HHsearch alignment for GI: 254781167 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=100.00 E-value=0 Score=596.14 Aligned_cols=311 Identities=49% Similarity=0.816 Sum_probs=300.4
Q ss_pred CCCCCCHHHHHHHHHHCCCEEEECCCCCCHHHHCCCHHHHHHCCCCCCCEEEEEECCCHHHHHHHHHHHHC-CCCCEEEE
Q ss_conf 97786078999999828982998170332477608978983027457846999826998999998875310-45377744
Q gi|254781167|r 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINL 79 (322)
Q Consensus 1 Mag~Td~~fR~l~r~~~~~~~~~TEmi~a~~l~~~~~~~~~~~~~~e~p~~~Ql~g~~p~~~~~aa~~~~~-~g~~~idl 79 (322)
T Consensus 8 M~d~TdrHfRYf~R~Lsk~~lLYTeMita~aIihgD~~~~l~~~~~E~PvAlQlgg~dp~~l~~ca~i~e~h~gydEiNL 87 (326)
T TIGR00742 8 MLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKDILKFSPEEKPVALQLGGSDPNDLAKCAKIAEKHRGYDEINL 87 (326)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEC
T ss_conf 34330268999999975222003554005778877678875017677865785078988999999999986458742215
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCC------CCCCCHHHHHHHHCCCC-CCHHH
Q ss_conf 256413677666889999855899999999985027906999861134566------53220145543200012-20121
Q gi|254781167|r 80 NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ------IPAVALRNLVKSIKKSG-VNGIW 152 (322)
Q Consensus 80 N~GCP~~~v~~~g~GaaLl~~p~~~~~iv~~~~~~~~~pvsvK~RlG~~~~------~~~~~~~~~~~~~~~~g-~~~it 152 (322)
T Consensus 88 NVGCPSdrvQng~fGACLMg~a~lVa~cv~~M~~~v~iPvtvK~RiGId~~ssdykndSYe~l~~Fv~~v~~~Gec~~Fi 167 (326)
T TIGR00742 88 NVGCPSDRVQNGNFGACLMGNADLVADCVKAMQEAVEIPVTVKHRIGIDELSSDYKNDSYEELCDFVEIVSGKGECQNFI 167 (326)
T ss_pred CCCCCCHHHHCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHH
T ss_conf 66883122204441111116823689999998971578822420147564433223233789999999861788611346
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHH
Q ss_conf 00135664025774212276610467876667388753025777789989888742035234412200012439999998
Q gi|254781167|r 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232 (322)
Q Consensus 153 iH~Rt~~~~g~s~~~~~~~~~~~~~~i~~l~~~~~~~~i~~NGdi~~~~~a~~~l~~~dgvMigRga~~~P~if~~I~~~ 232 (322)
T Consensus 168 vHARkAwL~GlSPKeNR~IPpL~y~~VYqLKkdfp~L~i~INGGI~~~E~~k~HL~~vD~VMvGR~Ay~NP~l~A~~dr~ 247 (326)
T TIGR00742 168 VHARKAWLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHLSHVDGVMVGREAYENPYLLANVDRE 247 (326)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCHHHHHCHHHHHHHHHH
T ss_conf 87899985788862257877987246776520032105633578553599997655643113022430052689999899
Q ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 71998888999889999999999999999999985228767998998999873899989999999862178110699999
Q gi|254781167|r 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312 (322)
Q Consensus 233 l~~~~~~~~p~~~~~~~~~~~~i~~~~~~y~~~~~~~~~~i~~irKhl~~y~kGlpgak~~R~~Ls~~~~~~~~~~~iie 312 (322)
T Consensus 248 ~~~~~~-~~~~--------~~~i~~~M~pYie~~l~~g~~ln~i~rHllg~f~~~~gAk~wRr~Ls~~~~k~~a~~e~l~ 318 (326)
T TIGR00742 248 IFNETD-EILT--------RKEIVEQMLPYIEERLSQGLSLNHITRHLLGLFQGKPGAKQWRRYLSENALKAGAGIEVLE 318 (326)
T ss_pred HHCCCC-CCCC--------HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCHHHHHHCCCHHHHH
T ss_conf 707787-7779--------7999998679999997436223379999999870881047886621514575026826899
Q ss_pred HHHHHHHH
Q ss_conf 99998652
Q gi|254781167|r 313 TAFNLMIE 320 (322)
Q Consensus 313 ~~~~~l~E 320 (322)
T Consensus 319 ~Al~~~~~ 326 (326)
T TIGR00742 319 TALELVKE 326 (326)
T ss_pred HHHHHHCC
T ss_conf 99986139