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

NucPred

Fetching P18947 from www.uniprot.org...

The NucPred score for your sequence is 0.64 (see score help below)

   1  MKSIIIASLVALAIAASPALDRTFSPKSEYVYKFDGLLLSGLPTTFSDAS    50
  51  QTLISCRTRLQAVDDRYIHLQLIDIQYSASHIPQSEQWPKIESLEQRELS   100
 101  DELKELLELPFRAQIRNGLVSEIQFSSEDAEWSKNAKRSILNLFSLRKSA   150
 151  PVDEMSQDQKDMESDKDSLFFNVHEKTMEGDCEVAYTIVQEGGKTIYTKS   200
 201  VNFDKCITRPETAYGLRFGSECKECEKEGQFVQPQTVYTYTFKNEKLQES   250
 251  EVNSIYTLNVNGQEVVKSETRAKVTFVEESKINREIKKVSGPKEEIVYSM   300
 301  ENEKLIEQFYKQGDKAEVNPFKAIEIEQKVEQLEEIFRQIQEHEQNTPET   350
 351  VHLIARAVRMFRMCTIEELKKVHTTIYTKAEKKVQLVIETTLAVAGTKNT   400
 401  IQHLIHHFEKKSITPLRAAELLKSVQETLYPSEHIADLLIQLAQSPLSEK   450
 451  YEPLRQSAWLAAGSVVRGFASKTQDLPLIRPASRQTKEKYVRVFMQHFRN   500
 501  ADSTYEKVLALKTLGNAGIDLSVYELVQLIQDPRQPLSIRTEAVDALRLL   550
 551  KDVMPRKIQKVLLPVYKNRQNKPELRMAALWRMMHTIPEEPVLAHIVSQM   600
 601  ENESNQHVAAFTYNVLRQFSKSTNPCYQQLAVRCSKVLLFTRYQPQEQML   650
 651  STYSQLPLFNSEWLSGVQFDFATIFEKNAFLPKEVQASFETVFGGNWNKY   700
 701  FAQVGFSQQNFEQVILKTLEKLSLYGKQSDELRSRRVQSGIQMLQEIVKK   750
 751  MNIRPRVQQTDSQNAHAVFYLRYKEMDYIVLPIDMETIDNVVEKYVRNGE   800
 801  FDIKSLLTFLTNDSKFELHRALFFYEAERRIPTTIGMPLTISGKMPTILS   850
 851  INGKVSIELEKLGARLVLDIVPTVATTHVTEMRFWYPVIEQGVKSLQSAR   900
 901  LHTPLRFESTVELKKNTLEITHKFVVPENKKTTVSVHTRPVAFIRVPKNQ   950
 951  DSEYVEAEEKTISHSQYQMSTEEIDRQYETFGLRINAQGNVLSQWTLPMV  1000
1001  LMTEQDFEFTLENKNRPVEFTARVTIGNLEKTDLSEIKFDKIFEKEFDLE  1050
1051  NNESENRRQYFHKMIREIQSEQGFKNLITLKLEAPQQMYWNTELRTVCDK  1100
1101  WIRMCKVEMDARRSPIEHENKEWTLRTELLAARPQMPSSLRQLREQPHRE  1150
1151  VQLALNAKWGSSKKSEITFNAQLEQSTEQKKFLRNIEREYKGIPEYELLI  1200
1201  KAARLNQVNVVSEYKLTPESEYTFSRIFDLIKAYNFWTVSEKRVQNEDRR  1250
1251  VVLQLSVEPLSRQYMNMTIQTPEQEVELKNVRIPRVVLPTIARRAMFQQT  1300
1301  WEKTGATCKVDQSEVSTFDNVIYRAPLTTCYSLVAKDCSEQPRFAVLAKK  1350
1351  INKNSEELLVKVVRREEEIVVKKSDDKFLVKVDGKKVNPTELEQYNIEIL  1400
1401  GDNLIVIRLPHGEVRFDGYTVKTNMPSVASQNQLCGLCGNNDGERDNEFM  1450
1451  TADNYETEDVEEFHRSYLLKNEECEVEKDRISEKKNYKNKWNREEKKSDY  1500
1501  ESSSDYESNYDEKETEKELVKKTLIKEFSNRVCFSIEPVSECRRGLESEK  1550
1551  TSNKKIRFTCMPRHSKNARRFLKEAREQTVADLVDFPVSFVESVKIPTAC  1600
1601  VAY                                                 1603

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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