HHsearch alignment for GI: 254780725 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=98.44  E-value=5.3e-05  Score=49.94  Aligned_cols=186  Identities=13%  Similarity=0.113  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHC---CCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCHHHCCCCC
Q ss_conf             89999976310---233222345675379997469887756899999999-99626994999978798986033438998
Q gi|254780725|r  139 VADIINSISAI---FTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFS-IASVFAMETLLADLDLPYGTANINFDKDP  214 (427)
Q Consensus       139 ~~~l~~ai~~~---~~~~~~~~~~~grvIav~g~KGGvGkTTiA~nLA~~-LA~~~~~~VlLvDlDl~~g~~~~~l~~~~  214 (427)
T Consensus        78 ~eEL~~~LG~~~~E~~~L~~~~~~-P~vilmvG-LQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~-------  148 (439)
T TIGR00959        78 HEELVAILGGKGRESAELKLAEKR-PTVILMVG-LQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAI-------  148 (439)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCC-CEEEEEEC-CCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHH-------
T ss_conf             689998516667325675556786-83899731-378857889999999999986389703403210347899-------


Q ss_pred             CCCHHHHHCCCCCHHHHHHHHHHHCCCCCEEEEE-CCCCCC--CHHCCCHHHHHHHHHHHH-HCCCEEEECCCCCCCHH-
Q ss_conf             7898886318456124337653202489806872-487612--032079999999899985-12888997388888989-
Q gi|254780725|r  215 INSISDAIYPVGRIDKAFVSRLPVFYAENLSILT-APAMLS--RTYDFDEKMIVPVLDILE-QIFPLVILDVPHVWNSW-  289 (427)
Q Consensus       215 ~~~l~d~l~~~~rlD~~~l~~~l~~~~~gL~lL~-a~~~~~--~~~~~~~~~l~~ll~~l~-~~yd~VIiD~p~~~~~~-  289 (427)
T Consensus       149 --------------~Q--L~~Lg~Q--~gVpvf~h~~~~~~p~~Pv----~ia~~Al~~Ak~~~~D~vI~DTAGRL~ID~  206 (439)
T TIGR00959       149 --------------EQ--LKVLGEQ--VGVPVFAHLGKGQSPDDPV----EIARQALEEAKENGFDVVIVDTAGRLQIDE  206 (439)
T ss_pred             --------------HH--HHHHHHH--CCCCCCCCCCCCCCCCCHH----HHHHHHHHHHHHCCCCEEEEECCCCHHHHH
T ss_conf             --------------99--9997675--2887110047888988778----999999999997489789972675125559


Q ss_pred             --H-----HHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCEEE
Q ss_conf             --9-----99986201254357877688999999999999819876753899956589875200599999984895379
Q gi|254780725|r  290 --T-----QEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVKTPKKPEISISDFCAPLGITPSA  361 (427)
Q Consensus       290 --~-----~~~L~~AD~vviV~~p~~~slr~a~~ll~~l~~~~~~~~~~~iVlNr~~~~~~~~i~~~~~~~~lg~~~~~  361 (427)
T Consensus       207 ~LM~EL~~iK~~~nP~EiLlVvD--aM~GQdAvn~A~~F~e-~--lgltG~vltK~DGDaRGGAAL-S~~~~tg~PIKF  279 (439)
T TIGR00959       207 ELMEELAEIKEILNPDEILLVVD--AMTGQDAVNTAKTFNE-R--LGLTGVVLTKLDGDARGGAAL-SVRSVTGKPIKF  279 (439)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCH--HCCHHHHHHHHHHHCC-C--CCCCEEEEECCCCCCHHHHHH-HHHHHHCCCEEE
T ss_conf             99999999988868870541220--1021699999986366-0--013547885475660578999-999996896188