HHsearch alignment for GI: 254780877 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=96.66  E-value=0.0014  Score=48.00  Aligned_cols=84  Identities=23%  Similarity=0.354  Sum_probs=40.1

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCCC--CCCCCCH---HHHCCCCCCCHHHCCCCHHCCCCCCCCCCHHH-------H
Q ss_conf             8987267861688999999987237765--3002244---77403453201304771120356677421132-------2
Q gi|254780877|r  600 SFMFLGPTGVGKTELVKSLARLLFDDEN--SMIRIDM---SEYMEKHSVSRLIGSPPGYVGYEEGGALTEAV-------R  667 (853)
Q Consensus       600 ~flf~GptGvGKTelak~la~~lf~~~~--~lir~dM---sey~e~~~vs~LiGappGYvG~~~gg~Lte~v-------r  667 (853)
T Consensus         2 Vi~lvGptGvGKTTTiaKLA~~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~v~-~~~~~~-~~~~~~~~~~~~~~~~   79 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVP-VFEEGE-GKDPVSIAKRAIEHAR   79 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHCCCE-EEECCC-CCCHHHHHHHHHHHHH
T ss_conf             99998999998899999999999976992899974887577999999999974985-992277-5587999999999987


Q ss_pred             CCCCCEEEEHHHHHCCHH
Q ss_conf             156410220214414989
Q gi|254780877|r  668 RHPYQVVLFDEIEKAHSD  685 (853)
Q Consensus       668 ~~P~sVil~DEiEKah~~  685 (853)
T Consensus        80 ~~~~D~IlIDTaGr~~~d   97 (173)
T cd03115          80 EENFDVVIVDTAGRLQID   97 (173)
T ss_pred             HCCCCEEEEECCCCCCCC
T ss_conf             568998999788878799