SERVERNAME: frsvr_SDP TARGET: T0085 PARAMETERS: excludefolds: 1kja 1hli 1bl0a include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDP.t0085 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1fcdc 4.90 144 24 2 1fgja_1-315 4.60 199 26 3 1tf6a 4.39 147 27 4 2mtac 4.17 119 24 5 153l 3.73 156 23 6 1trea 3.67 188 25 7 1ahja 3.63 146 22 8 1etpa 3.03 143 22 9 1cxa 2.96 110 27 10 1fcdc_81-174 2.75 86 22 11 155c 2.74 127 27 12 451c 2.71 81 20 13 2cdv 2.69 85 32 14 1cfo 2.67 63 24 15 1xra_232-383 2.58 139 20 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: 211 December 31, 1998 16:23 Type: P Check: 1809 .. 1 ADAPFEGRKK CSSCHKAQAQ SWKDTAHAKA MESLKPNVKK EAKQKAKLDP 51 AKDYTQDKDC VGCHVDGFGQ KGGYTIESPK PMLTGVGCES CHGPGRNFRG 101 DHRKSGQAFE KSGKKTPRKD LAKKGQDFHF EERCSACHLN YEGSPWKGAK 151 APYTPFTPEV DAKYTFKFDE MVKEVKAMHE HYKLEGVFEG EPKFKFHDEF 201 QASAKPAKKG K NAME: t0085 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: 1fcdc FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FCSD) RANK Z-SCORE FOLD LENGTHALI %ID 1 4.90 1fcdc 144 24 99--1-3--1-3 [alpha ; Cytochrome c] [All alpha ; Cytochrome c] [MULTIDOMAIN ; ] 99--1-3--1-3 [alpha ; Cytochrome c] [All alpha ; Cytochrome c] 2 4.60 1fgja_1-315 199 26 1998 3 4.39 1tf6a 147 27 199 4 4.17 2mtac 119 24 1-3 alpha ; Cytochrome c] 1-3-1-1-4-3-1- 5 3.73 153l 156 23 4-2 (a+b) ; Lysozyme-like] 4-2-1-4-1-1- 6 3.67 1trea 188 25 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-10-1-1-5-1- 7 3.63 1ahja 146 22 1998 8 3.03 1etpa 143 22 1997 new ; CYTOCHROME C4 FROM PSEUDOMONAS STUTZE 9 2.96 1cxa 110 27 1-3 alpha ; Cytochrome c] 1-3-1-1-2-3- 10 2.75 1fcdc_81-174 86 22 1-3 alpha ; Cytochrome c] 1-3-1-3-1-1-1- 11 2.74 155c 127 27 1-3 alpha ; Cytochrome c] 1-3-1-1-2-5- 12 2.71 451c 81 20 1-3 alpha ; Cytochrome c] 1-3-1-1-4-2- 13 2.69 2cdv 85 32 7-27 small ; Cytochrome c3] 7-27-1-1-1-2- 14 2.67 1cfo 63 24 1997 new ; CYTOCHROME C551.5, NMR, 20 STRUCTURES 15 2.58 1xra_232-383 139 20 4-61 (a+b) ; S-adenosylmethionine synthetase. MAT] 4-61-1-1-1-1-3- 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. bbbbb bbbb bb bb KDCVGCHVDGFGQKGGYTIESPKPM........LTGVGCESCHGP..GRN | ||| | | | | | || NNCAGCH.GTHGNSVGPASPSIAQMDPMVFVEVMEGFKSGEIASTIMGRI hh hhhhh hhhhhhhhhhhhhhh hhhhh hhhhhh hhhhhhhh hhhh FRG....DHRKSGQAFEK....SGKKTPRKDLAKKGQDFHFEERCSACHL | | | | | || | | | || AKGYSTADFEKMAGYFKQQTYQPAKQSFDTALADTGAKLH.DKYCEKCHV hh hhhhhhhhhhhhhh hhhhhhhhhhhh hhhh hh hhhhhhhhhhhhhhhhh NYEGSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMHEHY | | | | | E.GGKPL.ADEEDYHILAGQWTPYLQYAMSDFREERRPMEKKM h hhh hhhhhhhhhhhhhh hhhh 23% Additional information for your prediction can be found at the url: http://www.doe-mbi.ucla.edu/people/frsvr/preds/24518t0085/24518t0085.html p.s. if you need further information on this output, send an e-mail message to: fischer@mbi.ucla.edu