SERVERNAME: frsvr_SDPMA TARGET: T0068 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0068 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1rmg 6.12 323 17 2 1wba 4.72 163 18 3 1akp 3.26 106 11 4 1cgt 3.04 85 11 5 1sfp 3.00 109 12 6 1umua 2.82 93 20 7 1acx 2.77 100 15 8 1ulp 2.63 150 11 9 1pkn 2.58 97 10 10 1tocr 2.55 102 7 END NOTICE: the excludefolds excludes 2 library entries which are models. The server's output is: 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: mpa2_cryja pehx_erwch pgl1_arath pgl1_colln pgl1_erwca pgl1_sclsc pgl2_arath pgl2_erwca pglr_actch pglr_brana pglr_burso pglr_cocca pglr_gosba pglr_goshi pglr_maize pglr_maldo pglr_medsa pglr_oenor pglr_prupe pglr_tobac pgls_maize pglt_maize pglx_cocca 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: 376 December 21, 1998 16:59 Type: P Check: 614 .. 1 SDSRTVSEPK TPSSCTTLKA DSSTATSTIQ KALNNCDQGK AVRLSAGSTS 51 VFLSGPLSLP SGVSLLIDKG VTLRAVNNAK SFENAPSSCG VVDKNGKGCD 101 AFITAVSTTN SGIYGPGTID GQGGVKLQDK KVSWWELAAD AKVKKLKQNT 151 PRLIQINKSK NFTLYNVSLI NSPNFHVVFS DGDGFTAWKT TIKTPSTARN 201 TDGIDPMSSK NITIAYSNIA TGDDNVAIKA YKGRAETRNI SILHNDFGTG 251 HGMSIGSETM GVYNVTVDDL KMNGTTNGLR IKSDKSAAGV VNGVRYSNVV 301 MKNVAKPIVI DTVYEKKEGS NVPDWSDITF KDVTSETKGV VVLNGENAKK 351 PIEVTMKNVK LTSDSTWQIK NVNVKK NAME: t0068 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: MULT+gonnet+predss . Most similar fold: 1rmg MOL_ID: 1; 2 MOLECULE: RHAMNOGALACTURONASE A; 3 CHAIN: NULL; 4 SYNONYM: RGASE A; 5 EC: 3.2.1.-; 6 ENGINEERED: YES RANK Z-SCORE FOLD LENGTHALI %ID 1 6.12 1rmg 323 17 1998 2 4.72 1wba 163 18 1997 new ; WINGED BEAN ALBUMIN 3 3.26 1akp 106 11 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-6-1-4-1- 4 3.04 1cgt_495-579 85 11 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-1-5-2-1-2- 5 3.00 1sfp 109 12 199 6 2.82 1umua 93 20 1997 new ; STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF T 7 2.77 1acx 100 15 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-6-1-3-1- 8 2.63 1ulp 150 11 1997 new ; N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FI 9 2.58 1pkn_116-217 97 10 2-33 beta ; Pyruvate kinase beta-barrel domain] 2-33-1-1-1-1-1- 10 2.55 1tocr 102 7 1997 new ; STRUCTURE OF SERINE PROTEINASE 11 2.54 1sxl 93 10 4-26 (a+b) ; Ferredoxin-like] 4-26-7-1-2-1- 12 2.53 1ksr 91 18 1997 new ; THE REPEATING SEGMENTS OF THE F-ACTIN CROSS-LINKI 13 2.46 2mcm 98 9 2-1 beta ; Immunoglobulin-like beta-sandwich] 2-1-6-1-1-1- 14 2.41 1tit 87 13 1997 new ; TITIN, IG REPEAT 27, NMR, MINIMIZED AVERAGE STRUCTU 15 2.29 1bgh 83 7 2-21 beta ; OB-fold] 2-21-6-1-1-1- 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 ABOVE THIS THRESHOLD Additional information for your prediction can be found at the url: http://www.mbi.ucla.edu/people/frsvr/preds/24409t0068 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. hhhhhhhhhh bbbbb bbbb bbb bb TTLKADSSTATSTIQKALNNCDQGKAVRLSAGSTSVFLSGPLSLPSGVSL | | | | | | || | | | GAVADNSTDVGPAITSAWAACKSGGLVYIP........SGNYALNTWVTL h hhhhhhhhhhhhh bbbbb bbbbb bbb bbb bbbbb bbbb bbbbbbb b bbbb LIDKGVTLRAVNNAKSFENAPSSCGVVDKNGKGCDAFITAVSTTNSGIYG | | | || TGGSATAIQL.............DGIIYRTGTASGNMIAVTDTTDFELFS bbbbbbbbbb bbbbbbb bbbbbbbbbbbbbbbb bb hhhhhhhhh bbbbb bb P...GTIDGQGGVKLQDKKVSWWELAADAKVKKLKQNTPRLIQINKSKNF | | | | | | STSKGAVQGFGYVYHAE.................GTYGARILRLTDVTHF bbbbb hhhhhh bbbbbbbbbbb bbbbbbbb bbbbbb bbbbbb b TLYNVSLINSPNFHVVFSDGDGFTAWKTTIKTPSTARNTDGIDPMSSKNI | | || | |||| | || SVHDIILVDAPAFHFTMDTCSDGEVYNMAIRGGNEG.GLDGIDVWGS.NI bbbbbbbbb bbbbbbbbbbbbbbbbbbb bbbbbbb bb bbbbbbb bbb bb b bbbb TIAYSNIATGDDNVAIKAYKGRAETRNISILHNDFGTGHGMSIGS..ETM | | | || | || WVHDVEVTNKDECVTVKSP.....ANNILVESIYCNWSGGCAMGSLGADT bbbbbbbb bbbbbbbbb bbbbbbbbbbbbb bbbbbbb b bbbbbbbbbb bbbb b bbbbbbbhhh bbb GVYNVTVDDLKMNGTTNGLRIKSDKSAAGVVNGVRYSNVVMKNVAKPIVI | | | | | | | | DVTDIVYRNV.YTWSSNQMYMIKSNGGSGTVSNVLLENFIGHGNAYSLDI bbbbbbbbbb bbbb bbbbbbb bbbbbbbbbbbbbbbbb bbbb bbbbb bb b bbbbbb bb DTVYEKKEGSNVPDW..SDITFKD.....VTSETKGVVVLNGENAKKPIE | || | | DGYWSSMTAVAGDGVQLNNITVKNWKGTEANGATRPPIRVVCSDTAPCTD bb bbbbbbbbbbbbbbb bbbbbb bbb bb bb VTMKNVKL | LTLEDIAI bbbbbbbb 18%