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

NucPred

Fetching P09975 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MKQKLPKKKSLYKNLDLDEIQKIQNLGNPYTKWSLIRLLIAIFSNKRNFS    50
  51  TLLDFQILTSLFFRDLYNSKKKKKFLLNILVFLTLPFFVYILIDKSIVEQ   100
 101  QNFDFLKIQKQNFIEKNNKSILKNNFYFLNTKFDIFLHNFFSLKKKKWYK   150
 151  NSLLNLIDFRSILKKKEILNLHWWKFLVLEQIQSNWKISEESLSELKIVL   200
 201  EQKNIDELKHFFEFYINQKIYPNNNWEYYFYSIFINQLKIDIKNSKYNKN   250
 251  SIGFEVFLAFCEKLLFEVEFLSKPNNNNLQMKLNCLENFSFLDIFCILNK   300
 301  KLPWVNKKIFKNLQNFNESDKKLIESFFLLKIKGNLYFKNYIEFVTWQSY   350
 351  KKDCLDFNKFNELNNSEIYIKIEELFSDYIYKFSKYILYEGKKSKTIIKQ   400
 401  SFNNNIYYKKLNSIFNFNTIFYFDSNNLLFDWLKKNYYINNKPFLKSFLI   450
 451  YSSISNQFILFFKQKNSKSFNKNLVKKNSKDVITNVFSKENKIEINNFSK   500
 501  SIYYAFFEILSINEIDNKFVINKISLKNINKKKQKRFYLNKIKSSDNFRF   550
 551  INLWKIKNYSSQQFVSNNSFLLNPAFEILQQNYYLKKKNILFFKKLNEVF   600
 601  SNFFYFQYYKCKKLNIFLKFASLEKILKKRNKKFTISIKLFKKFYKNKLN   650
 651  ENGEYKIESQILQNEKELNKKRKKNFQFNPNIKILSFYNSSKKNIYLQNK   700
 701  YFFNKNLINNKLITWKKISNKLVISNSEYNKIIWNKKNMKFFSFSKNSVL   750
 751  DTFFFNKKSFNIITVIFDKLKKIQLNFQEIQKILNCFSLFFNSKNIKKTK   800
 801  IFKNSYFINENLTTTFSFNDKEFNIFFLELFISEINNDFLMRFFKKYLYY   850
 851  RIYKDKEILFNPIENRQLLQNFFEKTKILTFIDFLQDPELNYNNRFIFHL   900
 901  EKKTIKNNNLLYLRLLKIFLKDKRNFLLINEIKSFIEKKNNLFIKSQLSN   950
 951  VLLVKNSYKFFDNIFNFHFLKQKEKNIEIILNNQNYFEKSLLKKTYLKNL  1000
1001  NLNNSYSKFSYKIFIFQLLNILNKNNYKTFQWISELIFYSKNLNYKIQNK  1050
1051  IEKNNYCYNKNISYKKKKIKTVNFFEKNNLFQTNNSWFFTLEWWEYNTYI  1100
1101  LLQIIQETFFQITDVLEYFKKKKIIEKNLKFFLKSKKISLKTLSFHNFKL  1150
1151  KWNLRFFNEINYKKNYLLNFLWSDFNLINNCNNLYWVIFSLVIFIFLYYQ  1200
1201  KIFSIIIGSDCFHLWKNFEIIQYLTDRSRSLYFTKLTRRNKTALNKTENL  1250
1251  LSYFFQNLTHYITNIKFYLLTKKNLKKWLINNKTLDLSRRKRKLLVQSLI  1300
1301  THNKIQNYGFELNSNKQFFTSYFGYQITNQQGLLYFQYLAQFFQKNLINN  1350
1351  SLDLANKWIVFSFWHKIFSSQKLRQTNNIELGFQNIPVPLQFGLSYSKGI  1400
1401  LLIGPIETGRSYLIKNLAAESYVPLFKISINKLLYNKPDVITESWMNILI  1450
1451  ESLRRLNLTLDFAKKMSPCIIWIQNIHQLNVNRLTQNVESDPTFLLGILL  1500
1501  KYFQTDFSKTKKNNIIVIGSTHLPKKVDPALISPNRLDKIINVRLFNISQ  1550
1551  RKKQFPLLLKKKNFQLKENLFFLNEFGSRTMGYNLRDLSALTNEVLLISI  1600
1601  TKNRSFIDTDTLKLAFHRQIFGLTYTNNKLNFDRIFKIVIYKVGKTIIQN  1650
1651  ILIKSSSMNLLNIGNFLWKKNFYYLSKWYLEPSIDESIIKELTILTHILA  1700
1701  CLAGTAARDSWFLLEKKAESLLPIDKLVENDFTLAFSILESFFSEFPWLE  1750
1751  ICQTNVVNSKKNKIIEFSTKNSMNIMQNGIFAIANKKFIYTQNHLQYKSS  1800
1801  LSQQISFNKKKNYEFKNTSWSPRFWRLSFFRSNLFDWIKRPNDFEFSYKF  1850
1851  GFTKKKEYLFSANLQKKNNYGQFIEKKKKEQLLYERILPRIRRRNVQELE  1900
1901  SQFEEILLEEQFEILGFFRLSEQYPMEYQLYNKPRLFIGKRILWDPIGLF  1950
1951  FQIRHFVFSRREFFVDEEMLRRLYVTYGARRERERSRSSQKIKQFFLCRG  2000
2001  YNKDLISKLSIRWWSQLPINEKKNIDTLKRIEHISIQLKRPQIFTPVYLY  2050
2051  QRWLIENSPEKFFRFELLTHRKKWLKINSLLLNDSFIYTTLLEIYEYLLH  2100
2101  FFIANKKLLNQMTKILLKKGWLFENEIETIINETRQ                2136

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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