SERVERNAME: frsvr_SDPMA TARGET: T0080 PARAMETERS: excludefolds: 1an3b 1az7 1bd9a 1bg8a 1bl0a 1cdaa 1hli 1illg 1kja include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0080 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1a3aa 5.50 126 23 2 1ndk 5.33 144 19 3 1ghu 4.45 90 27 4 1ulp 3.36 133 19 5 1dih_131-240 3.19 108 16 6 1ab2 3.14 105 19 7 1aoic 3.05 109 20 8 1pspa 3.04 92 21 9 1u9a 2.82 144 15 10 2ts1_228-319 2.73 86 20 11 1pdnc 2.69 117 14 12 1paub 2.57 70 19 13 1lap_1-159 2.46 131 21 14 1bnca_1-114 2.38 103 27 15 1ak6 2.38 143 17 END The following are additional results for your prediction obtained using a multiple alignment of sequences homologous to your submitted sequence. The sequences in the multiple alignment (in addition to your sequence) are: 3mg_arath 3mg_human 3mg_mouse 3mg_rat This method (MULT+gonnet+predss) is still under testing. Comparing the results of the predictions for the homologous sequences may provide further information. You can obtain these by submitting them to this server. The three-dimensional fold predicted for your amino acid sequence is in the table below. HERE I INCLUDE ONLY THE RESULTS OF THE MULT+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. Your sequence was translated to: seq.seq Length: 219 January 4, 1999 15:35 Type: P Check: 4449 .. 1 KGHLTRLGLE FFDQPAVPLA RAFLGQVLVR RLPNGTELRG RIVETEAYLG 51 PEDEAAHSRG GRQTPRNRGM FMKPGTLYVY IIYGMYFCMN ISSQGDGACV 101 LLRALEPLEG LETMRQLRST LRKGTASRVL KDRELCSGPS KLCQALAINK 151 SFDQRDLAQD EAVWLERGPL EPSEPAVVAA ARVGVGHAGE WARKPLRFYV 201 RGSPWVSVVD RVAEQDTQA NAME: t0080full FROM: dfischer@indigo.cs.bgu.ac.il BY YOUR REQUEST I HAVE NOT USED THE FOLLOWING FOLDS: 1an3b 1az7 1bd9a 1bg8a 1bl0a 1cdaa 1hli 1illg 1kja The method used for this prediction was: MULT+gonnet+predss . Most similar fold: 1a3aa MOL_ID: 1; 2 MOLECULE: MANNITOL-SPECIFIC EII; 3 CHAIN: A, B, C, D; 4 FRAGMENT: IIA DOMAIN, RESIDUES 491 - 637; 5 EC: 2.7.1.69; 6 ENGINEERED: YES RANK Z-SCORE FOLD LENGTHALI %ID 1 5.50 1a3aa 126 23 199 2 5.33 1ndk 144 19 4-26 (a+b) ; Ferredoxin-like] 4-26-6-1-1-2- 3 4.45 1ghu 90 27 1997 new ; NMR SOLUTION STRUCTURE OF GROWTH FACTOR RECEPTOR-BOU 4 3.36 1ulp 133 19 1997 new ; N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FI 5 3.19 1dih_131-240 108 16 4-34 (a+b) ; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain] 4-34-1-2-1-1-1- 6 3.14 1ab2 105 19 4-41 (a+b) ; SH2-like] 4-41-1-1-7-1- 7 3.05 1aoic 109 20 199 8 3.04 1pspa 92 21 99--7-15--7-15 [MULTIDOMAIN ; ] [small ; Trefoil] [Small proteins ; Trefoil] 9 2.82 1u9a 144 15 1997 new ; HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 10 2.73 2ts1_228-319 86 20 1-42 alpha ; Tyrosyl-tRNA synthetase, middle domain] 1-42-1-1-1-1-1- 11 2.69 1pdnc 117 14 1-4 alpha ; DNA-binding 3-helical bundle] 1-4-1-4-1-1-1- 12 2.57 1paub 70 19 1997 new ; THE COMPLEX OF APOPAIN WITH 13 2.46 1lap_1-159 131 21 3-30 a/b ; Leucine aminopeptidase, N-terminal domain] 3-30-1-1-1-1-5- 14 2.38 1bnca_1-114 103 27 3-16 a/b ; Biotin carboxylase N-terminal domain-like] 3-16-1-1-1-1-1- 15 2.38 1ak6 143 17 1997 new ; DESTRIN, NMR, MINIMIZED AVERAGE STRUCTURE 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 5.0 +- 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. Additional information for your prediction can be found at the url: http://www.mbi.ucla.edu/people/frsvr/preds/24558t0080full 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. hhhhhhh hhhhhhhhh bbbbbbbbb TRLGLE..FFDQPAVPLARA..FLGQVLVRRLPNGTELRGRIVETE.... || | | | | | | || | | FKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTP hhhbbb hhhhhhhhhhhhhhhh hhhhhhhhhhhhhh bb bbb bbbbbbbb bbb AYLGPEDEAAHSRGGRQTPRNRGMFMKPGTLYVYIIYGMYF......... ||| | | | | | | TYLGESIAVPHG.....TVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIAR bbbb bbbb hhhhhhh bbbbbbbbbbbbb bbbb bbbb hhhhhhh hhhhhhhhhh .CMNISSQGDGACVLLRAL.EPLEGLETMRQLRST | | | | | LVIGIAARNNEHIQVITSLTNALDDESVIERLAHT bbbbbb hhhhhhhhhhhhh hhhhhhhhhhh 23%