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

NucPred

Fetching Q8TEK3 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPD    50
  51  LKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNT   100
 101  RPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDE   150
 151  IKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDR   200
 201  EFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVD   250
 251  HQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLK   300
 301  GSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQRESK   350
 351  SNAATPTKGPEGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLN   400
 401  KKGRKMAGRKRGRPKKMNTANPERKPKKNQTALDALHAQTVSQTAASSPQ   450
 451  DAYRSPHSPFYQLPPSVQRHSPNPLLVAPTPPALQKLLESFKIQYLQFLA   500
 501  YTKTPQYKASLQELLGQEKEKNAQLLGAAQQLLSHCQAQKEEIRRLFQQK   550
 551  LDELGVKALTYNDLIQAQKEISAHNQQLREQSEQLEQDNRALRGQSLQLL   600
 601  KARCEELQLDWATLSLEKLLKEKQALKSQISEKQRHCLELQISIVELEKS   650
 651  QRQQELLQLKSCVPPDDALSLHLRGKGALGRELEPDASRLHLELDCTKFS   700
 701  LPHLSSMSPELSMNGQAAGYELCGVLSRPSSKQNTPQYLASPLDQEVVPC   750
 751  TPSHVGRPRLEKLSGLAAPDYTRLSPAKIVLRRHLSQDHTVPGRPAASEL   800
 801  HSRAEHTKENGLPYQSPSVPGSMKLSPQDPRPLSPGALQLAGEKSSEKGL   850
 851  RERAYGSSGELITSLPISIPLSTVQPNKLPVSIPLASVVLPSRAERARST   900
 901  PSPVLQPRDPSSTLEKQIGANAHGAGSRSLALAPAGFSYAGSVAISGALA   950
 951  GSPASLTPGAEPATLDESSSSGSLFATVGSRSSTPQHPLLLAQPRNSLPA  1000
1001  SPAHQLSSSPRLGGAAQGPLPEASKGDLPSDSGFSDPESEAKRRIVFTIT  1050
1051  TGAGSAKQSPSSKHSPLTASARGDCVPSHGQDSRRRGRRKRASAGTPSLS  1100
1101  AGVSPKRRALPSVAGLFTQPSGSPLNLNSMVSNINQPLEITAISSPETSL  1150
1151  KSSPVPYQDHDQPPVLKKERPLSQTNGAHYSPLTSDEEPGSEDEPSSARI  1200
1201  ERKIATISLESKSPPKTLENGGGLAGRKPAPAGEPVNSSKWKSTFSPISD  1250
1251  IGLAKSADSPLQASSALSQNSLFTFRPALEEPSADAKLAAHPRKGFPGSL  1300
1301  SGADGLSPGTNPANGCTFGGGLAADLSLHSFSDGASLPHKGPEAAGLSSP  1350
1351  LSFPSQRGKEGSDANPFLSKRQLDGLAGLKGEGSRGKEAGEGGLPLCGPT  1400
1401  DKTPLLSGKAAKARDREVDLKNGHNLFISAAAVPPGSLLSGPGLAPAASS  1450
1451  AGGAASSAQTHRSFLGPFPPGPQFALGPMSLQANLGSVAGSSVLQSLFSS  1500
1501  VPAAAGLVHVSSAATRLTNSHAMGSFSGVAGGTVGGN               1537

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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