SERVERNAME: frsvr_SDP TARGET: T0062 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDP.t0062 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 2cnd 11.46 230 22 2 1ndh 9.62 216 26 3 1fdr 7.50 217 21 4 2cnd_125-270 6.42 137 21 5 1a8p 6.13 230 19 6 1ndh_126-272 5.08 134 25 7 2pia 4.50 224 24 8 1que 4.16 228 24 9 1fnr 3.81 228 22 10 2abk 3.51 184 23 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: 232 December 24, 1998 14:28 Type: P Check: 7806 .. 1 TTLSCKVTSV EAITDTVYRV RIVPDAAFSF RAGQYLMVVM DERDKRPFSM 51 ASTPDEKGFI ELHIGASEIN LYAKAVMDRI LKDHQIVVDI PHGEAWLRDD 101 EERPMILIAG GTGFSYARSI LLTALARNPN RDITIYWGGR EEQHLYDLCE 151 LEALSLKHPG LQVVPVVEQP EAGWRGRTGT VLTAVLQDHG TLAEHDIYIA 201 GRFEMAKIAR DLFCSERNAR EDRLFGDAFA FI NAME: t0062 FROM: dfischer@indigo.cs.bgu.ac.il BY YOUR REQUEST I HAVE NOT USED THE FOLLOWING FOLDS: 1hli 1kja The method used for this prediction was: gonnet+predss . Most similar fold: 2cnd NADH-DEPENDENT NITRATE REDUCTASE (CYTOCHROME B RE 2 FRAGMENT) (E.C.1.6.6.1) COMPLEXED WITH FAD 3 (SYNCHROTRON X-RAY DIFFRACTION) RANK Z-SCORE FOLD LENGTHALI %ID 1 11.46 2cnd 230 22 99--2-24--3-12 [MULTIDOMAIN ; ] 99--2-24--3-12 [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 2 9.62 1ndh 216 26 99--2-24--3-12 [MULTIDOMAIN ; ] [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3 7.50 1fdr 217 21 1997 new ; FLAVODOXIN REDUCTASE FROM E. COLI 4 6.42 2cnd_125-270 137 21 3-12 a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3-12-1-1-2-1-1- 5 6.13 1a8p 230 19 199 6 5.08 1ndh_126-272 134 25 3-12 a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3-12-1-1-3-1-1- 7 4.50 2pia 224 24 99--2-24--3-12--4-9 [beta ; Reductase/elongation factor common domain] [ a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] [(a+b) ; beta-Grasp] [MULTIDOMAIN ; ] 99--2-24--3-12--4-9 [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] [ (a+b) ; beta-Grasp] 8 4.16 1que 228 24 1997 new ; X-RAY STRUCTURE OF THE FERREDOXIN:NADP+ REDUCTASE 9 3.81 1fnr 228 22 1997 new ; FERREDOXIN 10 3.51 2abk 184 23 1-47 alpha ; Endonuclease III] 1-47-1-1-1-1- 11 3.21 1wab 175 18 1997 new ; PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE 12 2.77 1atr_2-188 160 21 3-34 a/b ; Ribonuclease H-like motif] 3-34-1-1-1-1-12- 13 2.71 1gria 175 21 99--2-19--4-41 [beta ; SH3-like barrel] [(a+b) ; SH2-like] [MULTIDOMAIN ; ] 99--2-19--4-41 [beta ; SH3-like barrel] [(a+b) ; SH2-like] 14 2.66 2pth 162 25 1998 15 2.63 1tyfa 141 22 199 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 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. bbbbbbbbbbb bbbbbb bbbbbbb TLSCKVTSVEAITDTVYRVRI...VPDAAFSFRAGQYLMVVMDERDK... | | | || | | | RIHCRLVAKKELSRDVRLFRFSLPSPDQVLGLPIGKHIFVCATIEGKLCM bbbbbbbbbbbb bbbbbbbbb bbbbbbbb bbbb bb bbbbbbb hhhh hhhhhhh b RPFSMASTPDEKGFIELHIGASEINLYAK....AVMDRILKDHQI..... | | || | | | | | | RAYTPTSMVDEIGHFDLLVKVYFKNEHPKFPNGGLMTQYLDSLPVGSYID bbb bbbbbbbbb hhhhhhhhhh bbbb bbb bb b bbbbb hhhhhhhhhhhhhh ......VVDIPHGEAWL...RDDEERPMILIAGGTGFSYARSILLTALAR | | | || | | | VKGPLGHVEYTGRGSFVINGKQRNARRLAMICGGSGITPMYQIIQAVLRD bbbbb bbb bbbb bbb bbbbbbbbb hhhhhhhhhhhhhhh bbbbb hhhhhhhhhhhhhhhh bbbbbb NP..NRDITIYWGGREEQHLYDLCELEALSLKHPG....LQVVPVVEQPE | | | || | | | || QPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQVKRPE bbbbbbbb hhhhh hhhhhhhhhhhh bbbbbbbbb hhh hhhhhhhhhhhh bbbb AGWRGRTGTVLTAVLQDHGTLAEHDIY || | | ||| | | EGWKYSVGFVTEAVLREHVPEGGDDTL hh bbb hhhhhhhhh bbb 22% Additional information for your prediction can be found at the url: http://www.doe-mbi.ucla.edu/people/frsvr/preds/24449t0062/24449t0062.html p.s. if you need further information on this output, send an e-mail message to: fischer@mbi.ucla.edu