PFRMAT AL 
TARGET T0054 
AUTHOR 7397-8542-2481 
METHOD We identified VanX-related proteins in the nonredundant database using 
METHOD BLAST (E-value cutoff of 0.1), aligned them in MACAW (E-value cutoff of 
METHOD e-10) and determined highly conserved motifs. We then searched the 
METHOD PathoSeq database (Incyte) recursively using BLAST and identified 
METHOD additional proteins containing the conserved motifs at E values between 
METHOD 0.1 and 10. These were D-alanyl-D-alanine carboxypeptidases (VanY, YokZ) 
METHOD and phage L-alanoyl-D-glutamate peptidases. We realigned the complete 
METHOD family in MACAW; used the conserved motifs, which now appeared 
METHOD sufficiently robust, in a regular expression search of the PDB; and 
METHOD detected their occurrence in 1LBU (Zn-DD-peptidase of S. albus) and 1VHH 
METHOD (mouse sonic hedgehog). At this point we discovered in MEDLINE that the 
METHOD same results had been published by McCafferty et al. in Biochemistry 
METHOD (36:10498) in 1997. We made the final alignment to the two structures in 
METHOD MACAW with guidance from a secondary structure prediction obtained from 
METHOD the JPred server and repeated reference to the structural features 
METHOD common to 1LBU and 1VHH. The last step included making automated models 
METHOD of VanX with different alignment assumptions in MODELLER. 
MODEL  1 
PARENT 1LBU 
V  15    T  82 
R  16    P  83 
W  17    V  84 
D  18    N  85 
A  19    F  86 
K  20    T  87 
Y  21    Y  88 
A  22    A  89 
T  23    E  90 
W  24    L  91 
D  25    N  92 
N  26    R  93 
F  27    C  94 
T  28    N  95 
G  29    S  96 
K  30    D  97 
P  31    W  98 
V  32    S  99 
D  33    G 100 
G  34    G 101 
Y  35    K 102 
E  36    V 103 
V  37    S 104 
N  38    A 106 
R  39    T 107 
G  42    A 108 
T  43    R 109 
Y  44    A 110 
E  45    N 111 
L  46    A 112 
A  47    L 113 
E  48    V 114 
S  49    T 115 
L  50    M 116 
L  51    W 117 
K  52    K 118 
A  53    L 119 
K  54    Q 120 
E  55    A 121 
L  56    M 122 
A  57    R 123 
A  58    H 124 
T  59    A 125 
Q  60    M 126 
G  61    G 127 
Y  62    D 128 
G  63    P 130 
L  64    I 131 
L  65    T 132 
L  66    V 133 
W  67    N 134 
D  68    G 135 
G  69    G 136 
Y  70    F 137 
R  71    R 138 
P  72    S 139 
K  73    V 140 
R  74    T 141 
A  75    C 142 
V  76    N 143 
N  77    S 144 
C  78    N 145 
F  79    V 146 
M  80    G 147 
V 110    G 148 
A 111    A 149 
S 112    S 150 
K 113    N 151 
S 114    S 152 
S 115    R 153 
H 116    H 154 
S 117    M 155 
R 118    Y 156 
G 119    G 157 
S 120    H 158 
A 121    A 159 
I 122    A 160 
D 123    D 161 
L 124    L 162 
T 125    G 163 
L 126    A 164 
R 163    F 169 
R 164    C 170 
R 165    A 171 
L 166    L 172 
R 167    A 173 
S 168    Q 174 
I 169    A 175 
M 170    A 176 
E 171    R 177 
N 172    N 178 
S 173    H 179 
G 174    G 180 
F 175    F 181 
E 176    T 182 
A 177    E 183 
Y 178    I 184 
S 179    L 185 
W 182    H 195 
W 183    T 196 
H 184    H 197 
Y 185    V 198 
V 186    A 199 
L 187    G 200 
R 188    G 201 
D 189    D 202 
E 190    G 203 
P 191    F 205 
Y 192    W 206 
P 193    S 207 
N 194    A 208 
S 195    P 209 
Y 196    S 210 
F 197    C 211 
D 198    G 212 
F 199    I 213 
TER 
END 
