SERVERNAME: frsvr_SDP TARGET: T0053 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDP.t0053 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 2tct 4.84 183 26 2 1ak1 4.30 251 16 3 1gne_80-232 4.08 130 25 4 1lrv 3.79 204 22 5 1gne 3.78 191 24 6 1aoa 3.59 220 20 7 1rgp 3.50 182 18 8 1bgla_334-625 3.43 200 24 9 1bed 2.75 166 20 10 1gsra 2.73 177 24 END NOTICE: the excludefolds excludes 2 library entries which are models. The three-dimensional fold predicted for your amino acid sequence is in the table below. HERE I INCLUDE ONLY THE RESULTS OF THE gonnet+predss METHOD. THE OTHER RESULTS CAN BE FOUND AT THE URL (www page) SPECIFIED AT THE END OF THIS MESSAGE. Please cite: Fischer, D. and Eisenberg, D. Fold Recognition Using Sequence-Derived Predictions. Protein Science, 5, 947-955, 1996. * * * * N O T E * * * * PLEASE CONSULT ALSO THE RESULTS OF gonnet+predss+multi Your sequence was translated to: seq.seq Length: 264 December 21, 1998 09:28 Type: P Check: 7024 .. 1 MKKALLVVSF GTSYHDTCEK NIVACERDLA ASCPDRDLFR AFTSGMIIRK 51 LRQRDGIDID TPLQALQKLA AQGYQDVAIQ SLHIINGDEY EKIVREVQLL 101 RPLFTRLTLG VPLLSSHNDY VQLMQALRQQ MPSLRQTEKV VFMGHGASHH 151 AFAAYACLDH MMTAQRFPAR VGAVESYPEV DILIDSLRDE GVTGVHLMPL 201 MLVAGDHAIN DMASDDGDSW KMRFNAAGIP ATPWLSGLGE NPAIRAMFVA 251 HLHQALNMAV EEAA NAME: t0053 FROM: dfischer@indigo.cs.bgu.ac.il BY YOUR REQUEST I HAVE NOT USED THE FOLLOWING FOLDS: 1hli 1kja The method used for this prediction was: gonnet+predss . Most similar fold: 2tct MOL_ID: 1; 2 MOLECULE: TETRACYCLINE REPRESSOR; 3 CHAIN: NULL; 4 SYNONYM: TET REPRESSOR, CLASS D; 5 ENGINEERED: YES RANK Z-SCORE FOLD LENGTHALI %ID 1 4.84 2tct 183 26 1-62 alpha ; Tetracyclin repressor (Tet-repressor, TetR)] 1-62-1-1-1-1- 2 4.30 1ak1 251 16 1998 3 4.08 1gne_80-232 130 25 1-31 alpha ; Glutathione S-transferases, C-terminal domain] 1-31-1-1-1-8-2- 4 3.79 1lrv 204 22 1997 new ; A LEUCINE-RICH REPEAT VARIANT WITH A NOVEL REPETITI 5 3.78 1gne 191 24 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 6 3.59 1aoa 220 20 1998 7 3.50 1rgp 182 18 1997 new ; GTPASE-ACTIVATION DOMAIN FROM RHOGAP 8 3.43 1bgla_334-625 200 24 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-1-3-4-1-1- 9 2.75 1bed 166 20 1997 new ; STRUCTURE OF DISULFIDE OXIDOREDUCTASE 10 2.73 1gsra 177 24 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 11 2.70 1a2oa 256 22 1998 12 2.68 1wab 198 19 1997 new ; PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE 13 2.53 1vpt 234 18 1997 new ; AS11 VARIANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPL 14 2.48 1guha 209 17 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 15 2.44 1pprm 238 15 1997 new ; PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CART LEGEND: COL. 1: RANK. The ranks are obtained by sorting the fold library, by Z-SCORES, in decreasing order. Only the 15 structures that are most compatible to your sequence are shown. COL. 2: Z-SCORE. The z-scores are computed using the distribution of raw scores (not shown) of all folds. COL. 3: FOLD. Protein Data Bank codes for the coordinates of the 3D structures. COL. 4: LENGTHALI. The number of residues from your sequence that were aligned to the fold. COL. 5: % ID. Percentage of identical residues in the alignment. RELIABILITY OF THIS PREDICTION: With this method the confidence threshold is a z-score of 4.8 +- 1.0. YOUR HIGHEST SCORING FOLD IS ABOVE THIS THRESHOLD BUT ONLY SLIGHTLY HIGHER. THE PREDICTION IS NOT VERY RELIABLE. You may conclude that: IF the fold of your sequence is similar to one already observed, THEN: - Our method is not sensitive enough to assign a fold for your sequence, and/or - It may be contained within a larger fold, and/or - The fold of your sequence is not included in our library of folds. IF your sequence corresponds to a new, unobserved fold, THEN: - Our method reflects this by a below threshold score. Below is the alignment of your sequence with the top hit structure. In the near future, all the alignments in a more readable format will be made available. hhhhhhhhhh hhhhhhhhhhbb hhhhhhhhhhhhhhhhhhhbbb LQALQKLAAQGYQDVAIQSLHIINGDEYEKIVREVQLLRPLFTRLTLGVP || | | | | | | | | | | DAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLD..ALAVE hhhhhhhhhhh hhhhhhhhhh hhhhhhhhh hhhhhhh hhhhh b hhh hhhhhhhhhhhh bbbbbb hhh LLSSHNDY.............VQLMQALRQQMPSLRQTEKVVFMGHGASH | | || | | | | | ILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAK.VHLGTRPDE hhhhhh hhhhhhhhhhhhhhhhhhh hhhh hhh hh hhhhhhhhhhhhhhhhh b bb hhhhhhhhh bbbbb HAFAAYACLDHMMTAQRFPARVGAVESYPEVDILIDSLRDEGVTGVHL.M || | | | | KQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALNL hhhhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhhhhhhhhhhh bbbbb hhhhhhhhh hhhhhhhh PLMLVAGDHAINDMASDDGDSWKMRFNAAGIPATPWLSGLGENPAIRAMF | | | | |||| | || || | PPLL...REALQIMDSDDGEQ.............AFLHGL..ESLIRG.F hhhh hhhhhhhh hhh hhhhhh hhhhhh h hhhhhhhhhh VAHLHQALNM | | EVQLTALLQI hhhhhhh 24% Additional information for your prediction can be found at the url: http://www.doe-mbi.ucla.edu/people/frsvr/preds/24403t0053/24403t0053.html p.s. if you need further information on this output, send an e-mail message to: fischer@mbi.ucla.edu