HHsearch alignment for GI: 254780601 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=96.18  E-value=0.11  Score=30.52  Aligned_cols=127  Identities=24%  Similarity=0.253  Sum_probs=65.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCC-HHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
Q ss_conf             99992898746899999999986104212255688279998499-89999999999998544698799998899879999
Q gi|254780601|r   40 VLVSAQTGSGKTVAFGLALASTLLAENDRFSPASAPLALAIAPT-RELAVQVGRELEWLYAKTGVVVAVCIGGVSVHRER  118 (573)
Q Consensus        40 ~i~~a~TGsGKT~af~lp~l~~l~~~~~~~~~~~~~~~lil~PT-rELa~Qv~~~~~~l~~~~~~~v~~~~gg~~~~~q~  118 (573)
T Consensus         3 i~lvGptGvGKTTTia-KLA~~~~~~-------~~kV~lit~Dt~R~gA---~eQL~~~a~~l~v~~~~~~~~~~~~~~~   71 (173)
T cd03115           3 ILLVGLQGVGKTTTAA-KLALYLKKK-------GKKVLLVAADTYRPAA---IEQLRVLGEQVGVPVFEEGEGKDPVSIA   71 (173)
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHHHC-------CCEEEEEECCCCCHHH---HHHHHHHHHHCCCEEEECCCCCCHHHHH
T ss_conf             9998999998899999-999999976-------9928999748875779---9999999997498599227755879999


Q ss_pred             H-HH----CCCC-EEEEECCCCHHHHHHCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCC
Q ss_conf             9-61----2897-5998223101332100012246431899961311001001235788875214334225631111222
Q gi|254780601|r  119 R-DL----QNGA-HIVVGTPGRLCDHIRGKGLNISHLKAVVLDEADEMLDLGFRDDIEFILDSSPKKRRMLMFSATISPA  192 (573)
Q Consensus       119 ~-~l----~~~~-~iiv~TPgrl~d~~~~~~l~l~~v~~lVlDEaD~ml~~gf~~~i~~i~~~~p~~~q~~l~SAT~~~~  192 (573)
T Consensus        72 ~~~~~~~~~~~~D~IlIDTaGr~~~-----------------d~~-------~~~el~~l~~~~~p~~~~LVl~a~~~~~  127 (173)
T cd03115          72 KRAIEHAREENFDVVIVDTAGRLQI-----------------DEN-------LMEELKKIKRVVKPDEVLLVVDAMTGQD  127 (173)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCC-----------------CHH-------HHHHHHHHHHHHCCCCCEEECCCCCHHH
T ss_conf             9999998756899899978887879-----------------999-------9999999986448972157424655065


Q ss_pred             CHHHHHHHC
Q ss_conf             001111210
Q gi|254780601|r  193 ITTLAKNYQ  201 (573)
Q Consensus       193 i~~l~~~~~  201 (573)
T Consensus       128 ~~~~~~~f~  136 (173)
T cd03115         128 AVNQAKAFN  136 (173)
T ss_pred             HHHHHHHHH
T ss_conf             899999987