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

NucPred

Fetching Q10250 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MNQFPNQPGNFGQNYYKPVQGSIPANSEATNFQQNNSRENKSECELRQNS    50
  51  IAASMSAYPNGMYAGAENHNVENHENYTMVGHDHMEEVYGDDLVNEPRIA   100
 101  YSSDIVATFDGKDFGSNLHVDDTLDQQWAHFAGKQQHPLEPREIPFPVTD   150
 151  PLNSKIEMKQFTNIAAVLRYRGVHSAKKTAFIILDNKGKEFTSITWEKLA   200
 201  SRAEKVAQVIRDKSGLFRSDRVVLMYRDCEAIDFVVSLFGCFIAGVVAVP   250
 251  INRFDDYNELSSILTTTSARLALTTDANLKAFQRDLNAKKLHWPKNVEWW   300
 301  KTNEFGGFHLKKKAEMPPLQVPDLAYIEFSRSPIGELHGVVISHRTILHQ   350
 351  MNCLAAIHATAPAYESDKLDYLSIDREYTEGLSKSGLFLTYLDLRQAIGL   400
 401  ILGVLHTVFSGYTTVWCPQNAVFVPGLWANLATRYRASFMLTDYAGLKTI   450
 451  AYNYQNDPKATLGFSKKHSVDLSSLRMCMVDCLNVDCEFQEIVSDRWLKP   500
 501  LGNQNPRATFVPLLCLPEHGGMVISMKDWIGGEEFMSPKGFKSPRTPENE   550
 551  ISEVLLEKEALKLNEVVVLAEDDKARRQSKHPNTIRVGAFWYPFVDATLA   600
 601  IVDPETQVLCLPNIVGEIWVDSPSLSGGFFALPKQTEAIFHARTSFISSD   650
 651  TFQPIPSNQEFLRTGLLGFIRKGKVYVLGLYEDRLQQKVEWVDNGKQDTI   700
 701  FFHHYTSHLVNTIMRKVSKVFDCSAFDIFVNSEHLPVVLLESPAANIPTE   750
 751  ANGNQVVINYGLLDLITTECVECLLEDHQVRVYCVLICAPFTLPRVTKNG   800
 801  RQEIGNMMCRRAFEHGTLPFLYVKFAVERAVLNLPVGEDAIDGIWSSYAS   850
 851  GIRQNLLSDQELQYSGFIDRSLRYDAKTSVDISSCHTMLQLLQLRVAKNA   900
 901  EDIAYITIDGRGREGKNITWRKFDQRVATIIRYLQKKKYIKPGRVVVLMY   950
 951  THSEDFVYALYACFYLGLIPIPVPPLDHMRLSEDVPAFLFLIKHYYVSAV  1000
1001  LVNSEADTALRAKTTSQHLKQSAMAAKVVLPSFIVTSKISKQTKSIKELN  1050
1051  VKLDPICLDPAFPALVWAFWSPDHRLTLTAYNHQTLLSICQIHKETCQMT  1100
1101  HKRPLLGHVRSMSGIGFFHTCLMGVFLGTTTYLLSPVDFANNPLLLFQII  1150
1151  SKYKIKDTYATFQTLNYIQNQQPTKWPNLSCLENLMIPHDGRISAFYIAS  1200
1201  LQKYFVKHGLSPYAFSTVYSNCLNPFISTRSYMGAIPTPQLLDLRALRHG  1250
1251  LIQPCESADKPYALPLLDSGMVPVSTQLAIVNPDTRELCRVGEYGEIWMR  1300
1301  SSANAISFFQSTDPVDMMRFNATNSDGFLGNGYVRTGDLGFLQITSHSMG  1350
1351  PNAPVVDMQLLYVLGPIGETFEVNGLSHFPSDIEDTIERSHPRIARGGTA  1400
1401  VFQSAGRVVVVIEALGQDFLAAIVPVVINSILDEHQIIADVVAFTSRGNF  1450
1451  PRSRLREKQRGKILASWVTGRLRTTQVFYIRGSGEGEFQSSYVPDYNPSL  1500
1501  RSTPSVSSRSTLPQRVF                                   1517

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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