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

NucPred

Fetching Q6FRZ9 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MENYQIRTLQDQLTSSKLRDRNAGLQELQSILKDNPGFIANEQINGLLNT    50
  51  LLSLLENEAGKYIDSIEDDTDSRQRKENISISRFSNITYTLRLFIETVIE   100
 101  KFKLSHLKLTISAVKDLFYNDARIIVPVINDVTYCILAIVKSEIFGNKIG   150
 151  PSQWLDVAEYTLWLIKITSSNRSNIRALTNSLDTFYVLLIKGSISLSKVA   200
 201  KEALVIITNLIVFEKGETATTNVLLSISSNLVARLHCQHYYDTTSLIIEC   250
 251  WKLYTRIGKTNNFNLLNDISKIDIFGGGLLQNQIPIMPGQEIMGSRISHS   300
 301  VVLSTLQDYIPMKVKEMLDVDHSLTIGIYDDLNNSNMDLTYNTFAKTHCK   350
 351  DLAWLRLFGLYDTLCLYYRLSNQERENNATQILKKIKYEGSLQSNLNQCN   400
 401  SLLDYSQSLLESGDPLIQLLGCKLFFLLNLDHPIACNTELIDRLCINTNN   450
 451  ISLTSWHLACIFTNISYDLWNFDETLYLKVLKYITPLLSTSEVNIMACLI   500
 501  FNKLLHSLTREPIDELSSLVNSIIASPDSVLPIEISSVTCEAWQHIFVFA   550
 551  INNLKVDNSLLLDSFSKWINHNITQTIHIEHLKLIFEFFLWSLDVVVGST   600
 601  SHNKQHNTYNLLNLKTSDSALAIWYFYENQRKFLTQTIQTSSQASVNTKS   650
 651  MVCPITSTNIKIQWLLNIIDNYFTTSKNHSLKYTFAISLIYFINFIEKSG   700
 701  KVYTYLNQELNQRLNSILIELDFLSFDKWEEGKQFIEIICNQETFFNRLH   750
 751  NDVVFKDNILLSLINLFEKEYSHFLNADNGSTAKTGNDIYLNQRSILRFR   800
 801  TDIKLMTQFFTCVDSNVPGKIGIYLDRLLLYSMGPNESLVLDELLSWVTN   850
 851  PSNNQYYEVHSLEKLCQFLAKSLLNSKYQLSDFSMIRLGLFLTSTIELWV   900
 901  NVKYNILNSDCNDFLIWITNNLVQNNFGETGTFVVLIRLFISVLKHNSTV   950
 951  NSSCAIKTQDLYSMLIFCMRNVAYSTLGNIVDELKAYMSKKSHKNRKTIL  1000
1001  DDLVELFEPMPESVEKAASSCFVLFGLLDCNDTNFVYTLDIFSNYGNIPH  1050
1051  ISFFLKKAVKNYVNNYYQGNKIQLLNVHILEVIRQWTKRNDTDRQLYFNS  1100
1101  VIGSLFGFGSIQEFERQYNREICALIFSRSDSESLERNFFSDRNTSKCEM  1150
1151  LRRSLYLLIPLSYYDNGVGDMVFNKLKDSFRGQLESVLSSNFIIVMRYAL  1200
1201  KLCDCSDYTSVLNEMQRPNQSSSLLELFMDSEMKNAINRMNIYITVHSVI  1250
1251  KIFKNCGRSRQTLLLDLRTLILWIISDIQKSESSWEQNNHLRQLQLLVFL  1300
1301  YEDTFLQSVLHIELMNWLSYLLKIENIEADVFLLLNCLLSLIKPNSLDKP  1350
1351  DSLTLFFLNVLHFYVRNKECLKIGDEDMNMLSNNLSTVNSIALKLLTNGQ  1400
1401  VTDLIYNQVGDLTSQMYFAEEVELFALLMTFAPPMPDYVSHKMNKKFIEY  1450
1451  VYKSNNLIDIDNFSLWFSDYSTQYSSLILELEENSSFCEKDGFGIDDMEI  1500
1501  VYDFSDSAVSAMYSVLFRSLISIKPTIGFKSFALSNIICHLISINILKDK  1550
1551  DLLSKFLRATKMKIAFSAKEIDETIIEHFGKSNCGCVISEHYLESEFFDT  1600
1601  NIPYKDWLVKLCMFFISQISLNSKEIQWFIPLCYESMDFCKQNVCIFFLA  1650
1651  AFSFDHRRMSSTWKHIFSRLNDLTMASDCLAKLTLLLSFIRLIRSGALQG  1700
1701  RKEYSNLYQKIEFKGVIDAALKIKDSKFALQLFEEAYMCENGDYDVALLT  1750
1751  SIYEQLDDVDMLYALPTPISLNGFIKNANRLSPHSLKALQLNGAYFDANF  1800
1801  NHLVDNGSHQLVNTLTGMGFNALADIADLRTSCDNPADAYLRCLQLDKWD  1850
1851  LPKPKAIDCKIVSFYNTAYDLRNTNIEFVDLLQNAEIQLYKAKANFSSKL  1900
1901  EWFETIREYVKTKRAIISLKTDTDISRFKIDHVINPDRYLENALISDIKI  1950
1951  NWQFRYLMLKIYVEREKFANEAMKCIPILELIHQTELSVDFHIQQTSLSR  2000
2001  ILSMEAAMKRFHIADTNLVEQLSRHVSYVTALALREFGETKAPLTILSKL  2050
2051  LSDKSYKLNYNTFVSDDEVRAQLIWDSYQAKVKSGIQIFENDVEHWDVSI  2100
2101  NNIRSAPDTIYKVANFLNLEISRLNGSDQLKEKQKSYRRTRQELKDIESV  2150
2151  VKSSNLSNEELLVGQKHYHNLKTHMENDRLAIENICLTRKKLIKRALDYY  2200
2201  VQILILTNNYDYDVLDRFCGLWFENDDDDDINTDLTSKLSQIPTWKFLPW  2250
2251  VNQFTSKLSLLKSKFQKQLWYIMKRLLYKLPFETGYAVINLQLYEKYSDK  2300
2301  LDEKISEKIKAANLIFDQLQNSQISVKEGEYLRTIQEFCYATLEIAELKV  2350
2351  KGKNAQISLETLNIGRYWITELPKKNLPLPTVTRTINSSQYTLDSSRNIV  2400
2401  KVIGNITITSTGLSLPKVMTLLLSDGSRHKVVIKYGSDDLRQDAIMEQVF  2450
2451  QQVNKIFGKDVEMRRSDLHMRTYNVVPLGPKAGLIEFVNNSLSLHSILTD  2500
2501  IHKDDNYSWLEARRSMKDVQSKSDKERILTYLDITKKISPKFRNFFFNSF  2550
2551  IDANGWICAKRKYTKGVATSSMVGYILGLGDRHLNNILIDTTTGEPIHID  2600
2601  LGIAFDQGRLLKIPELVPFRLTRDIIDGFGITGVEGIFRRTCEQVLNVLS  2650
2651  RDSEKVMCVLNILKWDPLYSWAVSPFKKHKYMYDDNLEGHMTTATNNSKV  2700
2701  IERKLTPKLDSDENQQSYRALKGVQEKLDRNGLTIEATVEKLIQEAVDES  2750
2751  NLALIFNGWSPFY                                       2763

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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