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

NucPred

Fetching Q7Z3T8 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MDSYFKAAVSDLDKLLDDFEQNPDEQDYLQDVQNAYDSNHCSVSSELASS    50
  51  QRTSLLPKDQECVNSCASSETSYGTNESSLNEKTLKGLTSIQNEKNVTGL   100
 101  DLLSSVDGGTSDEIQPLYMGRCSKPICDLISDMGNLVHATNSEEDIKKLL   150
 151  PDDFKSNADSLIGLDLSSVSDTPCVSSTDHDSDTVREQQNDISSELQNRE   200
 201  IGGIKELGIKVDTTLSDSYNYSGTENLKDKKIFNQLESIVDFNMSSALTR   250
 251  QSSKMFHAKDKLQHKSQPCGLLKDVGLVKEEVDVAVITAAECLKEEGKTS   300
 301  ALTCSLPKNEDLCLNDSNSRDENFKLPDFSFQEDKTVIKQSAQEDSKSLD   350
 351  LKDNDVIQDSSSALHVSSKDVPSSLSCLPASGSMCGSLIESKARGDFLPQ   400
 401  HEHKDNIQDAVTIHEEIQNSVVLGGEPFKENDLLKQEKCKSILLQSLIEG   450
 451  MEDRKIDPDQTVIRAESLDGGDTSSTVVESQEGLSGTHVPESSDCCEGFI   500
 501  NTFSSNDMDGQDLDYFNIDEGAKSGPLISDAELDAFLTEQYLQTTNIKSF   550
 551  EENVNDSKSQMNQIDMKGLDDGNINNIYFNAEAGAIGESHGINIICEIVD   600
 601  KQNTIENGLSLGEKSTIPVQQGLPTSKSEITNQLSVSDINSQSVGGARPK   650
 651  QLFSLPSRTRSSKDLNKPDVPDTIESEPSTADTVVPITCAIDSTADPQVS   700
 701  FNSNYIDIESNSEGGSSFVTANEDSVPENTCKEGLVLGQKQPTWVPDSEA   750
 751  PNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVC   800
 801  YETISKAQAFERMMSPTGSNLKSNHSDECTTVQPPQENQTSSIPSPATLP   850
 851  VSALKQPGVEGLCSKEQKRVWFADGILPNGEVADTTKLSSGSKRCSEDFS   900
 901  PLSPDVPMTVNTVDHSHSTTVEKPNNETGDITRNEIIQSPISQVPSVEKL   950
 951  SMNTGNEGLPTSGSFTLDDDVFAETEEPSSPTGVLVNSNLPIASISDYRL  1000
1001  LCDINKYVCNKISLLPNDEDSLPPLLVASGEKGSVPVVEEHPSHEQIILL  1050
1051  LEGESFHPVTFVLNANLLVNVKFIFYSSDKYWYFSTNGLHGLGQAEIIIL  1100
1101  LLCLPNEDTIPKDIFRLFITIYKDALKGKYIENLDNITFTESFLSSKDHG  1150
1151  GFLFITPTFQKLDDLSLPSNPFLCGILIQKLEIPWAKVFPMRLMLRLGAE  1200
1201  YKAYPAPLTSIRGRKPLFGEIGHTIMNLLVDLRNYQYTLHNIDQLLIHME  1250
1251  MGKSCIKIPRKKYSDVMKVLNSSNEHVISIGASFSTEADSHLVCIQNDGI  1300
1301  YETQANSATGHPRKVTGASFVVFNGALKTSSGFLAKSSIVEDGLMVQITP  1350
1351  ETMNGLRLALREQKDFKITCGKVDAVDLREYVDICWVDAEEKGNKGVISS  1400
1401  VDGISLQGFPSEKIKLEADFETDEKIVKCTEVFYFLKDQDLSILSTSYQF  1450
1451  AKEIAMACSAALCPHLKTLKSNGMNKIGLRVSIDTDMVEFQAGSEGQLLP  1500
1501  QHYLNDLDSALIPVIHGGTSNSSLPLEIELVFFIIEHLF             1539

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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