PFRMAT AL 
TARGET T0077 
AUTHOR 5529-3140-9255 
REMARK Prediction team BENNER-COHEN has two group leaders, 
REMARK but we will consistently use Steven Benner's predictor 
REMARK number to avoid confusion concerning a second team 
REMARK connected with Fred Cohen (called Cohen, Fred). 
REMARK (Fred Cohen's number as a group leader is 6140-7890-6093). 
REMARK Prediction team members: D.L.Gerloff, G.Cannarozzi, 
REMARK M.Joachimiak, F.E.Cohen & S.A.Benner. 
METHOD 
METHOD This submission is a threading alignment for T0077 
METHOD ribosomal protein L30 from yeast, with a parent 
METHOD structure suggested at a significant score by the fold 
METHOD recognition programs by D. Fischer and D. Rice, UCLA,  
METHOD as available through the UCLA-DOE fold recognition server.  
METHOD (Refs. D.Fischer & D. Eisenberg (1996). Protein Sci. 5:947-55), 
METHOD D.Rice & D.Eisenberg (1997). JMB 267:1026-38).  
METHOD 
METHOD OUR INTENTION WITH SUBMITTING THIS MANUAL THREADING ALIGNMENT 
METHOD IS TO ASSIST IN IMPROVING THE QUALITY OF AUTOMATED THREADING 
METHOD ALIGNMENTS BY UNCOVERING WHICH OF THE CLUES COMMONLY USED BY 
METHOD EXPERTS ALIGNING MANUALLY ARE MOST USEFUL AND COULD BE 
METHOD EXPLORED SYSTEMATICALLY. 
METHOD  
METHOD The proposed threading alignment was generated manually and 
METHOD takes into account sequence similarity between a T0077 align- 
METHOD ment of 14 sequences from SwissProt and a few prokaryotic 
METHOD genome projects and the template structure (for which we   
METHOD could not find more than 1 homolog in the databases), 
METHOD predicted secondary structures (an automated prediction  
METHOD by the program SAINT (Benner et al.), server-generated PHD  
METHOD predictions, the prediction by Chandonia&Cohen, and our manual  
METHOD predictions), predicted Surface/Interior positions (DARWIN &  
METHOD manual), but also strong consideration of which residues may be  
METHOD part of the functional epitope, and compensatory covariation. 
METHOD (Most importantly, T48, V81, and possibly S63, were brought to- 
METHOD gether due to a possible functional site in some of the homologs. 
METHOD Further, we used covariation between R35 and E55, and K64 and 
METHOD E94). 
METHOD  
METHOD Interestingly, our proposed alignment infers the replacement 
METHOD of a helix in 1fcd_A with a coil/turn structure over P49-S54. 
METHOD 
MODEL 1 
PARENT 1fcd_A 
K   5   E  132 
S   6   Q  133 
Q   7   T  134 
E   8   A  135 
S   9   I  136 
I  10   L  137 
N  11   R  138 
Q  12   K  139 
K  13   Q  140 
L  14   L  141 
A  15   E  142 
L  16   D  143 
V  17   M  144 
I  18   A  145 
K  19   D  146 
S  20   G  147 
G  21   G  148 
K  22   T  149 
Y  23   V  150 
T  24   V  151 
L  25   I  152 
G  26   A  153 
T  30   P  165 
V  31   Y  166 
K  32   E  167 
S  33   R  168 
L  34   A  169 
R  35   S  170 
Q  36   Q  171 
K  40   K  184 
L  41   V  185 
I  42   I  186 
I  43   I  187 
I  44   L  188 
A  45   D  189 
A  46   S  190 
N  47   S  191 
T  48   Q  192 
E  55   M  216 
L  56   I  217 
E  57   E  218 
Y  58   W  219 
Y  59   H  220 
A  60   P  221 
M  61   G  222 
S  63   P  223 
K  64   D  224 
T  65   S  225 
K  66   A  226 
V  67   V  227 
Y  68   V  228 
Y  69   K  229 
F  70   V  230 
Q  71   D  231 
G  72   G  232 
G  73   G  233 
N  74   E  234 
N  75   M  235 
E  76   M  236 
L  77   V  237 
G  78   E  238 
T  79   T  239 
A  80   A  240 
V  81   F  241 
G  82   G  242 
K  83   D  243 
L  84   E  244 
F  85   F  245 
R  86   K  246 
V  87   A  247 
G  88   D  248 
V  89   V  249 
V  90   I  250 
S  91   N  251 
I  92   L  252 
L  93   I  253 
E  94   P  254 
TER 
END 
