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

NucPred

Fetching Q8NEV4 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MFPLIGKTIIFDNFPDPSDTWEITETIGKGTYGKVFKVLNKKNGQKAAVK    50
  51  ILDPIHDIDEEIEAEYNILKALSDHPNVVRFYGIYFKKDKVNGDKLWLVL   100
 101  ELCSGGSVTDLVKGFLKRGERMSEPLIAYILHEALMGLQHLHNNKTIHRD   150
 151  VKGNNILLTTEGGVKLVDFGVSAQLTSTRHRRNTSVGTPFWMAPEVIACE   200
 201  QQLDTTYDARCDTWSLGITAIELGDGDPPLADLHPMRALFKIPRNPPPKL   250
 251  RQPELWSAEFNDFISKCLTKDYEKRPTVSELLQHKFITQIEGKDVMLQKQ   300
 301  LTEFIGIHQCMGGTEKARRERIHTKKGNFNRPLISNLKDVDDLATLEILD   350
 351  ENTVSEQLEKCYSRDQIYVYVGDILIALNPFQSLGLYSTKHSKLYIGSKR   400
 401  TASPPHIFAMADLGYQSMITYNSDQCIVISGESGAGKTENAHLLVQQLTV   450
 451  LGKANNRTLQEKILQVNNLVEAFGNACTIINDNSSRFGKYLEMKFTSSGA   500
 501  VVGAQISEYLLEKSRVIHQAIGEKNFHIFYYIYAGLAEKKKLAHYKLPEN   550
 551  KPPRYLQNDHLRTVQDIMNNSFYKSQYELIEQCFKVIGFTMEQLGSIYSI   600
 601  LAAILNVGNIEFSSVATEHQIDKSHISNHTALENCASLLCIRADELQEAL   650
 651  TSHCVVTRGETIIRPNTVEKATDVRDAMAKTLYGRLFSWIVNCINSLLKH   700
 701  DSSPSGNGDELSIGILDIFGFENFKKNSFEQLCINIANEQIQYYYNQHVF   750
 751  AWEQNEYLNEDVDARVIEYEDNWPLLDMFLQKPMGLLSLLDEESRFPKAT   800
 801  DQTLVEKFEGNLKSQYFWRPKRMELSFGIHHYAGKVLYNASGFLAKNRDT   850
 851  LPTDIVLLLRSSDNSVIRQLVNHPLTKTGNLPHSKTKNVINYQMRTSEKL   900
 901  INLAKGDTGEATRHARETTNMKTQTVASYFRYSLMDLLSKMVVGQPHFVR   950
 951  CIKPNSERQARKYDKEKVLLQLRYTGILETARIRRLGFSHRILFANFIKR  1000
1001  YYLLCYKSSEEPRMSPDTCATILEKAGLDNWALGKTKVFLKYYHVEQLNL  1050
1051  MRKEAIDKLILIQACVRAFLCSRRYQKIQEKRKESAIIIQSAARGHLVRK  1100
1101  QRKEIVDMKNTAVTTIQTSDQEFDYKKNFENTRESFVKKQAENAISANER  1150
1151  FISAPNNKGSVSVVKTSTFKPEEETTNAVESNNRVYQTPKKMNNVYEEEV  1200
1201  KQEFYLVGPEVSPKQKSVKDLEENSNLRKVEKEEAMIQSYYQRYTEERNC  1250
1251  EESKAAYLERKAISERPSYPVPWLAENETSFKKTLEPTLSQRSIYQNANS  1300
1301  MEKEKKTSVVTQRAPICSQEEGRGRLRHETVKERQVEPVTQAQEEEDKAA  1350
1351  VFIQSKYRGYKRRQQLRKDKMSSFKHQRIVTTPTEVARNTHNLYSYPTKH  1400
1401  EEINNIKKKDNKDSKATSEREACGLAIFSKQISKLSEEYFILQKKLNEMI  1450
1451  LSQQLKSLYLGVSHHKPINRRVSSQQCLSGVCKGEEPKILRPPRRPRKPK  1500
1501  TLNNPEDSTYYYLLHKSIQEEKRRPRKDSQGKLLDLEDFYYKEFLPSRSG  1550
1551  PKEHSPSLRERRPQQELQNQCIKANERCWAAESPEKEEEREPAANPYDFR  1600
1601  RLLRKTSQRRRLVQQS                                    1616

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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