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

NucPred

Fetching P18171 from www.uniprot.org...

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

   1  MRLFSLLPLLALLVVQAAGQSEVTSDDPATDAGSTTNSTTDTKPRIPSQD    50
  51  EILGQMPSINPIRTGNPQMDAFYMMFPALGSLLKWGSLFPAYSILGAIPD   100
 101  NLQPTAAASKVVLVLADDATAKTRVARQNPPPNPLGQLMNWPALPQDFQL   150
 151  PSMDLGPQVGSFLAQLPAMPTVPGLLGAAAPVPAPAPAPAAAPPPAPAPA   200
 201  ADPPAAPVPDAPQPAILGQAALQNAFTFFNPANFDASSLLGQSVPTFAPP   250
 251  NLDFVAQMQRQFFPGMTPAQPAAAGTDAQASDISEVRVRPEDPYSQEAQM   300
 301  KIKSALEMEQERQQQAQVKDQEQVPLLWFRMPTTQNQDATEEKTLEDLRV   350
 351  EAKLRAFERQVIAELRMLQKIELMAKQMRSSAAAQNGDSPYRISYPLSRT   400
 401  PIHKITRADIEQALRDDYVRRLVNKEAQRRARNSGINTQKANALKRQAKS   450
 451  QDQTLSKEDIVQIMAYAYRMANEQMESEKGKQDKVYAAYRTEQNPMMMQQ   500
 501  RQWSEEQAKIQQNQQQIQQNPMMMQQRQWSEEQAKIQQNQQQIQQNPMMM   550
 551  QQRQWSEEQAKIQQNQQQIQQNPMMMQQRQWSEEQAKIQQNQQQIQQNPM   600
 601  MVQQRQWSEEQAKIQQNQQQIQQNPMMMQQRQWSEEQAKIQHDQQMAQQM   650
 651  AQQGLMMTEQRQRQWSEDQAKIQQAQQMAQQTPMMMPQMQQRQWTEDPQM   700
 701  VQQMQQRQWAEDQTRMQMAQQNPMMQQQRQMAENPQMMQQRQWSEEQTKI   750
 751  EQAQQMAQQNQMMMQQMQQRQWSEDQAQIQQQQRQMMQQTPMMMKERQWA   800
 801  EENPQSVQQQGPMMMQQQMPSMMQREVEDEDNKAEDDLVGEAGPQMPENE   850
 851  GTARHKVDALGVGGNKRKKSKSKSAPPTVINYYYAAPQRPVVQSYGTSYG   900
 901  GGGYGSNAYGVPRPVNSYQSQGYRAAVGNDEVDEMLRQHQTMARTINPKQ   950
 951  PGEVGGSESQKSNSNPPTTLTPAPQEQPQEHRVHKRLAHFHRFGREAGLN  1000
1001  ATTSKGCGCGRLDCLCGRSCRCGRRGLESRVVSSRTSGTCQCKASHRNKR  1050
1051  SVEYGTLETIDEGSLNELRREYKLGLKEITLSPDEDPAEALMRYNAASIR  1100
1101  EALERASMEPLEIGGDQYEEDAQQEPMEEEQLQHDPNTEPQYNHKDFVRL  1150
1151  TTSTASPITSTTEAATPTGSDSTSEATVTPEVTTTTSTSTTTTTESTKDE  1200
1201  GLDMQQDSQAEAESSHVTKSISKQEAEIHQLHSIVEELKNEILKLNLRCS  1250
1251  TIISNNVAKEPVTEKNPPVVEEPSKQEDKPKVEEKVIAEEQAPVEQEEEL  1300
1301  EEDEDSTSISTTTETPSPSGSYSTKPGLSLGSPRVDEQSGSSNKLDYDDD  1350
1351  NNWQRILANRGYDTDYLTKSHERQFAQGQNLEMPKNCNYDGNGSQEYGPY  1400
1401  PEFQADEPSTDTEGKAKRALSVKQQAQLLNAALNDSGSDSSDGTTTTTTP  1450
1451  SPYAMRGKFVRRRSTARRVPIPKIGKASDEVWVRSPRQAKMPQRPKKSMS  1500
1501  KPKKQSSQVTTQATVSSTKLDSLVDVLKDLVRLQIQKEKKSSLLRTQSNN  1550
1551  LSKTKPKSIKPVKVIKRKRLRRRQHKSIATTIRSPIQTKA            1590

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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