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