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

NucPred

Fetching O08550 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MAAAAGGGSCPGPGSARGRFPGRPRGSGGGGGRGGRGNGAERVRVALRRG    50
  51  GGAAGPGGAEPGEDTALLRLLGLRRGLRRLRRLWAGARVQRGRGRGRGRG   100
 101  WGPNRGCMPEEESSDGESEEEEFQGFHSDEDVAPSSLRSALRSQRGRAPR   150
 151  GRGRKHKTTPLPPRLADVTPVPPKAPTRKRGEEGTERMVQALTELLRRSQ   200
 201  APQPPRSRARAREPSTPRRSRGRPPGRPAGPCRKKQQAVVLAEAAVTIPK   250
 251  PEPPPPVVPVKNKAGSWKCKEGPGPGPGTPKRGGQPGRGGRGGRGRGRGG   300
 301  LPLMIKFVSKAKKVKMGQLSQELESGQGHGQRGESWQDAPQRKDGDEPER   350
 351  GSCRKKQEQKLEEEEEEEEKEGEEKEEKDDNEDNNKQEEEEETERAVAEE   400
 401  EAMLAKEKEEAKLPSPPLTPPVPSPPPPLPPPSTSPPPPASPLPPPVSPP   450
 451  PPLSPPPYPAPEKQEESPPLVPATCSRKRGRPPLTPSQRAEREAARSGPE   500
 501  GTLSPTPNPSTTTGSPLEDSPTVVPKSTTFLKNIRQFIMPVVSARSSRVI   550
 551  KTPRRFMDEDPPKPPKVEASIVRPPVATSPPAPQEPVPVSSPPRVPTPPS   600
 601  TPVPLPEKRRSILREPTFRWTSLTRELPPPPPAPPPAPSPPPAPATPSRR   650
 651  PLLLRAPQFTPSEAHLKIYESVLTPPPLGALETPEPELPPADDSPAEPEP   700
 701  RAVGRTNHLSLPRFVPVVTSPVKVEVPPHGAPALSEGQQLQLQQPPQALQ   750
 751  TQLLPQALPPQQPQAQPPPSPQHTPPLEKARVASLGSLPLSGVEEKMFSL   800
 801  LKRAKVQLFKIDQQQQQKVAASMPLSPAVQTEEAVGTVKQTPDRGCVRSE   850
 851  DESMEAKRDRASGPESPLQGPRIKHVCRHAAVALGQARAMVPEDVPRLSA   900
 901  LPLRDRQDLATEDTSSASETESVPSRSQREKVESAGPGGDSEPTGSTGAL   950
 951  AHTPRRSLPSHHGKKMRMARCGHCRGCLRVQDCGSCVNCLDKPKFGGPNT  1000
1001  KKQCCVYRKCDKIEARKMERLAKKGRTIVKTLLPWDSDESPEASPGPPGP  1050
1051  RRGAGAGGSREEVGATPGPEEQDSLLLQRKSARRCVKQRPSYDVFEDSDD  1100
1101  SEPGGPPAPRRRTPREHELPVLEPEEQSRPRKPTLQPVLQLKARRRLDKD  1150
1151  ALAPGPFASFPNGWTGKQKSPDGVHRVRVDFKEDCDLENVWLMGGLSVLT  1200
1201  SVPGGPPMVCLLCASKGLHELVFCQVCCDPFHPFCLEEAERPSPQHRDTW  1250
1251  CCRRCKFCHVCGRKGRGSKHLLECERCRHAYHPACLGPSYPTRATRRRRH  1300
1301  WICSACVRCKSCGATPGKNWDVEWSGDYSLCPRCTELYEKGNYCPICTRC  1350
1351  YEDNDYESKMMQCAQCDHWVHAKCEGLSDEDYEILSGLPDSVLYTCGPCA  1400
1401  GATQPRWREALSGALQGGLRQVLQGLLSSKVAGPLLLCTQCGQDGKQLHP  1450
1451  GPCDLQAVGKRFEEGLYKSVHSFMEDVVAILMRHSEEGETPERRAGSQMK  1500
1501  GLLLKLLESAFCWFDAHDPKYWRRSTRLPNGVLPNAVLPPSLDHVYAQWR  1550
1551  QQESETPESGQPPGDPSAAFQSKDPAAFSHLDDPRQCALCLKYGDADSKE  1600
1601  AGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCELC  1650
1651  LKPGATVGCCLSSCLSNFHFMCARASYCIFQDDKKVFCQKHTDLLDGKEI  1700
1701  VTPDGFDVLRRVYVDFEGINFKRKFLTGLEPDVINVLIGSIRINSLGTLS  1750
1751  DLSDCEGRLFPIGYQCSRLYWSTVDARRRCWYRCRILEYRPWGPREEPVH  1800
1801  LEAAEENQTIVHSPTPSSDTDSLIPGDPVHHSPIQNLDPPLRTDSSNGPP  1850
1851  PTPRSFSGARIKVPNYSPSRRPLGGVSFGPLPSPGSPSSLTHHIPTVGDS  1900
1901  DFPAPPRRSRRPSPLATRPPPSRRTSSPLRTSPQLRVPLSTSVTALTPTS  1950
1951  GELAPPDLAPSPLPPSEDLGPDFEDMEVVSGLSAADLDFAASLLGTEPFQ  2000
2001  EEIVAAGAVGSSQGGPGDSSEEEASPTTHYVHFPVTVVSGPALAPSSLAG  2050
2051  APRIEQLDGVDDGTDSEAEAVQQPRGQGTPPSGPGVGRGGVLGAAGDRAQ  2100
2101  PPEDLPSEIVDFVLKNLGGPGEGAAGPREDSLPSAPPLANGSQPPQSLST  2150
2151  SPADPTRTFAWLPGAPGVRVLSLGPAPEPPKPATSKIILVNKLGQVFVKM  2200
2201  AGEGEPVAPPVKQPPLPPIIPPTAPTSWTLPPGPLLSVLPVVGVGVVRPA  2250
2251  PPPPPPPLTLVFSSGPPSPPRQAIRVKRVSTFSGRSPPVPPPNKTPRLDE  2300
2301  DGESLEDAHHVPGISGSGFSRVRMKTPTVRGVLDLNNPGEQPEEESPGRP  2350
2351  QDRCPLLPLAEAPSQALDGSSDLLFESQWHHYSAGEASSSEEEPPSPEDK  2400
2401  ENQVPKRVGPHLRFEISSDDGFSVEAESLEVAWRTLIEKVQEARGHARLR  2450
2451  HLSFSGMSGARLLGIHHDAVIFLAEQLPGAQRCQHYKFRYHQQGEGQEEP  2500
2501  PLNPHGAARAEVYLRKCTFDMFNFLASQHRVLPEGATCDEEEDEVQLRST  2550
2551  RRATSLELPMAMRFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVI  2600
2601  EYSGIVIRSVLTDKREKFYDGKGIGCYMFRMDDFDVVDATMHGNAARFIN  2650
2651  HSCEPNCFSRVIHVEGQKHIVIFALRRILRGEELTYDYKFPIEDASNKLP  2700
2701  CNCGAKRCRRFLN                                       2713

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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