HHsearch alignment for GI: 254781020 and conserved domain: TIGR00737
>TIGR00737 nifR3_yhdG putative TIM-barrel protein, nifR3 family; InterPro: IPR004652 This family represents one branch of COG0042 from COG (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family) and includes NifR3 itself, from Rhodobacter capsulatus. Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes , and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. ; GO: 0016491 oxidoreductase activity, 0050660 FAD binding, 0008033 tRNA processing.
Probab=97.20 E-value=0.0043 Score=36.60 Aligned_cols=123 Identities=18% Similarity=0.138 Sum_probs=80.3
Q ss_pred CCCHHHHCCHHHHH-HHHHHHHCCC---HHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCHHHHHHHCCCCCH
Q ss_conf 52022112866888-9999986640---1232202752123679989999877650898576253203566520688524
Q gi|254781020|r 93 GSQRVMFSDHNAIK-SFELRQYAPH---TVLISNLGAVQLNYDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNF 168 (337)
Q Consensus 93 g~~~~~~~~~~~~~-~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (337)
T Consensus 116 ~aGsaLl~~p~~~~~iv~~vV~AV~~~~iPVTVK~R~GWD~~h~n~~~~a~~a~~~Ga~Av~lHGRTRaQ------~Y~G 189 (336)
T TIGR00737 116 GAGSALLRDPDLIGKIVKAVVDAVDAQDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQ------GYEG 189 (336)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCEEEHHHHHHCC------CCCC
T ss_conf 6354323586899999999998751876651665515636244888999999987240002111000001------5788
Q ss_pred HHHHHHHHHHHHHCC----CCEEEEECCCCCCHHHHHHHH-HCCCCEEEEC-CCCCCCCCC
Q ss_conf 307999999998739----971785047866889999999-7699799945-888865100
Q gi|254781020|r 169 ADLSSKIALLSSAMD----VPLLLKEVGCGLSSMDIELGL-KSGIRYFDIA-GRGGTSWSR 223 (337)
Q Consensus 169 ~~~~~~i~~l~~~~~----~pii~k~v~~~~~~~~~~~a~-~aGad~i~v~-~~gG~~~~~ 223 (337)
T Consensus 190 ~A~wd~I~~vKq~v~~~GeiPVig--NGDi~~~~~A~~~L~~TG~DGvm~gRG~lG~PWl~ 248 (336)
T TIGR00737 190 EANWDIIARVKQAVRKEGEIPVIG--NGDIFSPEDAKAMLETTGADGVMIGRGALGNPWLF 248 (336)
T ss_pred CCCHHHHHHHHHHHHCCCCCCEEC--CCCCCCHHHHHHHHHHCCCCEEEEECHHCCCCHHH
T ss_conf 760689999999971687533222--77424678999998637886898500222787589