HHsearch alignment for GI: 254780129 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=94.54 E-value=0.32 Score=26.16 Aligned_cols=121 Identities=12% Similarity=0.079 Sum_probs=55.0
Q ss_pred EEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEE-CCCCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCEEE
Q ss_conf 999689998899999999999740899489972-3310137889999851553460699861121011223456766278
Q gi|254780129|r 23 ALWASMGSGKTVSVLFALSTIKILDPRPVLIIA-PLRVAQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYI 101 (220)
Q Consensus 23 ~l~~~~G~GKT~~ai~~~~~~~~~~~~~~LIi~-P~s~~~~~W~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 101 (220)
T Consensus 4 ~lvGptGvGKTTTiaKLA~~~~~~-~~kV~lit~Dt~--R~gA~eQL~~~a~~l~v~~~~~~~~~-----------~~-- 67 (173)
T cd03115 4 LLVGLQGVGKTTTAAKLALYLKKK-GKKVLLVAADTY--RPAAIEQLRVLGEQVGVPVFEEGEGK-----------DP-- 67 (173)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHC-CCEEEEEECCCC--CHHHHHHHHHHHHHCCCEEEECCCCC-----------CH--
T ss_conf 998999998899999999999976-992899974887--57799999999997498599227755-----------87--
Q ss_pred ECHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf 6566731000000002472000025122013654332036999999985137987998316532
Q gi|254780129|r 102 INFENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPS 165 (220)
Q Consensus 102 ~~~~~l~~~~~~~~~~~~~~~iIiDEaH~~kn~~~~~~~k~~k~l~~~~~~~~~~~l~LTgTPi 165 (220)
T Consensus 68 --~~~~~~~~-~~~~~~~~D~IlIDTaGr~--~~d~~~~~el~~l~~~~~-p~~~~LVl~a~~~ 125 (173)
T cd03115 68 --VSIAKRAI-EHAREENFDVVIVDTAGRL--QIDENLMEELKKIKRVVK-PDEVLLVVDAMTG 125 (173)
T ss_pred --HHHHHHHH-HHHHHCCCCEEEEECCCCC--CCCHHHHHHHHHHHHHHC-CCCCEEECCCCCH
T ss_conf --99999999-9987568998999788878--799999999999986448-9721574246550