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

NucPred

Fetching P22002 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MIRAFAQPSTPPYQPLSSCLSEDTERKFKGKVVHEAQLNCFYISPGGSNY    50
  51  GSPRPAHANMNANAAAGLAPEHIPTPGAALSWLAAIDAARQAKLMGSAGN   100
 101  ATISTVSSTQRKRQQYGKPKKQGGTTATRPPRALLCLTLKNPIRRACISI   150
 151  VEWKPFEIIILLTIFANCVALAIYIPFPEDDSNATNSNLERVEYLFLIIF   200
 201  TVEAFLKVIAYGLLFHPNAYLRNGWNLLDFIIVVVGLFSAILEQATKADG   250
 251  ANALGGKGAGFDVKALRAFRVLRPLRLVSGVPSLQVVLNSIIKAMVPLLH   300
 301  IALLVLFVIIIYAIIGLELFMGKMHKTCYNQEGIIDVPAEEDPSPCALET   350
 351  GHGRQCQNGTVCKPGWDGPKHGITNFDNFAFAMLTVFQCITMEGWTDVLY   400
 401  WMQDAMGYELPWVYFVSLVIFGSFFVLNLVLGVLSGEFSKEREKAKARGD   450
 451  FQKLREKQQLEEDLKGYLDWITQAEDIDPENEDEGMDEDKPRNMSMPTSE   500
 501  TESVNTENVAGGDIEGENCGARLAHRISKSKFSRYWRRWNRFCRRKCRAA   550
 551  VKSNVFYWLVIFLVFLNTLTIASEHYNQPHWLTEVQDTANKALLALFTAE   600
 601  MLLKMYSLGLQAYFVSLFNRFDCFIVCGGILETILVETKIMSPLGISCWR   650
 651  CVRLLRIFKITRYWNSLSNLVASLLNSLRSIASLLLLLFLFIIIFSLLGM   700
 701  QLFGGKFNFDEMQTRRSTFDNFPQSLLTVFQILTGEDWNSVMYDGIMAYG   750
 751  GPSFPGMLVCIYFIILFISPNYILLNLFLAIAVDNLADAESLTSAQKEEE   800
 801  EEKERKKLARTASPEKKQEVMEKPAVEESKEEKIELKSITADGESPPTTK   850
 851  INMDDLQPSENEDKSPHSNPDTAGEEDEEEPEMPVGPRPRPLSELHLKEK   900
 901  AVPMPEASAFFIFSPNNRFRLQCHRIVNDTIFTNLILFFILLSSISLAAE   950
 951  DPVQHTSFRNHILFYFDIVFTTIFTIEIALKMTAYGAFLHKGSFCRNYFN  1000
1001  ILDLLVVSVSLISFGIQSSAINVVKILRVLRVLRPLRINRAKGLKHVVQC  1050
1051  VFVAIRTIGNIVIVTTLLQFMFACIGVQLFKGKLYTCSDSSKQTEAESKG  1100
1101  NYITYKTGEVDHPIIQPRSWENSKFDFDNVLAAMMALFTVSTFEGWPELL  1150
1151  YRSIDSHTEDKGPIYNYRVEISIFFIIYIIIIAFFMMNIFVGFVIVTFQE  1200
1201  QGEQEYKNCELDKNQRQCVEYALKARPLPRYIPKNQHQYKVWYVVNSTYF  1250
1251  EYLMFVLILLNTICLAMQHYGQSCLFKIAMNILNMLFTGLFTVEMILKLI  1300
1301  AFKPKHYFCDAWNTFDALIVVGSIVDIAITEVHPAEHTQCSPSMSAEENS  1350
1351  RISITFFRLFRVMRLVKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLF  1400
1401  FIYAVIGMQVFGKIALNDTTEINRNNNFQTFPQAVLLLFRCATGEAWQDI  1450
1451  MLACMPGKKCAPESEPSNSTEGETPCGSSFAVFYFISFYMLCAFLIINLF  1500
1501  VAVIMDNFDYLTRDWSILGPHHLDEFKRIWAEYDPEAKGRIKHLDVVTLL  1550
1551  RRIQPPLGFGKLCPHRVACKRLVSMNMPLNSDGTVMFNATLFALVRTALR  1600
1601  IKTEGNLEQANEELRAIIKKIWKRTSMKLLDQVVPPAGDDEVTVGKFYAT  1650
1651  FLIQEYFRKFKKRKEQGLVGKPSQRNALSLQAGLRTLHDIGPEIRRAISG  1700
1701  DLTAEEELDKAMKEAVSAASEDDIFRRAGGLFGNHVSYYQSDSRSNFPQT  1750
1751  FATQRPLHINKTGNNQADTESPSHEKLVDSTFTPSSYSSTGSNANINNAN  1800
1801  NTALGRFPHPAGYSSTVSTVEGHGPPLSPAVRVQEAAWKLSSKRCHSRES  1850
1851  QGATVSQDMFPDETRSSVRLSEEVEYCSEPSLLSTDILSYQDDENRQLTC  1900
1901  LEEDKREIQPCPKRSFLRSASLGRRASFHLECLKRQKDQGGDISQKTALP  1950
1951  LHLVHHQALAVAGLSPLLQRSHSPSTFPRPRPTPPVTPGSRGRPLQPIPT  2000
2001  LRLEGAESSEKLNSSFPSIHCSSWSEETTACSGGSSMARRARPVSLTVPS  2050
2051  QAGAPGRQFHGSASSLVEAVLISEGLGQFAQDPKFIEVTTQELADACDMT  2100
2101  IEEMENAADNILSGGAQQSPNGTLLPFVNCRDPGQDRAVVPEDESCVYAL  2150
2151  GRGRSEEALPDSRSYVSNL                                 2169

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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