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

NucPred

Fetching P06125 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MKSIIIASLVALAIAASPALDRTFSPKSEYVYKFDGLLLSGLPTASSDAS    50
  51  QTLISCRTRLQAVDDRYIHLQLTDIQYSASHIPQSEQWPKIESLEQRELS   100
 101  DEFKELLELPFRAQIRNGLISEIQFSSEDAEWSKNAKRSILNLFSLRKSA   150
 151  PVDEMNQDQKDMESDKDSLFFNVHEKTMEGDCEVAYTIVQEGEKTIYTKS   200
 201  VNFDKCITRPETAYGLRFGSECKECEKEGQFVKPQTVYTYTFKNEKLQES   250
 251  EVHSVYTLNVNGQEVVKSETRAKVTFVEESKINREIKKVSGPKEEIVYSM   300
 301  ENEKLIEQFYQQGDKAEVNPFKAIEMEQKVEQLQEIFRQIQEHEQNTPET   350
 351  VHLIARAVRMFRMCTIEELKKVHTTIYTKAEKKVQLVIETTLAVAGTKNT   400
 401  IQHLIHHFEKKSITPLRAAELLKSVQETLYPSEHIADLLIQLAQSPLSEK   450
 451  YEPLRQSAWLAAGSVVRGFASKTQDLPLIRPASRQTKEKYVRVFMQHFRN   500
 501  ADSTYEKVLALKTLGNAGIDLSVYELVQIIQDPRQPLSIRTEAVDALRLL   550
 551  KDVMPRKIQKVLLPVYKNRQNKPELRMAALWRMMHTIPEEPVLAHIVSQM   600
 601  ENESNQHVAAFTYNVLRQFYKSTNPCYQQLAVRCSKILLFTRYQPQEQML   650
 651  STYSQLPLFNSEWLSGVQFDFATIFEKNAFLPKEVQASFETVFGGNWNKY   700
 701  FAQVGFSQQNFEQVILKTLEKLSLYGKQSDELRSRRVQSGIQMLQEIVKK   750
 751  MNIRPRVQQTDSQNAHAVFYLRYKEMDYIVLPIDMETIDTLVEKYVRNGE   800
 801  FDIKSLLTFLTNDSKFELHRALFFYEAERRIPTTIGMPLTISGKMPTILS   850
 851  INGKVSIELEKLGARLVLDIVPTVATTHVTEMRFWYPVIEQGVKSLQSAR   900
 901  LHTPLRFESTVELKKNTLEITHKFVVPENKKTTVSVHTRPVAFIRVPKNQ   950
 951  DSEYVEAEEKTISHSQYQMSTEEIDRQYETFGLRINAQGNVLSQWTLPMV  1000
1001  LMTEQDFEYTLENKNRPVEFTARVTIGNLEKTDLSEIKFDKIFEKEFDLE  1050
1051  NNESENRRQYFHKMIREIQSEQGFKNLITLKLEAPQQMYWNTELRTVCDK  1100
1101  WIRMCKVEMDARRSPMEHENKEWTLRTELLAARPQMPSSLRQLREQPHRE  1150
1151  VQLAFNAKWGSSKKSEITVNAQLEQSTEQKKFIRNIEREYKGIPEYELLI  1200
1201  KAARLNQVNVVSEYKLTPQSEYTFSRIFDLIKAYNFWTVSEKRVQNENRR  1250
1251  VVLQLSVEPLSRQYMNMTIQTPEQEVELKNVRIPRVVLPTIARSAMFQQT  1300
1301  WEKTGATCKVDQSEVSTFDNVIYRAPLTTCYSLVAKDCSEQPRFAVLAKK  1350
1351  INKNSEELLVKVVRREEEIVVKKSDDKFLVKVDGKKVNPTELEQYNIEIL  1400
1401  GDNLIVIRLPQGEVRFDGYTVKTNMPSVASQNQLCGLCGNNDGERDNEFM  1450
1451  TADNYETEDVEEFHRSYLLKNEECEVENDRISEKKNYRNKWNREEKKSDY  1500
1501  ESSSDYESNYDEKETEKELVKKTLIKEFSNRVCFSIEPVSECRRGLESEK  1550
1551  TSNKKIRFTCMPRHSKNARRFLKEAREQTVAELVDFPVSFVESVKIPTAC  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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