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

NucPred

Fetching P39109 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MAGNLVSWACKLCRSPEGFGPISFYGDFTQCFIDGVILNLSAIFMITFGI    50
  51  RDLVNLCKKKHSGIKYRRNWIIVSRMALVLLEIAFVSLASLNISKEEAEN   100
 101  FTIVSQYASTMLSLFVALALHWIEYDRSVVANTVLLFYWLFETFGNFAKL   150
 151  INILIRHTYEGIWYSGQTGFILTLFQVITCASILLLEALPKKPLMPHQHI   200
 201  HQTLTRRKPNPYDSANIFSRITFSWMSGLMKTGYEKYLVEADLYKLPRNF   250
 251  SSEELSQKLEKNWENELKQKSNPSLSWAICRTFGSKMLLAAFFKAIHDVL   300
 301  AFTQPQLLRILIKFVTDYNSERQDDHSSLQGFENNHPQKLPIVRGFLIAF   350
 351  AMFLVGFTQTSVLHQYFLNVFNTGMYIKSALTALIYQKSLVLSNEASGLS   400
 401  STGDIVNLMSVDVQKLQDLTQWLNLIWSGPFQIIICLYSLYKLLGNSMWV   450
 451  GVIILVIMMPLNSFLMRIQKKLQKSQMKYKDERTRVISEILNNIKSLKLY   500
 501  AWEKPYREKLEEVRNNKELKNLTKLGCYMAVTSFQFNIVPFLVSCCTFAV   550
 551  FVYTEDRALTTDLVFPALTLFNLLSFPLMIIPMVLNSFIEASVSIGRLFT   600
 601  FFTNEELQPDSVQRLPKVKNIGDVAINIGDDATFLWQRKPEYKVALKNIN   650
 651  FQAKKGNLTCIVGKVGSGKTALLSCMLGDLFRVKGFATVHGSVAYVSQVP   700
 701  WIMNGTVKENILFGHRYDAEFYEKTIKACALTIDLAILMDGDKTLVGEKG   750
 751  ISLSGGQKARLSLARAVYARADTYLLDDPLAAVDEHVARHLIEHVLGPNG   800
 801  LLHTKTKVLATNKVSALSIADSIALLDNGEITQQGTYDEITKDADSPLWK   850
 851  LLNNYGKKNNGKSNEFGDSSESSVRESSIPVEGELEQLQKLNDLDFGNSD   900
 901  AISLRRASDATLGSIDFGDDENIAKREHREQGKVKWNIYLEYAKACNPKS   950
 951  VCVFILFIVISMFLSVMGNVWLKHWSEVNSRYGSNPNAARYLAIYFALGI  1000
1001  GSALATLIQTIVLWVFCTIHASKYLHNLMTNSVLRAPMTFFETTPIGRIL  1050
1051  NRFSNDIYKVDALLGRTFSQFFVNAVKVTFTITVICATTWQFIFIIIPLS  1100
1101  VFYIYYQQYYLRTSRELRRLDSITRSPIYSHFQETLGGLATVRGYSQQKR  1150
1151  FSHINQCRIDNNMSAFYPSINANRWLAYRLELIGSIIILGAATLSVFRLK  1200
1201  QGTLTAGMVGLSLSYALQITQTLNWIVRMTVEVETNIVSVERIKEYADLK  1250
1251  SEAPLIVEGHRPPKEWPSQGDIKFNNYSTRYRPELDLVLKHINIHIKPNE  1300
1301  KVGIVGRTGAGKSSLTLALFRMIEASEGNIVIDNIAINEIGLYDLRHKLS  1350
1351  IIPQDSQVFEGTVRENIDPINQYTDEAIWRALELSHLKEHVLSMSNDGLD  1400
1401  AQLTEGGGNLSVGQRQLLCLARAMLVPSKILVLDEATAAVDVETDKVVQE  1450
1451  TIRTAFKDRTILTIAHRLNTIMDSDRIIVLDNGKVAEFDSPGQLLSDNKS  1500
1501  LFYSLCMEAGLVNEN                                     1515

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.)

Go back to the NucPred Home Page.