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

NucPred

Fetching Q6P4S8 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MNRAKPTTVRRPSAAAKPSGHPPPGDFIALGSKGQASESKTTSTLLKPAP    50
  51  SGLPSERKRDASASLSGTSALTGLTKRPKLSSTPPLSALGRLAEAAVAEK   100
 101  RAISPSIKEPSVVPIEVLPTVLLDEIEAAELEGNDDRIEGVLCGAVKQLK   150
 151  VTRAKPDSTLYLSLMYLAKIKPNIFATEGVIEALCSLLRRDASVNFKAKG   200
 201  NSLVSVLACNLLMAAYEEDENWPEIFVKVYIEDSLGERIWVDSPHCRTFV   250
 251  DNIQTAFNTKMPPKSVLLQGEGARSGGELGAGSSPHPSLTEEEDSQTELL   300
 301  IAEEKLSPEQEGQLMPRPRYDELTESVEEYVLDMLRDQLNRRQPIDNVSR   350
 351  NLLRLLTATCGYKEVRLLAVQRLEMWLQNPKLTRPAQDLLMSVCMNCNSH   400
 401  GSEDMDVISHLIKIRLKPKVLLNHYMLCIRELLNAHKDNLGTTIKFVIFN   450
 451  ELSNARNPNNMQILYTVLQHSSELAPKFLAMVFQDLLTNKDDYLRASRAL   500
 501  LREIIKQTKHEINFQAFCLGLMQERKEPQYLEMEFKERFVVHITDVLAVS   550
 551  MMLGITAQVKEAGVAWDKGEKRNLEVLRTFQNQIAAIQRDAVWWLHTVVP   600
 601  SVSKLAPKDYVHCLHKVLFTEQPETYYKWDNWPPESDRNFFLRLCSEVPI   650
 651  LEDTLMRVLVIGLSRELPLGPADAMELADHLVKRAAAVQADDVEVLKVER   700
 701  IQLIDAVLNLCTYHHPENIQLPPGYQPPNLAISTLYWKAWPLLLVVAAFN   750
 751  PENIGLAAWEEYPTLKMLMEMVMTNNYSYPPCTLTDEETRTEMINRELQI   800
 801  SQREKQEILAFEGHLAAASTKQTITESSSLLLSQLTSLDPQGPPRRPPPH   850
 851  ILDQVKALNQSLRLGHLLCRSRNPDFLLHIIQRQASSQSMPWLADLVQSS   900
 901  EGSLDVLPVQCLCEFLLHDAADSTASGEEDDEGESREQKAKKRQRQQKQR   950
 951  QLLGRLQDLLLGPKADEQTTCEVLDYFLRRLGSSQVASRVLAMKGLSLVL  1000
1001  SEGGLRDKEEKEPPMEEDIGETDALQGYQWLLRDLPRLPLFDSVRTTTAL  1050
1051  ALQQAIHMETDPQTISAYLIYLSQHTPVEEQGPHSDLALDVARLVVERST  1100
1101  IMAHLFSKPSCSTASDAVLSALLSVFSRYVRRMRKSKEGEEVYSWSESQD  1150
1151  QVFLRWSSGETATMHILVVHAMVILLTLGPPRSGDSEFSELLDIWFPEKK  1200
1201  PLPTAFLVDTSEEALLLPDWLKLRMIRSEVPRLVDAALQDLEPQQLLLFV  1250
1251  QSFGIPVSSMSKLLQYLDQAVAQDPQTLEQNIMDKNYMAHLVEVQHERGA  1300
1301  SGGQTFHSLLTASLPPRRDSTEAPKPESSPEPPPGQGRTRAGTQVPVLGP  1350
1351  EDDLAGIFLQIFPLSPDPRWQSSSPRPLALALQQALGQELARVRQGNPEV  1400
1401  PGITVRLLQAMTTLLSSPHGGTLALAMHHSHFLSCPLMRQLYQYQRAVPQ  1450
1451  DTGFSSLFLKVLMQILQWLDSPAVEDGPLQAQLKLFATRYSARHRISDVR  1500
1501  SGLLHLADALSFHGDLEVANSTARAVIATLRSGEKCPVEPELISKVLRGL  1550
1551  IEVRSPHLEELLTALFSATTETSCPSPASGPIVVVSSLLLQEKEELLGPS  1600
1601  KQEVEGASTEAMRLGPASGLLVDWLETLDPEVVCSCPDLQWKLLFSRRKG  1650
1651  KGHISAQVLSFRPYLLALLTHQASWSTLHCCIRVLLGKSREQRLDPSASL  1700
1701  DFLWACIHVPRIWQGRDQRTPQKRREELVLHVQGPELLSLVELILSEAET  1750
1751  RSQDGDSAARTLIQTRLPLLLSCCRSNDESIGKVTEHLTSCIQQWGDSVL  1800
1801  GQRCRDLLLQLYLQRPEVRVPVPEVLLQSEGATSSSICKLDGLVHRFITL  1850
1851  LADTSDSRSSESRVADANMACRKLAVAHPVLLLRHLPMIAALLHGRTHLN  1900
1901  FQEFRQQNHLAFFLHVLGILELLQPRVFQSEHQGALWDCLRSFIRLLLNY  1950
1951  RKSSRHLAPFISKFVQFIHKYVGCSAPAAVAFLQKHAEPLHDLSFDNSDL  2000
2001  VMLKSLLAGLSLPSRDGRTDQGLDEEGEDERSAGSLPLVSVSLSTPLTVA  2050
2051  DVAPHMKRLSRGRAVEDVLETLSDIDEMSRRRPEVLGFFSTNLQRLMSSA  2100
2101  EESCRNLAFSLALRSIQNNPSIAADFLPTFMYCLGSRDFEVVQTALRNLP  2150
2151  EYTLLCQEHAAVLLHRAFLVGVYGQIDTSAQISEALKILHMEAVM       2195

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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