SERVERNAME: frsvr_SDPMA TARGET: T0053 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0053 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1aoa 4.03 210 22 2 2tct 3.98 185 23 3 1ak1 3.94 243 18 4 1gne 3.46 207 21 5 1gne_80-232 3.40 135 23 6 1wab 3.21 198 19 7 1rgp 3.16 188 16 8 1lrv 2.97 205 23 9 1cola 2.72 188 20 10 1gsra 2.68 181 22 END NOTICE: the excludefolds excludes 2 library entries which are models. 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: cbik_salty 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: 264 December 21, 1998 09:28 Type: P Check: 7024 .. 1 MKKALLVVSF GTSYHDTCEK NIVACERDLA ASCPDRDLFR AFTSGMIIRK 51 LRQRDGIDID TPLQALQKLA AQGYQDVAIQ SLHIINGDEY EKIVREVQLL 101 RPLFTRLTLG VPLLSSHNDY VQLMQALRQQ MPSLRQTEKV VFMGHGASHH 151 AFAAYACLDH MMTAQRFPAR VGAVESYPEV DILIDSLRDE GVTGVHLMPL 201 MLVAGDHAIN DMASDDGDSW KMRFNAAGIP ATPWLSGLGE NPAIRAMFVA 251 HLHQALNMAV EEAA NAME: t0053 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: 1aoa MOL_ID: 1; 2 MOLECULE: T-FIMBRIN; 3 CHAIN: NULL; 4 FRAGMENT: ABD1 RANK Z-SCORE FOLD LENGTHALI %ID 1 4.03 1aoa 210 22 1998 2 3.98 2tct 185 23 1-62 alpha ; Tetracyclin repressor (Tet-repressor, TetR)] 1-62-1-1-1-1- 3 3.94 1ak1 243 18 1998 4 3.46 1gne 207 21 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 5 3.40 1gne_80-232 135 23 1-31 alpha ; Glutathione S-transferases, C-terminal domain] 1-31-1-1-1-8-2- 6 3.21 1wab 198 19 1997 new ; PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE 7 3.16 1rgp 188 16 1997 new ; GTPASE-ACTIVATION DOMAIN FROM RHOGAP 8 2.97 1lrv 205 23 1997 new ; A LEUCINE-RICH REPEAT VARIANT WITH A NOVEL REPETITI 9 2.72 1cola 188 20 6-1 MEMBR ; Toxins' membrane translocation domains] 6-1-1-1-1-1-1- 10 2.68 1gsra 181 22 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 11 2.67 1vpt 234 18 1997 new ; AS11 VARIANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPL 12 2.65 1lbd 202 18 1997 new ; LIGAND-BINDING DOMAIN OF THE HUMAN NUCLEAR RECEPT 13 2.47 1guha 209 17 99--1-31--3-27 [alpha ; Glutathione S-transferases, C-terminal domain] [ a/b ; Thioredoxin-like] [MULTIDOMAIN ; ] 14 2.44 1bcfa 140 19 1-21 alpha ; Ferritin like] 1-21-1-1-1-1-1- 15 2.40 1aky 185 18 3-21 a/b ; P-loop n. tri. hydrolases] 3-21-1-1-3-4- 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 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/24403t0053 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. hhhhhhhhhhhhhhh hhhhhhhh hhhhhh YHDTCEKNIVACERDLAASCPD...........RDLFRAFTSGMIIRK.. | | || ||| | | | YSEEEKYAFVNWINKALENDPDCRHVIPMNPNTDDLFKAVGDGIVLCKMI hhhhhhhhhhhhhhhh hhhhhhh hhhhhhhh hhhh hhhhhhhhhhh hhhhhhhhhhbb hhhh .LRQRDGIDID.......TPLQALQKLAAQGYQDVAIQSLHIIN.GDEYE | | || || | | | | | NLSVPDTIDERAINKKKLTPFIIQENLNL.ALNSASAIGCHVVNIGAEDL hhhh hhhhh hhhhhhhhhhh hhhhhhhh hhhhh hhhhhhhhhhhhhhhbbb b hhhhhhhhhhhhhhh bb KIVREVQLLRPLFTRLTLGV..PLLSSHNDYVQLMQALRQQMPSLRQTEK | | | | | | RAGKPHLVLGLLWQIIKIGLFADIELSRNEALTLEELMKL.......... hh hhhhhhhhhhhhhhhhhhhhhhh hhhhhhh bbbb hhhhhhhhhhhhhhhhhh hh b bb hhhhhh VVFMGHGASHHAFAAYACLDHMMTA....QRFPARVGAVESYPEVDILID | | | | | .......SPEELLLRWANFHLENSGWQKINNFSADIKDSKAYFH...LLN hhhhhhhhhhhhhhhhh hhhhhh hhh hhh bbbbb bbbbb hhhhhhhhh SLRDEGVTGVHLMPLMLVAGDHAINDMASDDGDSWKMRFNAAGIPATPWL | | | | | QIAPKGQKEGEPRIDINMSGFNETDDLKRAES....MLQQADKLGCRQFV hhh hhhhhhhh hhhhhh hhhhhhhhhhhhhh SG...LGENPAIRAMFVAHLHQ || ||| | TPADVVSGNPKLNLAFVANLFN hhhhhhh hhhhhhhhhhhhhh 19%