HHsearch alignment for GI: 254780928 and conserved domain: cd00862

>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=99.11  E-value=4.6e-09  Score=78.04  Aligned_cols=109  Identities=22%  Similarity=0.282  Sum_probs=88.3

Q ss_pred             CCCCCCCCEEEEEEECCC----HHHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEECHHHHHCCC
Q ss_conf             766555771489982697----6899999999999998798399971899998899999987799899998872874881
Q gi|254780928|r  369 TNNIKEMGPVLITTMDHD----SDSLSKYQMYTQMLRTAGIRAEMFLGSSKNFGNQLKYADRRNCPLAIIQGTGERSRGM  444 (496)
Q Consensus       369 ~~~~~~~~~v~V~~~~~~----~~~~~~~~~ia~~Lr~~Gi~~e~~~~~~~sl~~~~~~A~~~g~~~viiig~~e~~~~~  444 (496)
T Consensus         4 lPP~iAP~QVVIiPi~~k~~~~~~v~~~~~~i~~~L~~~~iRv~iD~rd~~~pG~K~~~wE~kGVPiRIEIGprDle~~~   83 (202)
T cd00862           4 LPPRVAPIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFNDWELKGVPLRIEIGPRDLEKNT   83 (202)
T ss_pred             CCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHCCCEEEEECHHHHHCCC
T ss_conf             68420585499997348723289999999999999986798899977878688888899998089779998715863791


Q ss_pred             EEEEECCCCCEEEEECCCHHHHHHCCCCCEEECHHHHHHHHHHHHHHHHHC
Q ss_conf             899787888364331120144320233510307999999999999864204
Q gi|254780928|r  445 LQIKDLAKGKELSREIKNNESWREARVAQITIPISELVSTVKKILQENKEE  495 (496)
Q Consensus       445 v~vK~l~~g~q~~~~~~~~~~~~~~~~~q~~v~~~~l~~~~~~~l~~~~~~  495 (496)
T Consensus        84 v~v~rRD~~~K------------------~~v~~~el~~~i~~~L~~iq~~  116 (202)
T cd00862          84 VVIVRRDTGEK------------------KTVPLAELVEKVPELLDEIQED  116 (202)
T ss_pred             EEEEEECCCCE------------------EEEEHHHHHHHHHHHHHHHHHH
T ss_conf             89999179957------------------8978899999999999999999