HHsearch alignment for GI: 254780434 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=99.73 E-value=2e-16 Score=130.47 Aligned_cols=234 Identities=21% Similarity=0.226 Sum_probs=162.6
Q ss_pred ECCEECCCCEEEC--CCC-CCCHHHHHHHHHCC-------CCEEECCCCCCCCCCCCCCCCEEEEECCCCCEEECCCCCC
Q ss_conf 8873359974853--468-88677988874036-------7524102001368789988626884255541000024777
Q gi|254780434|r 49 VAGISLSNPLGMA--AGY-DKNAEVPIELLKLG-------FGFVEIGTVTPHPQAGNPRPRVFRLTKDRAIINKLGFNNA 118 (362)
Q Consensus 49 ~~Gl~~~nPiglA--aG~-dk~~~~~~~l~~~G-------~G~v~~ktit~~p~~GNp~PR~~r~~~~~~iiN~~Gl~N~ 118 (362)
T Consensus 1 IG~~~L~s~V~~APmAGvtD~~FR~l~~~--~~~skvGtvagL~~~EMvs~~~-----------------~~~----~~- 56 (336)
T TIGR00737 1 IGNIQLKSRVVLAPMAGVTDLAFRRLVAE--YGQSKVGTVAGLTVSEMVSSEA-----------------IVY----KS- 56 (336)
T ss_pred CCCCCCCCCEEECCCCCCCCHHHHHHHHH--HCCCCCCCCCCCCEECCCCCHH-----------------HHH----HH-
T ss_conf 98722367656436778767178999998--5214433124100222004537-----------------886----23-
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCC------CCCCCCCCCHHHHHHHH
Q ss_conf 778899987641000121000110454246788776555420675526983033365------32211000023432111
Q gi|254780434|r 119 GYHTVFSRLSKIQPTSPIGINLGANKDSKDFILDYVSGIRLFFTIASYFTINISSPN------TPGLRSLQKKKNLERLL 192 (362)
Q Consensus 119 G~~~~~~~l~~~~~~~pi~vsI~~~~~s~~~~~dy~~~~~~~~~~aD~iEiNiSCPN------t~g~~~~~~~~~l~~~l 192 (362)
T Consensus 57 -r~~~~~~~~~~~~~~~~~~Ql~Gs~--P~~~aeAAk~i~-~~~ga~~IDiN~GCP~~Kitk~~aGsaLl~~p~~~~~iv 132 (336)
T TIGR00737 57 -RERTKKLLDIDEDETPISVQLFGSD--PDTMAEAAKLIN-EELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIV 132 (336)
T ss_pred -HHHHHHHHHHCCCCCCCEEEEECCC--HHHHHHHHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf -5557765321258885478764788--268999999985-305898885367654884216763543235868999999
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEC--CCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 122444556553126885178650--577774888999998764498299980665553234577544632211356454
Q gi|254780434|r 193 IHVMQTREEEKIKTGKFVPIFLKI--SPDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGGLSGSPLF 270 (362)
Q Consensus 193 ~~v~~~~~~~~~~~~~~~Pi~vKL--sPd~~~~~i~~ia~~a~~~g~dGiv~~NT~~~~~~~~~~~~~~~~GGlSG~~i~ 270 (362)
T Consensus 133 ~~vV~AV~~------~~iPVTVK~R~GWD~~h~n~~~~a~~a~~~Ga~Av~l----HGRTR---------aQ~Y~G~A~- 192 (336)
T TIGR00737 133 KAVVDAVDA------QDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTL----HGRTR---------AQGYEGEAN- 192 (336)
T ss_pred HHHHHHHCC------CCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCEEEH----HHHHH---------CCCCCCCCC-
T ss_conf 999987518------7665166551563624488899999998724000211----10000---------015788760-
Q ss_pred HHHHHHHHHHHHHCCCC--EEEEEECCCCCHHHHHHHHHC-CCCEEEECHHHHCCCHHHHHHHHHHH
Q ss_conf 24689999999740897--489996788999999999983-99975452787706978999999999
Q gi|254780434|r 271 LKSTIALAKIRQRVGPK--IAIIGTGGISSTKDALDKIMA-GANLIQLYSAMIYEGISLPKRIIQGL 334 (362)
Q Consensus 271 ~~al~~i~~i~~~~~~~--i~IIg~GGI~s~~Da~e~l~a-GAs~VQi~Tali~~Gp~~~~~I~~~L 334 (362)
T Consensus 193 ---wd~I~~vKq~v~~~GeiPVigNGDi~~~~~A~~~L~~TG~DGvm~gRG~-lG~PWl~~~i~~yL 255 (336)
T TIGR00737 193 ---WDIIARVKQAVRKEGEIPVIGNGDIFSPEDAKAMLETTGADGVMIGRGA-LGNPWLFKQIEQYL 255 (336)
T ss_pred ---HHHHHHHHHHHHCCCCCCEECCCCCCCHHHHHHHHHHCCCCEEEEECHH-CCCCHHHHHHHHHH
T ss_conf ---6899999999716875332227742467899999863788689850022-27875899999997