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

NucPred

Fetching Q9Y490 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MVALSLKISIGNVVKTMQFEPSTMVYDACRIIRERIPEAPAGPPSDFGLF    50
  51  LSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRKKQRPLKIRMLDGTVKTI   100
 101  MVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKEEITGTLRKDKT   150
 151  LLRDEKKMEKLKQKLHTDDELNWLDHGRTLREQGVEEHETLLLRRKFFYS   200
 201  DQNVDSRDPVQLNLLYVQARDDILNGSHPVSFDKACEFAGFQCQIQFGPH   250
 251  NEQKHKAGFLDLKDFLPKEYVKQKGERKIFQAHKNCGQMSEIEAKVRYVK   300
 301  LARSLKTYGVSFFLVKEKMKGKNKLVPRLLGITKECVMRVDEKTKEVIQE   350
 351  WNLTNIKRWAASPKSFTLDFGDYQDGYYSVQTTEGEQIAQLIAGYIDIIL   400
 401  KKKKSKDHFGLEGDEESTMLEDSVSPKKSTVLQQQYNRVGKVEHGSVALP   450
 451  AIMRSGASGPENFQVGSMPPAQQQITSGQMHRGHMPPLTSAQQALTGTIN   500
 501  SSMQAVQAAQATLDDFDTLPPLGQDAASKAWRKNKMDESKHEIHSQVDAI   550
 551  TAGTASVVNLTAGDPAETDYTAVGCAVTTISSNLTEMSRGVKLLAALLED   600
 601  EGGSGRPLLQAAKGLAGAVSELLRSAQPASAEPRQNLLQAAGNVGQASGE   650
 651  LLQQIGESDTDPHFQDALMQLAKAVASAAAALVLKAKSVAQRTEDSGLQT   700
 701  QVIAAATQCALSTSQLVACTKVVAPTISSPVCQEQLVEAGRLVAKAVEGC   750
 751  VSASQAATEDGQLLRGVGAAATAVTQALNELLQHVKAHATGAGPAGRYDQ   800
 801  ATDTILTVTENIFSSMGDAGEMVRQARILAQATSDLVNAIKADAEGESDL   850
 851  ENSRKLLSAAKILADATAKMVEAAKGAAAHPDSEEQQQRLREAAEGLRMA   900
 901  TNAAAQNAIKKKLVQRLEHAAKQAAASATQTIAAAQHAASTPKASAGPQP   950
 951  LLVQSCKAVAEQIPLLVQGVRGSQAQPDSPSAQLALIAASQSFLQPGGKM  1000
1001  VAAAKASVPTIQDQASAMQLSQCAKNLGTALAELRTAAQKAQEACGPLEM  1050
1051  DSALSVVQNLEKDLQEVKAAARDGKLKPLPGETMEKCTQDLGNSTKAVSS  1100
1101  AIAQLLGEVAQGNENYAGIAARDVAGGLRSLAQAARGVAALTSDPAVQAI  1150
1151  VLDTASDVLDKASSLIEEAKKAAGHPGDPESQQRLAQVAKAVTQALNRCV  1200
1201  SCLPGQRDVDNALRAVGDASKRLLSDSLPPSTGTFQEAQSRLNEAAAGLN  1250
1251  QAATELVQASRGTPQDLARASGRFGQDFSTFLEAGVEMAGQAPSQEDRAQ  1300
1301  VVSNLKGISMSSSKLLLAAKALSTDPAAPNLKSQLAAAARAVTDSINQLI  1350
1351  TMCTQQAPGQKECDNALRELETVRELLENPVQPINDMSYFGCLDSVMENS  1400
1401  KVLGEAMTGISQNAKNGNLPEFGDAISTASKALCGFTEAAAQAAYLVGVS  1450
1451  DPNSQAGQQGLVEPTQFARANQAIQMACQSLGEPGCTQAQVLSAATIVAK  1500
1501  HTSALCNSCRLASARTTNPTAKRQFVQSAKEVANSTANLVKTIKALDGAF  1550
1551  TEENRAQCRAATAPLLEAVDNLSAFASNPEFSSIPAQISPEGRAAMEPIV  1600
1601  ISAKTMLESAGGLIQTARALAVNPRDPPSWSVLAGHSRTVSDSIKKLITS  1650
1651  MRDKAPGQLECETAIAALNSCLRDLDQASLAAVSQQLAPREGISQEALHT  1700
1701  QMLTAVQEISHLIEPLANAARAEASQLGHKVSQMAQYFEPLTLAAVGAAS  1750
1751  KTLSHPQQMALLDQTKTLAESALQLLYTAKEAGGNPKQAAHTQEALEEAV  1800
1801  QMMTEAVEDLTTTLNEAASAAGVVGGMVDSITQAINQLDEGPMGEPEGSF  1850
1851  VDYQTTMVRTAKAIAVTVQEMVTKSNTSPEELGPLANQLTSDYGRLASEA  1900
1901  KPAAVAAENEEIGSHIKHRVQELGHGCAALVTKAGALQCSPSDAYTKKEL  1950
1951  IECARRVSEKVSHVLAALQAGNRGTQACITAASAVSGIIADLDTTIMFAT  2000
2001  AGTLNREGTETFADHREGILKTAKVLVEDTKVLVQNAAGSQEKLAQAAQS  2050
2051  SVATITRLADVVKLGAASLGAEDPETQVVLINAVKDVAKALGDLISATKA  2100
2101  AAGKVGDDPAVWQLKNSAKVMVTNVTSLLKTVKAVEDEATKGTRALEATT  2150
2151  EHIRQELAVFCSPEPPAKTSTPEDFIRMTKGITMATAKAVAAGNSCRQED  2200
2201  VIATANLSRRAIADMLRACKEAAYHPEVAPDVRLRALHYGRECANGYLEL  2250
2251  LDHVLLTLQKPSPELKQQLTGHSKRVAGSVTELIQAAEAMKGTEWVDPED  2300
2301  PTVIAENELLGAAAAIEAAAKKLEQLKPRAKPKEADESLNFEEQILEAAK  2350
2351  SIAAATSALVKAASAAQRELVAQGKVGAIPANALDDGQWSQGLISAARMV  2400
2401  AAATNNLCEAANAAVQGHASQEKLISSAKQVAASTAQLLVACKVKADQDS  2450
2451  EAMKRLQAAGNAVKRASDNLVKAAQKAAAFEEQENETVVVKEKMVGGIAQ  2500
2501  IIAAQEEMLRKERELEEARKKLAQIRQQQYKFLPSELRDEH           2541

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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