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

NucPred

Fetching Q9QZR8 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MPITQDNALLHLPLLYEWLQNSLREGGDSPEQRLCQAAIQKLQEYIQLNL    50
  51  AVDESTVPPDHSPPEMEICTVYLTKQLGDTETVGLSFGNIPVFGDYGEKR   100
 101  RGGKKRKTHQGPVLDVGCIWVTELRKNSPAGKSGKVRLRDEILSLNGQLM   150
 151  VGVDVTGASYLAEQCWNGGFIYLIMLRRFKQKAHVTYNGNSGNSSEPGET   200
 201  PTLELGDQTSKKGKRTRKFGVISRPSISKTPEDSKSSSGCDTADDPNSEL   250
 251  ENGADPELGNGHAFELENGPHSLKDVAGPHLERSEADSEVELRVPKTEAP   300
 301  LSDSNDKRRFSKTGKTDFQSSDCLAREEVGRIWKMELLKESDGLGIQVSG   350
 351  GRGSKRSPHAIVVTQVKEGGAAHRDGRLSLGDELLVINGHLLVGLSHEEA   400
 401  VAILRSATGMVQLVVASKMPGSEESQDVGSSEESKGNLESPKQGNCKTKL   450
 451  KSRLSGGVHRLESVEEYNELMVRNGDPRIRMLEVSRDGRKHSLPQLLDST   500
 501  GTSQEYHIVKKSTRSLSTTHVESPWRLIRPSVISIIGLYKEKGKGLGFSI   550
 551  AGGRDCIRGQMGIFVKTIFPNGSAAEDGRLKEGDEILDVNGIPIKGLTFQ   600
 601  EAIHTFKQIRSGLFVLTVRTKLLSPSLTPCSTPTHMSRSSSPSFNTNSGG   650
 651  TPAGGGQEEGGSSSLGRKAPGPKDRIVMEVTLNKEPRVGLGIGACCLALE   700
 701  NSPPGIYIHSLAPGSVAKMESNLSRGDQILEVNSVNVRHAALSKVHAILS   750
 751  KCPPGPVRLVIGRHPNPKVSEQEMDEVIARSTYQESREANSSPGLGTPLK   800
 801  SPSLAKKDSLLSESELSQYFVHDGQGSLSDFVVAGSEDEDHPGSGYETSE   850
 851  DGSLLPVPSAHKARANSLVTLGSQRTSGLLHKQVTVARQASLPGSPQVLR   900
 901  NPLLRQRRVRCYDSNGGSDDEDFDGEGDCISLPGVLPGPGKPLVEDDTRP   950
 951  ALTTSSKSIDVNKQEERLQKPLVSKACSVPLLGSSLDSEHSILNGAGGTP  1000
1001  PKVASLPGSGETPKNGPRGSGRKEMSGSRSSPKLEYRVPTDTQSPRSPEN  1050
1051  HTSPPQKSENLVSRHKPVARISPHYKRSDAEEAPGGTANGPCAQDLKVQA  1100
1101  SPVKDPVTSRQPGGTAEKELRGNPTPGDSSVPTNCGPASTPCHPNIGLPT  1150
1151  ENPQGAAPECGPHPGTGWDGSSEHLCSPGKSREVHPDSSETPTVAEQVHQ  1200
1201  PESLSQPVSPRTSEPESQGISKMKPPSQRCVSPREKASTPPDSSRAWAAP  1250
1251  GDSSPSTRRIAVPMSTGAAPATAIPQASLVSQERSRGLSGPSKGLGTKEL  1300
1301  CIPKSLKDGALLEDTAPASGKMSHASSPSGPVATERTLSGSPENPVTDID  1350
1351  NFIEEASEARLSQSPQKADCRAHGDTFESQPPGGAGSSSSHHAQMVRSDQ  1400
1401  TSSPRKTGGTGSPPPQQWALQPSVLDSIHPDKHLAVNKTFLNNYSRNFSN  1450
1451  FHEDSISLSGPGGSSEPSPSSMYGNAEDSSSDPESLAEDPGAAARNNWSP  1500
1501  PLSPESSPKEGSSESEDERIEICSTDGCPGTPVTAPPPTQVALCPVLPVQ  1550
1551  QRAVCKPVGDICERACFVPGASRTSIPDSSQPFSFLDVSSEEPETWASIN  1600
1601  ASQNHMPVCTEGIMDVTSTSSNMGDSQSSQMTRHCRNAPFVLGNPDMVND  1650
1651  LGRDLLDEGAPKEGAAAASVMRSVFALGAEGPKNGEAVLADLHIAERGNL  1700
1701  EDLLQKPKTISRRPILTWFKEINKDSQGSHLRSTSEKEQSSMLALGPGSK  1750
1751  ANMVNTGHRKGVTVPKSPPSRQKSQENKDLPPKSPVETLGNCQKPKCSPK  1800
1801  LKRLNSKGKASPEVPVAISTKGSRNDHRKTLPSPQASHKMFSKAVSHRLH  1850
1851  IADQEEPKNTAGDTPKPPQCVPESKPPQAALGSLRTSASDTSIRTFTSPL  1900
1901  TSPKLLPEQGANSRFHMAVYLESDTSCPTTSRSPRSGPEGKAPHANSGSA  1950
1951  SPPASRASLALAGIRQSKQFTPGRADLLVSEATQPQGICEKGAEKKVSDP  2000
2001  PQRTNQLKIVEISSERVPKNACGDRPPESDRKGGFLTQNNCQEKSAIRLR  2050
2051  QSEESSPEHTPFPPSQASQVEREIRWSFSMAKPATSSSSSLQLPAKLPES  2100
2101  FQGKSSQMPASVGVPKNGVPIGLAGEESPYFTPRPATRTYSMPAQFSSHF  2150
2151  GREGPSPHSPSHSPQDPQVPAMGGKLSEKTAKGVTNGQGVYSVKPLLETS  2200
2201  KNLSPVDGRDVSADPETSCLIPDKVKVTRRQYCCEQSWPHESTSFFSVKQ  2250
2251  RIKSFENLANSDRPTAKCATSPFLSVSSKPPINRRSSGSIPSGSPSDMTS  2300
2301  RSLRRSLSSCSESQSEASSLLPQMTKSPSSMTLTVSRQNPPDTSNKGPSP  2350
2351  DPKKSLVPVGIPTSTVSPASPSKRNKSSVRHAQPSPVSRSKLQERRTLSM  2400
2401  PDLDKLCNGEDDSASPGAVLFKTQLEITPRRSKGSQATSPAGSPARGHAD  2450
2451  FNGSTFLSCPMNGGTRAYTKGNSPPASEPAIATGSREEGESVWATPSGKS  2500
2501  WSVSLDRLLASVGNQQRLQGILSLVGSKSPILTLIQEAKAQSETKEDICF  2550
2551  IVLNKKEGSGLGFSVAGGADVEPKSVMVHRVFSQGVASQEGTVSRGDFLL  2600
2601  SVNGTSLAGLAHSEVTKVLHQAELHKHALMIIKKGNDQPGPSFKQEPPSA  2650
2651  NGKGPFPRRTLPLEPGAGRNGAAHDALCVEVLKTSAGLGLSLDGGKSSVS  2700
2701  GEGPLVIKRVYKGGAAERAGTIEAGDEILAINGKPLVGLVHFDAWNIMKS  2750
2751  VPEGPVQLVIRKHRDS                                    2766

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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