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

NucPred

Fetching Q8TEU7 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MNSPVDPGARQALRKKPPERTPEDLNTIYSYLHGMEILSNLREHQLRLMS    50
  51  ARARYERYSGNQVLFCSETIARCWYILLSGSVLVKGSMVLPPCSFGKQFG   100
 101  GKRGCDCLVLEPSEMIVVENAKDNEDSILQREIPARQSRRRFRKINYKGE   150
 151  RQTITDDVEVNSYLSLPADLTKMHLTENPHPQVTHVSSSQSGCSIASDSG   200
 201  SSSLSDIYQATESEVGDVDLTRLPEGPVDSEDDEEEDEEIDRTDPLQGRD   250
 251  LVRECLEKEPADKTDDDIEQLLEFMHQLPAFANMTMSVRRELCSVMIFEV   300
 301  VEQAGAIILEDGQELDSWYVILNGTVEISHPDGKVENLFMGNSFGITPTL   350
 351  DKQYMHGIVRTKVDDCQFVCIAQQDYWRILNHVEKNTHKVEEEGEIVMVH   400
 401  EHRELDRSGTRKGHIVIKATPERLIMHLIEEHSIVDPTYIEDFLLTYRTF   450
 451  LESPLDVGIKLLEWFKIDSLRDKVTRIVLLWVNNHFNDFEGDPAMTRFLE   500
 501  EFEKNLEDTKMNGHLRLLNIACAAKAKWRQVVLQKASRESPLQFSLNGGS   550
 551  EKGFGIFVEGVEPGSKAADSGLKRGDQIMEVNGQNFENITFMKAVEILRN   600
 601  NTHLALTVKTNIFVFKELLFRTEQEKSGVPHIPKIAEKKSNRHSIQHVPG   650
 651  DIEQTSQEKGSKKVKANTVSGGRNKIRKILDKTRFSILPPKLFSDGGLSQ   700
 701  SQDDSIVGTRHCRHSLAIMPIPGTLSSSSPDLLQPTTSMLDFSNPSDIPD   750
 751  QVIRVFKVDQQSCYIIISKDTTAKEVVFHAVHEFGLTGASDTYSLCEVSV   800
 801  TPEGVIKQRRLPDQFSKLADRIQLNGRYYLKNNMETETLCSDEDAQELVK   850
 851  ESQLSMLQLSTIEVATQLSMRDFDLFRNIEPTEYIDDLFKLNSKTGNTHL   900
 901  KRFEDIVNQETFWVASEILTEANQLKRMKIIKHFIKIALHCRECKNFNSM   950
 951  FAIISGLNLASVARLRGTWEKLPSKYEKHLQDLQDIFDPSRNMAKYRNIL  1000
1001  SSQSMQPPIIPLFPVVKKDMTFLHEGNDSKVDGLVNFEKLRMISKEIRQV  1050
1051  VRMTSANMDPAMMFRQRSLSQGSTNSNMLDVQGGAHKKRARRSSLLNAKK  1100
1101  LYEDAQMARKVKQYLSSLDVETDEEKFQMMSLQWEPAYGTLTKNLSEKRS  1150
1151  AKSSEMSPVPMRSAGQTTKAHLHQPHRVSQVLQVPAVNLHPIRKKGQTKD  1200
1201  PALNTSLPQKVLGTTEEISGKKHTEDTISVASSLHSSPPASPQGSPHKGY  1250
1251  TLIPSAKSDNLSDSSHSEISSRSSIVSNCSVDSMSAALQDERCSSQALAV  1300
1301  PESTGALEKTEHASGIGDHSQHGPGWTLLKPSLIKCLAVSSSVSNEEISQ  1350
1351  EHIIIEAADSGRGSWTSCSSSSHDNFQSLPNPKSWDFLNSYRHTHLDDPI  1400
1401  AEVEPTDSEPYSCSKSCSRTCGQCKGSLERKSWTSSSSLSDTYEPNYGTV  1450
1451  KQRVLESTPAESSEGLDPKDATDPVYKTVTSSTEKGLIVYCVTSPKKDDR  1500
1501  YREPPPTPPGYLGISLADLKEGPHTHLKPPDYSVAVQRSKMMHNSLSRLP  1550
1551  PASLSSNLVACVPSKIVTQPQRHNLQPFHPKLGDVTDADSEADENEQVSA  1600
1601  V                                                   1601

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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