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