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

NucPred

Fetching Q9VDW3 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MTAKPPPPIPPTLGGDDSGTHGPKLAPEIPRINSELAAQAALRGQQLLRK    50
  51  QGSQEQHATNTLPAHKTGAPPPLPPTQSRPVPAIPARGASDRAAPPEIPP   100
 101  KRHSLKSMPDGQPMMVPGLPPTMRQPPPLPRKPASTQSSAQNSAQSSPLA   150
 151  GMKFKDKPPPPPEKHSTLSAEGMAARRCSNPFEMPPPPPPLVLQSAVAAL   200
 201  SEQSSKNGLNPVPSPAPTRASEAKKINQRSIASPTEEFGSEDALRGIESG   250
 251  LRNMERAMQEQMNLRNMEAAVQNNFDLSFKASLAAGARHLGGGSVNLRTA   300
 301  NYERNLSLDEGRAGDSRQSLEELKQLRAQAQQQSLLNNSSSSSSNSQVEQ   350
 351  SMRSTIEHHMRSLDRNLPLELQYSRHRFQNNLNAVAAAGGGGGNSSTGNA   400
 401  VANSGTSGSQQPPMPLSSEFREQIRQQLLGNIPPQVVHNMGQSPGSAAAA   450
 451  ALLQHQAQSRAAAAAAAAAAAAAAAQVAAGSGALSREELRMRRRSSHDET   500
 501  QLTQNSSGGIQVTRLREHWDETSQCVLQRAAQLKNMLSDSQRFEAKRLEL   550
 551  EKWLARMEQRAERMGTIATTADILEAQQKEQKSFHAELHQNKQHFDIFNE   600
 601  LTQKLIAVYPNDDTTRIKKMTEVINQRYANLNSGVINRGKQLHAAVHSLQ   650
 651  SFDRAMDQFLAFLSETETLCENAESDIERNPLMFKDLQSEIETHRVVYDR   700
 701  LDGTGRKLLGSLTSQEDAVMLQRRLDEMNQRWNNLKSKSIAIRNRLESNS   750
 751  EHWNALLLSLRELTEWVIRKDTELSTLGLGPVRGDAVSLQKQLDDHKAFR   800
 801  RQLEDKRPIVESNLTSGRQYIANEAAVSDTSDTEANHDSDSRYMSAEEQS   850
 851  RELTRSIRREVGKLSEQWNNLIDRSDNWKHRLDEYMTKMRQFQKILEDLS   900
 901  SRVALAEQTKTSWLPPSSVGEANEQMQQLQRLRDKMTTASALLDDCNEQQ   950
 951  SFFTANQVLVPTPCLSKLEDLNTRMKLLQIAMDERQKVLCQAGAQQTHEN  1000
1001  GDDGRTTSNSGTIGPLPNLGQSVKPPWERATTAANVPYYIDHERETTHWD  1050
1051  HPEMIELMKGLADLNEIRFSAYRTAMKLRSVQKRLALDRISMSTACESFD  1100
1101  RHGLRAQNDKLIDIPDMTTVLHSLYVTIDKIDLTLMLDLAINWILNVYDS  1150
1151  QRTGQIRVLSFKVGLVLLCKGHLEEKYRYLFRLVADTDRRADQRRLGLLL  1200
1201  HDCIQVPRQLGEVAAFGGSNIEPSVRSCLEQAGISQEAIDGNQDISIELQ  1250
1251  HFLGWLQHEPQSLVWLPVLHRLAAAEAAKHQAKCNICKEYPIVGFRYRCL  1300
1301  KCFNFDMCQKCFFFGRNAKNHKLTHPMHEYCTTTTSTEDVRDFTRALKNK  1350
1351  FKSRKYFKKHPRVGYLPVQSVLEGDALESPAPSPQHTTHQLQNDMHSRLE  1400
1401  MYASRLAQVEYGGTGSNSTPDSDDEHQLIAQYCQALPGTSNGSAPKSPVQ  1450
1451  VMAAMDAEQREELEAIIRDLEEENANLQAEYQQLCSKEQSGMPEDSNGMQ  1500
1501  HSSSSMTGLSGQGEQGQDMMAEAKLLRQHKGRLEARMQILEDHNRQLEAQ  1550
1551  LQRLRQLLDEPNGGGSSATSSGLPSAPGSALNSKPNTLQTRSVTASQLNT  1600
1601  DSPAKMNQQNGHYEHNSKNSSGLVTVITEQELESINDDLEDSSSSNTTNT  1650
1651  TTTTTTTATTEKTCVELQK                                 1669

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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