SERVERNAME: frsvr_SDP 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_SDP.t0080 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1a3aa 4.98 126 24 2 1bccd 4.04 179 22 3 1ndk 4.03 146 21 4 1tml 3.72 195 27 5 1bbrh 3.42 126 25 6 2tmda_1-340 3.41 187 24 7 1a74a 3.36 134 25 8 1dhy_1-132 3.29 128 25 9 1shca 2.99 146 20 10 1pspa 2.90 92 21 11 3sdpa 2.80 159 18 12 1lap_1-159 2.67 131 25 13 2naca_1-374 2.65 130 24 14 1gnwa 2.57 184 20 15 1rypg 2.55 153 25 END 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: 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: 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 4.98 1a3aa 126 24 199 2 4.04 1bccd 179 22 199 3 4.03 1ndk 146 21 4-26 (a+b) ; Ferredoxin-like] 4-26-6-1-1-2- 4 3.72 1tml 195 27 3-2 a/b ; Cellulases] 3-2-1-1-1-1- 5 3.42 1bbrh 126 25 2-26 beta ; Trypsin-like serine proteases] 2-26-1-2-4-2-5- 6 3.41 2tmda_1-340 187 24 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-6-1-3-1-1- 7 3.36 1a74a 134 25 199 8 3.29 1dhy_1-132 128 25 4-16 (a+b) ; 2,3-Dihydroxybiphenyl dioxygenase (DHDB, BPHC enzyme)] 4-16-1-1-1-1-1- 9 2.99 1shca 146 20 1997 new ; SHC PTB DOMAIN COMPLEXED WITH A TRKA RECEPTOR 10 2.90 1pspa 92 21 99--7-15--7-15 [MULTIDOMAIN ; ] [small ; Trefoil] [Small proteins ; Trefoil] 11 2.80 3sdpa 159 18 99--1-2--4-18 [alpha ; Long alpha-hairpin] [(a+b) ; Fe,Mn superoxide dismutase (SOD), C-terminal domain] [MULTIDOMAIN ; ] 99--1-2--4-18 [alpha ; Long alpha-hairpin] [(a+b) ; Fe,Mn superoxide dismutase (SOD), C-terminal domain] 12 2.67 1lap_1-159 131 25 3-30 a/b ; Leucine aminopeptidase, N-terminal domain] 3-30-1-1-1-1-5- 13 2.65 2naca_1-374 130 24 3-11 a/b ; Flavodoxin-like] 3-11-10-1-1-1-1-1 RC: 14 2.57 1gnwa 184 20 1997 new ; STRUCTURE OF GLUTATHIONE S-TRANSFERASE 15 2.55 1rypg 153 25 1998 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. hhh hhhhhhhhhhhhh bbbbbbbbbb LTRLGLE..FFDQPAVP..LARAFLGQVLVRRLPNGTELRGRIVETEA.. | || | | | | | | || | | LFKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLT hhhbbb hhhhhhhhhhhhhhhh hhhhhhhhhhhhhh b bbb bbbbbbbb bbb ..YLGPEDEAAHSRGGRQTPRNRGMFMKPGTLYVYIIYGMYF........ ||| | | | | | | | PTYLGESIAVPH...GTVEAKDR..VLKTGVVFCQYPEGVRFGEEEDDIA bbbb bbbb hhhhhhh bbbbbbbbbbbbb bbb bbbb hhhhhhh hhhhhhhhhhh ..CMNISSQGDGACVLLRALEP.LEGLETMRQLRSTLRKGTASRVLKDRE | | | | | | | RLVIGIAARNNEHIQVITSLTNALDDESVIERLAHTTSVDEVLELLAGRK bbbbbbb hhhhhhhhhhhhh hhhhhhhhhhh hhhhhhhhh 23% Additional information for your prediction can be found at the url: http://www.doe-mbi.ucla.edu/people/frsvr/preds/24558t0080full/24558t0080full.html p.s. if you need further information on this output, send an e-mail message to: fischer@mbi.ucla.edu