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

NucPred

Fetching Q9QUK4 from www.uniprot.org...

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

   1  MAAQGEAVEEIICEFDDDLVSELSTLLRVDALSVLKRQQEEDHKTRMKMK    50
  51  KGFNSQMRSEAKRLKTFETYDKFRSWTPQEMAAAGFYHTGVKLGVQCFCC   100
 101  SLILFSTRLRKLPIENHKKLRPECEFLLGKDVGNIGKYDIRVKSPEKMLR   150
 151  GDKARYHEEEARLESFEDWPFYAHGTSPRVLSAAGFVFTGKRDTVQCFSC   200
 201  GGCLGNWEEGDDPWKEHAKWFPKCEFLQSKKSPEEITQYVQSYEGFLHVT   250
 251  GEHFVNSWVRRELPMVSAYCNDSVFANEELRMDTFKDWPHESPGAVEALV   300
 301  KAGLFYTGKRDIVQCFSCGGCMEKWAEGDNPIEDHTKFFPNCVFLQTLKS   350
 351  SAEVIPALQSHCALPEAMETTSESNHDDAAAVHSTVVDVSPSEAQELEPA   400
 401  SSLVSVLCRDQDHSEAQGRGCASSGTYLPSTDLGQSEAQWLQEARSLSEQ   450
 451  LRDTYTKATFRHMNLPEVYSSLGTDHLLSCDVSIISKHISQPVQGSLTIP   500
 501  EVFSNLNSVMCVEGEAGSGKTTFLKRIAFLWASGCCPLLYRFQLVFYLSL   550
 551  SSITPGQELAKIICAQLLGAGGCISEVCLSSIIQQLQHQVLFLLDDYSGL   600
 601  ASLPQALHTLITKNYLSRTCLLIAVHTNKVRGIRPYLDTSLEIKEFPFYN   650
 651  TVSVLRKLFSHDIMRVRKFINYFGFHEELQGIHKTPLFVAAVCTDWFKNP   700
 701  SDQPFQDVALFKAYMQYLSLKHKGAAKPLQATVSSCGQLALTGLFSSCFE   750
 751  FNSDNLAEAGVDEDEELTTCLMSKFTAQRLRPVYRFLGPLFQEFLAAVRL   800
 801  TELLSSDRQEDQDLGLYYLRQINSPLKAMSIYHTFLKYVSSHPSSKAAPT   850
 851  VVSHLLQLVDEKESLENMSENEDYMKLHPEALLWIECLRGLWQLSPESFS   900
 901  LFISENLLRICLNFAHESNTVAACSPVILQFLRGRTLDLKVLSLQYFWDH   950
 951  PETLLLLKSIKISLNGNNWVQRIDFSLIEKSFEKVQPPTIDQDYAIAFQP  1000
1001  INEVQKNLSEKKHIIKKYEDMKHQIPLNISTGYWKLSPKPYKIPKLEVQV  1050
1051  TNTGPADQALLQVLMEVFSASQSIEFRLSDSSGFLESIRPALELSKASVT  1100
1101  KCSMSRLELSREDQKLLLTLPTLQSLEVSETNQLPDQLFHNLHKFLGLKE  1150
1151  LCVRLDSKPDVLSVLPGEFPNLHHMEKLSIRTSTESDLSKLVKLIQNSPN  1200
1201  LHVFHLKCNFLSNCEPLMTVLASCKKLREIEFSGRCFEAMTFVNILPNFV  1250
1251  FLKILNLRDQQFPDKETSEKFAQALGSLRNLEKLFVPTGDGIHQVAKLIV  1300
1301  RQCLQLPCLRVLVFAETLDDDSVLEIAKGATRGGFQKLENLDLTLNHKIT  1350
1351  EEGYRNFFQVLDNLPNLKNLDISRHIPECIQIQAITVKALGQCVSRLPSL  1400
1401  TRLGMLSWLLDEEDIKVINDVKERHPQSKRLTVHWRWVVPFSPVIQK     1447

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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