HHsearch alignment for GI: 254780434 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=99.65  E-value=1.5e-14  Score=117.90  Aligned_cols=176  Identities=22%  Similarity=0.257  Sum_probs=126.7

Q ss_pred             HHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCC-CCCEEEEECCCCCC------CCCCCCCCHHHHHHHHHHHH
Q ss_conf             998764100012100011045424678877655542067-55269830333653------22110000234321111224
Q gi|254780434|r  124 FSRLSKIQPTSPIGINLGANKDSKDFILDYVSGIRLFFT-IASYFTINISSPNT------PGLRSLQKKKNLERLLIHVM  196 (362)
Q Consensus       124 ~~~l~~~~~~~pi~vsI~~~~~s~~~~~dy~~~~~~~~~-~aD~iEiNiSCPNt------~g~~~~~~~~~l~~~l~~v~  196 (362)
T Consensus        45 ~~~~~~~~~e~p~~~Ql~g~~-----p~~~~~aa~~~~~~g~d~IDlN~GCP~~~v~~~g~Ga~Ll~~p~~v~~iv~~~~  119 (231)
T cd02801          45 LRLLTRNPEERPLIVQLGGSD-----PETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVR  119 (231)
T ss_pred             HHHHCCCCCCCEEEEEECCCC-----HHHHHHHHHHHHHCCCCEEEEECCCCHHHHCCCCCCHHHHHCHHHHHHHHHHHH
T ss_conf             987244866780799875898-----999999999887539999998389996997089830787629789999999999


Q ss_pred             HHHHHHHHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             445565531268851786505--777748889999987644982999806655532345775446322113564542468
Q gi|254780434|r  197 QTREEEKIKTGKFVPIFLKIS--PDLSEEELDDIAVEVLSHKVEGIIVSNTTLSRKGVQCSDNHEQDGGLSGSPLFLKST  274 (362)
Q Consensus       197 ~~~~~~~~~~~~~~Pi~vKLs--Pd~~~~~i~~ia~~a~~~g~dGiv~~NT~~~~~~~~~~~~~~~~GGlSG~~i~~~al  274 (362)
T Consensus       120 ~~---------~~ipVsvKiRlg~~~-~~~~~~~~~~l~~~G~~~ltvH~----Rt~~q---------~~~~~a----~~  172 (231)
T cd02801         120 EA---------VPIPVTVKIRLGWDD-EEETLELAKALEDAGASALTVHG----RTREQ---------RYSGPA----DW  172 (231)
T ss_pred             HH---------CCCCEEEEEEECCCC-HHHHHHHHHHHHHCCCCEEEEEC----CCHHH---------CCCCCC----CH
T ss_conf             75---------699479999707786-34799999999976998999835----61441---------467762----26


Q ss_pred             HHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHC-CCCEEEECHHHHCCCHHHHHHHHHHH
Q ss_conf             9999999740897489996788999999999983-99975452787706978999999999
Q gi|254780434|r  275 IALAKIRQRVGPKIAIIGTGGISSTKDALDKIMA-GANLIQLYSAMIYEGISLPKRIIQGL  334 (362)
Q Consensus       275 ~~i~~i~~~~~~~i~IIg~GGI~s~~Da~e~l~a-GAs~VQi~Tali~~Gp~~~~~I~~~L  334 (362)
T Consensus       173 e~i~~~~~~~--~ipvi~NGdI~s~~d~~~~~~~tg~dgvMigRgal~n-P~iF~~i~~~~  230 (231)
T cd02801         173 DYIAEIKEAV--SIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGN-PWLFREIKELL  230 (231)
T ss_pred             HHHHHHHHCC--CCEEEEECCCCCHHHHHHHHHHHCCCEEEECHHHHHC-CHHHHHHHHHH
T ss_conf             9999998659--9779983890999999999985099999987888769-88999999975