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

NucPred

Fetching O35505 from www.uniprot.org...

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

   1  MVPLVQPTTPAYRPLPSHLSADTEVRGRGTLVHEAQLNCFYISPGGSNYG    50
  51  SPRPAHANINANAAAGLAPEHIPTPGAALSWQAAIDAGRQAKLMGSAGNT   100
 101  TISTVSSTQRKRQQYGKPKKQSGTTATRPPRALLCLTLKNPIRRACISIV   150
 151  EWKPFEIIILLTIFANCVALAIYIPFPEDDSNATNSNLERVEYLFLIIFT   200
 201  VEAFLKVIAYGLLFHPNAYLRNGWNLLDFIIVVVGLFSAILEQATKADGA   250
 251  NALGGKGAGFDVKALRAFRVLRPLRLVSGVPSLQVVLNSIIKAMVPLLHT   300
 301  ALLVLFVIIIYAIIGLELFMGKMHKTCYNQEGITDVPAEEDPSPCALESG   350
 351  HGRQCQNGTVCKPGWDGPKHGITNFDNFAFAMLTVFQCITMEGWTDVLYW   400
 401  MQDAMGYELPWVYFVSLVIFGSFFVLNLVLGVLSGEFSKEREKAKARGDF   450
 451  QKLREKQQLEEDLKGYLDWITQAEDIDPENEDEGVDEEKPRNMSMPTSET   500
 501  ESVNTENVAGGDIEGENCGARLAHRISKSKFSRYWRRWNRFCRRKCRAAV   550
 551  KSNVFYWLVIFLVFLNTLTIASEHYNQPHWLTEVQDTANKALLALFTAEM   600
 601  LLKMYSLGLQAYFVSLFNRLDCFIVCGGILETILVETKIMSPLGISVLRC   650
 651  VRLLRIFKITRYWNSLSNLVASLLNSVRSIASLLLLLFLFIIIFSLLGMQ   700
 701  LFGGKFNFDEMRTRRSTFDNFPQSLLTVFQILTGEDWNSVMYDGIMAYGG   750
 751  PSFPGMLVCIYFIILFICGNYILLNVFLAIAVDNLADAESLTSAQKEEEE   800
 801  EKERKKLARTASPEKKQEVVEKPAVEETKEEKIELKSITADGESPPTTKI   850
 851  NMDDLQPNENEDKSPYPNPDAAGEEDEEEPEMPVGPRPRPLSELHLKEKA   900
 901  VPMPEASAFFIFSPNNRFRLQCHRIVNDTIFTNLILFFILLSSISLAAED   950
 951  PVQHTSFRNHILFYFDIVFTTIFTIEIALKMTAYGAFLHKGSFCRNYFNI  1000
1001  LDLLVVSVSLISFGIQSSAINVVKILRVLRVLRPLRAINRAKGLKHVVQC  1050
1051  VFVAIRTIGNIVIVTTLLQFMFACIGVQLFKGKLYTCSDSSKQTEAECKG  1100
1101  NYITYKDGEVDQPIIQPRSWENSKFDFDNVLAAMMALFTVSTFEGWPELL  1150
1151  YRSIDSHTEDKGPIYNYRVEISIFFIIYIIIIAFFMMNIFVGFVIVTFQE  1200
1201  QGEQEYKNCELDKNQRQCVEYALKARPLRRYIPKNQHQYKVWYVVNSTYF  1250
1251  EYLMFVLILLNTICLAMQHYGQSCLFKIAMNILNMLFTGLFTVEMILKLI  1300
1301  AFKPKHYFCDAWNTFDALIVVGSIVDIAITEVNPAEHTQCSPSMNAEENS  1350
1351  RISITFFRLFRVMRLVKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLF  1400
1401  FIYAVIGMQVFGKIALNDTTEINRNNNFQTFPQAVLLLFRCATGEAWQDI  1450
1451  MLACMPGKKCAPESDPSNSTEGETPCGSSFAVFYFISFYMLCAFLIINLF  1500
1501  VAVVMDNFDYLTRDWSILGPHHLDEFKRIWAEYDPEAKGRIKHLDVVTLL  1550
1551  RRIQPPLGFGKLCPHRVACKRLVSMNMPLNSDGTAMFNATLFALVRTALR  1600
1601  IKTEGNLEQANEELRAIIKKIWKRTSMKLLDQVVPPAGDDEVTVGKFYAT  1650
1651  FLIQEYFRKFKKRKEQGLVGKPSQRNALSLQAGLRTLHDIGPEIRRAISG  1700
1701  DLTAEEELDKAMKEAVSAASEDDIFGRAGGLFGNHVSYYQSDSRSTFPQT  1750
1751  FTTQRPLHINKAGNNQGDTESPSHEKLVDSTFTPSSYSSTGSNANINNAN  1800
1801  NTALGRFPHPAGYPSTVSTVEGHRPPSSPATWAQEATRKLGAMRCHSRES  1850
1851  QIAVVCQEEPSQDKTYDVELNKDAEYCSEPSLLSTEMLSYKDDENRQLTP  1900
1901  PEEDKGDTRPSPKKGFLRSASLGRRASFHLECLKRQKNHGGDISQKTVLP  1950
1951  LHLVHHQALAVAGLSPLLQRSHSPTAIPRPCATPPATPGSRGWPPKPIPT  2000
2001  LRLEGAESCEKLNSSFPSIHCSSWSEEPSPCGGGSSAARRARPVSLMVPS  2050
2051  QAGAPGRQFHGSASSLAEAVLISEGLGQFAQDPKFIEVTTQELADACDMT  2100
2101  IGEMENAADNILSGGAPQSPNGTLLPFVNCRDPGQDRAGGDEDEGCACAL  2150
2151  GRGWSEEELADSRVHVRSL                                 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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