HHsearch alignment for GI: 254780975 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=95.68  E-value=0.2  Score=29.47  Aligned_cols=175  Identities=15%  Similarity=0.133  Sum_probs=99.1

Q ss_pred             HHHCCCCEEEEEEECCEECCCCCCCH-HHHHHHHH-CCCCEEEEEEEEEECCHHH---HHHCCCCCCEEEEECCC-----
Q ss_conf             99659989999734263458434178-99998641-2564168567885120336---76404776079997066-----
Q gi|254780975|r   26 ITKAGAKQIHFDVMDGCFVPNISFGA-DVIRSLRS-YSDSVFDCHLMISSIDSHI---NIIADAGCDIITFHPES-----   95 (224)
Q Consensus        26 l~~~~~d~iHiDImDg~fvpn~~~~~-~~i~~i~~-~t~~~~dvHLMv~~P~~~i---~~~~~~g~d~i~~H~E~-----   95 (224)
T Consensus        19 ~~~~g~~~~~T---Emv~a~~~~~~~~~~~~~~~~~~~e~p~~~Ql~g~~p~~~~~aa~~~~~~g~d~IDlN~GCP~~~v   95 (231)
T cd02801          19 CRRYGADLVYT---EMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKV   95 (231)
T ss_pred             HHHHCCCEEEE---CCEEEHHHHCCCHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHH
T ss_conf             99989398997---989987765388878987244866780799875898999999999887539999998389996997


Q ss_pred             ---------CCC---HHHHHHHHHHC-CCEEEEEEECCC----CHHHHHHHHHHCCEEEEEEEECCCCCCCCCC-HHHHH
Q ss_conf             ---------421---58999867764-982599852333----4478998862014028998306776533220-13577
Q gi|254780975|r   96 ---------SPH---IRRSLRTIHAM-GKKTGVAINPET----PVAILEDVIDEIDMILIMTVNPGFGGQQLIE-STIPK  157 (224)
Q Consensus        96 ---------~~~---~~~~i~~i~~~-g~k~Giai~p~T----~~~~i~~~l~~~D~vliM~V~PG~~Gq~f~~-~~l~k  157 (224)
T Consensus        96 ~~~g~Ga~Ll~~p~~v~~iv~~~~~~~~ipVsvKiRlg~~~~~~~~~~~~~l~~~-G~~~ltvH~Rt~~q~~~~~a~~e~  174 (231)
T cd02801          96 TKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDA-GASALTVHGRTREQRYSGPADWDY  174 (231)
T ss_pred             CCCCCCHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHC-CCCEEEEECCCHHHCCCCCCCHHH
T ss_conf             0898307876297899999999997569947999970778634799999999976-998999835614414677622699


Q ss_pred             HHHHHHHHHCCCCEEEEECCCC-HHHHHHHHH-CCCCEEEECHHHHCCCCHH
Q ss_conf             8998654313865269815899-889999996-7998999742663789989
Q gi|254780975|r  158 IRQAKALIGKRSISLEVDGGVT-SRNIKSLVQ-AGADLLVVGSSFFNQKGEI  207 (224)
Q Consensus       158 I~~l~~~~~~~~~~I~vDGGvn-~~~i~~l~~-~Gad~~V~Gsaif~~~d~~  207 (224)
T Consensus       175 i~~~~~---~~~ipvi~NGdI~s~~d~~~~~~~tg~dgvMigRgal~nP~iF  223 (231)
T cd02801         175 IAEIKE---AVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLF  223 (231)
T ss_pred             HHHHHH---CCCCEEEEECCCCCHHHHHHHHHHHCCCEEEECHHHHHCCHHH
T ss_conf             999986---5997799838909999999999850999999878887698899