00959       225 LLVVDAMT---G------------QDAV-NTAKTFNERLGLTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGVGEKIE  287 (439)
T ss_pred             EECCHHCC---H------------HHHH-HHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf             41220102---1------------6999-99986366001354788547566057899999999689618884177723