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

NucPred

Fetching P57999 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MFFATGRASAFSHPCGRTAVSLREERRIKKRKRQDGFYMLLDPKNAKPRQ    50
  51  KSVLLSPLSQSAGCLTLSFHYTLWGQSPGAALSVLASVLGSIRKHTLFSG   100
 101  QPSPNWQPVSVNYSGPGQIQFTVVGVFGDVPEPAVAVDAISIAPCGESFP   150
 151  QCVFEDAAHPFCDWLQASEDGGRWAWTDKDMLAQERSLMRESPHTGHHYI   200
 201  YLEADKFSRPGQSVRLVSRPFCAPGDVCVEFSYHMYGLGEGTTLQFLLGS   250
 251  PAGSTPVSLWNRVGSQSPDWLNASVTIPSGHQQPMQLVFEAIRGSNTAFV   300
 301  VAMSFILINHGTCHVPVPPVIPIKTLVIPTEQPTVPAEGTTEPPEGTIEL   350
 351  PEGTTKLPEETTELPEEITEPPKETTIPTEPPTVPTEPPTVPTEPPTVPT   400
 401  EKPTVLTEKPTVPTEETSIPTEPPTVPTEKPTVATEPPTVPTEEPTVATE   450
 451  KPTVPTEETTPPTTARSTLTSLEPTTHTPSTSLTSTTLSTTTTPSPTTVS   500
 501  CPANAHYESCACPASCKHPKASCKPPCQPGCVCDPGLVFSNNSCIKASSC   550
 551  PCLYNNNNYEPEAEWFSPNCTELCHCWPGGRIECQISQCKTHTKCQLKNG   600
 601  QYECQPYGTATCFVYGDPHYVTFDGRHFGFMGKCTYIVAQPCSKSTDSFF   650
 651  RVTAKNEERGQEGMSCLSRVDVTLSETVVTLLKGRRTLVGGQRVTLPAMP   700
 701  AKGVFLGPSGRFVELQTDFGLRVRWDGDQQLLVTVPSAYFQKLCGLCGNY   750
 751  DGHSSNDNLKADGQPAQSEEELGNSWQWAQDEDKECQKNQANPPSCDTAL   800
 801  QTKMSGPQFCGQLVDSRGVFKTCLLHLKASSFFDNCVFDTCNFQGLQLML   850
 851  CAHMSAVTAACQDAGYAVKPWREPQFCPLACPPNSRYSLCTSPCPKTCHT   900
 901  GYVGMPCPEQCLEGCECNPGFILSGLECVPSAQCGCLDPSRGYFKVGEQW   950
 951  FKSDCKQLCICEGSNQIRCQPWKCGPHEVCSQQSGIYGCHSQGSATCSAS  1000
1001  GDPHYLTFDGALHHFMGTCNYVLTQPCRHRPQENSFVVSATNEIRDGNLE  1050
1051  VSLRPSCPRCRSSALKISLVKGHKVVLNGRRVALPVWPSRGQVTVRPSGN  1100
1101  FMLLYTNFGLRVRYDGNHLVEVTVPSSYAGQLCGLCGNYNNNSLDDILGP  1150
1151  YKRPVGNSVQLGAAWKLEEGSETGCFLQGGKPSSCHEDMGDTWNKNCEVL  1200
1201  VNPLGPFSQCHKVVPPEVSFTSCVHGQCGTKGDSLTLCRSLQAYASLCSL  1250
1251  AGQALAWRNSTFCPLKCPPNSSYSPCGSPCPGTCLSLNHPKDCPITLPCV  1300
1301  EGCECQNGYILSGTSCVPLNQCGCTDFEGSYHLVRESWYTDNTCSRLCTC  1350
1351  SLHNNITCRQTACKPGQQCWAVDGLLRCRDSGMGVCQVTGDSRYLSFDGS  1400
1401  SHPLQGACTYVLAKVCHPNMDLPFFKVSASNEKSSAGGTNAVSLHQVYIE  1450
1451  FSGSLVTLQKGNLVLINGTRVALPATSQIRGLNISSSRTHTIVSFWIGAQ  1500
1501  IKFDGNHVLKITIPAAYYEKVCGICGNYNGEPEDELMMPSDELAASDLEF  1550
1551  VKSWKDNNIDPNCQKSQEGKGKPQEEQGPSGSSKKASCSPADLQKVQEQC  1600
1601  QAALQTPAWAECASRVDLRPFLLDCMNSLCEFRGSLQPLCKALQALGAAC  1650
1651  RSKGLQPPIWRNSSFCPLACPAYSTYTNCLPSCSPSCFDPDGRCEGARAP  1700
1701  SSCAEGCTCQPGYVLSKNKCVAKDQCSCRDAQGGSIPSGKSWVSSGCSQK  1750
1751  CACTEGSIQCRAFHCPSRSHCKLNSNGNSNCVSEKSDQCSIFGGPHYRTF  1800
1801  DRFSFGFRGRMTYVLIKTVDELPDGVERLLVQARNKMYPPWNKVFLQEII  1850
1851  TTVYGYKVQLQRDLVLVVNNQKMAVPYKPEDRLRVSMQGQRLFLITDFEM  1900
1901  VVSFDGRNAAVITLPSMYQGLVRGLCGNYDSDRRNEMMLPNGAITTNVDV  1950
1951  FGNSWEVKTEDSVLRFRRALQVEADGKEKETGSYRSECSQEQLALVNSTQ  2000
2001  ACRVLVDPQGPFAACHQTVAPEPFQEHCVSDLCASRDPKEHEELRCQVLS  2050
2051  GYSITCQEAGIALAGWRDHTHCAMVCPANTVYQSCMTPCPESCANLAAPR  2100
2101  DCEGPCVEGCASLPGYAFSGAQSLPLANCGCTSNGIYYQLGHSFVTADCS  2150
2151  QRCTCASSGVLLCEPFSCRPGESCTLGNLTRGCFRESPCLRNPCQNDGRC  2200
2201  REQGTSFTCECEPGYGGHLCTEPRDVLLPPKPDTSNLVAILLGMLVSLVV  2250
2251  TVPVLARKCVSRKRRRWREKTQSEPRSAPGRR                    2282

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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