 
PFRMAT AL 
TARGET T0062 
AUTHOR 7278-7379-8158 
METHOD  In order to explore Flavin Reductase's evolutionary relationship(s)  
METHOD  with other members of the Ferredoxin NADP Reductase superfamily (FNR)  
METHOD  we have employed an iterative strategy to primary sequence database (db)  
METHOD  searching. This approach combines conventional algorithms for detecting 
METHOD  pairwise sequence similarities such as BLAST, FASTA & SSEARCH with multiple  
METHOD  sequence alignments (CLUSTALW), profile analysis & secondary structure prediction  
METHOD  methods (PhD, DSC, etc). The general idea is to generate & refine evolving 
METHOD  regions of local similarities which can then be used in multiple rounds of  
METHOD  db scanning to identify distantly related members of this superfamily. 
METHOD  In addition, the library of HMMs of protein folds (FoReSst, typically used by  
METHOD  for CASP3 predictions), confirmed the proposed model below.  
METHOD  This the aforementioned combination of methods was used by Maria A. Cueto. 
METHOD  from Novartis Pharmaceuticals of Summit, NJ. 
REMARK  Flavin Reductase from E. Coli (sw:ubib_ecoli) contains two 
REMARK  domains. First, an N-terminal beta-barrel domain which may bind 
REMARK  a flavin cofactor on the outside. We have chosen the crystal 
REMARK  structure of the N-terminal domain of Phthalate Dioxygenase  
REMARK  Reductase (PDB code 2PIA; residues:8-74) to construct the structural alignment. 
REMARK  The second or C-terminal domain is an alpha/beta fold or pyrimidine 
REMARK  nucleotide binding domain. The crystal structure of the C-terminal 
REMARK  domain of Nitrate Reductase (PDB code 1CNF; residues:94-251) was used as   
REMARK  the parent template for generating the pairwise alignment.      
MODEL   1 
PARENT  1CNF 
N       70      G     94 
L       71      G     95 
Y       72      L     96 
A       73      M     97 
K       74      T     98 
A       75      Q     99 
V       76      Y    100 
M       77      L    101 
D       78      D    102 
R       79      S    103 
I       80      L    104 
L       81      P    105 
K       82      V    106 
D       83      G    107 
H       84      S    108 
Q       85      Y    109 
I       86      I    110 
V       87      D    111 
V       88      V    112 
D       89      K    113 
I       90      G    114 
P       91      P    115 
H       92      L    116 
G       93      G    125 
E       94      S    126 
A       95      F    127 
W       96      V    128 
L       97      I    129 
R       98      N    130 
D       99      G    131 
D      100      K    132 
R      103      R    137 
P      104      R    138 
M      105      L    139 
I      106      A    140 
L      107      M    141 
I      108      I    142 
A      109      C    143 
G      110      G    144 
G      111      G    145 
T      112      S    146 
G      113      G    147 
F      114      I    148 
S      115      T    149 
Y      116      P    150 
A      117      M    151 
R      118      Y    152 
S      119      Q    153 
I      120      I    154 
L      121      I    155 
L      122      Q    156 
T      123      A    157 
A      124      V    158 
L      125      L    159 
A      126      R    160 
R      127      D    161 
N      128      Q    162 
P      129      P    163 
N      130      H    166 
R      131      T    167 
D      132      E    168 
I      133      M    169 
T      134      H    170 
I      135      L    171 
Y      136      V    172 
W      137      Y    173 
G      138      A    174 
G      139      N    175 
R      140      R    176 
E      141      T    177 
E      142      E    178 
Q      143      D    179 
H      144      D    180 
L      145      I    181 
Y      146      L    182 
D      147      L    183 
L      148      R    184 
C      149      D    185 
E      150      E    186 
L      151      L    187 
E      152      D    188 
A      153      R    189 
L      154      W    190 
S      155      A    191 
L      156      A    192 
K      157      E    193 
H      158      Y    194 
P      159      P    195 
G      160      D    196 
V      163      V    203 
V      164      I    204 
P      165      D    205 
V      166      Q    206 
V      167      V    207 
E      168      K    208 
Q      169      R    209 
P      170      P    210 
E      171      E    211 
A      172      E    212 
G      173      G    213 
W      174      W    214 
R      175      K    215 
G      176      Y    216 
R      177      S    217 
T      178      V    218 
G      179      G    219 
T      180      F    220 
V      181      V    221 
L      182      T    222 
T      183      E    223 
A      184      A    224 
V      185      V    225 
L      186      L    226 
Q      187      R    227 
D      188      E    228 
H      189      H    229 
A      193      D    235 
E      194      D    236 
H      195      T    237 
D      196      L    238 
I      197      A    239 
Y      198      L    240 
I      199      A    241 
A      200      C    242 
G      201      G    243 
R      202      P    244 
F      203      P    245 
E      204      P    246 
M      205      M    247 
A      206      I    248 
K      207      Q    249 
I      208      F    250 
A      209      A    251 
TER 
END 
