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

NucPred

Fetching Q5VUA4 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MYRSSARSSVSSHRPKDDGGGGPRSGRSSGSSSGPARRSSPPPPPSGSSS    50
  51  RTPARRPRSPSGHRGRRASPSPPRGRRVSPSPPRARRGSPSPPRGRRLFP   100
 101  PGPAGFRGSSRGESRADYARDGRGDHPGDSGSRRRSPGLCSDSLEKSLRI   150
 151  TVGNDHFCVSTPERRRLSDRLGSPVDNLEDMDRDDLTDDSVFTRSSQCSR   200
 201  GLERYISQEEGPLSPFLGQLDEDYRTKETFLHRSDYSPHISCHDELLRGT   250
 251  ERNREKLKGYSIRSEERSREAKRPRYDDTVKINSMGGDHPSFTSGTRNYR   300
 301  QRRRSPSPRFLDPEFRELDLARRKREEEEERSRSLSQELVGVDGGGTGCS   350
 351  IPGLSGVLTASEPGYSLHRPEEVSVMPKKSILKKRIEVDIMEPSMQLESF   400
 401  SSSTSSSQDHPLYSGHPSLPLSGAIAAFASEIENKGTMVETALKEPQGNL   450
 451  YQWGPLPGIPKDNSPLREKFGSFLCHKDNLDLKAEGPERHTDFLLPHERA   500
 501  SQDGSGFSRILSMLADSTSTQEKRRRSFPDIEDEEKFLYGDEEEDLKAES   550
 551  VPKPLGSSESEVMRQKASSLPSSAPAVKLESLEETNPEYAKIHDLLKTIG   600
 601  LDIGVAEISQLAARTQERLHGKKPSLRSSADRRSSVDRYFSADHCSSVDH   650
 651  RFSADRCSSVDHCFSADRRSSDPHRLESREAHHSNTHSPEVSHPHPPSPV   700
 701  DPYLLTKNSPPFLKSDHPVGHISGPEVVGSGFQSSVAVRCMLPSAPSAPI   750
 751  RLPHTAALSQFHMPRASQFAAARIPPNYQGPAIPPASFDAYRHYMAYAAS   800
 801  RWPMYPTSQPSNHPVPEPHRIMPITKQATRSRPNLRVIPTVTPDKPKQKE   850
 851  SLRGSIPAAQVPVQVSIPSLIRYNPEKISDEKNRASQKQKVIEEREKLKN   900
 901  DREARQKKMYYLRTELERLHKQQGEMLRKKRREKDGHKDPLLVEVSRLQD   950
 951  NIMKDIAELRQEAEEAEKKQSELDKVAQILGINIFDKSQKSLSDSREPTE  1000
1001  KPGKAEKSKSPEKVSSFSNSSSNKESKVNNEKFRTKSPKPAESPQSATKQ  1050
1051  LDQPTAAYEYYDAGNHWCKDCNTICGTMFDFFTHMHNKKHTQTLDPYNRP  1100
1101  WASKTQSEAKQDAIKRTDKITVPAKGSEFLVPISGFYCQLCEEFLGDPIS  1150
1151  GEQHVKGHQHNEKYKKYVDENPLYEERRNLDRQAGLAVVLETERRRQSEL  1200
1201  KRKLSEKPKEEKKEKKAKAVKEVKEDDKVSEKLEDQLSEGRNSPEKAENK  1250
1251  RNTGIKLQLKEEVKKESPTSSSFGKFSWKKPEKEEEKSSLVTPSISKEEI  1300
1301  LESSKDKEDGKTEAGKAKPIKIKLSGKTVVAHTSPWMPVVTTSTQTKIRP  1350
1351  NLPIPSTVLRKSCSATMSKPAPLNTFLSIKSSGTTAKPLPVVKESSADLL  1400
1401  LPPDIISKAFGGEEVILKGSPEEKVVLAEKSEPSHLPEQILPPPPPPPPP  1450
1451  PPPPPPVIPHPAAPSAAQANAILAPVKSNPVVSQTLSPGFVGPNILNPVL  1500
1501  PVAIMASAQPAAIPSDETAPGVSESDRDQTLFSVLVRPPPPLSSVFSEQA  1550
1551  KKLEKRNSCLATANAKDLYDIFYSSGGKGAPETKGAPETKLSGGPLANGE  1600
1601  NSNLSRTKSSDTSSTSPLNSSASQEELHQDEGLVAAPIVSNSEKPIAKTL  1650
1651  VALGKWSVVEHVGPKSTGSTYGFLQPLTRLCQSRPYETITPKTDTLAIWT  1700
1701  SSSFQSDTSRDISPEKSELDLGEPGPPGVEPPPQLLDIQCKESQKLVEIH  1750
1751  LRESVNQDKESQELRKSEDCRESEIETNTELKERVKELSEGIVDEGVSTS  1800
1801  IGPHSIDDSNLNHGNRYMWEGEVKQPNLLMIDKEAEQSNKLMTGSETPSK  1850
1851  VVIKLSPQACSFTKAKLDSFLSEARSLLNPQDTPVKISAPELLLHSPARS  1900
1901  AMCLTGSPQEQGVSVVSEEGLENSAPESASRTSRYRSLKLKRERSKDFQV  1950
1951  KKIYELAVWDENKKRPETWESPEKPKTEALELQDVHPELTVTIESKALED  2000
2001  FEATDLKVEELTALGNLGDMPVDFCTTRVSPAHRSPTVLCQKVCEENSVS  2050
2051  PIGCNSSDPADFEPIPSFSGFPLDSPKTLVLDFETEGERNSPNPRSVRIP  2100
2101  SPNILKTGLTENVDRGLGGLEGTHQALDLLAGGMMPEEVKESSQLDKQES  2150
2151  LGLELKTINSAGLGPSPCLPDLVDFVTRTSGVQKDKLCSPLSEPGDPSKC  2200
2201  SSLELGPLQLEISNASTTEVAILQVDDDSGDPLNLVKAPVSRSPPREQVI  2250
2251  EDNMVPQGMPEQETTVGAIQDHTESSVHN                       2279

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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