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

NucPred

Fetching P11075 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MSEQNSVVNAEKGDGEISSNVETASSVNPSVKPQNAIKEEAKETNGEDQK    50
  51  CKGPENAGSTAETKETSNDATNGMKTPEETEDTNDKRHDDEGEDGDEDED   100
 101  EDEDEDEDNGDEDDEDVDSSSSETSSEDGEDSESVSGESTESSSGEDEES   150
 151  DESDGNTSNSSSGDESGSEEEEEEEEEEEEEENAGEPAIAHQDSVPTNDS   200
 201  TAPRSTHTRNISLSSNGSNTNSTIILVKTTLETILNDKDIKKNSNAQKAI   250
 251  ERTLQKFKEFDPQTTNNPHYVDSILVFEALRASCRTKSSKVQSLALDCLS   300
 301  KLFSFRSLDETLLVNPPDSLASNDQRQDAADGITPPPKQKIIDAAIDTIS   350
 351  DCFQGEGTDDRVELQIVRALSSCILEEDSSSLCHGASLLKAIRTIYNVFV   400
 401  FSLNPSNQGIAQATLTQIISSVYDKIDLKQSTSSAVSLSTKNHQQQSAIE   450
 451  LSEASENAETPAPLTLENMDKLNDDEERLMDAQQPDSIAITNQDLAVKDA   500
 501  FLVFRVMAKICAKPLETELDMRSHAVRSKLLSLHIIYSIIKDHIDVFLSH   550
 551  NIFLPGKERVCFIDSIRQYLRLVLSRNAASPLAPVFEVTLEIMWLLIANL   600
 601  RADFVKEIPVFLTEIYFPISELTTSTSQQKRYFLSVIQRICNDPRTLVEF   650
 651  YLNYDCNPGMPNVMEITVDYLTRLALTRVEITQTQRSYYDEQISKSLSTY   700
 701  NFSQLPLLTSSNLSSSPDVGQVNLLFPLDFALKMVSLNCIVSVLRSLSSW   750
 751  AHKALNPNTHTANKVLLNTTSSARQESRSSLSNDVRSSIMTSNDDFKPTY   800
 801  EDEESRSLSSQNIDADDPTQFENLKLRKTALSECIAIFNNKPKKAIPVLI   850
 851  KKGFLKDDSPISIAKWLLETEGLDMAAVGDYLGEGDDKNIAIMHAFVDEF   900
 901  DFTGMSIVDALRSFLQSFRLPGEGQKIDRFMLKFAERFVDQNPGVFSKAD   950
 951  TAYVLSYSLIMLNTDLHSSQIKNKMSLQEFLENNEGIDNGRDLPRDFLEG  1000
1001  LFNEIANNEIKLISEQHQAMLSGDTNLVQQQQSAFNFFNSRDLTREAYNQ  1050
1051  VSKEISSKTELVFKNLNKNKGGPDVYYAASHVEHVKSIFETLWMSFLAAL  1100
1101  TPPFKDYDDIDTTNKCLEGLKISIKIASTFRINDARTSFVGALVQFCNLQ  1150
1151  NLEEIKVKNVNAMVILLEVALSEGNYLEGSWKDILLVVSQMERLQLISKG  1200
1201  IDRDTVPDVAQARVANPRVSYESSRSNNTSFFDVWGKKATPTELAQEKHH  1250
1251  NQTLSPEISKFISSSELVVLMDNIFTKSSELSGNAIVDFIKALTAVSLEE  1300
1301  IESSENASTPRMFSLQKMVDVCYYNMDRIKLEWTPLWAVMGKAFNKIATN  1350
1351  SNLAVVFFAIDSLRQLSMRFLDIEELSGFEFQHDFLKPFEYTVQNSGNTE  1400
1401  VQEMIIECFRNFILTKSESIKSGWKPILESLQYTARSSTESIVLKTQLLV  1450
1451  SNDIVTNHFENVFSQEDAFSELVGVFREITKNKRFQKLSLHALESLRKMT  1500
1501  QNVADICFYNENKTEEERKHNDALLRGKDIFQDVWFPMLFCFNDTIMTAE  1550
1551  DLEVRSRALNYMFDALVAYGGKFNDDFWEKICKKLLFPIFGVLSKHWEVN  1600
1601  QFNSHDDLSVWLSTTLIQALRNLIALFTHYFESLNRMLDGFLGLLVSCIC  1650
1651  QENDTIARIGRSCLQQLILQNVSKFNEYHWNQIGDVFDKLFDLTTANELF  1700
1701  DYDPLQQGRKSSVSHHQTTNDTSQHSDDDSNDRRENDSNISETVERAHQE  1750
1751  ESSEDVGGDMVETLNGQTKLNNGNSVPTVKDELNPKPASLSIPKKTKHMK  1800
1801  RNESNEDIRRRINIKNSIVVKCVLQLLMIELLNELFENEDFAHCIPYKEA  1850
1851  IRITRLLEKSYEFSRDFNEDYGLRTRLVEARVVDKIPNLLKQETSAAAVL  1900
1901  LDIMFQLYLNDDEKKADLITRLITICIQVVEGYVSLDDRTMERSINAWRS  1950
1951  VIVEILQGYYEFDDEDFRLYCPAMYALVIQILDKSVPTELRHAIKQFLSR  2000
2001  VGELYLSTD                                           2009

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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