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

NucPred

Fetching Q13936 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MVNENTRMYIPEENHQGSNYGSPRPAHANMNANAAAGLAPEHIPTPGAAL    50
  51  SWQAAIDAARQAKLMGSAGNATISTVSSTQRKRQQYGKPKKQGSTTATRP   100
 101  PRALLCLTLKNPIRRACISIVEWKPFEIIILLTIFANCVALAIYIPFPED   150
 151  DSNATNSNLERVEYLFLIIFTVEAFLKVIAYGLLFHPNAYLRNGWNLLDF   200
 201  IIVVVGLFSAILEQATKADGANALGGKGAGFDVKALRAFRVLRPLRLVSG   250
 251  VPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFMGKMHKTCYN   300
 301  QEGIADVPAEDDPSPCALETGHGRQCQNGTVCKPGWDGPKHGITNFDNFA   350
 351  FAMLTVFQCITMEGWTDVLYWVNDAVGRDWPWIYFVTLIIIGSFFVLNLV   400
 401  LGVLSGEFSKEREKAKARGDFQKLREKQQLEEDLKGYLDWITQAEDIDPE   450
 451  NEDEGMDEEKPRNMSMPTSETESVNTENVAGGDIEGENCGARLAHRISKS   500
 501  KFSRYWRRWNRFCRRKCRAAVKSNVFYWLVIFLVFLNTLTIASEHYNQPN   550
 551  WLTEVQDTANKALLALFTAEMLLKMYSLGLQAYFVSLFNRFDCFVVCGGI   600
 601  LETILVETKIMSPLGISVLRCVRLLRIFKITRYWNSLSNLVASLLNSVRS   650
 651  IASLLLLLFLFIIIFSLLGMQLFGGKFNFDEMQTRRSTFDNFPQSLLTVF   700
 701  QILTGEDWNSVMYDGIMAYGGPSFPGMLVCIYFIILFICGNYILLNVFLA   750
 751  IAVDNLADAESLTSAQKEEEEEKERKKLARTASPEKKQELVEKPAVGESK   800
 801  EEKIELKSITADGESPPATKINMDDLQPNENEDKSPYPNPETTGEEDEEE   850
 851  PEMPVGPRPRPLSELHLKEKAVPMPEASAFFIFSSNNRFRLQCHRIVNDT   900
 901  IFTNLILFFILLSSISLAAEDPVQHTSFRNHILFYFDIVFTTIFTIEIAL   950
 951  KILGNADYVFTSIFTLEIILKMTAYGAFLHKGSFCRNYFNILDLLVVSVS  1000
1001  LISFGIQSSAINVVKILRVLRVLRPLRAINRAKGLKHVVQCVFVAIRTIG  1050
1051  NIVIVTTLLQFMFACIGVQLFKGKLYTCSDSSKQTEAECKGNYITYKDGE  1100
1101  VDHPIIQPRSWENSKFDFDNVLAAMMALFTVSTFEGWPELLYRSIDSHTE  1150
1151  DKGPIYNYRVEISIFFIIYIIIIAFFMMNIFVGFVIVTFQEQGEQEYKNC  1200
1201  ELDKNQRQCVEYALKARPLRRYIPKNQHQYKVWYVVNSTYFEYLMFVLIL  1250
1251  LNTICLAMQHYGQSCLFKIAMNILNMLFTGLFTVEMILKLIAFKPKGYFS  1300
1301  DPWNVFDFLIVIGSIIDVILSETNHYFCDAWNTFDALIVVGSIVDIAITE  1350
1351  VNPAEHTQCSPSMNAEENSRISITFFRLFRVMRLVKLLSRGEGIRTLLWT  1400
1401  FIKSFQALPYVALLIVMLFFIYAVIGMQVFGKIALNDTTEINRNNNFQTF  1450
1451  PQAVLLLFRCATGEAWQDIMLACMPGKKCAPESEPSNSTEGETPCGSSFA  1500
1501  VFYFISFYMLCAFLIINLFVAVIMDNFDYLTRDWSILGPHHLDEFKRIWA  1550
1551  EYDPEAKGRIKHLDVVTLLRRIQPPLGFGKLCPHRVACKRLVSMNMPLNS  1600
1601  DGTVMFNATLFALVRTALRIKTEGNLEQANEELRAIIKKIWKRTSMKLLD  1650
1651  QVVPPAGDDEVTVGKFYATFLIQEYFRKFKKRKEQGLVGKPSQRNALSLQ  1700
1701  AGLRTLHDIGPEIRRAISGDLTAEEELDKAMKEAVSAASEDDIFRRAGGL  1750
1751  FGNHVSYYQSDGRSAFPQTFTTQRPLHINKAGSSQGDTESPSHEKLVDST  1800
1801  FTPSSYSSTGSNANINNANNTALGRLPRPAGYPSTVSTVEGHGPPLSPAI  1850
1851  RVQEVAWKLSSNRERHVPMCEDLELRRDSGSAGTQAHCLLLRKANPSRCH  1900
1901  SRESQAAMAGQEETSQDETYEVKMNHDTEACSEPSLLSTEMLSYQDDENR  1950
1951  QLTLPEEDKRDIRQSPKRGFLRSASLGRRASFHLECLKRQKDRGGDISQK  2000
2001  TVLPLHLVHHQALAVAGLSPLLQRSHSPASFPRPFATPPATPGSRGWPPQ  2050
2051  PVPTLRLEGVESSEKLNSSFPSIHCGSWAETTPGGGGSSAARRVRPVSLM  2100
2101  VPSQAGAPGRQFHGSASSLVEAVLISEGLGQFAQDPKFIEVTTQELADAC  2150
2151  DMTIEEMESAADNILSGGAPQSPNGALLPFVNCRDAGQDRAGGEEDAGCV  2200
2201  RARGRPSEEELQDSRVYVSSL                               2221

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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