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

NucPred

Fetching P10180 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MQPTLPQAAGTADMDLTAVQSINDWFFKKEQIYLLAQFWQQRATLAEKEV    50
  51  NTLKEQLSTGNPDSNLNSENSDTAAAAATAAAVAAVVAGATATNDIEDEQ   100
 101  QQQLQQTASGGILESDSDKLLNSSIVAAAITLQQQNGSNLLANTNTPSPS   150
 151  PPLLSAEQQQQLQSSLQQSGGVGGACLNPKLFFNHAQQMMMMEAAAAAAA   200
 201  AALQQQQQQQSPLHSPANEVAIPTEQPAATVATGAAAAAAAAATPIATGN   250
 251  VKSGSTTSNANHTNSNNSHQDEEELDDEEEDEEEDEDEDDEEENASMQSN   300
 301  ADDMELDAQQETRTEPSATTQQQHQQQDTEDLEENKDAGEASLNVSNNHN   350
 351  TTDSNNSCSRKNNNGGNESEQHVASSAEDDDCANNNTNTSNNNNTSNTAT   400
 401  SNTNNNNNNNSSSGNSEKRKKKNNNNNNGQPAVLLAAKDKEIKALLDELQ   450
 451  RLRAQEQTHLVQIQRLEEHLEVKRQHIIRLEARLDKQQINEALAEATALS   500
 501  AAASTNNNNNSQSSDNNKKLNTAAERPMDASSNADLPESTKAPVPAEDDE   550
 551  EDEDQAMLVDSEEAEDKPEDSHHDDDEDEDEDREAVNATTTDSNELKIKK   600
 601  EQHSPLDLNVLSPNSAIAAAAAAAAAAACANDPNKFQALLIERTKALAAE   650
 651  ALKNGASDALSEDAHHQQQQHHQQQHQHQQQHHQQQHLHQQHHHHLQQQP   700
 701  NSGSNSNPASNDHHHGHHLHGHGLLHPSSAHHLHHQTTESNSNSSTPTAA   750
 751  GNNNGSNNSSSNTNANSTAQLAASLASTLNGTKSLMQEDSNGLAAVAMAA   800
 801  HAQHAAALGPGFLPGLPAFQFAAAQVAAGGDGRGHYRFADSELQLPPGAS   850
 851  MAGRLGESLIPKGDPMEAKLQEMLRYNMDKYANQALDTLHISRRVRELLS   900
 901  VHNIGQRLFAKYILGLSQGTVSELLSKPKPWDKLTEKGRDSYRKMHAWAC   950
 951  DDNAVMLLKSLIPKKDSGLPQYAGRGAGGAGGDDSMSEDRIAHILSEASS  1000
1001  LMKQSSVAQHREQERRSHGGEDSHSNEDSKSPPQSCTSPFFKVENQLKQH  1050
1051  QHLNPEQAAAQQREREREQREREQQQRLRHDDQDKMARLYQELIARTPRE  1100
1101  TAFPSFLFSPSLFGGAAGMPGAASNAFPAMADENMRHVFEREIAKLQQHQ  1150
1151  QQQQAAQAQAQFPNFSSLMALQQQVLNGAQDLSLAAAAAKDIKLNGQRSS  1200
1201  LEHSAGSSSCSKDGERDDAYPSSLHGRKSEGGGTPAPPAPPSGPGTGAGA  1250
1251  PPTAAPPTGGASSNSAAPSPLSNSILPPALSSQGEEFAATASPLQRMASI  1300
1301  TNSLITQPPVTPHHSTPQRPTKAVLPPITQQQFDMFNNLNTEDIVRRVKE  1350
1351  ALSQYSISQRLFGESVLGLSQGSVSDLLARPKPWHMLTQKGREPFIRMKM  1400
1401  FLEDENAVHKLVASQYKIAPEKLMRTGSYSGSPQMPQGLASKMQAASLPM  1450
1451  QKMMSELKLQEPAQAQHLMQQMQAAAMSAAMQQQQVAQAQQQAQQAQQAQ  1500
1501  QHLQQQAQQHLQQQQHLAQQQHPHQQHHQAAAAAAALHHQSMLLTSPGLP  1550
1551  PQHAISLPPSAGGAQPGGPGGNQGSSNPSNSEKKPMLMPVHGTNAMRSLH  1600
1601  QHMSPTVYEMAALTQDLDTHDITTKIKEALLANNIGQKIFGEAVLGLSQG  1650
1651  SVSELLSKPKPWHMLSIKGREPFIRMQLWLSDANNVERLQLLKNERREAS  1700
1701  KRRRSTGPNQQDNSSDTSSNDTNDFYTSSPGPGSVGSGVGGAPPSKKQRV  1750
1751  LFSEEQKEALRLAFALDPYPNVGTIEFLANELGLATRTITNWFHNHRMRL  1800
1801  KQQVPHGPAGQDNPIPSRESTSATPFDPVQFRILLQQRLLELHKERMGMS  1850
1851  GAPIPYPPYFAAAAILGRSLAGIPGAAAAAGAAAAAAAVGASGGDELQAL  1900
1901  NQAFKEQMSGLDLSMPTLKRERSDDYQDDLELEGGGHNLSDNESLEGQEP  1950
1951  EDKTTDYEKVLHKSALAAAAAYMSNAVRSSRRKPAAPQWVNPAGAVTNPS  2000
2001  AVVAAVAAAAAAAADNERIINGVCVMQASEYGRDDTDSNKPTDGGNDSDH  2050
2051  EHAQLEIDQRFMEPEVHIKQEEDDDEEQSGSVNLDNEDNATSEQKLKVIN  2100
2101  EEKLRMVRVRRLSSTGGGSSEEMPAPLAPPPPPPAASSSIVSGESTTSSS  2150
2151  SSSNTSSSTPAVTTAAATAAAGWNY                           2175

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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