SERVERNAME: frsvr_SDPMA2 TARGET: T0057 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA2.t0057 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 1gd1o 11.22 294 19 2 1llda 4.02 268 19 3 1gd1o_0-333 3.90 144 22 4 4mdha 3.87 300 19 5 1phh 3.64 301 17 6 1pda 3.38 249 20 7 1dapa 3.36 268 19 8 6ldh 3.35 281 16 9 1dik_2-376 3.33 303 14 10 4pfk 3.06 261 15 11 1a2oa 2.98 277 15 12 2cmd 2.94 266 16 13 1npx 2.90 327 20 14 1hlpa 2.89 271 17 15 1phh_1-394 2.84 266 17 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: g3p_metbr g3p_metfe g3p_metfo g3p_pyrwo g3p_sulso 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: 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: MULT2+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 11.22 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 4.02 1llda 268 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] 3 3.90 1gd1o_0-333 144 22 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-3-1-2-1-1 RC: 4 3.87 4mdha 300 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] 5 3.64 1phh 301 17 99--3-4--4-10 [ a/b ; FAD (also NAD)-binding motif] [(a+b) ; FAD-linked reductases, C-terminal domain] 3-4-1-2-2-1-4-1 R, [MULTIDOMAIN ; ] 99--3-4--4-10 [(a/b) ; FAD (also NAD)-binding motif] [ (a+b) ; FAD-linked reductases, C-terminal domain] 3-4-1-2-2-1-4-1 R 6 3.38 1pda 249 20 99--3-62--4-21 [ a/b ; Periplasmic binding protein-like II] [(a+b) ; dsRBD & PDA domains] [MULTIDOMAIN ; ] 99--3-62--4-21 [(a/b) ; Periplasmic binding protein-like II] [ (a+b) ; dsRBD & PDA domains] 7 3.36 1dapa 268 19 1997 new ; C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH N 8 3.35 6ldh 281 16 99--3-15--4-74 [MULTIDOMAIN ; ] [(a/b) ; NAD(P)-binding Rossmann-fold domains] [(a+b) ; Lactate & malate dehydrogenases, C-terminal domain] 9 3.33 1dik_2-376 303 14 4-66 (a+b) ; ATP-grasp] 4-66-1-4-1-1-1- 10 3.06 4pfk 261 15 3-60 a/b ; Phosphofructokinase] 3-60-1-1-1-2- 11 2.98 1a2oa 277 15 1998 12 2.94 2cmd 266 16 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] 13 2.90 1npx 327 20 99--3-4--3-4--4-38 [MULTIDOMAIN ; ] [(a/b) ; FAD (also NAD)-binding motif] [(a/b) ; FAD (also NAD)-binding motif] [ (a+b) ; FAD/NAD-linked reductases, dimerisation (C-terminal) domain] 3-4-1-3-3-1-1-1 R 14 2.89 1hlpa 271 17 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] 15 2.84 1phh_1-394 266 17 3-4 a/b ; FAD (also NAD)-binding motif] 3-4-1-2-2-1-4-1 R 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 |||| | | | | ..DIVVESTGRFTKREDAAKHLEAGAKKVIISAPANEDITI...VMGVNQ bbbb hhhh hhhh bbbb bb h hhh bbbbb bbbbhhhhhh EALGKKYIRVVS..CNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEV | | | | | | DKYDKAHHVISNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRI hh bbb hhhhhhhhhhhhhhhhh bbbbbbbbbbb bbb b bbbbb bbbbbb b KKGPINSL....VPDPATVPSHHAKD..VNSVIRNL..DIATMAVIAPTT | | | | | | || || LDLPHKDLRRARAAAESIIPTTTGAAKAVALVLPELKGKLNGMAMRVPTP bbbb hhhhh hhh bbbbbbbb bbbb bbbbbb hhhhhhh h bbbbbbb hhhhhhh LMHMHFINITLKDKVEKKDILSVL....ENTPRIVLISSKYDAEATAELV | | | | | | NVSVVDLVAELEKEVTVEEVNAALKAAAEGELKGILAYSEEPL....... bbbbbbbbb hhhhhhhhhhhhh bbbb hhhhhhhhh bbbbbbbbbbbb bbbbbhhh hhhhhh EVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAI | || | | | | .VSRDYN...GSTVSSTIDALSTMVIDGKMVKVVSWYDNETGYSHRVVDL hhhh bbbbhhh bbb bbbbbbbb hhhhhhhhhh hhhhhhh RASMKLMS | AAYIASKG hhhhhh 19%