PFRMAT AL 
TARGET T0082 
AUTHOR 2234-4819-7150 
REMARK Unrefined prediction (no energy minimization) 
METHOD Identification of PDB sequences related by evolution to the target 
METHOD (query) sequence was performed by PSI-BLAST run locally.   
METHOD The first search is performed with the CASP3 sequence against  
METHOD the non-redundant protein database ("nr").  Four runs of PSI-BLAST were 
METHOD run with an E-value cutoff of 0.001.  The final matrix  
METHOD (checkpoint file) was used to search the PDB.   
METHOD This search results in the following homologous chain: 
METHOD 
METHOD Chain                                                               Bits Evalue 
METHOD 1bol_  mol:protein length:222     The Ribonuclease Rh From Rhiz...   146  9e-37 
METHOD  
METHOD The alignments were checked against the structure. 
METHOD The alignment was adjusted manually to move gaps to loop regions.   
METHOD One stretch of amino acids of the target were not modeled (46-54). 
METHOD The final alignment for 1bol used was: 
METHOD 
METHOD Query: 1   FDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLT------------------NCPGSPFDITKI 58 
METHOD            +       QW P                  FT+HGLWP +   +         +                   +K    
METHOD Sbjct: 24  YGLVVLNMQWAPGY-----------GPDNAFTLHGLWPDKCSGAYAPSGGCDSNRASSSIASVI--------KSKD 80 
METHOD  
METHOD Query: 59  SHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTF-----------NQAAYFKLAVD 107 
METHOD            S L + + T WP+    NN  FWSHEW+KHGTC                    YF+ A+D 
METHOD Sbjct: 81  SSLYNSMLTYWPSNQGNNNV-FWSHEWSKHGTCVSTYDPDCYDNYEEGEDIVDYFQKAMD 139 
METHOD  
METHOD Query: 108 MRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVQVVACFAQDGSTLIDCTRDTCGANFIF 
METHOD            +R+ Y++  A   +   P G T +   ++  +++ FG    + C +   + V+    V  
METHOD Sbjct: 140 LRSQYNVYKAFSSNGITP-GGTYTATEMQSAIESYFGAKAKIDCSSGTLSDVALYFYVRGRDTYVITDALSTGSCSGDVEYPT 
METHOD  
METHOD 
MODEL  1 
PARENT 1bol 
F   1    Y   24 
D   2    G   25 
S   3    L   26 
F   4    V   27 
W   5    V   28 
F   6    L   29 
V   7    N   30 
Q   8    M   31 
Q   9    Q   32 
W  10    W   33 
P  11    A   34 
P  12    P   35 
A  13    G   36 
V  14    Y   37 
S  26    G   38 
G  27    P   39 
L  28    D   40 
R  29    N   41 
T  30    A   42 
F  31    F   43 
T  32    T   44 
I  33    L   45 
H  34    H   46 
G  35    G   47 
L  36    L   48 
W  37    W   49 
P  38    P   50 
Q  39    D   51 
Q  40    K   52 
S  41    C   53 
G  42    S   54 
T  43    G   55 
S  44    A   56 
L  45    Y   57 
T  46    A   58 
I  55    K   77 
T  56    S   78 
K  57    K   79 
I  58    D   80 
S  59    S   81 
H  60    S   82 
L  61    L   83 
Q  62    Y   84 
S  63    N   85 
Q  64    S   86 
L  65    M   87 
N  66    L   88 
T  67    T   89 
L  68    Y   90 
W  69    W   91 
P  70    P   92 
N  71    S   93 
V  72    N   94 
L  73    Q   95 
R  74    G   96 
A  75    N   97 
N  76    N   98 
N  77    N   99 
Q  78    V  100 
F  80    F  101 
W  81    W  102 
S  82    S  103 
H  83    H  104 
E  84    E  105 
W  85    W  106 
T  86    S  107 
K  87    K  108 
H  88    H  109 
G  89    G  110 
T  90    T  111 
C  91    C  112 
S  92    V  113 
E  93    S  114 
S  94    T  115 
T  95    Y  116 
F  96    D  117 
N  97    D  129 
Q  98    I  130 
A  99    V  131 
A 100    D  132 
Y 101    Y  133 
F 102    F  134 
K 103    Q  135 
L 104    K  136 
A 105    A  137 
V 106    M  138 
D 107    D  139 
M 108    L  140 
R 109    R  141 
N 110    S  142 
N 111    Q  143 
Y 112    Y  144 
D 113    N  145 
I 114    V  146 
I 115    Y  147 
G 116    K  148 
A 117    A  149 
L 118    F  150 
R 119    S  151 
P 120    S  152 
H 121    N  153 
A 122    G  154 
A 123    I  155 
G 124    T  156 
P 125    P  157 
G 127    G  158 
R 128    G  159 
T 129    T  160 
K 130    Y  161 
S 131    T  162 
R 132    A  163 
Q 133    T  164 
A 134    E  165 
I 135    M  166 
K 136    Q  167 
G 137    S  168 
F 138    A  169 
L 139    I  170 
K 140    E  171 
A 141    S  172 
K 142    Y  173 
F 143    F  174 
G 144    G  175 
K 145    A  176 
F 146    K  177 
P 147    A  178 
G 148    K  179 
L 149    I  180 
R 150    D  181 
C 151    C  182 
R 152    S  183 
T 153    S  184 
D 154    G  185 
P 155    T  186 
Q 156    L  187 
T 157    S  188 
K 158    D  189 
V 159    V  190 
S 160    A  191 
Y 161    L  192 
L 162    Y  193 
V 163    F  194 
Q 164    Y  195 
V 165    V  196 
V 166    R  197 
A 167    G  198 
C 168    R  199 
F 169    D  200 
A 170    T  201 
Q 171    Y  202 
D 172    V  203 
G 173    I  204 
S 174    T  205 
T 175    D  206 
L 176    A  207 
I 177    L  208 
D 178    S  209 
C 179    T  210 
T 180    G  211 
R 181    S  212 
D 182    C  213 
T 183    S  214 
C 184    G  215 
G 185    D  216 
A 186    V  217 
N 187    E  218 
F 188    Y  219 
I 189    P  220 
F 190    T  221 
TER 
END 
