HHsearch alignment for GI: 254780806 and conserved domain: cd03115

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=98.76  E-value=6.3e-08  Score=65.77  Aligned_cols=159  Identities=23%  Similarity=0.288  Sum_probs=78.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHCCCCCCCCCCEEEEEECCCCHHHCCCCCCCCCE
Q ss_conf             9999808898888999999999999879959999878776-801121246333454116763025771210244444420
Q gi|254780806|r    8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNL   86 (265)
Q Consensus         8 vI~v~s~KGGvGKTT~a~nlA~~la~~g~rVllID~D~q~-~~~~~l~~~~~~~~~ti~~~l~~~~~l~~~i~~~~~~~l   86 (265)
T Consensus         2 Vi~lv-GptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL--~------~~a~----------------~l~v   56 (173)
T cd03115           2 VILLV-GLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQL--R------VLGE----------------QVGV   56 (173)
T ss_pred             EEEEE-CCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHH--H------HHHH----------------HCCC
T ss_conf             99998-99999889999999999997699289997488757799999--9------9999----------------7498


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC--CCCCCC----HHH--HHHHCCCCCCCCCH
Q ss_conf             0014887457750001232222102333224765102782033101333--222210----112--33100111112311
Q gi|254780806|r   87 SIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPSF--NLLTMN----AMA--AADSILVPLQCEFF  158 (265)
Q Consensus        87 ~iipa~~~~~~~~~~l~~~~~~~~~l~~~l~~~l~~~yD~IiiD~pp~~--~~~~~~----al~--aad~viip~~p~~~  158 (265)
T Consensus        57 ~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~D~IlIDTaGr~~~d~~~~~el~~l~~~~~p~~~~LVl~a~-~  124 (173)
T cd03115          57 PVFEEG-----------EGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAM-T  124 (173)
T ss_pred             EEEECC-----------CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCC-C
T ss_conf             599227-----------7558799999999998756899899978887879999999999998644897215742465-5


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             3788875335777655432026774310020231253100112689998808520
Q gi|254780806|r  159 ALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKV  213 (265)
Q Consensus       159 s~~~~~~~~~~i~~~~~~~~~~~~~~~iv~N~~~~~~~~~~~~~~~l~~~~~~~v  213 (265)
T Consensus       125 ~----~~~~~~~~~f----~~~~~~~~~I~TKlDet~~~G~-~ls~~~~-~~~Pi  169 (173)
T cd03115         125 G----QDAVNQAKAF----NEALGITGVILTKLDGDARGGA-ALSIRAV-TGKPI  169 (173)
T ss_pred             H----HHHHHHHHHH----HHCCCCCEEEEEEECCCCCCCH-HHHHHHH-HCCCE
T ss_conf             0----6589999998----7427997899971438997579-9999999-89090