SERVERNAME: frsvr_SDPMA TARGET: T0054 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0054 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1cgme 4.77 148 20 2 1pp2l 4.72 112 22 3 3gapa_1-137 3.87 111 23 4 1poxa_183-365 3.73 156 21 5 1bvh 3.68 133 16 6 1pii_253-452 3.34 160 21 7 1lz1 3.23 126 18 8 1scub_245-388 3.17 143 13 9 2dlda_104-300 3.07 161 19 10 1rvea 2.99 177 19 11 1gdha_101-291 2.95 144 20 12 1occh 2.89 73 12 13 2pna 2.82 97 21 14 1ag2 2.81 89 21 15 1icea 2.73 158 14 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: vanx_entfa vanx_entfc 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: 202 December 30, 1998 09:44 Type: P Check: 7047 .. 1 MEIGFTFLDE IVHGVRWDAK YATWDNFTGK PVDGYEVNRI VGTYELAESL 51 LKAKELAATQ GYGLLLWDGY RPKRAVNCFM QWAAQPENNL TKESYYPNID 101 RTEMISKGYV ASKSSHSRGS AIDLTLYRLD TGELVPMGSR FDFMDERSHH 151 AANGISCNEA QNRRRLRSIM ENSGFEAYSL EWWHYVLRDE PYPNSYFDFP 201 VK NAME: t0054 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: 1cgme CUCUMBER GREEN MOTTLE MOSAIC VIRUS (CGMMV), WATER 2 STRAIN (FIBER DIFFRACTION) RANK Z-SCORE FOLD LENGTHALI %ID 1 4.77 1cgme 148 20 1-20 alpha ; Four-helical up-and-down bundle] 1-20-5-1-2-1-1- 2 4.72 1pp2l 112 22 1-70 alpha ; Phospholipase A2] 1-70-1-2-1-3-1- 3 3.87 3gapa_1-137 111 23 2-49 beta ; Double-stranded beta-helix] 2-49-2-1-1-1-2- 4 3.73 1poxa_183-365 156 21 3-17 a/b ; Pyruvate oxidase and decarboxylase, middle domain] 3-17-1-1-2-1-2- 5 3.68 1bvh 133 16 3-25 a/b ; Phosphotyrosine protein phosphatases I] 3-25-1-1-1-1- 6 3.34 1pii_253-452 160 21 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-7-1-2-1-1- 7 3.23 1lz1 126 18 4-2 (a+b) ; Lysozyme-like] 4-2-1-2-1-8- 8 3.17 1scub_245-388 143 13 3-11 a/b ; Flavodoxin-like] 3-11-3-1-2-1-1- 9 3.07 2dlda_104-300 161 19 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-4-4-1-1- 10 2.99 1rvea 177 19 3-32 a/b ; Restriction endonucleases] 3-32-1-2-1-1-4- 11 2.95 1gdha_101-291 144 20 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-4-2-1-1- 12 2.89 1occh 73 12 1997 new ; STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT T 13 2.82 2pna 97 21 4-41 (a+b) ; SH2-like] 4-41-1-1-6-1- 14 2.81 1ag2 89 21 1997 new ; PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 15 2.73 1icea 158 14 3-8 a/b ; Interleukin-1beta converting enzyme (a cysteine protease)] 3-8-1-1-1-1-1- 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/24503t0054 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 hhhhhhhhhhhhhhhhh bbbb hhhhh GKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNC | | || | | || YNPITPSKLIAFSASYVPVRTLLN..FLVASQG......TAFQTQAGRDS hhhhhh hhhhh hhhhhh hhh hhh hhhhhhhh bbbb bbbbb FMQ.WAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLY | | | | | | | | FRESLSALPSSVVDINSRFPD........AGFYAFLNGPVLRPIFVSLLS hhhhhhhh hhhhhhhh bb bbbb hhhhh hhhhhhhhh RLDTGELVPMGSRFDFMDERSHHAANGISCNEAQN......RRRLRSIME || | | | | | STDTRNRV.....IEVVDPSNPTTAESLNAVKRTDDASTAARAEIDNLIE hh hhhhhhhhhhhhhhhhhhhhh h bhhhhhhhh ..NSGFEAYSLEWWHYVL || | SISKGFDVYDRASFEAAF hhhh hhhhhhhhh 18%