SERVERNAME: frsvr_SDPMA TARGET: T0057 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA.t0057 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1gd1o 16.11 294 19 2 1gd1o_0-333 7.48 144 20 3 1gd1o_149-312 4.74 151 19 4 4mdha 4.18 298 18 5 1llda 3.96 280 19 6 1fmta 3.39 265 15 7 8adh_175-324 2.98 107 22 8 1dik_2-376 2.89 304 13 9 1dapa 2.85 268 19 10 1trka_338-534 2.84 159 17 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: g3p_metbr g3p_metfe g3p_metfo g3p_pyrwo g3p_sulso 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: 340 December 21, 1998 05:24 Type: P Check: 8932 .. 1 MINVAVNGYG TIGKRVADAI IKQPDMKLVG VAKTSPNYEA FIAHRRGIRI 51 YVPQQSIKKF EESGIPVAGT VEDLIKTSDI VVDTTPNGVG AQYKPIYLQL 101 QRNAIFQGGE KAEVADISFS ALCNYNEALG KKYIRVVSCN TTALLRTICT 151 VNKVSKVEKV RATIVRRAAD QKEVKKGPIN SLVPDPATVP SHHAKDVNSV 201 IRNLDIATMA VIAPTTLMHM HFINITLKDK VEKKDILSVL ENTPRIVLIS 251 SKYDAEATAE LVEVARDLKR DRNDIPEVMI FSDSIYVKDD EVMLMYAVHQ 301 ESIVVPENID AIRASMKLMS AEDSMRITNE SLGILKGYLI NAME: t0057 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: 1gd1o $HOLO-*D-*GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENAS 2 (E.C.1.2.1.12) RANK Z-SCORE FOLD LENGTHALI %ID 1 16.11 1gd1o 294 19 [MULTIDOMAIN ] 99--3-15--4-34 [(a/b) ; NAD(P)-binding Rossmann-fold domains] [ (a+b) ; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain] 3-15-1-3-1-2-1-1 RC:, 2 7.48 1gd1o_0-333 144 20 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-3-1-2-1-1 RC:, 3 4.74 1gd1o_149-312 151 19 4-34 (a+b) ; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain] 4-34-1-1-1-2-1-1 4 4.18 4mdha 298 18 99--3-15--4-74 a/b ; NAD(P)-binding Rossmann-fold domains] [(a+b) ; Lactate & malate dehydrogenases, C-terminal domain] [MULTIDOMAIN ; ] 99--3-15--4-74 [(a/b) ; NAD(P)-binding Rossmann-fold domains] [ (a+b) ; Lactate & malate dehydrogenases, C-terminal domain] 5 3.96 1llda 280 19 99--3-15--4-74 a/b ; NAD(P)-binding Rossmann-fold domains] [(a+b) ; Lactate & malate dehydrogenases, C-terminal domain] [MULTIDOMAIN ; ] 99--3-15--4-74 [(a/b) ; NAD(P)-binding Rossmann-fold domains] [ (a+b) ; Lactate & malate dehydrogenases, C-terminal domain] 6 3.39 1fmta 265 15 998 7 2.98 8adh_175-324 107 22 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-1-1-1-8-1 8 2.89 1dik_2-376 304 13 4-66 (a+b) ; ATP-grasp] 4-66-1-4-1-1-1-1 9 2.85 1dapa 268 19 1997 new ; C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH N ] 10 2.84 1trka_338-534 159 17 3-20 a/b ; Thiamin-binding] 3-20-1-2-1-1-1-2 11 2.83 1btma 238 18 3-1 a/b ; beta/alpha (TIM)-barrel] 3-1-10-1-1-7-1-1 12 2.71 1dkxa 205 18 1997 new ; THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH] 13 2.69 1hlpa 274 15 99--3-15--4-74 a/b ; NAD(P)-binding Rossmann-fold domains] [(a+b) ; Lactate & malate dehydrogenases, C-terminal domain] [MULTIDOMAIN ; ] 99--3-15--4-74 [(a/b) ; NAD(P)-binding Rossmann-fold domains] [ (a+b) ; Lactate & malate dehydrogenases, C-terminal domain] 14 2.69 1be1 121 20 998 15 2.65 1llda_7-149 131 18 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-5-3-6-1-1 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/24397t0057 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. bbbbb hhhhhhhhhh bbbbbb hhhhhhhhh MINVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHR..... | || | || | | | || | | AVKVGINGFGRIGRNVFRAALKNPDIEVVAVNDLTDANTLAHLLKYDSVH bbbbbb hhhhhhhhhh bbbbbbb hhhhhhhhhbb h bb hhhhhh hhh b hhhhhh ................RGIRIYVPQQSIKK...FEESGIPVAGTVEDLIK | | | | | GRLDAEVSVNGNNLVVNGKEIIVKAERDPENLAWGEIGV........... bb bbbb bbbb bbbbbb hhh hhhh bbbb hhhh bbb bbbbbbb hh TSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYN |||| | | | | ..DIVVESTGRFTKREDAAKHLEAGAKKVIISAPANEDITIVMGVNQDKY bbbb hhhh hhhh bbbb bb hhh hhh bbbbb bbbbhhhhhh EALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKK | || | | | | DK.AHHVISNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRILD bbb hhhhhhhhhhhhhhhhh bbbbbbbbbbb bbb b bbbbb bbbbbb bbb GPINSL....VPDPATVPSHHAKD..VNSVIRNL..DIATMAVIAPTTLM | | | | | | || || LPHKDLRRARAAAESIIPTTTGAAKAVALVLPELKGKLNGMAMRVPTPNV bbbb hhhhh hhh bbbbbbbb bb bbbbbb hhhhhhh h bbbbbbb hhhhhhhhh HMHFINITLKDKVEKKDILSVL....ENTPRIVLISSKYDAEATAELVEV | | | | | | | SVVDLVAELEKEVTVEEVNAALKAAAEGELKGILAYSEEPL........V bbbbbbbbb hhhhhhhhhhhhh bbbb hhhhhhh bbbbbbbbbbbb bbbbbhhh hhhhhhhh ARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRA || | | | | | SRDYN...GSTVSSTIDALSTMVIDGKMVKVVSWYDNETGYSHRVVDLAA hhhh bbbbhhh bbb bbbbbbbb hhhhhhhhhhhh hhh SMK YIA hhh 19%