HHsearch alignment for GI: 254781095 and conserved domain: pfam01565

>pfam01565 FAD_binding_4 FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.
Probab=99.68  E-value=1.7e-16  Score=124.47  Aligned_cols=129  Identities=27%  Similarity=0.412  Sum_probs=107.1

Q ss_pred             EEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCE-EEE-CCCCCCCCCEEEHHHHHH
Q ss_conf             89999689899999999856-299899984752036604884022022112344311-330-266512331122156777
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNI-EVR-NHCEMIVGARCSGKSLAN  116 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i-~~~-~~~~i~v~AG~~~~~l~~  116 (318)
T Consensus         2 ~~vv~P~s~~ev~~~v~~a~~~~~~v~~~g~G~~~~-~~~~~~gi~i~l~~--~~~i~~~d~~~~~v~v~aG~~~~~l~~   78 (138)
T pfam01565         2 AAVVRPESEEEVAAIVRLANEHGLPVLVRGGGSSLL-GDAVTGGVVLDLSR--LNGILEIDPENGTATVEAGVTLGDLVR   78 (138)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEECCCEECC-CCCCCCEEEEECCC--CCCCEEEECCCCEEEEECCCCHHHHHH
T ss_conf             899990999999999999998699689988966727-98639959999568--997268853884899957809999999


Q ss_pred             HHHHHHC-CCHHCCCCHHHHHHHHHCCCCCCCCCE----EEEEEEEEEEECCCCCEEEEC
Q ss_conf             7887520-120003872566324311573215831----345666434411232100001
Q gi|254781095|r  117 SALRHGI-GGFHFFYGIPGSIGGAAYMNAGANNCE----TSQYVVEVHGIDRKGNQHVIP  171 (318)
Q Consensus       117 ~~~~~gl-~GlE~l~gIPGTVGGAi~mNAGayG~e----i~d~i~~V~~~d~~g~~~~l~  171 (318)
T Consensus        79 ~l~~~g~~~~~~~~~~~~~tvGG~i~~~~~G~~~~~~G~~~d~v~~~~vV~~~G~iv~~s  138 (138)
T pfam01565        79 ALAAKGLLLGLEPGSGIPGTVGGAIATNGGGYGSEKYGLTRDNVLSLEVVLADGEVVRLS  138 (138)
T ss_pred             HHHHCCCEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCHHHEEEEEEEECCCCCEEEEC
T ss_conf             999729988631676676203121248965567456464887489999996897199949