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

NucPred

Fetching P34706 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSDEPPIVLPTEEDGPFSNCVSIAFVNDKSIPVELRIRKAIRGKVTFTQE    50
  51  LVVAARRLYLDGELERPDLNYHVAADFYDPFMIPVPDHRNWEYNPLYPRE   100
 101  WPRLIDRDLVQKIKMSNTYKKNQARRKRRRLLRIFHRKRGGEFLNYLWHS   150
 151  KENDVHYKRYMAAYQFPLPFEKCIRDVVREELKDPETSFSKPPSVVHHSK   200
 201  IRPATPDLLKLAKYLGKDRFCFIVTPFKFRSQFRLRYYKKSPFKRSNILE   250
 251  KWLKFKKVRDQGVFNIRDAAREVKKLLQRKNVYHMTDPQCEQEFWDVYRL   300
 301  QMQWLEEDNIEENITMLRENLSKVTDEEFNRSVYIMRPENRASIHDDVTF   350
 351  TTDAEINLKPIVLELFRNNMPLEDIRQVKECIDDMINLTVCQELIPQVAT   400
 401  IETVRDYSGVEQHRLKYIRPENELEIMFQLATVLVKNENTHDQEITSPMF   450
 451  ALLRTEQYLWSIPLRPFLRMYTDWRKTKLNFKKFRKFSPELVSKAPIDLF   500
 501  KVFLTTNMDKKGVATKDTDCFDYRTASEIKKLYHEEFIRVRPIIEHQRFH   550
 551  RCYTSVITEEPLPNPFYWVHRGQWEKVYECNWKQRVKPLAGRFSWKTKHP   600
 601  NICDLPRLEKDDKQEMEMLAKMREKIREYNKEKEKHPFYVSSSLPEFAST   650
 651  SDFVKFPISNTGIKYTAPRRNQPKVQRSLVTYTRFRLAELEDKDFSFPEE   700
 701  KMLEKNRLLEKLNFEERLQLDALMSKDVKYKPRMIPEKGFLQLQDEKLIL   750
 751  KRLCEKEDEWSGKQKRRFPDLYEQATQEAERLGDPDASTSGTSNKELGLL   800
 801  PVWKHDDFRDLKKINVLGSKEYPISSPYLIKRLHYDIHLEIVRDKLKSWI   850
 851  YRTELWEKMKPVYERLKRDKEKREKEWHEMRAAQRAQKEKEEEDQRRMDM   900
 901  GIEHGQESLLKSITPEVEQQILLPISRENSFEEMLPAPQEAYDEDLDQDI   950
 951  DIHFDGAESVCTGIRLDSEDRELVDSPDQVENEEPERVEAVTENIRQEMS  1000
1001  DAEMRDLMRKKREQYSMLFPNVPQPFQPLNRFDVTAPGAGIVPPYDEAPD  1050
1051  FDLSAYLEEDHVRIPTLSTVEINSLLKDQDLVEEQEIVEEEETPLVVEEP  1100
1101  DIPAAPVLSAEEKASRISREMSALRKLPDAAFNYASDRDGVVVEEVETIE  1150
1151  EIQEIYNDKLEKMIAARLGSIAQGANIERLSEDQLLGDQGSEDISFEEIQ  1200
1201  VDLLLESGVEVQVNQSVTISRSSTSFESLLVEDPEEHPEQLPVSASEKAN  1250
1251  NQIVPEVEVEGSVVPVTNQQEENVTSEGPTLQEGSSIPSSSHIYTVDELL  1300
1301  GTESPGPEATETPVAEESPKKKSGKTTRGRPKKVKENLKKRIQPRRGQKE  1350
1351  EAAHEPEVVEEQEQVEPEVGPEVVHEPVPAPAAQLETEPIEQQIEEPDKV  1400
1401  FEPIIEALPLFETSPVPAPEGNIPSRAHSSDDDVQVISSETDPNGPINLV  1450
1451  EQVQNDKLTAYQYSTEELLGEYGELDEAGAPSPSEIVVHDEVLQDEVLQP  1500
1501  NPKSSKKRGRRRKKTPPHIAKARKVFTSISKTEEIELAPTPTQQSRKRMA  1550
1551  NVSSEEATATRRQKRAKVEEPNDSDVSRVLTPEPEDLHETERPGHVGEEG  1600
1601  FETPSLRTGRESTASSVKTSRSKRLFLSKNNPVPRMRIQSQAGTNASPTP  1650
1651  ARRTGVARDSVSPDGASEKLKQLPKSVQDIFEVFDVERSAERGESATVTN  1700
1701  LEGPVKIEIEDENWMAPPAITETSRKSKKRLRAEKQQQILDDIKLELNGE  1750
1751  PPQKRECEILMERVQVKIEEGVENADCRIVQANFNCKSVEEHETLPLKII  1800
1801  RVFEENEKPVHKFFMTQIIWKEINEAFMTDPEKFMLLVRILFSDRNISGQ  1850
1851  IYKISMTVTDRIKGFDDDFIKLLTQFPKKLSQEHKPLVDYNKLAHALREK  1900
1901  ASLHLNNHKITPFTFHGVISNITEMKEKIIGRCEIGMLTDGDRDVLNSTE  1950
1951  NMLLGAYMKSVLRMTAQSQVSWAHPEYIKRRLEMIYYGWRMFLGSGGFFR  2000
2001  VALAINRKDVKPMSQQFRDFFIEYLKDVNENYAKAVELVQMDEDKLMEAM  2050
2051  IEKAGLSSIDLLALDEDVQGQVSESHKHKCVQCSIRNQSVYFSSYSLLEL  2100
2101  HGKLHQNLHELAPEDADDCQDCYETLTSSFEVIVHRINHHHSRRCFFADD  2150

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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