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

NucPred

Fetching Q21286 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MKREKDNPKAKTTSFNQGKLNIGEETCDLYAYKETIGRQILFWLLTIVTL    50
  51  GFYQLLAYWVKSLFVKVRFQPTSHDECEYVMVEDIHGTQTIKEVFKAESD   100
 101  VGLARPTRSGKQEKVKVMRFFTYRKIKYIWYEKDQEWLNPADMDSAAPFN   150
 151  IYQKLTLDVIGLKEQDVIASRKIYNMNALALALTPILVILFKEVLGPFYL   200
 201  FQCFSVALWYSDNYAYYASVIVIITVGSAAVAVYQMRAQEKRIRNMVGDT   250
 251  ISVIVRRDGHDITIDASEIVPMDILILPSNTFILPCDCLLMNGTVIVNEA   300
 301  MLTGESVPVTKASLKEADECGPEIRLSSEHNRHTLFSGTTVLQTRNYKGQ   350
 351  PVMARVIRTGFSTLKGQLVRSIMYPKPQEKEALKDVMVFILVLGFIALIG   400
 401  FIYTVIEMVSRGESLKHIIIRSLDIITIVVPPALPAAMSVGIINANSRLK   450
 451  KKKIFCTSPTTVNVCGLINVACFDKTGTLTEDGLDFNCLKAIRKNEDGKP   500
 501  EFTSEFEELDPVKLSAENANLNIVVAAASCHSLTRIDGTLHGDPLELILV   550
 551  EKSKWIIEEAVNSDEETQDFDTVQPTVLRPPPEQATYHPENNEYSVIKQH   600
 601  PFNSALQRMSVIISTPSEHSAHDMMVFTKGSPEMIASLCIPDTIPEDYME   650
 651  VVDEYAQRGFRLIAVASKAVHLNFAKALKTPRDIMESELEFLGLIVMENR   700
 701  LKDVTLSVINELSVANIRCVMVTGDNLLTAMSVARECGIIRPTKKAFLIT   750
 751  HSKTEKDPLGRTKLFIKESVSSSENDIDTDSEVRAFDRKAVLRTATYQMA   800
 801  IAGPTYSVITHEYPELVDRITAMCDVYARMAPDQKAQLIGALQEIGAKVS   850
 851  MCGDGANDCAALKAAHAGISLSQAEASIAAPFTSNVPDIRCVPTVIKEGR   900
 901  CALVTSYAVSKYMAAYSLNEFLSVMLLYNDGTNISDGQFLYIDLVLITLV   950
 951  ALFLGNTEASRKLSGIPPPRRLATSAFYFSVFGQMFFNIITQTTGYLLVR  1000
1001  GQSWYVPNPEELDNTTTMIGTTVFFTSCCMYLGYAFVYSKGHPYRRSVFT  1050
1051  NWLLCGIIFVIGAINMVMIFTNMGFLMNLMGFVYVPSTSMRFILLAISLA  1100
1101  GVFLSLLYEHFFVEKVVAIHFESYLRQRRLRNGDPSLSAYEKILAAIGSS  1150
1151  PRWFEDEINLSKSIDRKETIESKC                            1174

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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