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

NucPred

Fetching Q8LK56 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MNSRADPGDRYFRVPLENQTQQEFMGSWIPFTPKKPRSSLMVDERVINQD    50
  51  LNGFPGGEFVDRGFCNTGVDHNGVFDHGAHQGVTNLSMMINSLAGSHAQA   100
 101  WSNSERDLLGRSEVTSPLAPVIRNTTGNVEPVNGNFTSDVGMVNGPFTQS   150
 151  GTSQAGYNEFELDDLLNPDQMPFSFTSLLSGGDSLFKVRQYGPPACNKPL   200
 201  YNLNSPIRREAVGSVCESSFQYVPSTPSLFRTGEKTGFLEQIVTTTGHEI   250
 251  PEPKSDKSMQSIMDSSAVNATEATEQNDGSRQDVLEFDLNKTPQQKPSKR   300
 301  KRKFMPKVVVEGKPKRKPRKPAELPKVVVEGKPKRKPRKAATQEKVKSKE   350
 351  TGSAKKKNLKESATKKPANVGDMSNKSPEVTLKSCRKALNFDLENPGDAR   400
 401  QGDSESEIVQNSSGANSFSEIRDAIGGTNGSFLDSVSQIDKTNGLGAMNQ   450
 451  PLEVSMGNQPDKLSTGAKLARDQQPDLLTRNQQCQFPVATQNTQFPMENQ   500
 501  QAWLQMKNQLIGFPFGNQQPRMTIRNQQPCLAMGNQQPMYLIGTPRPALV   550
 551  SGNQQLGGPQGNKRPIFLNHQTCLPAGNQLYGSPTDMHQLVMSTGGQQHG   600
 601  LLIKNQQPGSLIRGQQPCVPLIDQQPATPKGFTHLNQMVATSMSSPGLRP   650
 651  HSQSQVPTTYLHVESVSRILNGTTGTCQRSRAPAYDSLQQDIHQGNKYIL   700
 701  SHEISNGNGCKKALPQNSSLPTPIMAKLEEARGSKRQYHRAMGQTEKHDL   750
 751  NLAQQIAQSQDVERHNSSTCVEYLDAAKKTKIQKVVQENLHGMPPEVIEI   800
 801  EDDPTDGARKGKNTASISKGASKGNSSPVKKTAEKEKCIVPKTPAKKGRA   850
 851  GRKKSVPPPAHASEIQLWQPTPPKTPLSRSKPKGKGRKSIQDSGKARGPS   900
 901  GELLCQDSIAEIIYRMQNLYLGDKEREQEQNAMVLYKGDGALVPYESKKR   950
 951  KPRPKVDIDDETTRIWNLLMGKGDEKEGDEEKDKKKEKWWEEERRVFRGR  1000
1001  ADSFIARMHLVQGDRRFSPWKGSVVDSVIGVFLTQNVSDHLSSSAFMSLA  1050
1051  ARFPPKLSSSREDERNVRSVVVEDPEGCILNLNEIPSWQEKVQHPSDMEV  1100
1101  SGVDSGSKEQLRDCSNSGIERFNFLEKSIQNLEEEVLSSQDSFDPAIFQS  1150
1151  CGRVGSCSCSKSDAEFPTTRCETKTVSGTSQSVQTGSPNLSDEICLQGNE  1200
1201  RPHLYEGSGDVQKQETTNVAQKKPDLEKTMNWKDSVCFGQPRNDTNWQTT  1250
1251  PSSSYEQCATRQPHVLDIEDFGMQGEGLGYSWMSISPRVDRVKNKNVPRR  1300
1301  FFRQGGSVPREFTGQIIPSTPHELPGMGLSGSSSAVQEHQDDTQHNQQDE  1350
1351  MNKASHLQKTFLDLLNSSEECLTRQSSTKQNITDGCLPRDRTAEDVVDPL  1400
1401  SNNSSLQNILVESNSSNKEQTAVEYKETNATILREMKGTLADGKKPTSQW  1450
1451  DSLRKDVEGNEGRQERNKNNMDSIDYEAIRRASISEISEAIKERGMNNML  1500
1501  AVRIKDFLERIVKDHGGIDLEWLRESPPDKAKDYLLSIRGLGLKSVECVR  1550
1551  LLTLHNLAFPVDTNVGRIAVRMGWVPLQPLPESLQLHLLELYPVLESIQK  1600
1601  FLWPRLCKLDQRTLYELHYQLITFGKVFCTKSRPNCNACPMRGECRHFAS  1650
1651  AYASARLALPAPEERSLTSATIPVPPESYPPVAIPMIELPLPLEKSLASG  1700
1701  APSNRENCEPIIEEPASPGQECTEITESDIEDAYYNEDPDEIPTIKLNIE  1750
1751  QFGMTLREHMERNMELQEGDMSKALVALHPTTTSIPTPKLKNISRLRTEH  1800
1801  QVYELPDSHRLLDGMDKREPDDPSPYLLAIWTPGETANSAQPPEQKCGGK  1850
1851  ASGKMCFDETCSECNSLREANSQTVRGTLLIPCRTAMRGSFPLNGTYFQV  1900
1901  NELFADHESSLKPIDVPRDWIWDLPRRTVYFGTSVTSIFRGLSTEQIQFC  1950
1951  FWKGFVCVRGFEQKTRAPRPLMARLHFPASKLKNNKT               1987

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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