SERVERNAME: frsvr_SDPMA2 TARGET: T0062 PARAMETERS: excludefolds: 1kja 1hli include h3p2 URL: http://www.cs.bgu.ac.il/~dfischer/cafasp1/frsvr_SDPMA2.t0062 SERVER'S URL: http://www.doe-mbi.ucla.edu/people/frsvr/submit.html RANK FOLD SCORE LENGTH_ALIGNMENT SEQ_ID% 1 2cnd 10.23 228 21 2 1ndh 8.96 227 21 3 1fdr 7.78 222 21 4 1fnr 7.10 228 20 5 1que 7.09 229 20 6 1a8p 7.04 231 19 7 2cnd_125-270 6.11 136 19 8 1ndh_126-272 5.40 135 23 9 2pia 4.78 220 19 10 2pia_104-223 2.51 120 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: ascd_yerps dmpp_psepu luxg_phole luxg_vibfi luxg_vibha rfbi_salty tmof_pseme ubib_ecoli ubib_pholu ubib_vibfi ubib_vibha ubib_vibor 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: 232 December 24, 1998 14:28 Type: P Check: 7806 .. 1 TTLSCKVTSV EAITDTVYRV RIVPDAAFSF RAGQYLMVVM DERDKRPFSM 51 ASTPDEKGFI ELHIGASEIN LYAKAVMDRI LKDHQIVVDI PHGEAWLRDD 101 EERPMILIAG GTGFSYARSI LLTALARNPN RDITIYWGGR EEQHLYDLCE 151 LEALSLKHPG LQVVPVVEQP EAGWRGRTGT VLTAVLQDHG TLAEHDIYIA 201 GRFEMAKIAR DLFCSERNAR EDRLFGDAFA FI NAME: t0062 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: 2cnd NADH-DEPENDENT NITRATE REDUCTASE (CYTOCHROME B RE 2 FRAGMENT) (E.C.1.6.6.1) COMPLEXED WITH FAD 3 (SYNCHROTRON X-RAY DIFFRACTION) RANK Z-SCORE FOLD LENGTHALI %ID 1 10.23 2cnd 228 21 99--2-24--3-12 [MULTIDOMAIN ; ] 99--2-24--3-12 [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 2 8.96 1ndh 227 21 99--2-24--3-12 [MULTIDOMAIN ; ] [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3 7.78 1fdr 222 17 1997 new ; FLAVODOXIN REDUCTASE FROM E. COLI 4 7.10 1fnr 228 20 1997 new ; FERREDOXIN 5 7.09 1que 229 20 1997 new ; X-RAY STRUCTURE OF THE FERREDOXIN:NADP+ REDUCTASE 6 7.04 1a8p 231 19 199 7 6.11 2cnd_125-270 136 23 3-12 a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3-12-1-1-2-1-1- 8 5.40 1ndh_126-272 135 23 3-12 a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3-12-1-1-3-1-1- 9 4.78 2pia 220 19 99--2-24--3-12--4-9 [beta ; Reductase/elongation factor common domain] [ a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] [(a+b) ; beta-Grasp] [MULTIDOMAIN ; ] 99--2-24--3-12--4-9 [beta ; Reductase/elongation factor common domain] [(a/b) ; Ferredoxin reductase-like, C-terminal NADP-linked domain] [ (a+b) ; beta-Grasp] 10 2.51 2pia_104-223 120 17 3-12 a/b ; Ferredoxin reductase-like, C-terminal NADP-linked domain] 3-12-1-2-1-1-1- 11 2.46 1scub_245-388 143 15 3-11 a/b ; Flavodoxin-like] 3-11-3-1-2-1-1- 12 2.27 1trka_535-680 133 19 3-28 a/b ; Transketolase, C-terminal domain] 3-28-1-1-1-1-1- 13 2.21 1sto 158 18 3-37 a/b ; Phosphoribosyltransferases (PRTases)] 3-37-1-1-3-1- 14 2.15 2pia_1-103 93 19 2-24 beta ; Reductase/elongation factor common domain] 2-24-1-2-1-1-1- 15 1.91 1llda_7-149 120 19 3-15 a/b ; NAD(P)-binding Rossmann-fold domains] 3-15-1-5-3-6-1- 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/24449t0062 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. bbbbbbbbbbb b bbbbb bbbbbbb TLSCKVTSVEAITDTV..YRVRIV.PDAAFSFRAGQYLMVVMDERDK... | | | || | | | RIHCRLVAKKELSRDVRLFRFSLPSPDQVLGLPIGKHIFVCATIEGKLCM bbbbbbbbbbbb bbbbbbbbb bbbbbbbb bbbb bb bbbbbbb hhhhhhhhhhh bb RPFSMASTPDEKGFIELHIG........ASEINLYAKAVMDRILKDHQIV | | || | | | | RAYTPTSMVDEIGHFDLLVKVYFKNEHPKFPNGGLMTQYLDSLPVGSYID bbb bbbbbbbbb hhhhhhhhhh bbbb bb bb b bbbbb hhhhhhhhhhhhhh VDIP........HGEAWL..RDDEERPMILIAGGTGFSYARSILLTALAR | | | | | || | | | VKGPLGHVEYTGRGSFVINGKQRNARRLAMICGGSGITPMYQIIQAVLRD bbbbb bbb bbbb bbb bbbbbbbbb hhhhhhhhhhhhhhh bbbbb hhhhhhhhhhhhhhhh bbbbbb NPNR..DITIYWGGREEQHLYDLCELEALSLKHPG....LQVVPVVEQPE | | | || | | | || QPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQVKRPE bbbbbbbb hhhhh hhhhhhhhhhhh bbbbbbbbb hhh hhhhhhhhhhhh bb bbb hhhhhhhhhhhhhhh AGWRGRTGTVLTAVLQDHGTLAEHD..IYIAGRFEMAKIARDLFCSERNA || | | ||| | | | | | EGWKYSVGFVTEAVLREHVPEGGDDTLALACGPPPMIQFAISPNLEKMKY hh bbb hhhhhhhhh bbbbbbb hhhhhhh hhhhhhh hhhhh REDRLF | DMANSF hhhhhb 21%