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

NucPred

Fetching Q4WLK5 from www.uniprot.org...

The NucPred score for your sequence is 0.68 (see score help below)

   1  MAYFLPSFFQKRLLRYALSRLELVDTEALDLDSLGIRWGQRSTVELRDIG    50
  51  LRLELPASSELLSAKVQFLKITVPADIYSSGIICEASGINVHLQLPSEES   100
 101  FSTAKDGNPNSRSPSKAGTHDSSSDHILPTPADLAESFLDAEPKEEKEEL   150
 151  QAAITSRSQMLQRTSASISDDEEELGLGNEGVSLPSFVAAFLKGVAERLQ   200
 201  VRVDNVSIRVDMEMKQEGVVKREPENKPDNVTGLLTVREVSVGAVSSATS   250
 251  SSEQEKLFRNRPIVISDINMALISEPIVFSNYSRFAPPASPTTPVQPKSS   300
 301  EPSSRIPSPLPGHTPDADSFLAMTRSTILETQQEHWIQDIEEPGVGRMEG   350
 351  SAYTYDGRFSDADTDAEDRSDGYLEGAQQFLDNDKLLDNPAYLDSVIDSQ   400
 401  LHDDDLEPPEDLVPQDDQFPPSSATPRPPKPEVHMYRETSPSGIDTEQTA   450
 451  PFSHYGDGFFMDRSPHGSQPYLGPDHVATRNASHSASSPSGSLPSREISN   500
 501  RQTAPPSESGSIGSSDFANGGELSESKLFSTEEAQSMYMSAISHGSSRSF   550
 551  VPNVPGAWDLWESTVAQDMHAGTQLTDAADAKQDVQDETSISTPKLTAQA   600
 601  ASAFTEKRSFGEQSECLSEAREPDLAPLSPTLSKLSDVAKRFLRIDRISI   650
 651  SIPVGEDRRHTDETVHSSDLNLASDSPKDSTVHSGHSSAESEFLSSTMYA   700
 701  SARLRSDSINLAPSFEGTLPRSLPRQGKKADHDPISKSQPGDIAVEISAV   750
 751  DIRFDNAVGWLVVKIGQRVLHAFRDGGNVSSGKPAPESVQTRHSLALTLH   800
 801  DFSIKYVDHIPGQTYALNDYDPHSSSFFGLPHEDIILRAEASGLTARYLA   850
 851  DKSATKFSLDVSKFVFGFAWDDLISFSESLKMRESTRDVLAPVNGDISLS   900
 901  LTKSSDSASLTITTLPLRLHLNVQRLEEIFGRVGGLSTILELGSSISSAS   950
 951  TGFSTAKNMQRDSPRRARGVHFESSPPPENILPANPQLSWKVNARVGGIV  1000
1001  FDVVGETHYLRLKTTAVKVVSRFEGIGVQIDKAKLSGPLPLDDSRDAPAK  1050
1051  INLSNIRVEFLYSPKEPDLDRLLAIITPSKDKYDEDDDIMLDTLFRQRRQ  1100
1101  GSVLRTTVADAKIIISRTSDLESLSQLEEELGKLSTVAKYLPEDDRPGIL  1150
1151  TLTLIRELECQVYLGGPVGNITTHLRNAEAAYISMPSLIAAQLGTIKVVR  1200
1201  NGSEELVGEALPASGSQGQNQSQLPILMARYIADEMDPTIKIKSHNLRVE  1250
1251  YTIPSIIAFLGLSEDQTTGDVAANMANSLANIAESQHLHRNASETSIGSK  1300
1301  GRQASAKPRKLAFALRDCVLALNPRCTTAKGLVVLTNAKFSAAISDSGCS  1350
1351  EAMLDLKKASIMVIDDVKNMGLAENLQRGRSTIPQSDQIQSFIDMGFVPV  1400
1401  SSISSAMATVKLLQLDDDGTKSVDVELKDDLLILETCADSTQTLISIING  1450
1451  LQPPTPPSVAVKYRTEVLPIEDMLASFSGDAFAMDPPPGQAEITEAPTIV  1500
1501  EPEDGGPRIEDELEYVSDFYPVKSGPDNLAPTGSAVPSESNELLDSFHSQ  1550
1551  YYVSSSVSDLEFKEDHFANHSAVGGTAHRWDSTQNTYGLTDDSKIRKSPL  1600
1601  RIRVRDAHIIWNLFDGYDWQRTRDTISKAVKDVEKRATERRARAGSRASP  1650
1651  GFEEEEESVIGDCLFNSIYIGIPANKDPRELRNDINRNIDDLVSETGSYA  1700
1701  TTTTVTGATARQAQSPSYRGRRLKLSRSKYHKMTFELKGICADFVVFPPG  1750
1751  SEETQSSLDVRVNDLEIFDHVPTSTWKKFATYMHEAGERESGASMVHLEM  1800
1801  LTVRPVPELAASELVLKATLLPLRLHVDQDALDFICRFFEFRDDTAPTPS  1850
1851  SPADIPFLQRVEVNAVPVKLDFKPKRVDYAGLRSGRTTEFMNFFVLDGAD  1900
1901  MVMRHVIIYGVSGFDKLGQTLNDIWMPDIKRNQLPGVLAGLAPIRSLVNV  1950
1951  GGGVKDLVVVPMREYRKDGRIVRSIQKGALAFAKTTSNELVKLGAKLAIG  2000
2001  TQTVLQGAEEMLTAPTATTLGSEEDMIDEEEANKISPYADQPVGVVQGLR  2050
2051  GAFRGLERDLLLARDAIVAVPGEIVESGSAKAAAKAVLKRAPTVILRPAI  2100
2101  GVSKAVGQTLLGAGNTLDPSNRRKIEDVSVMVKYVSRVCLLTSLLRNINA  2150
2151  IKTVGHIGQL                                          2160

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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