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

NucPred

Fetching O75691 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MKTKPVSHKTENTYRFLTFAERLGNVNIDIIHRIDRTASYEEEVETYFFE    50
  51  GLLKWRELNLTEHFGKFYKEVIDKCQSFNQLVYHQNEIVQSLKTHLQVKN   100
 101  SFAYQPLLDLVVQLARDLQMDFYPHFPEFFLTITSILETQDTELLEWAFT   150
 151  SLSYLYKYLWRLMVKDMSSIYSMYSTLLAHKKLHIRNFAAESFTFLMRKV   200
 201  SDKNALFNLMFLDLDKHPEKVEGVGQLLFEMCKGVRNMFHSCTGQAVKLI   250
 251  LRKLGPVTETETQLPWMLIGETLKNMVKSTVSYISKEHFGTFFECLQESL   300
 301  LDLHTKVTKTNCCESSEQIKRLLETYLILVKHGSGTKIPTPADVCKVLSQ   350
 351  TLQVASLSTSCWETLLDVISALILGENVSLPETLIKETIEKIFESRFEKR   400
 401  LIFSFSEVMFAMKQFEQLFLPSFLSYIVNCFLIDDAVVKDEALAILAKLI   450
 451  LNKAAPPTAGSMAIEKYPLVFSPQMVGFYIKQKKTRSKGRNEQFPVLDHL   500
 501  LSIIKLPPNKDTTYLSQSWAALVVLPHIRPLEKEKVIPLVTGFIEALFMT   550
 551  VDKGSFGKGNLFVLCQAVNTLLSLEESSELLHLVPVERVKNLVLTFPLEP   600
 601  SVLLLTDLYYQRLALCGCKGPLSQEALMELFPKLQANISTGVSKIRLLTI   650
 651  RILNHFDVQLPESMEDDGLSERQSVFAILRQAELVPATVNDYREKLLHLR   700
 701  KLRHDVVQTAVPDGPLQEVPLRYLLGMLYINFSALWDPVIELISSHAHEM   750
 751  ENKQFWKVYYEHLEKAATHAEKELQNDMTDEKSVGDESWEQTQEGDVGAL   800
 801  YHEQLALKTDCQERLDHTNFRFLLWRALTKFPERVEPRSRELSPLFLRFI   850
 851  NNEYYPADLQVAPTQDLRRKGKGMVAEEIEEEPAAGDDEELEEEAVPQDE   900
 901  SSQKKKTRRAAAKQLIAHLQVFSKFSNPRALYLESKLYELYLQLLLHQDQ   950
 951  MVQKITLDCIMTYKHPHVLPYRENLQRLLEDRSFKEEIVHFSISEDNAVV  1000
1001  KTAHRADLFPILMRILYGRMKNKTGSKTQGKSASGTRMAIVLRFLAGTQP  1050
1051  EEIQIFLDLLFEPVRHFKNGECHSAVIQAVEDLDLSKVLPLGRQHGILNS  1100
1101  LEIVLKNISHLISAYLPKILQILLCMTATVSHILDQREKIQLRFINPLKN  1150
1151  LRRLGIKMVTDIFLDWESYQFRTEEIDAVFHGAVWPQISRLGSESQYSPT  1200
1201  PLLKLISIWSRNARYFPLLAKQKPGHPECDILTNVFAILSAKNLSDATAS  1250
1251  IVMDIVDDLLNLPDFEPTETVLNLLVTGCVYPGIAENIGESITIGGRLIL  1300
1301  PHVPAILQYLSKTTISAEKVKKKKNRAQVSKELGILSKISKFMKDKEQSS  1350
1351  VLITLLLPFLHRGNIAEDTEVDILVTVQNLLKHCVDPTSFLKPIAKLFSV  1400
1401  IKNKLSRKLLCTVFETLSDFESGLKYITDVVKLNAFDQRHLDDINFDVRF  1450
1451  ETFQTITSYIKEMQIVDVNYLIPVMHNCFYNLELGDMSLSDNASMCLMSI  1500
1501  IKKLAALNVTEKDYREIIHRSLLEKLRKGLKSQTESIQQDYTTILSCLIQ  1550
1551  TFPNQLEFKDLVQLTHYHDPEMDFFENMKHIQIHRRARALKKLAKQLMEG  1600
1601  KVVLSSKSLQNYIMPYAMTPIFDEKMLKHENITTAATEIIGAICKHLSWS  1650
1651  AYMYYLKHFIHVLQTGQINQKLGVSLLVIVLEAFHFDHKTLEEQMGKIEN  1700
1701  EENAIEAIELPEPEAMELERVDEEEKEYTCKSLSDNGQPGTPDPADSGGT  1750
1751  SAKESECITKPVSFLPQNKEEIERTIKNIQGTITGDILPRLHKCLASTTK  1800
1801  REEEHKLVKSKVVNDEEVVRVPLAFAMVKLMQSLPQEVMEANLPSILLKV  1850
1851  CALLKNRAQEIRDIARSTLAKIIEDLGVHFLLYVLKELQTTLVRGYQVHV  1900
1901  LTFTVHMLLQGLTNKLQVGDLDSCLDIMIEIFNHELFGAVAEEKEVKQIL  1950
1951  SKVMEARRSKSYDSYEILGKFVGKDQVTKLILPLKEILQNTTSLKLARKV  2000
2001  HETLRRITVGLIVNQEMTAESILLLSYGLISENLPLLTEKEKNPVAPAPD  2050
2051  PRLPPQSCLLLPPTPVRGGQKAVVSRKTNMHIFIESGLRLLHLSLKTSKI  2100
2101  KSSGECVLEMLDPFVSLLIDCLGSMDVKVITGALQCLIWVLRFPLPSIET  2150
2151  KAEQLTKHLFLLLKDYAKLGAARGQNFHLVVNCFKCVTILVKKVKSYQIT  2200
2201  EKQLQVLLAYAEEDIYDTSRQATAFGLLKAILSRKLLVPEIDEVMRKVSK  2250
2251  LAVSAQSEPARVQCRQVFLKYILDYPLGDKLRPNLEFMLAQLNYEHETGR  2300
2301  ESTLEMIAYLFDTFPQGLLHENCGMFFIPLCLMTINDDSATCKKMASMTI  2350
2351  KSLLGKISLEKKDWLFDMVTTWFGAKKRLNRQLAALICGLFVESEGVDFE  2400
2401  KRLGTVLPVIEKEIDPENFKDIMEETEEKAADRLLFSFLTLITKLIKECN  2450
2451  IIQFTKPAETLSKIWSHVHSHLRHPHNWVWLTAAQIFGLLFASCQPEELI  2500
2501  QKWNTKKTKKHLPEPVAIKFLASDLDQKMKSISLASCHQLHSKFLDQSLG  2550
2551  EQVVKNLLFAAKVLYLLELYCEDKQSKIKEDLEEQEALEDGVACADEKAE  2600
2601  SDGEEKEEVKEELGRPATLLWLIQKLSRIAKLEAAYSPRNPLKRTCIFKF  2650
2651  LGAVAMDLGIDKVKPYLPMIIAPLFRELNSTYSEQDPLLKNLSQEIIELL  2700
2701  KKLVGLESFSLAFASVQKQANEKRALRKKRKALEFVTNPDIAAKKKMKKH  2750
2751  KNKSEAKKRKIEFLRPGYKAKRQKSHSLKDLAMVE                 2785

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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