HHsearch alignment for GI: 254781020 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=99.39  E-value=7.5e-11  Score=82.27  Aligned_cols=206  Identities=16%  Similarity=0.129  Sum_probs=122.0

Q ss_pred             CEEEECHHHHHHHHCHHHHHHHHHHHHHHCCEEECCCCHHH-H-CCHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCHH
Q ss_conf             86850126633430002569999999980990660520221-1-286688899999866401232202752123679989
Q gi|254781020|r   58 PLLISSMTGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVM-F-SDHNAIKSFELRQYAPHTVLISNLGAVQLNYDFGVQ  135 (337)
Q Consensus        58 Pv~iapmsgg~~~~~~~~~~~lA~aa~~~g~~~~~g~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (337)
T Consensus         1 k~~lAPM~g~td~-------~fR~l~~~~g~~~~~TEmv~a~~~~~~~~~~~~~~~~~~~e~p~~~Ql~g~~p~---~~~   70 (231)
T cd02801           1 KLILAPMVGVTDL-------PFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPE---TLA   70 (231)
T ss_pred             CEEEECCCCCCCH-------HHHHHHHHHCCCEEEECCEEEHHHHCCCHHHHHHHCCCCCCCEEEEEECCCCHH---HHH
T ss_conf             9898378998479-------999999998939899798998776538887898724486678079987589899---999


Q ss_pred             HHHHHHHHHCCCEEEECCCCHHHHHHHCCCC-----CHHHHHHHHHHHHHHCCCCEEEEE---CCCC-CCHHHHHHHHHC
Q ss_conf             9998776508985762532035665206885-----243079999999987399717850---4786-688999999976
Q gi|254781020|r  136 KAHQAVHVLGADGLFLHLNPLQEIIQPNGNT-----NFADLSSKIALLSSAMDVPLLLKE---VGCG-LSSMDIELGLKS  206 (337)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~i~~l~~~~~~pii~k~---v~~~-~~~~~~~~a~~a  206 (337)
T Consensus        71 ~aa~~~~~~g~d~IDlN~GCP~~~v~~~g~Ga~Ll~~p~~v~~iv~~~~~~~~ipVsvKiRlg~~~~~~~~~~~~~l~~~  150 (231)
T cd02801          71 EAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDA  150 (231)
T ss_pred             HHHHHHHHCCCCEEEEECCCCHHHHCCCCCCHHHHHCHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHC
T ss_conf             99998875399999983899969970898307876297899999999997569947999970778634799999999976


Q ss_pred             CCCEEEECCCCCCCCCCHHHHCCCCCCCCHHHHHCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHH-CCCEEH
Q ss_conf             9979994588886510012310234432324431063468899999852289879972988888999999983-888523
Q gi|254781020|r  207 GIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIIL-GASLGG  285 (337)
Q Consensus       207 Gad~i~v~~~gG~~~~~~~~~r~~~~~~~~~~~~~gi~~~~al~~~~~~~~~v~IiadGGIr~g~Dv~kAlal-GAdaV~  285 (337)
T Consensus       151 G~~~ltvH~Rt~---------~q--~~~-------~~a~~e~i~~~~~-~~~ipvi~NGdI~s~~d~~~~~~~tg~dgvM  211 (231)
T cd02801         151 GASALTVHGRTR---------EQ--RYS-------GPADWDYIAEIKE-AVSIPVIANGDIFSLEDALRCLEQTGVDGVM  211 (231)
T ss_pred             CCCEEEEECCCH---------HH--CCC-------CCCCHHHHHHHHH-CCCCEEEEECCCCCHHHHHHHHHHHCCCEEE
T ss_conf             998999835614---------41--467-------7622699999986-5997799838909999999999850999999


Q ss_pred             HHHHHHH
Q ss_conf             3479999
Q gi|254781020|r  286 LASPFLK  292 (337)
Q Consensus       286 iGr~~l~  292 (337)
T Consensus       212 igRgal~  218 (231)
T cd02801         212 IGRGALG  218 (231)
T ss_pred             ECHHHHH
T ss_conf             8788876