HHsearch alignment for GI: 254781020 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=96.71 E-value=0.038 Score=31.03 Aligned_cols=191 Identities=13% Similarity=0.104 Sum_probs=113.9
Q ss_pred CCHHHHHCCCCCCCCCCCCHHHHHHHHHH-HCCCEEEECCCCHHHHHHHCC-----CCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf 40123220275212367998999987765-089857625320356652068-----852430799999999873997178
Q gi|254781020|r 115 PHTVLISNLGAVQLNYDFGVQKAHQAVHV-LGADGLFLHLNPLQEIIQPNG-----NTNFADLSSKIALLSSAMDVPLLL 188 (337)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~i~~l~~~~~~pii~ 188 (337)
T Consensus 53 ~E~PvAlQlgg~dp---~~l~~ca~i~e~h~gydEiNLNVGCPSdrvQng~fGACLMg~a~lVa~cv~~M~~~v~iPvtv 129 (326)
T TIGR00742 53 EEKPVALQLGGSDP---NDLAKCAKIAEKHRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQEAVEIPVTV 129 (326)
T ss_pred CCCCEEEEECCCCH---HHHHHHHHHHHHHCCCCEEECCCCCCCHHHHCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCEE
T ss_conf 77865785078988---999999999986458742215668831222044411111168236899999989715788224
Q ss_pred E---ECCCC------CCHHHHHHHHHCCCCEEEECCCC-CCCCCCHHHHCCCCCCCCHHHHHCCCCHHH--HHHHHHHHC
Q ss_conf 5---04786------68899999997699799945888-865100123102344323244310634688--999998522
Q gi|254781020|r 189 K---EVGCG------LSSMDIELGLKSGIRYFDIAGRG-GTSWSRIESHRDLESDIGIVFQDWGIPTPL--SLEMARPYC 256 (337)
Q Consensus 189 k---~v~~~------~~~~~~~~a~~aGad~i~v~~~g-G~~~~~~~~~r~~~~~~~~~~~~~gi~~~~--al~~~~~~~ 256 (337)
T Consensus 130 K~RiGId~~ssdykndSYe~l~~Fv~~------v~~~Gec~~F--ivHARkAwL~GlSPKeNR~IPpL~y~~VYqLKkdf 201 (326)
T TIGR00742 130 KHRIGIDELSSDYKNDSYEELCDFVEI------VSGKGECQNF--IVHARKAWLSGLSPKENREIPPLRYERVYQLKKDF 201 (326)
T ss_pred EECCCCCCCCCCCCCCCHHHHHHHHHH------HHCCCCCCHH--HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCC
T ss_conf 201475644332232337899999998------6178861134--68789998578886225787798724677652003
Q ss_pred CCCEEEECCCCCCHHHHHHHHHHCCCEEHHHHHH-----HHHH------------CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8987997298888899999998388852334799-----9984------------14668999999999999999999
Q gi|254781020|r 257 NEAQFIASGGLRNGVDILKSIILGASLGGLASPF-----LKPA------------MDSSDAVVAAIESLRKEFIVSMF 317 (337)
Q Consensus 257 ~~v~IiadGGIr~g~Dv~kAlalGAdaV~iGr~~-----l~~~------------~~G~~gv~~~l~~l~~el~~~m~ 317 (337)
T Consensus 202 p~L~i~INGGI~~~E~~k~HL~~-vD~VMvGR~Ay~NP~l~A~~dr~~~~~~~~~~~~~~i~~~M~pYie~~l~~g~~ 278 (326)
T TIGR00742 202 PHLTIEINGGIKNSEQIKQHLSH-VDGVMVGREAYENPYLLANVDREIFNETDEILTRKEIVEQMLPYIEERLSQGLS 278 (326)
T ss_pred CCCEEEECCCCCCHHHHHHHHHH-HHHHHHCHHHHHCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf 21056335785535999976556-431130224300526899998997077877779799999867999999743622