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

NucPred

Fetching Q9Y7K2 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MKEFPGLKSRNEEIRNKAANDLYEYVIAYSRELSGEALVQFNNDVNKYVY    50
  51  TLIHSTDPLDRLAGVTAINRLIDYEGEDTTRITRFANYLRIILPGTDQKA   100
 101  TVLAAKALGRLAVPGGALTSEFVNFEVKRALEWLQGERNENRRYAAVLIL   150
 151  KELAKNTSTLIYAHIDSIFELLWHGLRDPKVTIRIASADALSEFLKIVRQ   200
 201  RDSSIRLQWYTSILNEAQRGVAQGSSDYIHGSLLVYRQLFLKAGMFMHER   250
 251  YREVSDIILQFRDHKDLLIRKTVTELIATLAAYNPDEFVSNYLHVCMLHL   300
 301  LNLLKKENVKMLAFATIGKVAVAITNSIIPYLDPICDSIKESLKIHIRNK   350
 351  SASDAAIFQCISLLSIALGQAFSNYAYDLFDLIFASGLSEASYRALSDLA   400
 401  HNIPPLLPVIQERLLDMLSKILSGRPFIPPGCPPQYVARSLKSSKSASLK   450
 451  TGFFPNDVYILALKVLGNFDFSGYILNEFVKDCVVVYLENNDPEVRKTAS   500
 501  ITCSQLFARDPILSQTSDHAIQVVAEVLEKLLTVGICDTVPDIRLTVLNS   550
 551  LDSRFNKHLAQADKIRLLFIAINDENFAVRESALRIIGRLNVYNPAYVMP   600
 601  YLRKIMLKTLTILDYSTIIRTKEENAKLLCLLIAAAPRLIESHVEPILQI   650
 651  LLPKAKDSSSIVAASIVNSLGEICQISGEVIVPFIKDLMPLIIEALQDQS   700
 701  SPIRRAAALKALGNLSSSTGYVIDPYIEFPSLLDILIGITKTEQDITIRR   750
 751  ETIKLIGTLGALDPNRHRVLEKGTEKVVPEQKNIPPDISLLMSGIGPSSD   800
 801  EYYPTVVITALMSILKDPSLTIHHTAVIQAVMYIFKTMGLRCAPFLSQII   850
 851  PEFIAVMRTCPTNILEFYFQQLSILVLIVRQHIRSFLPDLFKLIKDFWNP   900
 901  HSNLQFTILSLIESLARAMQGEFKPYLPSLLVMMLQIFDSDVSVDSVSTK   950
 951  KVLHAFIVFGDTLADYFHMLLDPILRLYERNDVSIGIKESIMITIGRLSM  1000
1001  VINLSEYASRIIHPVMRMLSCNNASLIRVSMDTVCALIYQLNVDFAIFIP  1050
1051  MIDKCLKMNGVTHETYSILVEQFLQEQPLPIKLNPYEKYDKPKLDVVASA  1100
1101  ADITSKKLPVNQEILRNAWEASQRSTKDDWQEWIRRLGVALLRESPSHAL  1150
1151  RACAALAAAYQPLARDLFNASFVSCWSELYDHFQEELVKSIEIALTSPHI  1200
1201  SPEIIQILLNLAEFMEHDDKPLPIDIRTLGAYAAKCHAFAKALHYKELEF  1250
1251  IEEELVTKPSVDTIEALISINNQLQQPDAAIGILKHAQQHDKMNLKETWY  1300
1301  EKLQRWEDALSAYEKREAAGAGNFEITMGKLRCLHALGEWDRLSQLAQEN  1350
1351  WIHAGHDARRYIAPLSVAAAWGLGQWEQMDEYISVMKSESPDKAFFNAIV  1400
1401  ALHRSQFEEAASYITRARDLLDTELTALVGESYNRAYSVAVRVQMLSELE  1450
1451  EIITYKKAEDKPEVREMIKKTWVRRLKGCQRNVDVWQRMLRIRSLVISPR  1500
1501  DNMEMWIKFANLCRKSGRISLAKKSLNLLLEDDENLDNSLVLKKTHPSIV  1550
1551  YANLKFLWAVDDKRKALNSMQEFTSQLISDINVDPALFVQSTSVNTQKSQ  1600
1601  EEIQYYFHLLARCYHKQGQWQQEIENNWSEGSFDGVLQSYMYATQFDSKW  1650
1651  YKAWHSWALANFEAVKFLEQSEEQIPSAAYEQYIIPAVKGFFKSIALSKG  1700
1701  NLQDTLRLLNLWFKFGNNSNVINTLNVGISTVNIDIWLDVIPQLIARIHA  1750
1751  SSLSVRKSVHQLLSDVGRAHPQALVYPLTVAAKSQSSARQNAALAIMDSL  1800
1801  KTHSPRLVEQARLVSHELIRAAILWHEQWHEGLEEASRLYFGDHNIEGMF  1850
1851  AVLRPLHEMLERGPETLREISFQQAFGRDLVEARDCCIRFEQTGDISDLN  1900
1901  QAWDLYYQVFKKIRKQLPQLTTLDLQYVSPKLLHVHDLELAVPGTYVSGK  1950
1951  PVIRIVKFYPTFNVITSKQRPRRLSIKGSDGKDYQYVLKGHEDIRQDERV  2000
2001  MQLFGLCNNLLLADPETFKRLLSIQRYPVIPLSPDSGLLGWVLDSDTLHV  2050
2051  LIRDYRESRKILLNIEHRLIIQMAPDYDRLTLLQKVEVFEYALLSTTGQD  2100
2101  LYRVLWLKSRSSEAWLNRRTNYSRTLAVMSMVGYILGLGDRHPSNLMLDR  2150
2151  YTGNIIHIDFGDCFEVAMHREKFPEKIPFRLTRMLVNAMEVSGIEGTFRI  2200
2201  TCEHVMRVLRTNKESVMAVLEAFVYDPLINWRLAPAYSPSIDEKQSNEPN  2250
2251  TLLGETIDGLHRKRLNEEGITLEERQKPEILNQRAITVLNRVSNKLTGRD  2300
2301  FKPQQQLDVPSQVEKLILQATSIENLCLCYIGWCSFW               2337

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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