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

NucPred

Fetching P48120 from www.uniprot.org...

The NucPred score for your sequence is 0.45 (see score help below)

   1  MSENLFSKKKIFFNQTIGKKEVKNVIAWAFTSYGAARTAYLVEQLKDLGF    50
  51  HYATKAGISLSVEDLLIPPLKDSLLQTAENEIKATLNRYLLGEITEVERF   100
 101  QKVIDIWHRTSETLKDEVVDYFKSTDPLNSLYMMSFSGARGNLSQVHQLV   150
 151  GMRGLMADPQGEIIDFPIRSNFKEGLTTTEYLISSYGARKGVVDTALRTA   200
 201  DSGYLTRRLVDIAQEVIIREIDCETPRGVILTALKENGKILISLKDRLVG   250
 251  RVLLHNLYHPKTHSLIAQKNESISVLLADDIIKAGLKEVWIRSPLTCKAT   300
 301  RSVCQYCYGWNLAHGRLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVF   350
 351  TAEVAKQITAPFPGRIYYPLNTTFREIRTRYGDNAWWVENNAKLRLEGEN   400
 401  GKRVSFNLTQGSIIRIKDQSWVETNDLLAEIASTAPNTRRAKEKTTRELR   450
 451  TDIAGEVYFQNLEIDEAGGQVDTAGGSIWILGGNVYNLSSNFDVILKNGD   500
 501  FILNGSILARTQFISQYGGYVRLTDDNLTVEVIPASLKIQNAKIFIDETD   550
 551  QPCLHFKNNETFELKIQNETQLKHGQVVAERYLTTEMGGIIRYADLDAKT   600
 601  TNKNGYEITKSGSLLWIPEETHEVNTEAKNVLVKNGQYIPSGTQLIKNKK   650
 651  IRNKHSGVVELVHKKNFVIEIIIKPGIVLKIKNNVSFSKKAKRFIQPGEY   700
 701  LFSKFVVEDLRYLDYIITSTGIILLLRPVVEYKVESPKTIIRDDKNHLKI   750
 751  SSIQSILYKDGERIKSVQGIELFKIQLKLQVRKGLKHLPIKTNFIPSSQN   800
 801  SFELEFLIIESILPKNDKYFDSTVLESLAKAQTKILVKNNQLVKKGELIA   850
 851  QIEIISINQGEIRWIGDNTAKQIRRLLLITEKQIVTIPIQNLTKLKNKNL   900
 901  NLGNFIRAGEEIEETIKIPNSGQIIEITSTYIRLRISRPYLISARAIIRV   950
 951  LTGDLVQSGESLALLVFERAKTGDIIQGLPRIEELLEARKPKDNCVLSTH  1000
1001  PGFTQLYYSETIELKIKSLDKINTLLELQPGVFPTVTNNQFIEAGAPLSE  1050
1051  GDISVHEILEIFFNLYFKNRVNCLSLADAIHLSLQKIQQFLVSEVQSVYQ  1100
1101  SQGIDISDKHIEIIIKQMTNKVKIEEGGDTTLLPNELIEFQQIEKMNEKF  1150
1151  STSNGQLASYTPILLGITKSSLNTQSFISAASFQETTRVLAKAAVEGKID  1200
1201  QLRGLKENVIIGNLIPAGTGFSAYNDNAVFQNEDIESIEVKTSVLNSPAE  1250
1251  SDTNSDLDDIILNKD                                     1265

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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