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

NucPred

Fetching P61243 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MKQELSKNKYLYKRLKLEEIQNPRYFFEVWSESNLVKFLIRIFFNKENFI    50
  51  KLFDFRIISSLILQDLHSSKSNKSSILKTFLLLTLSVFLYHLNNKAIIEK   100
 101  KHLNLVKIVYGHINYSKYKEKNLKENFNKKNISTFTNHSLSKILSLKKKK   150
 151  KYSIIKTNLKKRIHAISTYNQNLVGDSEWWKLCIIEQILPSWKISSSSIK   200
 201  KVEILLKEKTTDDLKHFFEFYIDNILCQNYNWETKFNFIFCKTIKNNKKL   250
 251  NLSTDNKILTNSLIFQIFSAFCEKLLFEIENPLNLNQLNSTIKLKNNQLF   300
 301  FSFSKSYQKKNSVELLYLLKKNVSQNFKFWGENDSLIVKSYIFIKKKGWF   350
 351  FFNNYAEFYIWQLYKNSLVQYEDDLDNFNENKSNLKLFKLNFLQNKKKNL   400
 401  KINSDLSEISYQITKYILYKVKNSNKAINNYKIIDKNFKFGNKKKTEIKK   450
 451  TLNLVETNFFISNKNFFKWILYKKNLNNKNVKQNIDSTIWDLCFFFKNEN   500
 501  NKIKSNFFLSPFFKKYLLYWIKNLFREEEKYITNPNFFENKKNLNFSNNS   550
 551  FSNSLFIDELNMAFSLTKKYRKNFEIIKQQKNKFFRNRKKSDIHRLIRLC   600
 601  KIKKTYQKLNSFIFSDYFYKIIYKKKYDINNLNLSTNLKLYTNHFYLLKS   650
 651  LINNHFNIEKYNKFLLFQIKYFVNLIISLDQINLLIIKQNLLFSKKINND   700
 701  IHYQTNENFKLKKKLLVNKIIYKKTKIYLKYDLKKKFQSYNFVTNSFIKN   750
 751  RISYKYIYNNYYKNLTESLNHLLLIFSSDKKINLKNITKNIIDQKIVNWK   800
 801  KKGKSYFSYKIIKKNIFNYWKYNKYKLIDKKNKNKNTFKFFIKKQRNLIV   850
 851  LSNKTKFIDNKNSIIKWSKKLNKKNTYIFYKTFLVIFYENFNNISKLLLY   900
 901  YSKIFNIQNNFLKKKLNETNLVQQIKFNIYYKLKIHFYFDKILTTKFLIN   950
 951  YFNNNQIYLESFNNNIFSLILQNQKSYFNSIQMSDKILLNSQFCKADTSK  1000
1001  LVSFLYYSDLNYKKKLNFYLKKKKSNLSYLELIKIFSIKKKKTLSTNELT  1050
1051  FFSKILNENSNIELKIYKTFLFEKLEQFNNENLLFIHNFNLNKLANSFVS  1100
1101  FNPIFSTKKYLEKNISLQKSLKKNNDFYPIDSSENYLLSEFFIKIQNENT  1150
1151  RIINKINKLFIINSNSEKFLINNILKKNTNNKKFNSETNKKRILSFSKNS  1200
1201  IKLIPQTERFKIFKNSSFSLKLSSLFEKYIPWFFTFKWWKYFQNLFLNLY  1250
1251  LEISLNISDQFYYILPTILQNRKKNLDYLVENLFFNLKNKFFGNSFGIWN  1300
1301  SRLLKQINKQHKSKENQLPWFSLNLVNKWNRHYVVTISLVIFSYFILQKY  1350
1351  FSILLGSDYLELWADFKIIQYLVDSSRGIYLDNLLHNNSIKFIKSENLLI  1400
1401  HFFKNSKHYIKNIKFYLFTKKKINKLLIKNKGIDLSRRERKLLVQSLITD  1450
1451  KSIDRYRPNFIYNTNSTNFQFGNQIIKQQKIKNYLENLTEDYQKNLINYP  1500
1501  SHQFYLAENLVFLSSWQKATSLNTLWQINTLKSTFYKKPIPLELRLFSSK  1550
1551  GILLIGSQETGRSYLVKNLAANSFIPLIKISINKLLYNKPDILTESWINI  1600
1601  LMESLRRLNLILELAEKLSPCIIWMPNIHELNVNRSTQNVESDPTFLLGI  1650
1651  FLKYFQTGFSKKNTNNIIIIGSTHLPKKVDPALISPNRLDRLINIRTFNI  1700
1701  LQRQKKISILLYSKYSKYFYSKKKKSSLNEFGSRTIGYNARDLAGLINEI  1750
1751  LLISINQNQSTIQKKTIRLAFHRQTLGSTYINNKINFTKNYGILFYKIGK  1800
1801  AIVQNLFIKNSSKNPLYFGNDLWKKNFYYLSKWYLEPSIFESTIKEFTIL  1850
1851  PHILGCLAGLAARDSWFILKNKPDNLISLDKYAENDFYLACGILESLLRD  1900
1901  FSWLEIFEEKNINKKNFFNFQFQTKNPLHMVKKGLYQLTSNIVWAPKISR  1950
1951  LNFIRTNLFNWINRPNEFEITSNLKKADKKNITGSSDNSHSFEIIQHKIK  2000
2001  EQLPYERILSRIRRRNVQELESQLEDILLEEQFVILGFSRLFTEYRMESQ  2050
2051  LSNKPLIFIGGRFLWDPTGLLYQNHNFIFSRQDLSIDGEMLRRLYVTYGA  2100
2101  RREREKSRSSQKIKQFFLRRGYGRDSINNFSINWWNQLPFIEKNNIETFK  2150
2151  RIEGIGVQLKRPQVFTPVYLYQRWLIENPQKILTRFELLNNQQKWLKTNK  2200
2201  LLLNDSLIYNTLLEIYQYLLQFFILHQVLLNEMTNVLLKNKWLFQNEIED  2250
2251  FMNIINKNN                                           2259

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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