HHsearch alignment for GI: 254780325 and conserved domain: cd04661

>cd04661 MRP_L46 Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the Nudix hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. MRP L46 appears to contain a modified nudix motif.
Probab=98.49  E-value=9.4e-07  Score=59.33  Aligned_cols=98  Identities=28%  Similarity=0.398  Sum_probs=67.5

Q ss_pred             CEEEEEEECCCCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCC--EEEEEEEECCCCC-------CEEEEEE
Q ss_conf             869999917898889838225731017874889999888876265202442--0255665205788-------6069999
Q gi|254780325|r   22 GKVLLSCRPKDKSHGEFWEFPGGKIEDGETPEEALTRELFEELAIVVKPFS--LVPLTFISHPYEK-------FHLLMPF   92 (141)
Q Consensus        22 ~~iLl~~R~~~~~~~g~W~lPGG~ve~gEs~~~a~~REv~EEtgi~~~~~~--~~~~~~~~~~~~~-------~~~~~~~   92 (141)
T Consensus        13 tLyLlVk~k~--g~~~~W~fP~~~~~~~EtLr~~Aer~L~~~~G~~~~~~~vgnaP~g~~k~k~p~~~~~~~~~G~K~Ff   90 (132)
T cd04661          13 TLVLLVQQKV--GSQNHWILPQGKREEGETLRQTAERTLKELCGNNLKAKFYGNAPVGFYKYKYPKAVRNEGIVGAKVFF   90 (132)
T ss_pred             EEEEEEEECC--CCCCEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCEEEEEEECCCCCCCCCCCCEEEEE
T ss_conf             3999999537--98888028842466785489999999998607773678962687588987568522444666347999


Q ss_pred             EEEEEECCEECCC-HHHEEEECCHHHHCCC
Q ss_conf             9999754837688-2331570277883248
Q gi|254780325|r   93 FVCHCFEGIPQSC-EGQQLQWVALDDLQNY  121 (141)
Q Consensus        93 ~~~~~~~~~~~~~-E~~~~~Wi~~~el~~~  121 (141)
T Consensus        91 ~ka~~~~G~~~~~~~~~df~Wltk~EL~~~  120 (132)
T cd04661          91 FKARYMSGQFELSQNQVDFKWLAKEELQKY  120 (132)
T ss_pred             EEEEEECCCCCCCCCCCEEEECCHHHHHHH
T ss_conf             999995586465677520387089999876