HHsearch alignment for GI: 254780434 and conserved domain: TIGR00742

>TIGR00742 yjbN TIM-barrel protein, yjbN family; InterPro: IPR004653 This family represents one branch of COG0042 from COG (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family) although NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family catalyse 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 . They show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase.; GO: 0016491 oxidoreductase activity, 0050660 FAD binding, 0008033 tRNA processing.
Probab=98.28  E-value=8.3e-06  Score=58.95  Aligned_cols=201  Identities=18%  Similarity=0.211  Sum_probs=134.5

Q ss_pred             HHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHCCC--CCEEEEECCCC-----CCC-CCCCCCCHHHHHHHHHHHHHH
Q ss_conf             7641000121000110454246788776555420675--52698303336-----532-211000023432111122444
Q gi|254780434|r  127 LSKIQPTSPIGINLGANKDSKDFILDYVSGIRLFFTI--ASYFTINISSP-----NTP-GLRSLQKKKNLERLLIHVMQT  198 (362)
Q Consensus       127 l~~~~~~~pi~vsI~~~~~s~~~~~dy~~~~~~~~~~--aD~iEiNiSCP-----Nt~-g~~~~~~~~~l~~~l~~v~~~  198 (362)
T Consensus        48 l~~~~~E~PvAlQlgg~d-----p~~l~~ca~i~e~h~gydEiNLNVGCPSdrvQng~fGACLMg~a~lVa~cv~~M~~-  121 (326)
T TIGR00742        48 LKFSPEEKPVALQLGGSD-----PNDLAKCAKIAEKHRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQE-  121 (326)
T ss_pred             HCCCCCCCCEEEEECCCC-----HHHHHHHHHHHHHHCCCCEEECCCCCCCHHHHCCCCCHHHCCCHHHHHHHHHHHHH-
T ss_conf             501767786578507898-----89999999999864587422156688312220444111111682368999999897-


Q ss_pred             HHHHHHHCCCCCEEEEEC-------CCC---CCHHHHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             556553126885178650-------577---77488899999876449-829998066555323457754463221135-
Q gi|254780434|r  199 REEEKIKTGKFVPIFLKI-------SPD---LSEEELDDIAVEVLSHK-VEGIIVSNTTLSRKGVQCSDNHEQDGGLSG-  266 (362)
Q Consensus       199 ~~~~~~~~~~~~Pi~vKL-------sPd---~~~~~i~~ia~~a~~~g-~dGiv~~NT~~~~~~~~~~~~~~~~GGlSG-  266 (362)
T Consensus       122 --------~v~iPvtvK~RiGId~~ssdykndSYe~l~~Fv~~v~~~Gec~~Fiv----HARkAw--------L~GlSPK  181 (326)
T TIGR00742       122 --------AVEIPVTVKHRIGIDELSSDYKNDSYEELCDFVEIVSGKGECQNFIV----HARKAW--------LSGLSPK  181 (326)
T ss_pred             --------HCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHH----HHHHHH--------HCCCCCC
T ss_conf             --------15788224201475644332232337899999998617886113468----789998--------5788862


Q ss_pred             --CCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             --645424689999999740897489996788999999999983999754527877069789999999999999983899
Q gi|254780434|r  267 --SPLFLKSTIALAKIRQRVGPKIAIIGTGGISSTKDALDKIMAGANLIQLYSAMIYEGISLPKRIIQGLSDFLNKENEV  344 (362)
Q Consensus       267 --~~i~~~al~~i~~i~~~~~~~i~IIg~GGI~s~~Da~e~l~aGAs~VQi~Tali~~Gp~~~~~I~~~L~~~l~~~G~~  344 (362)
T Consensus       182 eNR~IPpL~y~~VYqLKkdf-p~L~i~INGGI~~~E~~k~HL~~-vD~VMvGR~-Ay~NP~l~A~~dr~~~~--~~~~~~  256 (326)
T TIGR00742       182 ENREIPPLRYERVYQLKKDF-PHLTIEINGGIKNSEQIKQHLSH-VDGVMVGRE-AYENPYLLANVDREIFN--ETDEIL  256 (326)
T ss_pred             CCCCCCCCCCHHHHHHHCCC-CCCEEEECCCCCCHHHHHHHHHH-HHHHHHCHH-HHHCHHHHHHHHHHHHC--CCCCCC
T ss_conf             25787798724677652003-21056335785535999976556-431130224-30052689999899707--787777


Q ss_pred             CHHHHHCCCCHHHH
Q ss_conf             77896169752664
Q gi|254780434|r  345 NFENIRGSYTEYWA  358 (362)
Q Consensus       345 si~e~iG~~~~~~~  358 (362)
T Consensus       257 ~~~~i~~~M~pYie  270 (326)
T TIGR00742       257 TRKEIVEQMLPYIE  270 (326)
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             97999998679999