SERVERNAME: frsvr_SDP TARGET: T0070 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDP.t0070 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 2omf 11.14 284 24 2 1prn 10.79 273 25 3 2por 10.40 280 23 4 1a0tp 5.77 290 28 5 1nbca 4.78 146 21 6 1csee 4.48 215 23 7 1mal 4.24 304 20 8 1jxra 3.49 255 23 9 3cox_5-318 3.47 241 24 10 1thm 3.44 263 16 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: 332 December 25, 1998 04:18 Type: P Check: 4899 .. 1 QSSVTLFGIV DTNVAYVNKD AAGDSRYGLG TSGASTSRLG LRGTEDLGGG 51 LKAGFWLEGE IFGDDGNASG FNFKRRSTVS LSGNFGEVRL GRDLVPTSQK 101 LTSYDLFSAT GIGPFMGFRN WAAGQGADDN GIRANNLISY YTPNFGGFNA 151 GFGYAFDEKQ TIGTADSVGR YIGGYVAYDN GPLSASLGLA QQKTAVGGLA 201 TDRDEITLGA SYNFGVAKLS GLLQQTKFKR DIGGDIKTNS YMLGASAPVG 251 GVGEVKLQYA LYDQKAIDSK AHQITLGYVH NLSKRTALYG NLAFLKNKDA 301 STLGLQAKGV YAGGVQAGES QTGVQVGIRH AF NAME: t0070 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: 2omf MOL_ID: 1; 2 MOLECULE: MATRIX PORIN OUTER MEMBRANE PROTEIN F; 3 CHAIN: NULL; 4 SYNONYM: MATRIX PORIN, OMPF PORIN; 5 BIOLOGICAL_UNIT: TRIMER (CRYSTALLOGRAPHIC) RANK Z-SCORE FOLD LENGTHALI %ID 1 11.14 2omf 284 24 6-6 MEMBR ; Porins] 6-6-1-1-1-1- 2 10.79 1prn 273 25 6-6 MEMBR ; Porins] 6-6-1-1-1-3- 3 10.40 2por 280 23 6-6 MEMBR ; Porins] 6-6-1-1-1-2- 4 5.77 1a0tp 290 28 1998 5 4.78 1nbca 146 21 1997 new ; BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN 6 4.48 1csee 215 23 3-23 a/b ; Subtilases] 3-23-1-1-1-1-1- 7 4.24 1mal 304 20 6-6 MEMBR ; Porins] 6-6-1-2-1-1- 8 3.49 1jxra 255 23 1997 new ; STRUCTURE OF YEAST PROTEINASE 9 3.47 3cox_5-318 241 24 3-4 a/b ; FAD (also NAD)-binding motif] 3-4-1-2-1-1-1- 10 3.44 1thm 263 16 3-23 a/b ; Subtilases] 3-23-1-1-2-1- 11 2.96 1ctn_133-441 266 22 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-1-6-4-1-1- 12 2.69 2er7e 278 20 2-29 beta ; Acid proteases] 2-29-1-2-1-1-2- 13 2.68 2ayh 172 25 2-17 beta ; ConA-like lectins/glucanases] 2-17-1-2-1-2- 14 2.62 6tmne 242 21 99--1-41--4-40 [MULTIDOMAIN ; ] [alpha ; Thermolysin-like metalloproteases, C-terminal domain] [(a+b) ; Metzincins, catalytic (N-terminal) domain] 15 2.60 1yna 170 22 1997 new ; ENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4 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. bbbbbbbb b bbb QSSVTLFGIVDTNVAYVNKDAAGDSRYGLGTSGASTSRLGLRGTEDLGGG | | | | | | || | ||| | GNKVDLYGKA.VGLHYFSK.GNGENSYG.GNGDMTYARLGFKGETQINSD bbbbbbbbbb bbbbbb bbbbbbbbbbbbbbbb b bbbbbbb b bbbbbb bbbb LKAGFWLEGEIFGDDGNASGFNFKRRSTVSLSGNF....GEVRLGRDLVP | | | | | || LTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYG. bbbbbbbbbbbbb bbbbbbbbbbbb bbbbbbbbbb bb bbbbbbb TSQKLTSYDLFSATGIGPFMGFRNWAAGQGADDNGI...RANNLISYYTP || | | | | | | | .....VVYDALGYTDMLPEFG......GDTAYSDDFFVGRVGGVATYRNS hhhhhhhhh bbbbbbbbbbb bbb bbb b bbbbbb bbb NFGGFNAGFGYAFDEKQTIGTAD......SVGRYIGGYVAYDNG..PLSA || | | | | | | | || | NFFGLVDGLNFAV...QYLGKNERDTARRSNGDGVGGSISYEYEGFGIVG hhhhh bbbbbb bbbb bbbbbbbbbbb bbbbbb bb h hhhhhhhh SLGLA.....QQKTAVG..........GLATDRDEITLGASYNFGVAKLS | | | | || | | | | | | AYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAA..NYGETRNA bbbbbbbhhhhhh bbbbbbbbbbbbbb bbbbbb bbbbbbb hhhhh bbb bb bbbbbbbb GLLQQTKFKRDIGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSK || | || | | | | TPI.TNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGI bbb bb bbbbbbbbbbbbbbbbbb bbbbbbbbbbbbbbbb bbbbb bb bbbbb hhhhhhh bbbbbbbbbbb A.....HQITLGYVHNLSKRTALYGNLAFLKNKDASTLGLQAKGVYAGGV | | | || | | GDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGI bbbbbbbbbbbbbbbbb bbbbbbbbbbbb bbbbbb 23% Additional information for your prediction can be found at the url: http://www.doe-mbi.ucla.edu/people/frsvr/preds/24455t0070/24455t0070.html p.s. if you need further information on this output, send an e-mail message to: fischer@mbi.ucla.edu