HHsearch alignment for GI: 254780276 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=95.82  E-value=0.15  Score=31.96  Aligned_cols=186  Identities=11%  Similarity=0.123  Sum_probs=101.6

Q ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             99999999999769989998672325010899999998654311012344300367410278999975343210244320
Q gi|254780276|r   22 DAFVEHIEWQITEGSGGLVPAGTTGESSTLSHEEHCRIIELCVKTVASRVPVMAGIGSNNTRESVELAQYAHSIGADALL  101 (292)
Q Consensus        22 ~~~~~~i~~l~~~gv~gi~~~G~tGE~~~Ls~~Er~~~~~~~~~~~~~r~pii~gv~~~~~~~~i~~a~~a~~~Gad~i~  101 (292)
T Consensus        13 ~~fR~l~~~~---g~~~~~TEmv~a~~~~~~~~~~----~~~~~~~~~e~p~~~Ql~g~~p~~~~~aa~~~~~~g~d~ID   85 (231)
T cd02801          13 LPFRLLCRRY---GADLVYTEMISAKALLRGNRKR----LRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGID   85 (231)
T ss_pred             HHHHHHHHHH---CCCEEEECCEEEHHHHCCCHHH----HHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             9999999998---9398997989987765388878----98724486678079987589899999999988753999999


Q ss_pred             E--ECCCC----------CCCCHHHHHHHHHHHHHHHCCCCEEEECHHHCCCCCC---HHHHHHHHHHCCHHHHHH----
Q ss_conf             0--12343----------3431788999999987530233012100111112111---068999743203023310----
Q gi|254780276|r  102 V--VIPYY----------NKPNRRGLLAHFGEIATTVSSPIYIYNNPSRTVIEMD---VDTMAELAATYPNIVGVK----  162 (292)
Q Consensus       102 v--~~P~~----------~~~~~~~i~~~~~~i~~~~~~pi~iYn~P~~~g~~~~---~~~l~~L~~~~pni~giK----  162 (292)
T Consensus        86 lN~GCP~~~v~~~g~Ga~Ll~~p~~v~~iv~~~~~~~~ipVsvK---iRlg~~~~~~~~~~~-~~l~~~G-~~~ltvH~R  160 (231)
T cd02801          86 LNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVK---IRLGWDDEEETLELA-KALEDAG-ASALTVHGR  160 (231)
T ss_pred             EECCCCHHHHCCCCCCHHHHHCHHHHHHHHHHHHHHCCCCEEEE---EEECCCCHHHHHHHH-HHHHHCC-CCEEEEECC
T ss_conf             83899969970898307876297899999999997569947999---970778634799999-9999769-989998356


Q ss_pred             ------CCCCCHHHHHHHHHHCCCCEEECCCCCC---CHHHHHH-HCCCCCCCCCCCC-CCCHHHHHHH
Q ss_conf             ------0122113589999735984032013221---0012432-0334455222232-1100244444
Q gi|254780276|r  163 ------DATGKIELVSEQRLSCGFDFIQLSGEDS---SALGFNA-HGGVGCISVTANV-VPRICAEFQQ  220 (292)
Q Consensus       163 ------~~~~~~~~~~~~~~~~~~~~~v~~G~~~---~~~~~~~-~G~~G~is~~~n~-~P~~~~~l~~  220 (292)
T Consensus       161 t~~q~~~~~a~~e~i~~~~~~~~ip-vi~NGdI~s~~d~~~~~~~tg~dgvMigRgal~nP~iF~~i~~  228 (231)
T cd02801         161 TREQRYSGPADWDYIAEIKEAVSIP-VIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKE  228 (231)
T ss_pred             CHHHCCCCCCCHHHHHHHHHCCCCE-EEEECCCCCHHHHHHHHHHHCCCEEEECHHHHHCCHHHHHHHH
T ss_conf             1441467762269999998659977-9983890999999999985099999987888769889999999