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

NucPred

Fetching P16875 from www.uniprot.org...

The NucPred score for your sequence is 0.30 (see score help below)

   1  MDITESEFTIFEVTPDPNELNNKRIKEIKGGKVNIKELFRYAGVFEIILL    50
  51  IIGIIGSIGVGCLNPLLMILTGDVVDTFVNGENFSKEGGSIKITTEEMNY   100
 101  EIMNSISDTINKLVLKMLYFAIGNMVAGFLQTICFFVLSEYQGIKIRSLY   150
 151  FKALLRQDPGWFDCHKTGELTSKIINDIQKIQDGMSLKFGRLFQTFSSFI   200
 201  TGYLIGFIKCWDLTLVVLCMFPFIMVSMMGLGMSAGIFTMKSHKPFSEAC   250
 251  SIAEQTIGNIRTVHSLTQERSFCESYNTKIMETDKYNIKKSIGIGTGLGC   300
 301  MMFFIMSSNALGSWYGNFVVRGKGGSDNVKAGTVLTVFMSVLLATQSLSQ   350
 351  ISTPINILNSAKVAAFNVYQTIDRIPDIDCQSIGGECPTECNGNIRFEDV   400
 401  QFVYPTRLSHHVLKGLDLEIKKGQTIALVGASGCGKSTTIQLIQRNYDPN   450
 451  GGRVTLDGKDIRELNIKWLRNQIGLVGQEPVLFAGTIRENIMLGAKEGAT   500
 501  PSEEEMIECAKMANAHDFISKLPEGYDTIIGEKGALLSGGQKQRIAIARA   550
 551  LIRNPSILLLDEATSALDTQSEKIVQEALEKASKGRTTIIVAHRLTTVRN   600
 601  ADKICVFHQGEIIEQGKHQELMDLKGTYYGLVKRQSMEEEVDQETVENDL   650
 651  KKFREQEDKEVENISLEQTNLHNENSIVKQIKQEYKEEQKKLKHSNRFVL   700
 701  FRVIWNNYKHEYIFCTLGLIGGIGAGAAFPFYSLNFVDLIRVLMKLHPGI   750
 751  NLTDEQANSILRSCMIIICIGIITMISFFCYVGLFMAAGEKMIGRIRRRF   800
 801  YYSIMHQNVSWFDRRENMVGAVTTKLTSDPTSLQGISAERVGDIIEIMST   850
 851  VGFGFGIGLYFSWKLSLCILAVFPIISFFMFINGQLNSKNAAPAKAAYEQ   900
 901  CGVTLVEVVEAMKTVQSLGKEDYFSQKYNNDLQIPKRGIIKWGPLLSITN   950
 951  AITNLLTFSINAYGYYLGICFMKKTINYQQDVPNFVDEIIDTFGDIQKAL  1000
1001  MTINSATTSFAQIGNVLPDVGKAVGAAKSIYNIIDRKPSIDCYSEEGETF  1050
1051  NDVKGEIEFKNIHFRYPTRADNEVLKGISFKAEQGKTIALVGASGCGKST  1100
1101  TIQLIERFYDPTSGEVLLDGHNIKDLNIHFLRNQIGLVGQEPVLFAESVI  1150
1151  DNIKRGVPEGVEVSNEQIYAAAKMANAHDFISAMPEGYNTMVGDRGSQLS  1200
1201  GGQKQRIAIARALIRNPKVLLLDEATSALDSESEKIVQDALDKASKGRTT  1250
1251  IVIAHRLSTIQNADKIYVIMRGKIVEQGKHQELIDLKGFYYTLAMQQFGT  1300
1301  VN                                                  1302

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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