SERVERNAME: frsvr_SDPMA TARGET: T0063 PARAMETERS: excludefolds: 1an3b 1az7 1bd9a 1bg8a 1bl0a 1cdaa 1hli 1illg 1kja include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0063 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 2rspa 4.20 107 15 2 1ltsd 3.13 85 15 3 4fgf 3.05 118 9 4 1kul 3.03 94 15 5 1cgt_495-579 2.99 80 15 6 1nbta 2.98 65 12 7 1cto 2.95 107 15 8 1whi 2.89 109 10 9 2pia_1-103 2.85 97 7 10 3dpa2 2.81 97 13 11 2cnd_11-124 2.79 94 18 12 3hlab 2.75 85 7 13 2taaa_374-478 2.69 98 11 14 1ata 2.52 61 11 15 1pse 2.48 67 13 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: efp_helpy if51_caeel if51_chick if51_nicpl if51_soltu if51_yeast if52_chick if52_nicpl if52_yeast if53_soltu if54_soltu if55_soltu if5a_dicdi if5a_human if5a_maize if5a_medsa if5a_metja if5a_neucr if5a_rabit if5a_schpo if5a_sulac 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: 138 January 4, 1999 15:33 Type: P Check: 4692 .. 1 MVLKWVMSTK YVEAGELKEG SYVVIDGEPC RVVEIEKSKT GKHGSAKARI 51 VAVGVFDGGK RTLSLPVDAQ VEVPIIEKFT AQILSVSGDV IQLMDMRDYK 101 TIEVPMKYVE EEAKGRLAPG AEVEVWQILD RYKIIRVK NAME: t0063full 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: 2rspa ROUS SARCOMA VIRUS PROTEASE (/RSV PR$) RANK Z-SCORE FOLD LENGTHALI %ID 1 4.20 2rspa 107 15 2-29 beta ; Acid proteases] 2-29-1-1-4-1-1- 2 3.13 1ltsd 85 15 2-21 beta ; OB-fold] 2-21-1-1-1-1-1- 3 3.05 4fgf 118 9 2-23 beta ; beta-Trefoil] 2-23-1-1-1-1- 4 3.03 1kul 94 15 1997 new ; GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NM 5 2.99 1cgt_495-579 80 15 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-1-5-2-1-2- 6 2.98 1nbta 65 12 7-5 small ; Snake toxin-like] 7-5-1-1-10-1-3- 7 2.95 1cto 107 15 1997 new ; NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF THE 8 2.89 1whi 109 10 1997 new ; RIBOSOMAL PROTEIN L 9 2.85 2pia_1-103 97 7 2-24 beta ; Reductase/elongation factor common domain] 2-24-1-2-1-1-1- 10 2.81 3dpa2 97 13 199 11 2.79 2cnd_11-124 94 18 2-24 beta ; Reductase/elongation factor common domain] 2-24-1-1-2-1-1- 12 2.75 3hlab 85 7 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-1-2-4-4-1- 13 2.69 2taaa_374-478 98 11 2-41 beta ; alpha-Amylases, beta-sheet domain] 2-41-1-1-2-2-2- 14 2.52 1ata 61 11 7-24 small ; Ascaris trypsin inhibitor] 7-24-1-1-1-1- 15 2.48 1pse 67 13 2-19 beta ; SH3-like barrel] 2-19-5-1-1-1- 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 BELOW THIS THRESHOLD YOUR PREDICTION IS NOT 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/24557t0063full 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. bbbb bbbbbbbb bbbbbbbbbbb YVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVF.DGGKRTLSLPVDAQ | || | | | | AMTMEHKDRPLVRVILTNTGSHPVKQRSVYITALLDSGADITIISEEDWP bbbbbbbb bbbbbbbb bbb bbbbb bbbbb VEVPIIEKFTAQILSVSGDVIQLMDMRDYKTIEVP | | | | | | | | TDWPVMEAAGIPMRK.SRDMIELGVINRDGSLERP bbb bbb b bbbbbb 18%