PFRMAT AL 
TARGET T0044 
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 the first 
METHOD domain of T0044, RNA-terminal cyclase, with a parent 
METHOD structure suggested at a significant score by the fold 
METHOD recognition programs by Danny Fischer, UCLA, as available 
METHOD through the UCLA-DOE fold recognition server. (Ref. D.Fischer 
METHOD & D. Eisenberg (1996). Protein Sci. 5:947-55). Notably, the 
METHOD programs also returned a significant match with the second 
METHOD domain of T0044, 1cnp, calcyclin. However, because of the 
METHOD conception that T0044 may function as a monomer, while the 
METHOD top matches returned for the second domain involved structures 
METHOD which seem unfit to exist other than in a dimer, we decided 
METHOD not to follow up on the match for the second domain, in light 
METHOD of restricted time also.  
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 putative domain boundaries were obtained by constructing 
METHOD a multiple sequence for T0044 using DARWIN (G.H. Gonnet et al.). 
METHOD We found similarity with SwissProt-sequences 5H1A_*, beginning 
METHOD with the starting residues of those proteins, over the second 
METHOD domain only, which was predicted to begin around res. 211 of  
METHOD the target sequence. 
METHOD  
METHOD The proposed threading alignment was generated manually and 
METHOD takes into account sequence similarity between a T0044 align- 
METHOD ment (SP-seqs rtca_ecoli 1-215, rtca_metja 1-210, rtc1_human 
METHOD 1-210, rtc1_schpo 1-208, rtc1_yeast 1-210, rtc1_caeel 1-215) 
METHOD and a sequence alignment for the parent (cheb_salty, cheb_ecoli, 
METHOD cheb_bacsu, frzg_myxxa), predicted secondary structures (an 
METHOD automated prediction by the program SAINT (Benner et al.), two 
METHOD different server-generated PHD predictions (PredictProtein and 
METHOD UCLA-DOE servers), and our manual predictions), predicted  
METHOD Surface/Interior positions (DARWIN & manual), but also conside- 
METHOD ration of which residues may be part of the active site of the 
METHOD cyclase (most importantly, H158 or R157 in the target was regar- 
METHOD ded the potential adenylation site postulated by the published 
METHOD hypotheses regarding the cyclase mechanism, W. Filipowicz (1982), 
METHOD Proc.Natl.Acad.Sci. USA 82:1316-1320), and which residues 
METHOD could best be deleted in the parent structure, if necessary. 
METHOD  
METHOD Interestingly, our proposed alignment infers an extension of the 
METHOD excursion from the core fold found in 1chd, between strands S4 
METHOD and a loop region L2, as named in the pdb-entry. One possibility 
METHOD to extend this insertion is to extend the beta-hairpin by an 
METHOD additional pair of strands which may fold over this, or another 
METHOD part of the structure, possibly even into the second domain. We 
METHOD have chosen this possibility in our model. However, it is also 
METHOD conceivable that the insertion would consist of a 4-stranded  
METHOD antiparallel sheet in T0044, with the new strands either being 
METHOD inserted at the N-terminus, or the C-terminus of the original 
METHOD insertion found in 1chd. 
METHOD  
METHOD A further characteristic of our model is that helix D in 1chd 
METHOD (res. 287-297) would have been replaced by an extended cross-over 
METHOD loop in T0044 (res. 160-166). This is especially interesting, 
METHOD and unusual, because of the proximity of this region at the  
METHOD putative active site vicinity of T0044. This observation could 
METHOD of course also have arisen from a mistake in our prediction, as 
METHOD the sequence conservation/variation patterns tend to be more  
METHOD difficult to interpret in structural context, but are dominated 
METHOD by functional context instead. 
METHOD 
METHOD NOTE: Due to the sparse multiple sequence alignment for T0044, 
METHOD no separate secondary structure prediction by the SAINT system 
METHOD will be submitted for this target. The SAINT output was, however, 
METHOD used together with other secondary structure predictions (see 
METHOD above), to guide this threading alignment partially. 
METHOD 
MODEL  1 
PARENT 1chd 
R   4   S   155 
M   5   E   156 
I   6   K   157 
A   7   L   158 
L   8   I   159 
D   9   A   160 
G   10   I   161 
A   11   G   162 
Q   12   A   163 
G   13   S   164 
E   14   T   165 
G   15   G   166 
G   16   G   167 
G   17   T   168 
Q   18   E   169 
I   19   A   170 
L   20   I   171 
R   21   R   172 
S   22   H   173 
A   23   V   174 
L   24   L   175 
S   25   Q   176 
L   26   P   177 
S   27   L   178 
M   28   P   179 
T   30   L   180 
G   31   S   181 
Q   32   S   182 
P   33   P   183 
F   34   A   184 
T   35   V   185 
I   36   I   186 
T   37   I   187 
S   38   T   188 
I   39   Q   189 
R   40   H   190 
A   41   M   191 
G   47   P   192 
L   48   P   193 
L   49   G   194 
R   50   F   195 
Q   51   T   196 
H   52   R   197 
L   53   S   198 
T   54   F   199 
A   55   A   200 
V   56   E   201 
K   57   R   202 
A   58   L   203 
A   59   N   204 
T   60   K   205 
E   61   L   206 
C   63   C   207 
G   64   Q   208 
A   65   I   209 
T   66   S   210 
V   67   V   211 
E   68   K   212 
G   69   E   213 
A   70   A   214 
E   71   E   215 
L   72   D   216 
G   73   G   217 
S   74   E   218 
Q   75   R   219 
R   76   V   220 
L   77   L   221 
L   78   P   222 
F   79   G   223 
R   80   H   224 
P   81   A   225 
G   82   Y   226 
T   83   I   227 
V   84   A   228 
R   85   P   229 
G   86   G   230 
G   87   D   231 
D   88   K   232 
R   90   H   233 
F   91   M   234 
A   92   E   235 
I   93   L   236 
G   94   A   237 
S   95   R   238 
A   96   S   239 
G   97   G   240 
S   98   A   241 
P   116   N   242 
S   117   Y   243 
R   118   Q   244 
V   119   I   245 
E   120   K   246 
V   121   I   247 
S   122   D   249 
G   123   G   250 
G   124   P   251 
T   125   P   252 
D   126   V   253 
N   127   N   254 
P   128   R   255 
S   129   H   256 
A   130   R   257 
P   131   P   258 
P   132   S   259 
A   133   V   260 
D   134   D   261 
F   135   V   262 
I   136   L   263 
R   137   F   264 
R   138   H   265 
V   139   S   266 
L   140   V   267 
E   141   A   268 
P   142   K   269 
L   143   H   270 
L   144   A   271 
A   145   G   272 
K   146   R   273 
I   147   N   274 
G   148   A   275 
I   149   V   276 
H   150   G   277 
Q   151   V   278 
Q   152   I   279 
T   153   L   280 
T   154   T   281 
L   155   G   282 
L   156   M   283 
R   157   G   284 
H   158   N   285 
G   159   D   286 
F   160   G   287 
V   167   G   298 
V   168   A   299 
A   169   W   300 
T   170   T   301 
E   171   I   302 
V   172   A   303 
S   173   Q   304 
P   174   E   306 
V   175   A   307 
A   176   S   308 
S   177   C   309 
F   178   V   310 
Q   182   V   311 
L   183   F   312 
G   184   G   313 
E   185   M   314 
R   186   P   315 
G   187   R   316 
N   188   E   317 
I   189   A   318 
V   190   I   319 
Q   191   N   320 
M   192   M   321 
R   193   G   322 
G   194   G   323 
E   195   V   324 
V   196   S   325 
L   197   E   326 
L   198   V   327 
A   199   V   328 
G   200   D   329 
V   201   L   330 
P   202   S   331 
R   203   Q   332 
H   204   V   333 
V   205   S   334 
A   206   Q   335 
E   207   Q   336 
R   208   M   337 
E   209   L   338 
I   210   A   339 
TER 
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