PFRMAT AL 
TARGET T0075 
AUTHOR 7397-8542-2481 
METHOD A MACAW alignment of ETS1 pointed domain sequences from the nr database 
METHOD showed a distant similarity between the N-terminal and C-terminal halves 
METHOD of the domain, suggesting the existance of some internal symmetry. 
METHOD Secondary structure prediction using the JPRED server yielded four  
METHOD helices, each of which had the 4-3 periodicity of hydrophobic residues 
METHOD typically found in four-helix bundles.   
METHOD A structure based alignment of classical up-down-up-down four helical 
METHOD bundles was constructed using the STAMP program (Russell & Barton, 
METHOD PROTEINS, 1992).  Only two families of proteins adopting the four  
METHOD helical bundles had helices of approximately the correct length for the 
METHOD ETS1 secondary structure prediction: plant mosaic virus (e.g. TMV), 
METHOD and FK506-binding protein (1fap-b).  The later appeared to have an 
METHOD internal symmetry in agreement with that proposed for ETS1.   
METHOD The alignment to 1fap-b was made by choosing the best overlap between 
METHOD conserved hydrophobic positions of ETS1 and core residues of 1fap-b.  
MODEL  1 
PARENT 1fap_B 
Q  47    R 2018 
A  48    V 2019 
L  49    A 2020 
K  50    I 2021 
A  51    L 2022 
T  52    W 2023 
F  53    H 2024 
S  54    E 2025 
G  55    M 2026 
F  56    W 2027 
T  57    H 2028 
K  58    E 2029 
E  59    G 2030 
Q  60    L 2031 
Q  61    E 2032 
R  62    E 2033 
L  63    A 2034 
G  64    S 2035 
I  65    R 2036 
P  66    L 2037 
E  74    V 2044 
T  75    K 2045 
H  76    G 2046 
V  77    M 2047 
R  78    F 2048 
D  79    E 2049 
W  80    V 2050 
V  81    L 2051 
M  82    E 2052 
W  83    P 2053 
A  84    L 2054 
V  85    H 2055 
N  86    A 2056 
E  87    M 2057 
F  88    M 2058 
D  94    K 2066 
F  95    E 2067 
Q  96    T 2068 
K  97    S 2069 
F  98    F 2070 
C  99    N 2071 
M 100    Q 2072 
S 101    A 2073 
G 102    Y 2074 
A 103    G 2075 
A 104    R 2076 
L 105    D 2077 
C 106    L 2078 
A 107    M 2079 
L 108    E 2080 
G 109    A 2081 
K 110    Q 2082 
E 111    E 2083 
C 112    W 2084 
F 113    C 2085 
L 114    R 2086 
E 115    K 2087 
L 116    Y 2088 
G 122    L 2097 
D 123    T 2098 
I 124    Q 2099 
L 125    A 2100 
W 126    W 2101 
E 127    D 2102 
H 128    L 2103 
L 129    Y 2104 
E 130    Y 2105 
I 131    H 2106 
L 132    V 2107 
Q 133    F 2108 
K 134    R 2109 
E 135    R 2110 
D 136    I 2111 
V 137    S 2112 
TER 
END 
