HHsearch alignment for GI: 254780831 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=98.39  E-value=4.8e-07  Score=66.93  Aligned_cols=237  Identities=17%  Similarity=0.293  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCEEEC----CCEEEEEEE--CCEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCE-
Q ss_conf             20289999987203384797643635----876556988--99899999966878478999999999998606763423-
Q gi|254780831|r    3 QILKNQIVDSLKVLSIPGEKNNIVEM----QRLSEIFIV--HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNA-   75 (341)
Q Consensus         3 ~it~~~I~e~L~~V~DPel~~dIv~l----GlI~~I~I~--~~~V~i~l~lt~~~cp~~~~l~~~i~~~l~~i~gv~~v-   75 (341)
T Consensus        20 ~itE~~i~~al~EiR~ALLeADV-nl~VvK~Fi~~V~ekA~G~eV~-------~~~~P~Qq~iKIV~eEL~~~LG~~~~E   91 (439)
T TIGR00959        20 TITEKNIKEALREIRLALLEADV-NLQVVKDFIKKVKEKALGQEVL-------KSLSPGQQFIKIVHEELVAILGGKGRE   91 (439)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHH-------CCCCCCHHEEHHHHHHHHHHCCCCCCC
T ss_conf             75889999999999998877315-7689999999888875225441-------267802012022468999851666732


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHHH--HCCCCCEEEEEECCCCCCC-CCCEECCCCCCCCC
Q ss_conf             55032223433322234654201024466654257899998987--2357750698822467876-53100024563112
Q gi|254780831|r   76 VVTLTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTVVNIACA--LKNKGKNVAILDADVYGPS-IPKLLKISGKVEIS  152 (341)
Q Consensus        76 ~V~lt~~~~~~~~~~~~~~~~iiav~SgKGGVGKSt~s~nLa~a--la~~G~~V~liDaDi~~ps-~~~~lg~~~~~~~~  152 (341)
T Consensus        92 ~~~L~~~~~~P---------~vil-mvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~Lg~Q~---  158 (439)
T TIGR00959        92 SAELKLAEKRP---------TVIL-MVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVLGEQV---  158 (439)
T ss_pred             CCCCCCCCCCC---------EEEE-EECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHHHHHC---
T ss_conf             56755567868---------3899-7313788578899999999999863897034032103478999999976752---


Q ss_pred             CCCCCCCCCCCCEEECC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCC---------HHH
Q ss_conf             33445766322303223-33435522100013420247899986752137775899745564442100---------000
Q gi|254780831|r  153 DKKFLKPKENYGIKIMS-MASLVDENVAMIWRGPMVQSAIMHMLHNVVWGQLDFLLIDMPPGTGDAHL---------TIA  222 (341)
Q Consensus       153 ~~~~i~p~~~~gi~~~s-~g~l~~~~~~~~~rg~~~~~~l~~~l~~~~w~~~D~liiD~ppG~gd~~l---------sl~  222 (341)
T Consensus       159 -----------gVpvf~h~~~~~~p~~Pv~----ia~~Al~~Ak~----~~~D~vI~DT---AGRL~ID~~LM~EL~~iK  216 (439)
T TIGR00959       159 -----------GVPVFAHLGKGQSPDDPVE----IARQALEEAKE----NGFDVVIVDT---AGRLQIDEELMEELAEIK  216 (439)
T ss_pred             -----------CCCCCCCCCCCCCCCCHHH----HHHHHHHHHHH----CCCCEEEEEC---CCCHHHHHHHHHHHHHHH
T ss_conf             -----------8871100478889887789----99999999997----4897899726---751255599999999998


Q ss_pred             HCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEECCCCCH-HHHHHHHHCCCE
Q ss_conf             00223402674214431134566677764001221144554420245877886651247765-899999847978
Q gi|254780831|r  223 QKIPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMIENMSYFLASDTGKKYDLFGNGG-ARFEAEKIGIPF  296 (341)
Q Consensus       223 ~~~~~~~~iiVttP~~~s~~da~r~~~~~~~~~~~i~GiV~NMs~~~~~~~~~~~~~fg~~~-~~~~a~~~~i~~  296 (341)
T Consensus       217 ~~~nP~EiLlVv--DaM~GQdAvn~A~~F~e-~lgltG~vltK--~D----GD-----aRGGAALS~~~~tg~PI  277 (439)
T TIGR00959       217 EILNPDEILLVV--DAMTGQDAVNTAKTFNE-RLGLTGVVLTK--LD----GD-----ARGGAALSVRSVTGKPI  277 (439)
T ss_pred             HHHCCCEEEECC--HHCCHHHHHHHHHHHCC-CCCCCEEEEEC--CC----CC-----CHHHHHHHHHHHHCCCE
T ss_conf             886887054122--01021699999986366-00135478854--75----66-----05789999999968961