HHsearch alignment for GI: 254780146 and conserved domain: cd00403

>cd00403 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Probab=100.00  E-value=0  Score=350.02  Aligned_cols=200  Identities=47%  Similarity=0.783  Sum_probs=190.8

Q ss_pred             HHHHHHHHHHCC--CCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCCCEEEEECHHHHHHHHHCCCCCCCHHHH
Q ss_conf             899999998608--789986299999953787645443013799527788654069997504457687412000027899
Q gi|254780146|r   24 LSDAVVMLKERA--TARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDL  101 (232)
Q Consensus        24 i~eAi~~lk~~~--~~kf~esvel~i~L~id~~k~~~~irg~v~LPh~~gk~~kV~Vf~~~~~~~~Ak~aGa~~vg~~el  101 (232)
T Consensus         1 ~~~Aik~l~~~~~~~~~~~~~v~l~i~l~~~~~~~~~~~~~~v~LPh~~~~~~~i~v~~~~~~~~~a~~~ga~vvg~~~L   80 (208)
T cd00403           1 LEEAIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGEDL   80 (208)
T ss_pred             CHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHCCCCEECHHHH
T ss_conf             96899999970667788663499999827988987765789998899999860899975788789998769857358999


Q ss_pred             HHHHHCCC-----CCCCEEEECHHHHHHHHH-HHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEE
Q ss_conf             99975175-----333468864467788886-433200100174223356665579999998601110223575267875
Q gi|254780146|r  102 FEIVKGGQ-----IDFDRCIATPDMMPLVGR-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAG  175 (232)
Q Consensus       102 i~~i~~~~-----~~fd~~iAt~~~m~~i~k-lgriLGPkglMPn~k~GTv~~di~~~i~~~k~g~i~~r~~k~g~i~~~  175 (232)
T Consensus        81 ~~~~k~~~~kkl~~~fD~fla~~~~~~~l~~~LGk~l~~k~kmP~~~~~t~~~dl~~~i~~~~~-~~~~~~~~~~~~~v~  159 (208)
T cd00403          81 KKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKS-SVEFRLDKGGCIHVP  159 (208)
T ss_pred             HHHHHCCHHHHHHHCCCEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHC-CEEEEECCCCEEEEE
T ss_conf             9887563156676328999987899899998751452103788855368774659999998738-489998899748876


Q ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf             31577898999999999999998608662544337799999238972774
Q gi|254780146|r  176 IGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKV  225 (232)
Q Consensus       176 IG~~~m~~e~i~eNi~~~~~~i~~~kp~~~kg~~Ik~v~lssTmGp~i~i  225 (232)
T Consensus       160 VG~~~m~~e~l~eNi~a~~~~i~~~~p~-~~~~~I~~v~lktt~~~~l~I  208 (208)
T cd00403         160 VGKVSMSPEQLVENIEAVINALVKKLPS-KKGQNIKSIYLKTTMGPSLPI  208 (208)
T ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHCCC-CCCCEEEEEEEECCCCCCEEC
T ss_conf             6136699999999999999999984787-567629899998999986479