
PFRMAT AL
TARGET T0118
AUTHOR 6801-5605-9478
REMARK
REMARK  Alignment of T0118 (Endodeoxyribonuclease I) w/ 1DDQ_A. by CS
REMARK
REMARK                          METHODS
REMARK                          -------
METHOD  This alignment with the PDB file 1DDQ-A was based on the 
METHOD  Cafasp result with PDB-Blast. A preliminary alignment with 
METHOD  ClustalW and the Gonnet matrix indicated a stretch of good 
METHOD  identity near the C-terminal of the target with residues 150-
METHOD  172 of the template file.  However, the alignments with the 
METHOD  Blossom matrix or the identity matrix indicated different 
METHOD  results.  A multiple alignment with other a-factors of RNA 
METHOD  polymerases from various bacteria and fungi yielded the 
METHOD  alignment between DDQ and T118 given here.
METHOD  (The blossom matrix and standard gapping parameters were 
METHOD  used in Clustal W).
REMARK
MODEL  1
PARENT 1DDQ_A
M 1 E 29               
A 2 R 30               
G 3 G 31               
Y 4 F 32               
G 5 G 33               
TER
PARENT 1DDQ_A                                                   
A 6 T 35               
K 7 L 36               
G 8 G 37               
TER
PARENT 1DDQ_A                                                   
I 9 L 40               
R 10 R 41               
K 11 R 42               
V 12 I 43               
G 13 L 44               
A 14 L 45               
F 15 S 46               
R 16 S 47               
S 17 I 48               
G 18 P 49               
L 19 G 50               
E 20 T 51               
D 21 A 52               
K 22 V 53               
V 23 T 54               
S 24 S 55               
K 25 V 56               
Q 26 Y 57               
L 27 I 58               
E 28 E 59               
S 29 D 60               
K 30 V 61               
G 31 L 62               
I 32 H 63               
K 33 E 64               
F 34 F 65               
E 35 S 66               
TER
PARENT 1DDQ_A                                                   
Y 36 V 71               
E 37 K 72               
E 38 E 73               
W 39 D 74               
K 40 V 75               
V 41 V 76               
P 42 E 77               
Y 43 I 78               
V 44 I 79               
I 45 L 80               
P 46 N 81               
A 47 L 82               
S 48 K 83               
N 49 E 84               
H 50 L 85               
T 51 V 86               
Y 52 V 87               
T 53 R 88               
P 54 F 89               
D 55 L 90               
F 56 D 91               
L 57 P 92               
L 58 R 93               
P 59 W 94               
N 60 R 95               
TER
PARENT 1DDQ_A                                                   
G 61 T 97               
I 62 L 98               
F 63 I 99               
V 64 L 100               
E 65 R 101               
T 66 A 102               
K 67 E 103               
G 68 G 104               
L 69 P 105               
W 70 K 106               
E 71 E 107               
S 72 V 108               
TER
PARENT 1DDQ_A                                                   
D 73 V 111               
D 74 D 112               
R 75 F 113               
K 76 T 114               
K 77 P 115               
H 78 S 116               
L 79 A 117               
L 80 D 118               
I 81 V 119               
R 82 E 120               
E 83 I 121               
Q 84 M 122               
H 85 N 123               
P 86 P 124               
E 87 D 125               
L 88 L 126               
D 89 H 127               
I 90 I 128               
R 91 A 129               
I 92 T 130               
V 93 L 131               
F 94 E 132               
S 95 E 133               
S 96 G 134               
S 97 G 135               
TER
PARENT 1DDQ_A                                                   
R 98 Y 138               
T 99 M 139               
K 100 E 140               
L 101 V 141               
Y 102 R 142               
K 103 V 143               
G 104 D 144               
S 105 R 145               
P 106 G 146               
T 107 V 147               
S 108 G 148               
Y 109 Y 149               
TER
PARENT 1DDQ_A                                                   
E 111 V 150               
F 112 P 151               
C 113 A 152               
E 114 E 153               
K 115 R 154               
H 116 H 155               
G 117 G 156               
I 118 I 157               
K 119 K 158               
F 120 D 159               
A 121 R 160               
D 122 I 161               
K 123 N 162               
L 124 A 163               
I 125 I 164               
P 126 P 165               
A 127 V 166               
E 128 D 167               
W 129 A 168               
I 130 I 169               
K 131 F 170               
E 132 S 171               
P 133 P 172               
TER
PARENT 1DDQ_A                                                   
V 137 V 176               
P 138 A 177               
F 139 F 178               
D 140 Q 179               
R 141 V 180               
L 142 E 181               
K 143 D 182               
R 144 T 183               
K 145 R 184               
G 146 L 185               
G 147 G 186               
K 148 Q 187               
K 149 R 188               
TER
END
Kizhake V Soman, Ph.D., Sealy Center for Structural Biology,
   Department of Human Biological Chemistry & Genetics
     University of Texas Medical Branch at Galveston
         Route: 1157; Galveston, TX 77555-1157
     http://www.scsb.utmb.edu/comp_biol.html/ksoman/
     ksoman@nmr.utmb.edu        Phone: 409-747-6815

