SERVERNAME: frsvr_SDPMA TARGET: T0085 PARAMETERS: excludefolds: 1kja 1hli 1bl0a 1an3b 1az7 1bd9a 1bg8a 1cdaa 1illg 1bst include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0085 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1fcdc 4.94 148 24 2 2mtac 4.89 111 24 3 1tf6a 4.59 147 25 4 153l 3.96 153 22 5 1ahja 3.91 146 22 6 1apya 3.47 153 14 7 155c 3.02 127 27 8 3c2c 3.01 91 29 9 451c 3.00 82 21 10 1fcdc_81-174 2.98 86 22 11 1ycc 2.96 94 22 12 2cdv 2.75 85 27 13 1xra_232-383 2.75 140 19 14 1cxa 2.64 114 25 15 1fgja_1-315 2.60 190 22 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: c554_niteu 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: 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 1bst The method used for this prediction was: MULT+gonnet+predss . Most similar fold: 1fcdc FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FCSD) RANK Z-SCORE FOLD LENGTHALI %ID 1 4.94 1fcdc 148 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 4.89 2mtac 111 24 1-3 alpha ; Cytochrome c] 1-3-1-1-4-3-1- 3 4.59 1tf6a 147 25 199 4 3.96 153l 153 22 4-2 (a+b) ; Lysozyme-like] 4-2-1-4-1-1- 5 3.91 1ahja 146 22 1998 6 3.47 1apya 153 14 1997 new ; HUMAN ASPARTYLGLUCOSAMINIDA 7 3.02 155c 127 27 1-3 alpha ; Cytochrome c] 1-3-1-1-2-5- 8 3.01 3c2c 91 29 1-3 alpha ; Cytochrome c] 1-3-1-1-2-1- 9 3.00 451c 82 21 1-3 alpha ; Cytochrome c] 1-3-1-1-4-2- 10 2.98 1fcdc_81-174 86 22 1-3 alpha ; Cytochrome c] 1-3-1-3-1-1-1- 11 2.96 1ycc 94 22 1-3 alpha ; Cytochrome c] 1-3-1-1-1-1- 12 2.75 2cdv 85 27 7-27 small ; Cytochrome c3] 7-27-1-1-1-2- 13 2.75 1xra_232-383 140 19 4-61 (a+b) ; S-adenosylmethionine synthetase. MAT] 4-61-1-1-1-1-3- 14 2.64 1cxa 114 25 1-3 alpha ; Cytochrome c] 1-3-1-1-2-3- 15 2.60 1fgja_1-315 190 22 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 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/24518t0085 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 b bbbb bb bb KDCVGC...HVDGFGQKGGYTIESPKPM.....LTGVGCESCHGP..GRN | || | | | || | || NNCAGCHGTHGNSVGPASP.SIAQMDPMVFVEVMEGFKSGEIASTIMGRI hh hhhhh hhhhhhhhhhhhhhh hhhhh hhhhhh hhhhhhhh hhhh FRG....DHRKSGQAFEK....SGKKTPRKDLAKKGQDFHFEERCSACHL | | | | | || | | | || AKGYSTADFEKMAGYFKQQTYQPAKQSFDTALADTGAKLH.DKYCEKCHV hh hhhhhhhhhhhhhh hhhhhhhhhhhh hhhh hh hhhhhhhhhhhhhhhhh bbbb NYEGSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMHEHY..KLEGV | | | | | || E.GGKPL.ADEEDYHILAGQWTPYLQYAMSDFREERRPMEKKMASKLREL h hhh hhhhhhhhhhhhhh hhhhhhhhhhh b hhhh FEGEPKFKFHDEFQ | | LKAEGDAGLDALFA hhhhhhhhhhhhhh 22%