
PFRMAT AL
TARGET T0110
AUTHOR 7023-8870-2129
METHOD I took the alignment from PHD of RBFA sequences, and combined this with 
METHOD the secondary structure predictions from the CAFASP server.  
METHOD So the predictions are fairly convincing, and there appear to be
METHOD sufficient homologues to derive good conservation patterns.
METHOD By this I get:
METHOD alpha - beta - beta - alpha - (beta) - beta - alpha
METHOD          1      2               3       4
METHOD (though the beta in parentheses is possibly missing or very short)
METHOD The burial order based on conservation of hydrophobics is
METHOD 2 > 4 > 1 > 3
METHOD So this would be: 1243 or 1423
METHOD 1243 has several matches in SCOP, but only one really agrees with
METHOD the prediction, the fold of honing endonucleases
METHOD http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.1.004.079.000.000.000.html
METHOD So this is alpha - beta - beta - alpha - beta - beta - alpha with 1243 order
METHOD I created a stamp alignment of the honing endonucleases structures.
METHOD The strands appear to be quite a bit shorter, but there is some variation across
METHOD the various diversity.
METHOD I did a hand-crafted alignment trying to match the conserved hydrophobics/phillics
METHOD with the core.
MODEL 1
PARENT 1bp7A
D   9    N   2
R  10    T   3
V  11    K   4
A  12    Y   5
Q  13    N   6
E  14    K   7
I  15    E   8
Q  16    F   9
K  17    L  10
E  18    L  11
I  19    Y  12
A  20    L  13
V  21    A  14
I  22    G  15
L  23    F  16
Q  24    V  17
R  25    D  18
E  26    G  19
V  27    D  20
K  28    G  21
D  29    S  22
P  30    I  23
R  31    I  24
I  32    A  25
G  33    Q  26
S  38    P  29
D  39    N  30
V  40    Q  31
E  41    S  32
V  42    Y  33
S  43    K  34
S  44    F  35
D  45    H  37
L  46    Q  38
S  47    L  39
Y  48    S  40
A  49    L  41
K  50    T  42
I  51    F  43
F  52    Q  44
V  53    V  45
I  64    T  46
E  65    Q  47
Q  66    K  48
G  67    T  49
M  68    Q  50
K  69    R  51
G  70    R  52
L  71    W  53
E  72    F  54
K  73    L  55
A  74    D  56
S  75    K  57
P  76    L  58
Y  77    V  59
I  78    D  60
R  79    E  61
S  80    I  62
L  81    G  63
L  82    V  64
A  85    G  65
M  86    Y  66
R  87    V  67
L  88    R  68
R  89    D  69
I  90    R  70
P  92    V  73
E  93    S  74
I  94    D  75
R  95    Y  76
F  96    I  77
I  97    L  78
Y  98    S  79
D  99    E  80
E 104    I  81
G 105    K  82
M 106    P  83
R 107    L  84
M 108    H  85
S 109    N  86
N 110    F  87
L 111    L  88
V 112    T  89
T 113    Q  90
N 114    L  91
V 115    Q  92
V 116    P  93
R 117    F  94
E 118    L  95
D 119    K  96
E 120    L  97
K 121    K  98
K 122    Q  99
H 123    K 100
V 124    Q 101
E 125    A 102
E 126    N 103
S 127    L 104
N 128    V 105
TER
END

