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

NucPred

Fetching P32639 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MTEHETKDKAKKIREIYRYDEMSNKVLKVDKRFMNTSQNPQRDAEISQPK    50
  51  SMSGRISAKDMGQGLCNNINKGLKENDVAVEKTGKSASLKKIQQHNTILN   100
 101  SSSDFRLHYYPKDPSNVETYEQILQWVTEVLGNDIPHDLIIGTADIFIRQ   150
 151  LKENEENEDGNIEERKEKIQHELGINIDSLKFNELVKLMKNITDYETHPD   200
 201  NSNKQAVAILADDEKSDEEEVTEMSNNANVLGGEINDNEDDDEEYDYNDV   250
 251  EVNSKKKNKRALPNIENDIIKLSDSKTSNIESVPIYSIDEFFLQRKLRSE   300
 301  LGYKDTSVIQDLSEKILNDIETLEHNPVALEQKLVDLLKFENISLAEFIL   350
 351  KNRSTIFWGIRLAKSTENEIPNLIEKMVAKGLNDLVEQYKFRETTHSKRE   400
 401  LDSGDDQPQSSEAKRTKFSNPAIPPVIDLEKIKFDESSKLMTVTKVSLPE   450
 451  GSFKRVKPQYDEIHIPAPSKPVIDYELKEITSLPDWCQEAFPSSETTSLN   500
 501  PIQSKVFHAAFEGDSNMLICAPTGSGKTNIALLTVLKALSHHYNPKTKKL   550
 551  NLSAFKIVYIAPLKALVQEQVREFQRRLAFLGIKVAELTGDSRLSRKQID   600
 601  ETQVLVSTPEKWDITTRNSNNLAIVELVRLLIIDEIHLLHDDRGPVLESI   650
 651  VARTFWASKYGQEYPRIIGLSATLPNYEDVGRFLRVPKEGLFYFDSSFRP   700
 701  CPLSQQFCGIKERNSLKKLKAMNDACYEKVLESINEGNQIIVFVHSRKET   750
 751  SRTATWLKNKFAEENITHKLTKNDAGSKQILKTEAANVLDPSLRKLIESG   800
 801  IGTHHAGLTRSDRSLSEDLFADGLLQVLVCTATLAWGVNLPAHTVIIKGT   850
 851  DVYSPEKGSWEQLSPQDVLQMLGRAGRPRYDTFGEGIIITDQSNVQYYLS   900
 901  VLNQQLPIESQFVSKLVDNLNAEVVAGNIKCRNDAVNWLAYTYLYVRMLA   950
 951  SPMLYKVPDISSDGQLKKFRESLVHSALCILKEQELVLYDAENDVIEATD  1000
1001  LGNIASSFYINHASMDVYNRELDEHTTQIDLFRIFSMSEEFKYVSVRYEE  1050
1051  KRELKQLLEKAPIPIREDIDDPLAKVNVLLQSYFSQLKFEGFALNSDIVF  1100
1101  IHQNAGRLLRAMFEICLKRGWGHPTRMLLNLCKSATTKMWPTNCPLRQFK  1150
1151  TCPVEVIKRLEASTVPWGDYLQLETPAEVGRAIRSEKYGKQVYDLLKRFP  1200
1201  KMSVTCNAQPITRSVMRFNIEIIADWIWDMNVHGSLEPFLLMLEDTDGDS  1250
1251  ILYYDVLFITPDIVGHEFTLSFTYELKQHNQNNLPPNFFLTLISENWWHS  1300
1301  EFEIPVSFNGFKLPKKFPPPTPLLENISISTSELGNDDFSEVFEFKTFNK  1350
1351  IQSQVFESLYNSNDSVFVGSGKGTGKTAMAELALLNHWRQNKGRAVYINP  1400
1401  SGEKIDFLLSDWNKRFSHLAGGKIINKLGNDPSLNLKLLAKSHVLLATPV  1450
1451  QFELLSRRWRQRKNIQSLELMIYDDAHEISQGVYGAVYETLISRMIFIAT  1500
1501  QLEKKIRFVCLSNCLANARDFGEWAGMTKSNIYNFSPSERIEPLEINIQS  1550
1551  FKDVEHISFNFSMLQMAFEASAAAAGNRNSSSVFLPSRKDCMEVASAFMK  1600
1601  FSKAIEWDMLNVEEEQIVPYIEKLTDGHLRAPLKHGVGILYKGMASNDER  1650
1651  IVKRLYEYGAVSVLLISKDCSAFACKTDEVIILGTNLYDGAEHKYMPYTI  1700
1701  NELLEMVGLASGNDSMAGKVLILTSHNMKAYYKKFLIEPLPTESYLQYII  1750
1751  HDTLNNEIANSIIQSKQDCVDWFTYSYFYRRIHVNPSYYGVRDTSPHGIS  1800
1801  VFLSNLVETCLNDLVESSFIEIDDTEAEVTAEVNGGDDEATEIISTLSNG  1850
1851  LIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRA  1900
1901  LLVKLSKRLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDI  1950
1951  LEKVVPLINVVVDILSANGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHF  2000
2001  NNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNNYPN  2050
2051  VELTYSLNNSDSLISGVKQKITIQLTRDVEPENLQVTSEKYPFDKLESWW  2100
2101  LVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCDSYL  2150
2151  DADKELSFEINVK                                       2163

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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