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

NucPred

Fetching P29994 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MSDKMSSFLHIGDICSLYAEGSTNGFISTLGLVDDRCVVQPEAGDLNNPP    50
  51  KKFRDCLFKLCPMNRYSAQKQFWKAAKPGANSTTDAVLLNKLHHAADLEK   100
 101  KQNETENRKLLGTVIQYGNVIQLLHLKSNKYLTVNKRLPALLEKNAMRVT   150
 151  LDEAGNEGSWFYIQPFYKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQL   200
 201  VDNPGCNEVNSVNCNTSWKIVLFMKWSDNKDDILKGGDVVRLFHAEQEKF   250
 251  LTCDEHRKKQHVFLRTTGRQSATSATSSKALWEVEVVQHDPCRGGAGYWN   300
 301  SLFRFKHLATGHYLAAEVDPDFEEECLEFQPSVDPDQDASRSRLRNAQEK   350
 351  MVYSLVSVPEGNDISSIFELDPTTLRGGDSLVPRNSYVRLRHLCTNTWVH   400
 401  STNIPIDKEEEKPVMLKIGTSPLKEDKEAFAIVPVSPAEVRDLDFANDAS   450
 451  KVLGSIAGKLEKGTITQNERRSVTKLLEDLVYFVTGGTNSGQDVLEVVFS   500
 501  KPNRERQKLMREQNILKQIFKLLQAPFTDCGDGPMLRLEELGDQRHAPFR   550
 551  HICRLCYRVLRHSQQDYRKNQEYIAKQFGFMQKQIGYDVLAEDTITALLH   600
 601  NNRKLLEKHITAAEIDTFVSLVRKNREPRFLDYLSDLCVSMNKSIPVTQE   650
 651  LICKAVLNPTNADILIETKLVLSRFEFEGVSTGENALEAGEDEEEVWLFW   700
 701  RDSNKEIRSKSVRELAQDAKEGQKEDRDVLSYYRYQLNLFARMCLDRQYL   750
 751  AINEISGQLDVDLILRCMSDENLPYDLRASFCRLMLHMHVDRDPQEQVTP   800
 801  VKYARLWSEIPSEIAIDDYDSSGASKDEIKERFAQTMEFVEEYLRDVVCQ   850
 851  RFPFSDKEKNKLTFEVVNLARNLIYFGFYNFSDLLRLTKILLAILDCVHV   900
 901  TTIFPISKMTKGEENKGSNVMRSIHGVGELMTQVVLRGGGFLPMTPMAAA   950
 951  PEGNVKQAEPEKEDIMVMDTKLKIIEILQFILNVRLDYRISCLLCIFKRE  1000
1001  FDESNSQSSETSSGNSSQEGPSNVPGALDFEHIEEQAEGIFGGSEENTPL  1050
1051  DLDDHGGRTFLRVLLHLTMHDYPPLVSGALQLLFRHFSQRQEVLQAFKQV  1100
1101  QLLVTSQDVDNYKQIKQDLDQLRSIVEKSELWVYKGQGPDEPMDGASGEN  1150
1151  EHKKTEEGTSKPLKHESTSSYNYRVVKEILIRLSKLCVQESASVRKSRKQ  1200
1201  QQRLLRNMGAHAVVLELLQIPYEKAEDTKMQEIMRLAHEFLQNFCAGNQQ  1250
1251  NQALLHKHINLFLNPGILEAVTMQHIFMNNFQLCSEINERVVQHFVHCIE  1300
1301  THGRNVQYIKFLQTIVKAEGKFIKKCQDMVMAELVNSGEDVLVFYNDRAS  1350
1351  FQTLIQMMRSERDRMDENSPLFMYHIHLVELLAVCTEGKNVYTEIKCNSL  1400
1401  LPLDDIVRVVTHEDCIPEVKIAYINFLNHCYVDTEVEMKEIYTSNHMWKL  1450
1451  FENFLVDICRACNNTSDRKHADSVLEKYVTEIVMSIVTTFFSSPFSDQST  1500
1501  TLQTRQPVFVQLLQGVFRVYHCNWLMPSQKASVESCIRVLSDVAKSRAIA  1550
1551  IPVDLDSQVNNLFLKSHNIVQKTAMNWRLSARNAARRDSVLAASRDYRNI  1600
1601  IERLQDIVSALEDRLRPLVQAELSVLVDVLHRPELLFPENTDARRKCESG  1650
1651  GFICKLIKHTKQLLEENEEKLCIKVLQTLREMMTKDRGYGEKQISIDELE  1700
1701  NAELPQPPEAENSTEQELEPSPPLRQLEDHKRGEALRQILVNRYYGNIRP  1750
1751  SGRRESLTSFGNGPLSPGGPSKPGGGGGGPGSGSTSRGEMSLAEVQCHLD  1800
1801  KEGASNLVIDLIMNASSDRVFHESILLAIALLEGGNTTIQHSFFCRLTED  1850
1851  KKSEKFFKVFYDRMKVAQQEIKATVTVNTSDLGNKKKDDEVDRDAPSRKK  1900
1901  AKEPTTQITEEVRDQLLEASAATRKAFTTFRREADPDDHYQSGEGTQATT  1950
1951  DKAKDDLEMSAVITIMQPILRFLQLLCENHNRDLQNFLRCQNNKTNYNLV  2000
2001  CETLQFLDCICGSTTGGLGLLGLYINEKNVALINQTLESLTEYCQGPCHE  2050
2051  NQNCIATHESNGIDIITALILNDINPLGKKRMDLVLELKNNASKLLLAIM  2100
2101  ESRHDSENAERILYNMRPKELVEVIKKAYMQGEVEFEDGENGEDGAASPR  2150
2151  NVGHNIYILAHQLARHNKELQTMLKPGGQVDGDEALEFYAKHTAQIEIVR  2200
2201  LDRTMEQIVFPVPSICEFLTKESKLRIYYTTERDEQGSKINDFFLRSEDL  2250
2251  FNEMNWQKKLRAQPVLYWCARNMSFWSSISFNLAVLMNLLVAFFYPFKGV  2300
2301  RGGTLEPHWSGLLWTAMLISLAIVIALPKPHGIRALIASTILRLIFSVGL  2350
2351  QPTLFLLGAFNVCNKIIFLMSFVGNCGTFTRGYRAMVLDVEFLYHLLYLL  2400
2401  ICAMGLFVHEFFYSLLLFDLVYREETLLNVIKSVTRNGRPIILTAALALI  2450
2451  LVYLFSIVGYLFFKDDFILEVDRLPNETAGPETGESLANDFLYSDVCRVE  2500
2501  TGENCTSPAPKEELLPVEETEQDKEHTCETLLMCIVTVLSHGLRSGGGVG  2550
2551  DVLRKPSKEEPLFAARVIYDLLFFFMVIIIVLNLIFGVIIDTFADLRSEK  2600
2601  QKKEEILKTTCFICGLERDKFDNKTVTFEEHIKEEHNMWHYLCFIVLVKV  2650
2651  KDSTEYTGPESYVAEMIRERNLDWFPRMRAMSLVSSDSEGEQNELRNLQE  2700
2701  KLESTMKLVTNLSGQLSELKDQMTEQRKQKQRIGLLGHPPHMNVNPQQPA  2750

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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