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

NucPred

Fetching Q8CGC7 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MAALCLTVNAGNPPLEALLAVEHVKGDVSISVEEGKENLLRVSETVAFTD    50
  51  VNSILRYLARIATTSGLYGTNLMEHTEIDHWLEFSATKLSSCDRLTSAIN   100
 101  ELNHCLSLRTYLVGNSLTLADLCVWATLKGSAAWQEHLKQNKTLVHVKRW   150
 151  FGFLEAQQAFRSVGTKWDVSGNRATVAPDKKQDVGKFVELPGAEMGKVTV   200
 201  RFPPEASGYLHIGHAKAALLNQHYQVNFKGKLIMRFDDTNPEKEKEDFEK   250
 251  VILEDVAMLHIKPDQFTYTSDHFETIMKYAEKLIQEGKAYVDDTPAEQMK   300
 301  AEREQRTESKHRKNSVEKNLQMWEEMKKGSQFGQSCCLRAKIDMSSNNGC   350
 351  MRDPTLYRCKIQPHPRTGNKYNVYPTYDFACPIVDSIEGVTHALRTTEYH   400
 401  DRDEQFYWIIEALGIRKPYIWEYSRLNLNNTVLSKRKLTWFVNEGLVDGW   450
 451  DDPRFPTVRGVLRRGMTVEGLKQFIAAQGSSRSVVNMEWDKIWAFNKKVI   500
 501  DPVAPRYVALLKKEVVPVNVLDAQEEMKEVARHPKNPDVGLKPVWYSPKV   550
 551  FIEGADAETFSEGEMVTFINWGNINITKIHKNADGKITSLDAKLNLENKD   600
 601  YKKTTKITWLAESTHALSIPAVCVTYEHLITKPVLGKDEDFKQYINKDSK   650
 651  HEELMLGDPCLKDLKKGDIIQLQRRGFFICDQPYEPVSPYSCREAPCILI   700
 701  YIPDGHTKEMPTSGSKEKTKVEISKKETSSAPKERPAPAVSSTCATAEDS   750
 751  SVLYSRVAVQGDVVRELKAKKAPKEDIDAAVKQLLTLKAEYKEKTGQEYK   800
 801  PGNPSAAAVQTVSTKSSSNTVESTSLYNKVAAQGEVVRKLKAEKAPKAKV   850
 851  TEAVECLLSLKAEYKEKTGKDYVPGQPPASQNSHSNPVSNAQPAGAEKPE   900
 901  AKVLFDRVACQGEVVRKLKAEKASKDQVDSAVQELLQLKAQYKSLTGIEY   950
 951  KPVSATGAEDKDKKKKEKENKSEKQNKPQKQNDGQGKDSSKSQGSGLSSG  1000
1001  GAGEGQGPKKQTRLGLEAKKEENLAEWYSQVITKSEMIEYYDVSGCYILR  1050
1051  PWSYSIWESIKDFFDAEIKKLGVENCYFPIFVSQAALEKEKNHIEDFAPE  1100
1101  VAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPVRLNQWCNV  1150
1151  VRWEFKHPQPFLRTREFLWQEGHSAFATFEEAADEVLQILELYARVYEEL  1200
1201  LAIPVVRGRKTEKEKFAGGDYTTTIEAFISASGRAIQGATSHHLGQNFSK  1250
1251  MCEIVFEDPKTPGEKQFAYQCSWGLTTRTIGVMVMVHGDNMGLVLPPRVA  1300
1301  SVQVVVIPCGITNALSEEDREALMAKCNEYRRRLLGANIRVRVDLRDNYS  1350
1351  PGWKFNHWELKGVPVRLEVGPRDMKSCQFVAVRRDTGEKLTIAEKEAEAK  1400
1401  LEKVLEDIQLNLFTRASEDLKTHMVVSNTLEDFQKVLDAGKVAQIPFCGE  1450
1451  IDCEDWIKKMTARDQDVEPGAPSMGAKSLCIPFNPLCELQPGAMCVCGKN  1500
1501  PAKFYTLFGRSY                                        1512

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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