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

NucPred

Fetching Q69ZK6 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MQGPYSLNGYRVRVYRQDSATQWFTGIITHHDLFTRTMIVMNDQVLEPQN    50
  51  VDPSMVQMTFLDDVVHSLLKGENIGITSRRRSRASQNISTVHGHYTRAQA   100
 101  NSPRPAMNSQAAVPKQNTHQQQQQRSIRPNKRKGSDSSIPDEEKMKEDKY   150
 151  DCVSRGENPKGKNKHVVTKRRKPEEAEKRLSMKRLRTDNASDASESSDAE   200
 201  SSSKRVTETSSSEPMPEYEPKNKVTSKVNGEEGQSQAAEEAGEETLIDTR   250
 251  PPWDQMQEDKNHNEGEKPKSTDSHLQDKMTLRSSEQATVADHNSNDSVLQ   300
 301  ECNVENQRTVELLPKDRLVSRTPTPKCVTDIKNDTHSERAAQENLNTFGL   350
 351  QTPENMDPNVSDSKHSNAKYLETAKQDCDQSWVSDVVKVDLTQSSVTNAP   400
 401  SGSDKRDTEKERNHYVSYMSSLSAVSVTEDQLHKRSPPPETIKAKLTTSV   450
 451  DTQKAKSSSSPEVVKPKITHSPDSVKSKAAYGNSQAVGERRLANKIEHEL   500
 501  SRGSFHPVPTRGSALETTKSPLIIDKNEHFTVYRDPALIGSETGANHISP   550
 551  FLSQHPFSLHSSSHRTCLNPGTHHPALTPGPHLLAGSTSQTPLPTINTHP   600
 601  LTSGPHHPVHHPHLLPTVLPGVPTASLLGGHPRLESAHASSLSHLALAHQ   650
 651  QQQQLLQHQSPHLLGQAHPSASYNQLGLYPIIWQYPNGTHAYSGLGLPSS   700
 701  KWVHPENAVNAEASLRRNSPSPWLHQPTPVTSADGIGLLSHIPVRPSSAE   750
 751  PHRPHKITVHSSPPLTKTLADHHKEELERKAFMEPLRSNASTSVKGDLDL   800
 801  NRSQAGKDCHLHRHFVGPRPPQETGERLNKYKEEHRRILQESIDVAPFTT   850
 851  KIKGHEVERENYSRVVPSSSSPKSHAIKQDKDVDRSVSEIYKMKHSVPQS   900
 901  LPQSNYFTTLSNSVVNEPPRSYPSKEVSNIYTEKQNNNLSATANPQTHSF   950
 951  ISSLSKPPPLIKHQPESESLVGKIPDHLPHQSASHSVTTFRSDCRSPTHL  1000
1001  TVSSTNALRSMPALHRAPVFHPPIHHSLERKESSYSSLSPPTLTPVMPVN  1050
1051  AGGKVQESQKPPTLIPEPKDSQSNFKNSSDQSLTEMWRSNNNLNREKAEW  1100
1101  PVEKSSGKSQAAVASVIVRPPSSTKVDSVPSVPLASKDRVCERSSSGANK  1150
1151  TDYLKPEAGETGRIILPNVNLESAHVKSEKNFEAVSQGNVPVSVMSAVNV  1200
1201  VSTTKADVFTSAATTTSVSSLSSAETSYSLSNTISASTPFECTSSKSVVS  1250
1251  QAVAQAKDCTVSTAVPGTLACSKTGSAVQPGSGFSGTTDFIHLKKHKAAL  1300
1301  AAAQFKNSSVSEAELNTVRNQTVAASLPLDSTMTCTASNKAISVGNGPAA  1350
1351  QSSQPNYHTKLKKAWLTRHSEEDKNTNKMENSGNSVSEIIKPCSVNLIAS  1400
1401  TSNDIENRADGRVAVDKYGRDEKVSRRKAKRTYESGSESGDSDESESKSE  1450
1451  QRTKRQPKPTYKKKQNDLQKRKGEVEEDSKPNGVLSRSAKDKSKLKLQNS  1500
1501  NSAGVPRSVLKDWRKVKKLKQTGESFLQDDSCCEIGPNLQKCRECRLIRS  1550
1551  KKGEESTHSPVFCRFYYFRRLSFSKNGVVRIDGFSSPDQYDDEAMSLWTH  1600
1601  ENYEDDEVDVETSKYILDIIGDKFCQLVTSEKTALSWVKKDAKIAWKRAV  1650
1651  RGVREMCDACEATLFNVHWVCRKCGFVACLDCYKAKERKSSRDKELYAWM  1700
1701  KCVKGQPHDHKHLMLTQIIPGSVLTDLLDAMHILREKYGIKSHCHCTNRQ  1750
1751  NLQGGNVPTMNGVSQVLQNVLHHSNKTSVSLPESQQQNSPQKSQTNGNSS  1800
1801  PGSASTDSRLTPPESQSPLHWLADLAEQKSREEKQENKEFTLEREIKEDG  1850
1851  DQDASDSPNGSTSPPASQSNEQGSTLRDLLTTTAGKLRVGSTDAGIAFAP  1900
1901  VYSMGTSSGKGGRTMPNILDDIIASVVENKIPPNKTSKINIKSEPNEEPK  1950
1951  ESSLPATDESNKSYRDIPHSWICDQHILWLKDYKNSNNWKLFKECWKQGQ  2000
2001  PAVVSGVHKKMNISLWKAESISLDFGDHQADLLNCKDSIVSNANVKEFWD  2050
2051  GFEEVSKRQKNKGGETVVLKLKDCPSGEDFKAMMPTRYEDFLRCLPLPEY  2100
2101  CNPEGKFNLASHLPGFFVRPDLGPRLCSAYGVAAAKDHDIGTTNLHIEAS  2150
2151  DVVNVLVYVGIAKGNGVLSKAGILKKFEEEELDDVLRKRLKDSSEIPGAL  2200
2201  WHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNRKLRQRLL  2250
2251  EEYGVRACTLIQFLGDAIVLPAGTLHQVQNFHSCVQVTEDFVSPEHLVQS  2300
2301  FHLTQELRLLKEEINYDDKLQVKNILYHAVKEMVRALKMHEDEVEDMEDT  2350

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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