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

NucPred

Fetching Q04958 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MRSMNCTTNNTNNTGQNTKNSLGSSFNSSNYTSYRFQTCLTDQIISEAQT    50
  51  WSLSSLFNFSWVVSYFVMGASRMIFRYGWYLATLSLLRIPKWIFFKLHHV   100
 101  QFTLSFWLILFALAVIVFVTYTIMKERILSQYKRLTPEFLPLENTGKSGS   150
 151  SANINAASTQSANAPPAIGSSTTGASSIIDSKKHSLKDGNENETFLSSYL   200
 201  DQFLSAIKIFGYLEKPVFHDLTKNMKTQKMDEGEILLLDSTIGFAIVVEG   250
 251  TLQLYHEVDHSDKDHGDETDHSDTDGLDDQDRDEEDEEEDDDIDNYDTKS   300
 301  CSSNLIDEEDESVGYIHLKNGLGNFQLLNTVKPGNPLTSLVSILNLFTHS   350
 351  MSSYGNSNFPSELSSPIDTTVSVNNMFCSSEQNFSNTDSMTNSTNSFPTF   400
 401  PSSMPKLVARAATDCTIGIIPPQSFAKLTAKYPRSASHIIQMVLTKLYHV   450
 451  TFQTAHDYLGLTKEIMDIEVLLNKSIVYELPYYLKEAVIRKFKTVDKSSG   500
 501  SADLEPKPKNSNASSKLKKPPKAKPSDGIIQSLKIANANANTSSNSLSLK   550
 551  PEFTHHPSSRHVVLGSRDQFNPGDLLSNVPLSRTMDILSPNPIHNNNRNK   600
 601  SNGINTSTSNQHKRSSRSSSNNASVHSKKFSSLSPELRNAQLSTSPLSLD   650
 651  NTSVHDHIHPSPVHLKGRVSPRPNLLPTTSFSAAQEETEDSALRMALVEA   700
 701  MLTYLGVNKSNMSVSSSSIANMSSLNSPQLNEMYSRRPSNASFLMSPHCT   750
 751  PSDISVASSFASPQTQPTMLRILPKEYTISNKRHNKSKSQDKKKPRAYKE   800
 801  ELTPNLDFEDVKKDFAQGIQLKFFKKGTTIVEQNARGKGLFYIISGKVNV   850
 851  TTNSSSSVVSSMSKPEQVSAQSSHKGENPHHTQHLLYSVGSGGIVGYLSS   900
 901  LIGYKSFVNIVAKSDVYVGFLSSATLERLFDKYFLIYLRISDSLTKLLSS   950
 951  RLLKLDHALEWVHLRASETLFSQGDSANGIYVVLNGRLRQLQQQSLSNSN  1000
1001  TSSEEVETQNIILGELAQGESFGEVEVLTAMNRYSTIVAVRDSELARIPR  1050
1051  TLFELLALEHPSIMIRVSRLVAKKIVGDRTVPALTGDPLSIKENDFTSLI  1100
1101  PPTKASYSSSLSHKPQNITSGTITFRTITILPITSGLPVEAFAMKLVQAF  1150
1151  KQVGRTTIGLNQRTTLTHLGRHAFDRLSKLKQSGYFAELEEMYQTVVYIS  1200
1201  DTPVKSNWTRTCIAQGDCILLLADARSPSAEIGEYEKLLLNSKTTARTEL  1250
1251  ILLHPERYVEPGLTHKWLRYRPWVHSHHHIQFSLTGTTLMNEGKMHVLNN  1300
1301  GALALMDKLIQTEFSRKTQQNISKLLPDSIKNTVENFSSRFMKSKRQYYT  1350
1351  PVHRHKNDFLRLARILSGQAIGLVLGGGGARGISHLGVIQAIEEQGIPVD  1400
1401  VIGGTSIGSFVGGLYAKDYDLVPIYGRVKKFAGRISSIWRMLTDLTWPVT  1450
1451  SYTTGHEFNRGIWKTFGDTRIEDFWIQYYCNSTNITDSVQEIHSFGYAWR  1500
1501  YIRASMSLAGLLPPLEENGSMLLDGGYVDNLPVTEMRARGCQTIFAVDVG  1550
1551  SADDRTPMEYGDSLNGFWIIFNRWNPFSSHPNIPNMAEIQVRLGYVASVN  1600
1601  ALEKAKNTPGVVYVRPPIEEYATLDFSKFEEIYHVGVDYGRIFLQGLIDD  1650
1651  DKMPYIPGSQETTLNSQVPEFLLHRRNSI                       1679

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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