PFRMAT AL 
TARGET T0062 
AUTHOR 2234-4819-7150 
REMARK Only segments of query sequence that aligned with PDB sequence are given (N-terminal 65 aa) 
METHOD Identification of PDB sequences related by evolution to the target 
METHOD (query) sequence was performed by PSI-BLAST run locally.  The first search is performed  
METHOD with the CASP3 sequence against the non-redundant protein database ("nr").  Four runs of PSI-BLAST were 
METHOD run with an E-value cutoff of 0.001.  The final matrix (checkpoint file) was 
METHOD used to search the PDB.   
METHOD This search results in the following homologous chains: 
METHOD  Chain                                                              Score E-value 
METHOD gi|1064998|pdb|1CNF|  Nitrate Reductase (Cytochrome B Reductase...   207  4e-55 
METHOD gi|999817|pdb|1NDH|  Cytochrome B5 Reductase (E.C.1.6.2.2)           203  1e-53 
METHOD gi|1064997|pdb|1CNE|  Nitrate Reductase (Cytochrome B Reductase...   202  2e-53 
METHOD gi|1065268|pdb|1FNB|  Ferredoxin:nadp+ Oxidoreductase (Ferredox...   159  2e-40 
METHOD gi|3318958|pdb|1AMO|A Chain A, Three-Dimensional Structure Of N...   157  7e-40 
METHOD gi|349931|pdb|2PIA|  Phthalate Dioxygenase Reductase (E.C.1.18.1.)   154  5e-39 
METHOD gi|1065318|pdb|1FRN|  Ferredoxin: Nadp+ Oxidoreductase (Ferredo...   154  5e-39 
METHOD gi|2554655|pdb|1QUF|  X-Ray Structure Of A Complex Nadp+-Ferred...   145  2e-36 
METHOD gi|2194029|pdb|1QUE|  X-Ray Structure Of The Ferredoxin:nadp+ R...   144  5e-36 
METHOD gi|2554661|pdb|1FDR|  Flavodoxin Reductase From E. Coli Flavodo...   119  1e-28 
METHOD gi|3318932|pdb|1A8P|  Ferredoxin Reductase From Azotobacter Vin...   114  7e-27 
METHOD 
METHOD The positions of the insertions and deletions between the PDB sequences and the target sequence 
METHOD in the structures were examined.  Chain 2PIA had the fewest changes and these 
METHOD were mostly in loops.  With reference to the 1CNF alignment, one insertion was 
METHOD moved along the sequence by 7 amino acids.  The target has a long insertion (residues 165-175, 11 aa) 
METHOD at position 174-175 in 2PIA.  This is a much longer loop in 1CNF, compared to 2PIA, indicating that 
METHOD the alignment is approximately correct in this region. All other insertions and deletions are small (<=3 aa). 
METHOD 
METHOD It should be noted that a simple BLAST search of the PDB without the profiling 
METHOD provided by PSI-BLAST gives much poorer scores, many fewer hits, and much shorter alignments: 
METHOD 
METHOD gi|1064998|pdb|1CNF|  Nitrate Reductase (Cytochrome B Reductase...    40  2e-04 
METHOD gi|1064997|pdb|1CNE|  Nitrate Reductase (Cytochrome B Reductase...    40  2e-04 
MODEL  1 
PARENT 2pia 
L   3    L    9 
S   4    R   10 
C   5    L   11 
K   6    K   12 
V   7    I   13 
T   8    A   14 
S   9    S   15 
V  10    K   16 
E  11    E   17 
A  12    K   18 
I  13    I   19 
T  14    A   20 
D  15    R   21 
T  16    D   22 
V  17    I   23 
Y  18    W   24 
R  19    S   25 
V  20    F   26 
R  21    E   27 
I  22    L   28 
V  23    T   29 
P  24    G   33 
D  25    A   34 
A  26    P   35 
A  27    L   36 
F  28    P   37 
S  29    P   38 
F  30    F   39 
R  31    E   40 
A  32    A   41 
G  33    G   42 
Q  34    A   43 
Y  35    N   44 
L  36    L   45 
M  37    T   46 
V  38    V   47 
V  39    A   48 
M  40    V   49 
D  41    P   50 
E  42    N   51 
R  43    G   52 
D  44    S   53 
K  45    R   54 
R  46    R   55 
P  47    T   56 
F  48    Y   57 
S  49    S   58 
M  50    L   59 
A  51    C   60 
S  52    N   61 
T  53    D   62 
P  54    S   63 
D  55    Q   64 
E  56    E   65 
K  57    R   66 
G  58    N   67 
F  59    R   68 
I  60    Y   69 
E  61    V   70 
L  62    I   71 
H  63    A   72 
I  64    V   73 
G  65    K   74 
A  66    R   75 
S  67    D   76 
E  68    S   77 
I  69    N   78 
N  70    G   79 
L  71    R   80 
Y  72    G   82 
A  73    S   83 
K  74    I   84 
A  75    S   85 
V  76    F   86 
M  77    I   87 
D  78    D   88 
R  79    D   89 
I  80    T   90 
L  81    S   91 
K  82    E   92 
D  83    G   93 
H  84    D   94 
Q  85    A   95 
I  86    V   96 
V  87    E   97 
V  88    V   98 
D  89    S   99 
I  90    L  100 
P  91    P  101 
H  92    R  102 
G  93    N  103 
E  94    E  104 
A  95    F  105 
W  96    P  106 
L  97    L  107 
R  98    D  108 
D  99    K  109 
D 100    R  110 
E 102    A  111 
R 103    K  112 
P 104    S  113 
M 105    F  114 
I 106    I  115 
L 107    L  116 
I 108    V  117 
A 109    A  118 
G 110    G  119 
G 111    G  120 
T 112    I  121 
G 113    G  122 
F 114    I  123 
S 115    T  124 
Y 116    P  125 
A 117    M  126 
R 118    L  127 
S 119    S  128 
I 120    M  129 
L 121    A  130 
L 122    R  131 
T 123    Q  132 
A 124    L  133 
L 125    R  134 
A 126    A  135 
R 127    E  136 
N 128    G  137 
N 130    L  138 
R 131    R  139 
D 132    S  140 
I 133    F  141 
T 134    R  142 
I 135    L  143 
Y 136    Y  144 
W 137    Y  145 
G 138    L  146 
G 139    T  147 
R 140    R  148 
E 141    D  149 
E 142    P  150 
Q 143    E  151 
H 144    G  152 
L 145    T  153 
Y 146    A  154 
D 147    F  155 
L 148    F  156 
C 149    D  157 
E 150    E  158 
L 151    L  159 
E 152    D  162 
A 153    E  163 
L 154    W  164 
S 155    R  165 
L 156    S  166 
K 157    D  167 
H 158    V  168 
P 159    K  169 
G 160    I  170 
L 161    H  171 
Q 162    H  172 
V 163    D  173 
V 164    H  174 
G 176    G  175 
R 177    D  176 
T 178    P  177 
G 179    T  178 
T 180    K  179 
V 181    A  180 
L 182    F  181 
T 183    D  182 
A 184    F  183 
V 185    W  184 
L 186    S  185 
Q 187    V  186 
D 188    F  187 
H 189    E  188 
G 190    K  189 
T 191    S  190 
L 192    K  191 
A 193    P  192 
E 194    A  193 
H 195    Q  194 
D 196    H  195 
I 197    V  196 
Y 198    Y  197 
I 199    C  198 
A 200    C  199 
G 201    G  200 
R 202    P  201 
F 203    Q  202 
E 204    A  203 
M 205    L  204 
A 206    M  205 
K 207    D  206 
I 208    T  207 
A 209    V  208 
R 210    R  209 
D 211    D  210 
L 212    M  211 
F 213    T  212 
C 214    G  213 
S 215    H  214 
A 219    W  215 
R 220    P  216 
E 221    S  217 
D 222    G  218 
R 223    T  219 
L 224    V  220 
F 225    H  221 
G 226    F  222 
D 227    E  223 
A 228    S  224 
F 229    F  225 
TER 
END 
