SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q92616 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MAADTQVSETLKRFAGKVTTASVKERREILSELGKCVAGKDLPEGAVKGL    50
  51  CKLFCLTLHRYRDAASRRALQAAIQQLAEAQPEATAKNLLHSLQSSGIGS   100
 101  KAGVPSKSSGSAALLALTWTCLLVRIVFPSRAKRQGDIWNKLVEVQCLLL   150
 151  LEVLGGSHKHAVDGAVKKLTKLWKENPGLVEQYLSAILSLEPNQNYAGML   200
 201  GLLVQFCTSHKEMDVVSQHKSALLDFYMKNILMSKVKPPKYLLDSCAPLL   250
 251  RYLSHSEFKDLILPTIQKSLLRSPENVIETISSLLASVTLDLSQYAMDIV   300
 301  KGLAGHLKSNSPRLMDEAVLALRNLARQCSDSSAMESLTKHLFAILGGSE   350
 351  GKLTVVAQKMSVLSGIGSVSHHVVSGPSSQVLNGIVAELFIPFLQQEVHE   400
 401  GTLVHAVSVLALWCNRFTMEVPKKLTEWFKKAFSLKTSTSAVRHAYLQCM   450
 451  LASYRGDTLLQALDLLPLLIQTVEKAASQSTQVPTITEGVAAALLLLKLS   500
 501  VADSQAEAKLSSFWQLIVDEKKQVFTSEKFLVMASEDALCTVLHLTERLF   550
 551  LDHPHRLTGNKVQQYHRALVAVLLSRTWHVRRQAQQTVRKLLSSLGGFKL   600
 601  AHGLLEELKTVLSSHKVLPLEALVTDAGEVTEAGKAYVPPRVLQEALCVI   650
 651  SGVPGLKGDVTDTEQLAQEMLIISHHPSLVAVQSGLWPALLARMKIDPEA   700
 701  FITRHLDQIIPRMTTQSPLNQSSMNAMGSLSVLSPDRVLPQLISTITASV   750
 751  QNPALRLVTREEFAIMQTPAGELYDKSIIQSAQQDSIKKANMKRENKAYS   800
 801  FKEQIIELELKEEIKKKKGIKEEVQLTSKQKEMLQAQLDREAQVRRRLQE   850
 851  LDGELEAALGLLDIILAKNPSGLTQYIPVLVDSFLPLLKSPLAAPRIKNP   900
 901  FLSLAACVMPSRLKALGTLVSHVTLRLLKPECVLDKSWCQEELSVAVKRA   950
 951  VMLLHTHTITSRVGKGEPGAAPLSAPAFSLVFPFLKMVLTEMPHHSEEEE  1000
1001  EWMAQILQILTVQAQLRASPNTPPGRVDENGPELLPRVAMLRLLTWVIGT  1050
1051  GSPRLQVLASDTLTTLCASSSGDDGCAFAEQEEVDVLLCALQSPCASVRE  1100
1101  TVLRGLMELHMVLPAPDTDEKNGLNLLRRLWVVKFDKEEEIRKLAERLWS  1150
1151  MMGLDLQPDLCSLLIDDVIYHEAAVRQAGAEALSQAVARYQRQAAEVMGR  1200
1201  LMEIYQEKLYRPPPVLDALGRVISESPPDQWEARCGLALALNKLSQYLDS  1250
1251  SQVKPLFQFFVPDALNDRHPDVRKCMLDAALATLNTHGKENVNSLLPVFE  1300
1301  EFLKNAPNDASYDAVRQSVVVLMGSLAKHLDKSDPKVKPIVAKLIAALST  1350
1351  PSQQVQESVASCLPPLVPAIKEDAGGMIQRLMQQLLESDKYAERKGAAYG  1400
1401  LAGLVKGLGILSLKQQEMMAALTDAIQDKKNFRRREGALFAFEMLCTMLG  1450
1451  KLFEPYVVHVLPHLLLCFGDGNQYVREAADDCAKAVMSNLSAHGVKLVLP  1500
1501  SLLAALEEESWRTKAGSVELLGAMAYCAPKQLSSCLPNIVPKLTEVLTDS  1550
1551  HVKVQKAGQQALRQIGSVIRNPEILAIAPVLLDALTDPSRKTQKCLQTLL  1600
1601  DTKFVHFIDAPSLALIMPIVQRAFQDRSTDTRKMAAQIIGNMYSLTDQKD  1650
1651  LAPYLPSVTPGLKASLLDPVPEVRTVSAKALGAMVKGMGESCFEDLLPWL  1700
1701  METLTYEQSSVDRSGAAQGLAEVMAGLGVEKLEKLMPEIVATASKVDIAP  1750
1751  HVRDGYIMMFNYLPITFGDKFTPYVGPIIPCILKALADENEFVRDTALRA  1800
1801  GQRVISMYAETAIALLLPQLEQGLFDDLWRIRFSSVQLLGDLLFHISGVT  1850
1851  GKMTTETASEDDNFGTAQSNKAIITALGVERRNRVLAGLYMGRSDTQLVV  1900
1901  RQASLHVWKIVVSNTPRTLREILPTLFGLLLGFLASTCADKRTIAARTLG  1950
1951  DLVRKLGEKILPEIIPILEEGLRSQKSDERQGVCIGLSEIMKSTSRDAVL  2000
2001  YFSESLVPTARKALCDPLEEVREAAAKTFEQLHSTIGHQALEDILPFLLK  2050
2051  QLDDEEVSEFALDGLKQVMAIKSRVVLPYLVPKLTTPPVNTRVLAFLSSV  2100
2101  AGDALTRHLGVILPAVMLALKEKLGTPDEQLEMANCQAVILSVEDDTGHR  2150
2151  IIIEDLLEATRSPEVGMRQAAAIILNIYCSRSKADYTSHLRSLVSGLIRL  2200
2201  FNDSSPVVLEESWDALNAITKKLDAGNQLALIEELHKEIRLIGNESKGEH  2250
2251  VPGFCLPKKGVTSILPVLREGVLTGSPEQKEEAAKALGLVIRLTSADALR  2300
2301  PSVVSITGPLIRILGDRFSWNVKAALLETLSLLLAKVGIALKPFLPQLQT  2350
2351  TFTKALQDSNRGVRLKAADALGKLISIHIKVDPLFTELLNGIRAMEDPGV  2400
2401  RDTMLQALRFVIQGAGAKVDAVIRKNIVSLLLSMLGHDEDNTRISSAGCL  2450
2451  GELCAFLTEEELSAVLQQCLLADVSGIDWMVRHGRSLALSVAVNVAPGRL  2500
2501  CAGRYSSDVQEMILSSATADRIPIAVSGVRGMGFLMRHHIETGGGQLPAK  2550
2551  LSSLFVKCLQNPSSDIRLVAEKMIWWANKDPLPPLDPQAIKPILKALLDN  2600
2601  TKDKNTVVRAYSDQAIVNLLKMRQGEEVFQSLSKILDVASLEVLNEVNRR  2650
2651  SLKKLASQADSTEQVDDTILT                               2671

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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