PFRMAT AL 
TARGET T0079 
AUTHOR 7397-8542-2481 
METHOD A MACAW alignment of sequences belonging to the araC DNA-binding domain 
METHOD family revealed the existance of an internal duplication.  Secondary  
METHOD structure prediction using the JPRED server showed that each half of  
METHOD marA consists of three helices.  Literature searches and sequence  
METHOD comparisons showed that the third of these helices is the DNA-binding 
METHOD helix.  A comparison of HTH structures in PDB gave us the position  
METHOD of the three helices, which is conserved in all HTH proteins.  Because 
METHOD the araC monomer binds two consecutive major grooves, and this property 
METHOD is expected to be preserved in marA, we chose the cMyb DNA-binding  
METHOD repeats as a template.   
MODEL  1 
PARENT 1mse_C 
M   1    M   89 
T   2    L   90 
M   3    I   91 
R   5    K   92 
R   6    G   93 
N   7    P   94 
T   8    W   95 
D   9    T   96 
A  10    K   97 
I  11    E   98 
T  12    E   99 
I  13    D  100 
H  14    Q  101 
S  15    R  102 
I  16    V  103 
L  17    I  104 
D  18    K  105 
W  19    L  106 
I  20    V  107 
E  21    Q  108 
D  22    K  109 
N  23    Y  110 
L  24    G  111 
L  28    K  113 
S  29    R  114 
L  30    W  115 
E  31    S  116 
K  32    V  117 
V  33    I  118 
S  34    A  119 
E  35    K  120 
R  36    H  121 
S  37    L  122 
G  38    G  124 
Y  39    R  125 
S  40    I  126 
K  41    G  127 
W  42    K  128 
H  43    Q  129 
L  44    C  130 
Q  45    R  131 
R  46    E  132 
M  47    R  133 
F  48    W  134 
K  49    H  135 
K  50    N  136 
E  51    H  137 
T  52    L  138 
R  61    T  148 
S  62    E  149 
R  63    E  150 
K  64    E  151 
M  65    D  152 
T  66    R  153 
E  67    I  154 
I  68    I  155 
A  69    Y  156 
Q  70    Q  157 
K  71    A  158 
L  72    H  159 
K  73    K  160 
E  74    R  161 
S  75    L  162 
N  76    G  163 
E  77    N  164 
P  78    R  165 
I  79    W  166 
L  80    A  167 
Y  81    E  168 
L  82    I  169 
A  83    A  170 
E  84    K  171 
R  85    L  172 
Y  86    L  173 
G  87    P  174 
F  88    G  175 
E  89    R  176 
S  90    T  177 
Q  91    D  178 
Q  92    N  179 
T  93    A  180 
L  94    I  181 
T  95    K  182 
R  96    N  183 
T  97    H  184 
F  98    W  185 
K  99    N  186 
N 100    S  187 
Y 101    T  188 
F 102    M  189 
D 103    R  190 
V 104    R  191 
P 105    K  192 
P 106    V  193 
TER 
END 
