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

NucPred

Fetching Q8NIV6 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MSNSMRDLIDGEAELDDEEDDESFDEEAGDRPRRRPNIDDSSEEEEDDED    50
  51  EEEARKIREGFIVDEDEEDEAEDSDARERRRRKKRRREREEEEQLDEEDL   100
 101  DLIGEAIPEWERKPQPQRLKRGHRDDHRPTERRGLAEIFSDEDEEHDDRG   150
 151  YGRPSGRAQADEFDDFIEDDYPEDDEERRHREEDEEVARPKDRGLNIDTT   200
 201  GLDKDALEDMDAIFGNGEDYEWALQLEEEQEHAERTKEDIELQDVFEPSQ   250
 251  LKEKLLTDEDNRIRFNDEPERFQLDRKAFKNLQMTSDQFKEEARWISNLM   300
 301  LPSKNLSSELHGPFNKAVGKVLEFFVIDGVEVPYVFQHRRDYLIHAKKMR   350
 351  NPNRRDDPDAPEYTVDAEKLLTQDDLWKVLDLDIRFRSFLEKRNALEQTY   400
 401  DKLKEKTRDDILEEMIRQAQSIEELQDLQDYLNFQYSAELKDLAANDNSA   450
 451  QREIKRAGGRTAQFERIRRSNAYKFVQALGITPDRLAKNILRESSKVTSE   500
 501  DDSRLPDDLADTLVDADFPTGELVINAARQMLAEEMFASPRMRKHFRKNF   550
 551  YGMGIVSCRRTDKGLRKIDEANPYYEVKYLKNMSIADLAVRPELFLKMMK   600
 601  AEEEGLIEIKVSLENDREFRQQLFSDFASENFSELADKWNAERQKVIDLA   650
 651  FDKLVKVIVKGVKDSLRTACQDELLKTCRELYFKRLDQAPYKPKGMVIGT   700
 701  TPRVLTLSNGMGDPNREPVSWVSMDEDGRILEHGTFTNLARDESQREALA   750
 751  ELVRRRQPDVIGISGFSADTHRLIKDVEGLVSEKGLVGPEYDDPETNEYR   800
 801  SDLLEVIVINDEVARLYKDSPRAVADHPSLNPMTRYCIALARYMQNPMKE   850
 851  YAALGKDVTSLQIHPYQQYLPQAKLLKHLETAMVDMVNLVGVDINVAMQD   900
 901  ANTAHLLPYVAGLGPRKAQLLIKGINKNGGVVTSRDELVGDPERHKLPVL   950
 951  GPRVWNNCASFLFIEYEPTNPESDPLDNTRIHPEDYDLARKVAADALGLD  1000
1001  EEDVKAETDENGAGAIVRKLFKDDEQDKVNELILEEYAEQLEREYQQRKR  1050
1051  ATLETIRAELQVPYEELRKKFESLTVDQVFTMLTGENRDSLCEGMIVAAN  1100
1101  VRVVKDDFAIVKLDCGIEGRIESHDVSYRHSIKDVLHVGQVVQAKLIDLN  1150
1151  RKEFVSKLSMRDEEMRRPFRRHFDHGRDQWDYRKEDEDREELREKDKSTG  1200
1201  RAQRVVNHPLFKPFNSTQAEEYLGSQPSGEVVIRPSSKGNDHLAVTWKVA  1250
1251  DGVFQHVDVLELQKENEFAVGRVLRVGKYTYQDLDELIVDHVKAMAKKVD  1300
1301  ELMQCDKFQKGSRNETEKWLTTYMDANPNRSTYAFCIDTKHPGYFFLCFK  1350
1351  ASRNSRVNAWPVRVIPHAFELMKSQYPDVRALCNGFKLRYQSEMLKQQSG  1400
1401  GR                                                  1402

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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