HHsearch alignment for GI: 254780438 and conserved domain: cd02801

>cd02801 DUS_like_FMN Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze 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. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.
Probab=90.58  E-value=1.3  Score=25.70  Aligned_cols=197  Identities=12%  Similarity=0.130  Sum_probs=104.3

Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCC--HHHHHHHHHHHCCCCCCCEE--EEEECCCHHHHHHHHHHCCCEEEEE-----
Q ss_conf             99999997499899982478833488--89999988740001367415--8883485689999985072128971-----
Q gi|254780438|r   28 HIGKIALQSGASGLTVHPRPDQRHIR--YTDLPEIRRLIDEQFPKAEL--NIEGYPNETFLNLCERYKPEQITLV-----   98 (261)
Q Consensus        28 ~~a~~~~~~GadgITvH~R~DrRHI~--~~Dv~~l~~~~~~~~~~~el--NiEg~p~~e~i~ia~~ikP~qvtLV-----   98 (261)
T Consensus        14 ~fR~l~~~~g~~-~~~TEmv~a~~~~~~~~~~~~~~~~~~---~e~p~~~Ql~g~~p~~~~~aa~~~~~~g~d~IDlN~G   89 (231)
T cd02801          14 PFRLLCRRYGAD-LVYTEMISAKALLRGNRKRLRLLTRNP---EERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMG   89 (231)
T ss_pred             HHHHHHHHHCCC-EEEECCEEEHHHHCCCHHHHHHHCCCC---CCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             999999998939-899798998776538887898724486---6780799875898999999999887539999998389


Q ss_pred             -ECCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-CCEEEEEE----CCC-CCCHHHHHHHHCCCCEEEECCCCCHHHHHH
Q ss_conf             -01655533357822133378899999862026-96389972----544-441479999740661465112111024443
Q gi|254780438|r   99 -PDDPHQLTSDHGWDFLQNQALLTKTVARLHNL-GSRISLFA----DGN-GNEHSLQAAKLTGADCIELYTGPYGACYNN  171 (261)
Q Consensus        99 -Pe~r~elTTegGldv~~~~~~L~~~i~~l~~~-girvSLFI----Dpd-~~q~~i~~a~~~Gad~VElhTG~Ya~a~~~  171 (261)
T Consensus        90 CP~~~-v~~~g~Ga~Ll~~p~~v~~iv~~~~~~~~ipVsvKiRlg~~~~~~~~~~~~~l~~~G~~~ltvH~Rt~~q~~~~  168 (231)
T cd02801          90 CPSPK-VTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQRYSG  168 (231)
T ss_pred             CCHHH-HCCCCCCHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCHHHCCCC
T ss_conf             99699-70898307876297899999999997569947999970778634799999999976998999835614414677


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHCCCCEEEEEHHHHHHH-HHHHHHH
Q ss_conf             5643366688999876654156235207898987799999736996388425999999-9994099
Q gi|254780438|r  172 PQQERIFLNKLAITAQLAQKMDLQINAGHDLTIQNIPNLINAIPYISEISVGHAFAAT-ALECGVK  236 (261)
Q Consensus       172 ~~~~~~el~~i~~aa~~A~~lgL~VnAGHgLn~~Nl~~~i~~Ip~I~EvsIGHaiIse-Al~~GL~  236 (261)
T Consensus       169 ~a~----~e~i~~~~~-~~~ipvi~NGd-I~s~~d~~~~~~-~tg~dgvMigRgal~nP~iF~~i~  227 (231)
T cd02801         169 PAD----WDYIAEIKE-AVSIPVIANGD-IFSLEDALRCLE-QTGVDGVMIGRGALGNPWLFREIK  227 (231)
T ss_pred             CCC----HHHHHHHHH-CCCCEEEEECC-CCCHHHHHHHHH-HHCCCEEEECHHHHHCCHHHHHHH
T ss_conf             622----699999986-59977998389-099999999998-509999998788876988999999