 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q9QX47 from www.uniprot.org...
The NucPred score for your sequence is 0.98 (see score help below)
1 MAADIEQVFRSFVVSKFREIQQELSSGRSEGQLNGETNPPIEGNQAGDTA 50
51 ASARSLPNEEIVQKIEEVLSGVLDTELRYKPDLKEASRKSRCVSVQTDPT 100
101 DEVPTKKSKKHKKHKNKKKKKKKEKEKKYKRQPEESESKLKSHHDGNLES 150
151 DSFLKFDSEPSAAALEHPVRAFGLSEASETALVLEPPVVSMEVQESHVLE 200
201 TLKPATKAAELSVVSTSVISEQSEQPMPGMLEPSMTKILDSFTAAPVPMS 250
251 TAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKVVEPSE 300
301 TLTIVSETPTEVHPEPSPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSM 350
351 TRPQESLELPKTTAVELQESTVASALELPGPPATSILELQGPPVTPVPEL 400
401 PGPSATPVPELSGPLSTPVPELPGPPATVVPELPGPSVTPVPQLSQELPG 450
451 PPAPSMGLEPPQEVPEPPVMAQELSGVPAVSAAIELTGQPAVTVAMELTE 500
501 QPVTTTEFEQPVAMTTVEHPGHPEVTTATGLLGQPEAAMVLELPGQPVAT 550
551 TALELSGQPSVTGVPELSGLPSATRALELSGQSVATGALELPGQLMATGA 600
601 LEFSGQSGAAGALELLGQPLATGVLELPGQPGAPELPGQPVATVALEISV 650
651 QSVVTTSELSTMTVSQSLEVPSTTALESYNTVAQELPTTLVGETSVTVGV 700
701 DPLMAQESHMLASNTMETHMLASNTMDSQMLASNTMDSQMLASNTMDSQM 750
751 LASSTMDSQMLASSTMDSQMLATSTMDSQMLATSSMDSQMLATSSMDSQM 800
801 LATSSMDSQMLATSSMDSQMLATSSMDSQMLATSSMDSQMLATSSMDSQM 850
851 LATSSMDSQMLASGAMDSQMLASGTMDAQMLASGTMDAQMLASSTQDSAM 900
901 MGSKSPDPYRLAQDPYRLAQDPYRLGHDPYRLGHDAYRLGQDPYRLGHDP 950
951 YRLTPDPYRVSPRPYRIAPRSYRIAPRPYRLAPRPLMLASRRSMMMSYAA 1000
1001 ERSMMSSYERSMMSYERSMMSPMAERSMMSAYERSMMSAYERSMMSPMAE 1050
1051 RSMMSAYERSMMSAYERSMMSPMADRSMMSMGADRSMMSSYSAADRSMMS 1100
1101 SYSAADRSMMSSYTDRSMMSMAADSYTDSYTDSYTEAYMVPPLPPEEPPT 1150
1151 MPPLPPEEPPMTPPLPPEEPPEGPALSTEQSALTADNTWSTEVTLSTGES 1200
1201 LSQPEPPVSQSEISEPMAVPANYSMSESETSMLASEAVMTVPEPAREPES 1250
1251 SVTSAPVESAVVAEHEMVPERPMTYMVSETTMSVEPAVLTSEASVISETS 1300
1301 ETYDSMRPSGHAISEVTMSLLEPAVTISQPAENSLELPSMTVPAPSTMTT 1350
1351 TESPVVAVTEIPPVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEP 1400
1401 PTMATPELCSLSVSEPPVAVSELPALADPEHAITAVSGVSSLEPSVPILE 1450
1451 PAVSVLQPVMIVSEPSVPVQEPTVAVSEPAVIVSEHTQITSPEMAVESSP 1500
1501 VIVDSSVMSSQIMKGMNLLGGDENLGPEVGMQETLLHPGEEPRDGGHLKS 1550
1551 DLYENEYDRNADLTVNSHLIVKDAEHNTVCATTVGPVGEASEEKILPISE 1600
1601 TKEITELATCAAVSEADIGRSLSSQLALELDTVGTSKGFEFVTASALISE 1650
1651 SKYDVEVSVTTQDTEHDMVISTSPSGGSEADIEGPLPAKDIHLDLPSTNF 1700
1701 VCKDVEDSLPIKESAQAVAVALSPKESSEDTEVPLPNKEIVPESGYSASI 1750
1751 DEINEADLVRPLLPKDMERLTSLRAGIEGPLLASEVERDKSAASPVVISI 1800
1801 PERASESSSEEKDDYEIFVKVKDTHEKSKKNKNRDKGEKEKKRDSSLRSR 1850
1851 SKRSKSSEHKSRKRTSESRSRARKRSSKSKSHRSQTRSRSRSRRRRRSSR 1900
1901 SRSKSRGRRSVSKEKRKRSPKHRSKSRERKRKRSSSRDNRKAARARSRTP 1950
1951 SRRSRSHTPSRRRRSRSVGRRRSFSISPSRRSRTPSRRSRTPSRRSRTPS 2000
2001 RRSRTPSRRSRTPSRRRRSRSAVRRRSFSISPVRLRRSRTPLRRRFSRSP 2050
2051 IRRKRSRSSERGRSPKRLTDLDKAQLLEIAKANAAAMCAKAGVPLPPNLK 2100
2101 PAPPPTIEEKVAKKSGGATIEELTEKCKQIAQSKEDDDVIVNKPHVSDEE 2150
2151 EEEPPFYHHPFKLSEPKPIFFNLNIAAAKPTPPKSQVTLTKEFPVSSGSQ 2200
2201 HRKKEADSVYGEWVPVEKNGEESKDDDNVFSSSLPSEPVDISTAMSERAL 2250
2251 AQKRLSENAFDLEAMSMLNRAQERIDAWAQLNSIPGQFTGSTGVQVLTQE 2300
2301 QLANTGAQAWIKKDQFLRAAPVTGGMGAVLMRKMGWREGEGLGKNKEGNK 2350
2351 EPILVDFKTDRKGLVAVGERAQKRSGNFSAAMKDLSGKHPVSALMEICNK 2400
2401 RRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNCMFFLNRY 2444
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
What does the NucPred score mean?
| You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper. |
| NucPred score threshold | Specificity | Sensitivity |
| see above | fraction of proteins predicted to be nuclear that actually are nuclear | fraction of true nuclear proteins that are predicted (coverage) |
| 0.10 | 0.45 | 0.88 |
| 0.20 | 0.52 | 0.83 |
| 0.30 | 0.57 | 0.77 |
| 0.40 | 0.63 | 0.69 |
| 0.50 | 0.70 | 0.62 |
| 0.60 | 0.71 | 0.53 |
| 0.70 | 0.81 | 0.44 |
| 0.80 | 0.84 | 0.32 |
| 0.90 | 0.88 | 0.21 |
| 1.00 | 1.00 | 0.02 |
| Sequences which score >= 0.8 with NucPred and which
are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.) |
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