 
PFRMAT AL 
TARGET T0085 
AUTHOR 9070-5088-8627 
REMARK  
REMARK Prediction date: Monday June 22, 1998 
REMARK Group name: UCSC-compbio 
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, 
REMARK 	 Kevin Karplus, David Haussler, and Richard Hughey 
REMARK University of California, Santa Cruz 
REMARK  
METHOD Overview 
METHOD  
METHOD Fold recognition was performed using the Target98 (SAM-T98) method 
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed 
METHOD by this group for CASP2 [2].  This method attempts to find and multiply  
METHOD align a set of homologs to a given sequence, then create an HMM from that  
METHOD multiple alignment. 
METHOD  
METHOD First, a set of sequence weights is determined from the alignment.  Next,  
METHOD Modelfromalign is used to build the model from the alignment and the  
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring  
METHOD of the sequences, using a reversed-sequence normalization feature. 
METHOD  
METHOD The weighting method, detailed in upcoming publications [3,4], 
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an 
METHOD entropy method to set the final weights. 
METHOD  
METHOD Alignment generation 
METHOD  
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set 
METHOD of very close homologs, and once to produce a set of possible homologs. 
METHOD  
METHOD The method then uses multiple iterations of a selection, training, and  
METHOD alignment procedure.  Each iteration involves an initial alignment, a set  
METHOD of search sequences, a threshold value, and a transition regularizer.  
METHOD  
METHOD The first iteration uses a single sequence (or seed alignment) as the  
METHOD initial alignment and the close homologs found by BLASTP are used as the  
METHOD search set.  The threshold is set very strictly, so that only good matches  
METHOD to the sequence are considered.  This iteration uses a transition regularizer  
METHOD that was designed to match the gap costs used by BLASTP. 
METHOD  
METHOD On subsequent iterations the input alignment is the output from the 
METHOD previous iteration, the search set is the larger set of possible 
METHOD homologs found by BLASTP, and the thresholds are gradually loosened. 
METHOD The second through second-from-last iteration use a ``long-match'' 
METHOD transition regularizer, and the final iteration uses a transition regularizer  
METHOD trained on FSSP alignments. 
METHOD  
METHOD References 
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996. 
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.   
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R. 
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and  
METHOD     Genetics, Suppl. 1, 134-9, 1997. 
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06, 
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998. 
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, 
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998. 
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994. 
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. 
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996. 
METHOD  
METHOD  
METHOD There are four obvious heme-binding sites in T0085: CSSCHK, CVGCHV, 
METHOD CESCHG, and CSACHL. 
METHOD  
METHOD Our prediction for T0085 should be considered in three parts.   
METHOD  
METHOD The first part includes the first three heme-binding sites.  We are 
METHOD submitting an automatic alignment to 2cthA, which had a summed score 
METHOD of -63. For scores in this range, we had no false positives in our 
METHOD fold-recognition tests.  While 2cthA is a tetraheme protein, it does 
METHOD not appear that T0085 binds heme where 2cthA binds its second heme 
METHOD group. 
METHOD  
METHOD Since the 2cthA left much of T0085, including one heme-binding group, 
METHOD unaligned, we looked further down our list of hits until we found one 
METHOD that aligned well near the remaining heme-binding site. 
METHOD The 1ycc alignment looked good around the heme-binding site, but not so 
METHOD good on the back side of the heme, so we removed that part of the 
METHOD automatic alignment. 
METHOD  
METHOD In place of 1ycc for the fourth heme-binding site, we considered 
METHOD cytochromes 1cor and 1c52, since they associate electrostatically with 
METHOD phospholipid membranes, as T0085 does.  Because of what we considered 
METHOD structural problems, we chose to submit 1ycc plus an alignment to 1avc 
METHOD for the C-terminus instead. 
METHOD  
METHOD  
METHOD  
MODEL 1 
PARENT 1avc 
G 148 G 355 
A 149 T 356 
K 150 V 357 
A 151 R 358 
P 152 P 359 
Y 153 A 360 
T 154 G 361 
P 155 D 362 
F 156 F 363 
T 157 N 364 
P 158 P 365 
E 159 D 366 
V 160 A 367 
D 161 D 368 
A 162 A 369 
K 163 K 370 
Y 164 A 371 
T 165 L 372 
F 166 R 373 
K 167 K 374 
F 168 T 381 
D 169 D 382 
E 170 E 383 
M 171 D 384 
V 172 T 385 
K 173 I 386 
E 174 I 387 
V 175 D 388 
K 176 I 389 
A 177 I 390 
M 178 T 391 
H 179 H 392 
E 180 R 393 
H 181 S 394 
Y 182 N 395 
K 183 A 396 
L 184 Q 397 
E 185 R 398 
G 186 Q 399 
V 187 Q 400 
F 188 I 401 
E 189 R 402 
G 190 Q 403 
E 191 T 404 
P 192 F 405 
K 193 K 406 
F 194 S 407 
K 195 H 408 
F 196 F 409 
H 197 G 410 
D 198 R 411 
E 199 D 412 
F 200 L 413 
Q 201 M 414 
A 202 A 415 
S 203 D 416 
A 204 L 417 
K 205 K 418 
P 206 S 419 
A 207 E 420 
K 208 L 421 
K 209 S 422 
G 210 G 423 
K 211 D 424 
TER 
END 
