PFRMAT AL 
TARGET T0046 
AUTHOR 7397-8542-2481 
METHOD Homologs of the gamma adaptin ear domain were identified in the nr  
METHOD database using PSI-BLAST, and the sequences were aligned in MACAW. 
METHOD The alignment was submitted to the JPRED server and eight beta strands 
METHOD were predicted. The prediction was used to derive a pattern for the  
METHOD MAP program.  Searches found numerous Immunoglobulin-type beta  
METHOD sandwiches in the top scoring hits,  and accounted for all of the  
METHOD predicted beta strands.  An initial alignment was performed using 
METHOD MAP and a BLOSUM62 matrix (where predicted strands were required to  
METHOD align to the strands matched using MAP).  This alignment was 
METHOD refined by eye after considering all predictions returned from JPRED, 
METHOD then homologues of gamma-adaptin and homologues of the top scoring 
METHOD Ig-type fold (1cid C2 domain from CD4) that were aligned using the  
METHOD STAMP structure comparison algorithm. 
MODEL  1 
PARENT 1cid 
I   1    L 104 
P   2    V 105 
S   3    V 106 
I   4    M 107 
T   5    K 108 
A   6    V 109 
Y   7    T 110 
S   8    Q 111 
K   9    S 114 
N  10    N 115 
G  11    T 116 
L  12    L 117 
K  13    T 118 
I  14    C 119 
E  15    E 120 
F  16    V 121 
T  17    M 122 
F  18    G 123 
E  19    P 124 
S  26    K 128 
V  27    M 129 
T  28    R 130 
V  29    L 131 
I  30    I 132 
T  31    L 133 
I  32    K 134 
Q  33    Q 135 
D  44    A 140 
F  45    R 141 
V  46    V 142 
F  47    S 143 
Q  48    R 144 
A  49    Q 145 
K  53    K 147 
T  54    V 148 
F  55    I 149 
Q  56    Q 150 
L  57    V 151 
Q  58    Q 152 
L  59    A 153 
T  74    G 157 
I  75    V 158 
T  76    W 159 
Q  77    Q 160 
V  78    C 161 
I  79    L 162 
K  80    L 163 
V  81    S 164 
L  82    E 165 
R  90    E 168 
M  91    V 169 
R  92    K 170 
I  93    M 171 
K  94    D 172 
L  95    S 173 
T  96    K 174 
Y  97    I 175 
N  98    Q 176 
H  99    V 177 
TER 
END 
