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

NucPred

Fetching Q80U44 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MDSYFKAAVSGLDKLLDDFEQNPDKQDYLPDAYAFNQCSVSSESASPQLA    50
  51  LLSKDQRCISTCASSEACCEDANETFLEGKIHEGLTSRPNEKNVAGLDLL   100
 101  SSVDASTSDEIQPSCMRRCSKPVCDLISDMGNLVHATNSEEDIKQLLPDD   150
 151  PKSSADTLITLDSSSVSEALTVSSVDCGSNAVREEQNNINAGIKNRDISI   200
 201  KELGVKVDMALFDSCKYNRTENLKDKIISNELETVDFDMPSVLMEQSSEM   250
 251  SNTKDNPQYKRLPCELLKDDGCLAEEKVAVAVNNTECLEEGGGSNTIAMP   300
 301  CKLPENEGISPSDPASKDENFKLPDFPLQENRTSVFMKQTVKEDSRNLDL   350
 351  KDNNDIVHVSGDDVPPSLSCLSLSGSLCGSLIHNNEHSDILPPNESEGQN   400
 401  NDAVTIHEEIQKSDVLDGETDLSKKETCRSIFLQPVNEKKGEGKVEVEEM   450
 451  VISGESLESPEDASSAAAAGSPVALSAASVPEAPGPCEGLTFPSSDMDGQ   500
 501  ELDYFNIDESMRSGILISDAELDAFLKEQCLSNSNTMSAGENVNDSQLQM   550
 551  NQITMKGLHDENAGDIYFNAEAGAAGENGGVGNCETSDKENTENNGLSIG   600
 601  EKGAIPTERELSACQPDIRDELPVPSIKTQAVGGARPKQLLSLPPGTRSS   650
 651  KELNKPDVVDVPESEPCTANATAVSTCSADHIPDSQVSFNSNYIDIESNF   700
 701  EDGSSFVTANKDSLPENKRKESLVLGQKQPTWVPDSEAPNCMNCQVKFTF   750
 751  TKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVICYETINKAQAFER   800
 801  MMSPGGSCLKSNHSNECATDQPLQETQTSSTPSPTTLPISALKQPNVEGP   850
 851  CSKEQKRVWFADGILPNGEVADTTKLSSGSKRCSDDFSPVLPDVPTMINK   900
 901  VDRTHSPTVEKPNNGLGDIIRSEISQSPTCHTAPVERLPGNTGTEGLPMP   950
 951  GPFTLEDDVFVDSEEPSTPTVVPANSGLPVASISDYRLLCSVAKCVCNNI  1000
1001  SLLPDDDIGLPPLLATSGEDGSVPVVQERPSHEQIILLLEGEGFPPATFV  1050
1051  LNANLLVNVKLVLYSSEKYWYFSTNGLHGLGQAEIIVLLQCLPNEDTVPK  1100
1101  DIFRLFITIYKDALKGKYIENLDNLTFTESFLNSKDHGGFLFITPTFQNL  1150
1151  DGLPVPRSPFLCGILIQKLEIPWAKVFPMRLMLRLGAEYKAYPAPLTSVR  1200
1201  GRKPLFGEIGHTIMNLLVDLRNYQYTLHNIDQLLIHMEMGKSCIKIPRKK  1250
1251  YSDVMKVIHSSNEHVISIGASFSTEADSHLVCVQSDGVYQTQANSATGQP  1300
1301  RKVTGASFVVFNGALKTSSGFLAKSSIVEDGLMVQITPETMEGLRLALRE  1350
1351  QKDFRIQCGKVDAVDLREYVDICWVDSEERKNKGVISSVDGMSVEGFPSE  1400
1401  KIKLETDFETEEKTVKCTEVFYFLKDQDISILSSSYQFAKEIAVACSAAL  1450
1451  CPHLRTLKSNRMNKIGLRVSIDTDMVEFQAGCEGQLLPQHYLNDLDSALI  1500
1501  PVIHGGTSNSSLPLEIELAFFILENLSE                        1528

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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