SERVERNAME: frsvr_SDPMA TARGET: T0083 PARAMETERS: excludefolds: 1an3b 1az7 1bd9a 1bg8a 1bl0a 1cdaa 1hli 1illg 1kja include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0083 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1lmb3 3.22 86 26 2 1vhba 2.96 130 12 3 1env 2.90 112 21 4 1dkga 2.54 130 23 5 1jli 2.53 105 12 6 1cpq 2.47 113 17 7 1ash 2.43 126 12 8 1a7va 2.43 108 16 9 1bmfg 2.42 120 13 10 2wrpr 2.38 103 15 11 1r69 2.24 63 16 12 1beo 2.23 98 18 13 1gfi_61-181 2.20 108 14 14 2hie 2.18 135 7 15 2end 2.18 113 18 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: cyns_ecoli cyns_synp7 cyns_syny3 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: 156 January 4, 1999 15:30 Type: P Check: 5589 .. 1 MIQSQINRNI RLDLADAILL SKAKKDLSFA EIADGTGLAE AFVTAALLGQ 51 QALPADAARL VGAKLDLDED SILLLQMIPL RGCIDDRIPT DPTMYRFYEM 101 LQVYGTTLKA LVHEKFGDGI ISAINFKLDV KKVADPEGGE RAVITLDGKY 151 LPTKPF NAME: T0083full 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: 1lmb3 LAMBDA REPRESSOR/OPERATOR COMPLEX RANK Z-SCORE FOLD LENGTHALI %ID 1 3.22 1lmb3 86 26 1-25 alpha ; lambda repressor-like DNA-binding domains] 1-25-1-2-1-1-1- 2 2.96 1vhba 130 12 1998 3 2.90 1env 112 21 1997 new ; ATOMIC STRUCTURE OF THE ECTODOMAIN FROM HIV-1 GP41 4 2.54 1dkga 130 23 1997 new ; THE NUCLEOTIDE EXCHANGE FACT 5 2.53 1jli 105 12 1997 new ; HUMAN INTERLEUKIN 3 (IL-3) MUTANT WITH TRUNCATION 6 2.47 1cpq 113 17 1997 new ; CYTOCHROME C' FROM RHODOPSEUDOMONAS CAPSULA 7 2.43 1ash 126 12 1-1 alpha ; Globin-like] 1-1-1-1-10-1- 8 2.43 1a7va 108 16 199 9 2.42 1bmfg 120 13 1997 new ; BOVINE MITOCHONDRIAL F1-ATPA 10 2.38 2wrpr 103 15 1-57 alpha ; Trp repressor] 1-57-1-1-1-1-1- 11 2.24 1r69 63 16 1-25 alpha ; lambda repressor-like DNA-binding domains] 1-25-1-2-2-1- 12 2.23 1beo 98 18 1997 new ; BETA-CRYPTOGEIN 13 2.20 1gfi_61-181 108 14 1-40 alpha ; Transducin (alpha subunit), insertion domain] 1-40-1-1-1-2-3- 14 2.18 2hie 135 7 10-1 NON ; Theoretical Models] 10-1-1-3-1-1- 15 2.18 2end 113 18 1-14 alpha ; T4 endonuclease V] 1-14-1-1-1-1- 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/24555T0083full 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. hhhhhhhhhhhhhhhhhhhhhh hhhhhhhh hhhhhhhhhhhhhhh QSQINRNIRLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQA | | | || || | | | | | LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINA hhhhhhhhhhhhhhhhhhhhhhh hhhhhhhhh hhhhhhhhhh hhhhhhhhhhhh hhhhhhh hhhhhhhhhh LPADAARLVGAKLDLDEDSILLLQMIPLRGCIDDRIPTDPTMYRFYEML | | | | | | | || LNAYNAALLAKILKVSVEE............FSPSIARE..IYEMYEAV hhhhhhhhhhhhh hhhh hhhhhhhh hhhhhh 24%