SERVERNAME: frsvr_SDPMA2 TARGET: T0068 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA2.t0068 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1rmg 12.85 323 17 2 1wba 4.27 163 18 3 1mdah 4.11 302 13 4 1gof_151-537 3.52 342 13 5 1ulp 3.44 150 11 6 2fbjh 2.96 205 12 7 2pec 2.96 273 15 8 1tie 2.78 152 12 9 1pgs 2.58 279 10 10 1fnf 2.57 298 13 11 1ppfe 2.45 189 12 12 1hgea 2.44 309 13 13 1afna_11-166 2.42 142 14 14 1idja 2.25 337 12 15 2bbkh 2.20 312 11 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: 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 (MULT2+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 MULT2+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: MULT2+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 12.85 1rmg 323 17 1998 2 4.27 1wba 163 18 1997 new ; WINGED BEAN ALBUMIN 3 4.11 1mdah 302 13 2-39 beta ; 7-bladed beta-propeller] 2-39-2-1-1-1-3- 4 3.52 1gof_151-537 342 13 2-39 beta ; 7-bladed beta-propeller] 2-39-1-1-1-1-1- 5 3.44 1ulp 150 11 1997 new ; N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FI 6 2.96 2fbjh 205 12 99--2-1--2-1 [MULTIDOMAIN ; ] [beta ; Immunoglobulin-like beta-sandwich] [All beta ; Immunoglobulin-like beta-sandwich] 7 2.96 2pec 273 15 2-47 beta ; Single-stranded right-handed beta-helix] 2-47-1-1-1-1- 8 2.78 1tie 152 12 2-23 beta ; beta-Trefoil] 2-23-3-1-1-1- 9 2.58 1pgs 279 10 99--2-10--2-10 [MULTIDOMAIN ; ] [beta ; Glycosyl-asparaginase] [All beta ; Glycosyl-asparaginase] 10 2.57 1fnf 298 13 99--2-1--2-1--2-1--2-1 [beta ; Immunoglobulin-like beta-sandwich] 11 2.45 1ppfe 189 12 2-26 beta ; Trypsin-like serine proteases] 2-26-1-2-3-1-1- 12 2.44 1hgea 309 13 2-13 beta ; Segmented RNA-genome viruses' proteins] 2-13-1-2-1-1-7- 13 2.42 1afna_11-166 142 14 2-5 beta ; Cupredoxins] 2-5-1-3-1-2-1- 14 2.25 1idja 337 12 1997 new ; PECTIN LYASE A 15 2.20 2bbkh 312 11 2-39 beta ; 7-bladed beta-propeller] 2-39-2-1-1-1-1- 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 | | | | | | | | | | GAVADNSTDVGPAITSAWAACKSGGLVYIPS........GNYALNTWVTL 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 bbb bbbbbb DTVYEKKEGSNVPDWSDITFKDVT..........SETKGVVVLNGENAKK | | | DGYW...SSMTAVAGDGVQLNNITVKNWKGTEANGATRPPIRVVCSDTAP bb bbbbbbbbbbbbbbb bbbbbb bbbb bb PIEVTMKNVKL | CTDLTLEDIAI bbbbbbbbbbb 17%