HHsearch alignment for GI: 254781167 and conserved domain: cd02940

>cd02940 DHPD_FMN Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.
Probab=99.68  E-value=1.9e-16  Score=141.05  Aligned_cols=175  Identities=23%  Similarity=0.341  Sum_probs=140.4

Q ss_pred             CCCEEEEEEC-CCHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEC
Q ss_conf             7846999826-998999998875310453777442564136776668899998558999999999850279069998611
Q gi|254781167|r   47 EKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI  125 (322)
Q Consensus        47 e~p~~~Ql~g-~~p~~~~~aa~~~~~~g~~~idlN~GCP~~~v~~~g~GaaLl~~p~~~~~iv~~~~~~~~~pvsvK~Rl  125 (322)
T Consensus        99 ~~~~i~si~~~~~~~~~~~~a~~~~~~gad~lElNiScPN-~~~~~~~g~~~~~~~~~l~~i~~~v~~~~~~Pi~vKLs-  176 (299)
T cd02940          99 DKILIASIMCEYNKEDWTELAKLVEEAGADALELNFSCPH-GMPERGMGAAVGQDPELVEEICRWVREAVKIPVIAKLT-  176 (299)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEECC-
T ss_conf             9737988517898789999999998718888998267889-87612345552449999999999998624786489628-


Q ss_pred             CCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHH--------------------HHCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             3456653220145543200012201210013566--------------------40257742122766104678766673
Q gi|254781167|r  126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--------------------LKGLSPKDNRKIPNLDYDIVYEIKKE  185 (322)
Q Consensus       126 G~~~~~~~~~~~~~~~~~~~~g~~~itiH~Rt~~--------------------~~g~s~~~~~~~~~~~~~~i~~l~~~  185 (322)
T Consensus       177 -----P~~~~i~~ia~~~~~~gadgiv~~Nt~~~~~~i~~d~~~~~~~~~~~~~~GGlSG~~---l~~~al~~v~~i~~~  248 (299)
T cd02940         177 -----PNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPA---VKPIALRAVSQIARA  248 (299)
T ss_pred             -----CCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH---HHHHHHHHHHHHHHH
T ss_conf             -----871549999999998599899997666775654422356665645677778455878---899999999999996


Q ss_pred             C-CCCCCCCCCCCCCHHHHHHHH-HCCCCEEEECCCC-CHHHHHHHHHH
Q ss_conf             8-875302577778998988874-2035234412200-01243999999
Q gi|254781167|r  186 N-PDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY-KNSAMLTTVDE  231 (322)
Q Consensus       186 ~-~~~~i~~NGdi~~~~~a~~~l-~~~dgvMigRga~-~~P~if~~I~~  231 (322)
T Consensus       249 ~~~~i~Iig~GGI~s~~Da~e~i~aGAs~Vqv~Tal~~~Gp~~i~~I~~  297 (299)
T cd02940         249 PEPGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFTIVDDMCT  297 (299)
T ss_pred             CCCCCCEEEECCCCCHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHC
T ss_conf             4899778998995999999999984998999989999809899999972