PFRMAT AL 
TARGET T0062 
AUTHOR 7397-8542-2481 
METHOD A HMMER (v 2.0) hidden Markov model was constructed from an alignment of 
METHOD UBIB homologues from the JPRED server.  This profile was used to align 
METHOD UBIB homologues with various nitrate/cytochrome B5 reductases of known 
METHOD three-dimensional structure (1cne, 1ndh, 2cnd).  1cne was found to be the 
METHOD closest match to UBIB using conventional sequence comparison methods. 
METHOD The alignment was modified slightly by hand in an attempt to correct 
METHOD regions that appeared to be incorrectly aligned: namely around the 
METHOD domain-linker region and the C-terminus.  
MODEL  1 
PARENT 1cne 
T   1    G   11 
T   2    R   12 
L   3    I   13 
S   4    H   14 
C   5    C   15 
K   6    R   16 
V   7    L   17 
T   8    V   18 
S   9    A   19 
V  10    K   20 
E  11    K   21 
A  12    E   22 
I  13    L   23 
T  14    S   24 
D  15    R   25 
T  16    D   26 
V  17    V   27 
Y  18    R   28 
R  19    L   29 
V  20    F   30 
R  21    R   31 
I  22    F   32 
V  23    S   36 
P  24    P   37 
D  25    D   38 
A  26    Q   39 
A  27    V   40 
F  28    L   41 
S  29    G   42 
F  30    L   43 
R  31    P   44 
A  32    I   45 
G  33    G   46 
Q  34    K   47 
Y  35    H   48 
L  36    I   49 
M  37    F   50 
V  38    V   51 
V  39    C   52 
M  40    A   53 
D  41    T   54 
E  42    I   55 
R  43    E   56 
D  44    G   57 
K  45    K   58 
R  46    R   62 
P  47    A   63 
F  48    Y   64 
S  49    T   65 
M  50    P   66 
A  51    T   67 
S  52    S   68 
T  53    M   69 
P  54    V   70 
D  55    D   71 
E  56    E   72 
K  57    I   73 
G  58    G   74 
F  59    H   75 
I  60    F   76 
E  61    D   77 
L  62    L   78 
H  63    L   79 
I  64    V   80 
G  65    K   81 
A  66    V   82 
S  67    Y   83 
E  68    N   93 
I  69    G   94 
N  70    G   95 
L  71    L   96 
Y  72    M   97 
A  73    T   98 
K  74    Q   99 
A  75    Y  100 
V  76    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  117 
E  94    H  118 
A  95    V  119 
W  96    E  120 
L  97    Y  121 
R  98    K  132 
D  99    Q  133 
D 100    R  134 
E 101    N  135 
E 102    A  136 
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    E  164 
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 
L 161    L  198 
Q 162    K  199 
V 163    V  200 
V 164    W  201 
P 165    Y  202 
V 166    V  203 
V 167    I  204 
E 168    D  205 
Q 169    Q  206 
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 
G 190    V  230 
T 191    P  231 
A 193    E  232 
E 194    G  233 
H 195    G  234 
D 196    D  235 
I 197    A  239 
Y 198    L  240 
I 199    A  241 
A 200    S  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 
D 211    I  252 
L 212    S  253 
F 213    P  254 
C 214    N  255 
S 215    L  256 
E 216    E  257 
R 217    K  258 
R 223    M  259 
L 224    K  260 
F 225    Y  261 
G 226    D  262 
D 227    M  263 
A 228    A  264 
F 229    N  265 
A 230    S  266 
F 231    F  267 
I 232    V  268 
TER 
END 
